BACKGROUND
hypothetical proteins  are generally known as proteins of unknown structures and functions  <cit> .
they constitute approximately 25% of any sequenced genome even in simple, model organisms such as escherichia coli, bacillus subtilis and saccharomyces cerevisiae <cit> .
annotating their biological function has remained a challenge due to their low sequence and structural homology to other known proteins  <cit> .
this in turn creates difficulties in attempts to understand a biological system as a whole due to the information gaps posed by these “orphan” proteins.
therefore, efforts in trying to unravel their structures and functions are crucial in filling these information gaps for any particular system and hence, should be encouraged.
to deepen our understanding on these proteins, in silico methods of analysis are the most time and cost effective in generating a wealth of reliable and useful information on hps ranging from their localization, properties to their possible structures and functions.
it also provides a quick means to preliminary screen and chooses potential hps for subsequent downstream in vitro and in vivo experiments, particularly to initiate structural genomic projects in the future  <cit> .
with the wealth of information which can be generated using the in silico approach, this present study highlights the utilization of various in silico tools and methods to functionally predict and cluster all hps present in the complete genome of a locally isolated alkaliphile, bacillus lehensis g <dig>  with the purpose of establishing a platform to mine and later select specific hps to be studied further in greater detail.
whilst the genome of this alkaliphile has been completely sequenced  <cit> , the structural and functional omics of this extremophile is not well characterised, particularly its hps.
hence, our attempt at firstly predicting their functions and clustering them accordingly will serve as a platform in mining and selecting specific hps to be studied further in greater detail.
stemming from this effort, our attention was led to a particular hp, bleg1_ <dig>  in the metalloprotein category of the cluster.
this hp contained a sco <dig> domain of the thioredoxin  superfamily and showed up to 50% of sequence identity to other bacterial hps and 47% to bacterial sco proteins.
it is important to note that sco proteins are present in both prokaryotic and eukaryotic organisms and are required for the proper assembly of cytochrome c oxidase , a terminal enzyme in the respiratory chain  <cit> .
sco was suggested to be involved in the delivery of copper ion to cox complex  <cit> – <cit> .
to date, the only bacterial sco <dig> protein which was structurally studied and analysed at length is from bacillus subtilis <cit>  while its eukaryotic counterpart is from yeast  <cit> , human  <cit>  and plant  <cit> .
sco proteins have garnered importance in recent years due to their roles in the correct assembly of the copper center  of cox subunit ii .
improper assembly of cox has been reported to cause fatal infantile encephalopathy due to mutations in sco <dig> and sco <dig> genes in humans  <cit> .
due to the physiological relevance of sco proteins, we embarked on the task of building the structure of hp bleg1_ <dig> of b. lehensis g <dig> via homology modelling to investigate the structural similarities and differences between this protein with sco <dig> protein from b. subtilis , yeast and human.
as sco <dig> was suggested to be involved in the delivery of copper ion to cox complex, specifically coxii  <cit> – <cit> , we subsequently mined the genome of b. lehensis g <dig> for the sequence encoding coxii by performing a blastp search.
as a result, bleg1_ <dig> was retrieved and its structure was built via homology modelling.
docking of both hp bleg1_ <dig> and bleg1_ <dig> models was performed to investigate their possible interaction.
based on the results obtained, the possible structure, function and mechanism of hp bleg1_ <dig> from b. lehensis g <dig> are duly discussed.
lastly, the structure of hp bleg1_ <dig> of b. lehensis g <dig> was compared to other sco proteins to highlight its similarity and distinctness.
methods
domain and sequence similarity analysis of hps of b. lehensis g1: development of an hp cluster
all sequences encoding hps in the genome of b. lehensis g <dig> were firstly subjected to interproscan  <cit>  and conserved domain search   <cit>  analyses to detect possible functional domains within the sequences.
sequence similarity of all the hps with other proteins in the database was investigated also using blastp  <cit> .
based on the predicted functional domains and sequence similarity, an hp cluster was built to categorize the proteins accordingly.
a scan on hps which showed acceptable similarity to other proteins with low e-value was carried out and the potential candidate was chosen for further analyses and structure prediction.
sequence analysis of selected hp  and putative cytochrome c oxidase subunit ii, coxii
from the above scan, a particular hp in the metal-binding group of proteins encoded by bleg1_ <dig> gene was chosen for further analyses based on the presence of the conserved copper chaperone sco <dig> domain related to trx-like superfamily.
firstly, the possible presence of consensus amino acids pattern in bleg1_ <dig> sequence was identified using scanprosite  <cit> .
important and metal-binding residues were subsequently identified using consurf  <cit>  and metaldetector v  <dig>   <cit>  respectively.
the physicochemical aspect of the protein such as its theoretical pi value was investigated using protparam  <cit> .
sigcleave from emboss  <cit>  was used to investigate the possible presence of signal peptide in bleg1_ <dig>  while the evolutionary relatedness of the protein with other known proteins was investigated using phylip  <cit> .
subsequently, a genome-wide scan for bleg1_ <dig> redox partner i.e.
cytochrome c oxidase subunit ii , was performed.
as a result, bleg1_ <dig>  a putative coxii protein was identified from the genome sequence of b. lehensis g <dig>  further analyses similar to the ones mentioned above were performed on bleg1_ <dig>
homology modeling of hp bleg1_ <dig> and bleg1_2337
psi-blast  <cit>  search against protein data bank  was performed to retrieve potential templates for bleg1_ <dig> and bleg1_ <dig> model construction.
subsequently, multiple sequence alignment  of the templates with the query sequences was performed using clustalw  <cit>  to determine the degree of similarity and conservation of specific motifs and amino acids in the sequences.
3d models of both proteins were developed via homology modeling using modeller 9v <dig>  <cit> .
the best built models for bleg1_ <dig> and bleg1_ <dig> were chosen based on their lowest discrete optimized protein energy  values and ga  <dig> score of one, which signify that the models resemble the native structure and hence, reliable.
the generated models were visualized by pymol  <cit> .
to aid assessment and ease discussion on the models, a color gradient scheme representing different levels of hydrophobicity of the amino acid side chains  <cit>  were utilized.
further confirmation on the validity of the models was made based on their root mean square deviation  calculated by superimposing them with their respective templates using chimera uscf  <dig> .
<dig>  <cit> .
model refinement and validation
refinement of the built models was performed using foldx  <cit>   to remove van der waals clashes and bad contacts of amino acid side chains.
subsequently, structural evaluation and stereochemical analyses of the refined models were performed using errat which sets a 95% confidence limit being the cut-off value to evaluate any incorrect residues present in the protein structure based on the average of six atomic interactions in the protein i.e.
ƒ, ƒ, ƒ, ƒ, ƒ and ƒ  <cit> .
further supporting analysis to evaluate the models was performed using procheck ramachandran plot  <cit> .
docking of bleg1_ <dig> and bleg1_ <dig> models and energy minimization of protein complex
both of the models were docked by using cluspro v  <dig>   <cit>  to predict protein interaction.
subsequently, the docked protein complex was refined using amber force in yasara  <cit> .
RESULTS
domain and sequence similarity analyses and clustering of hps of b. lehensis g1
based on the bleg1db v <dig>  complete genome of the locally isolated alkaliphilic b. lehensis g <dig> , the  <dig>  mbp genome consisted of  <dig> predicted genes, in which  <dig> of them encode proteins with putative functions while  <dig> of them encode uncharacterized, hypothetical proteins .
interproscan analysis on all the hps revealed that  <dig> % of them were predicted with functions, while  <dig> % were of unknown functions and hence categorized as unknown proteins .
in the category of proteins with predicted functions, majority of the hps  were signal peptides, in which  <dig> of them were transmembrane peptides.
other than these signal peptides, there were other  <dig> transmembrane proteins as well.
the second most abundant type of hps  was predicted to have enzymatic functions.
the remaining numbers of hps were predicted to be regulatory proteins , metal-binding proteins  and antibiotic-related  .
bleg1_ <dig> and bleg1_ <dig>  sequence analyses
within the pool of metal-binding proteins, hp bleg1_ <dig> which consists of  <dig> amino acids was discovered to possess a copper chaperone sco <dig> domain related to trx-like superfamily from both interproscan and ncbi-cdd analyses .
sequence similarity analysis of the hp using blastp indicated that bleg1_ <dig> is similar to hps of other bacillus species with 40-50% identities .
additionally in the top  <dig> hits of the blastp analysis, results also indicated that bleg1_ <dig> shared similarity to electron transport protein sco <dig> of various microorganisms.
sco1/senc protein from planococcus antarcticus dsm  <dig> has the highest identity of 47% while the model sco <dig> protein from b. subtilis  surprisingly shared only 35% identity with bleg1_ <dig> .
further analysis on bleg1_ <dig> using scanprosite revealed that amino acids 31– <dig> matched a thioredoxin_ <dig> consensus pattern with total score of  <dig>  apart from this, analysis on the degree of amino acids conservation in bleg1_ <dig> using consurf revealed that cys- <dig>  cys- <dig> and his- <dig> were highly conserved and similar to the ones in the top  <dig> hits from the uniref  <dig> database of the consurf program.
the hits include the assembly factor of copper ii  site of cox in b. atrophaeus  <dig>  sco <dig> protein homolog from b. subtilis  and putative uncharacterized protein from b. clausii ksm- <dig>  in addition to this, these residues were also identified as potential metal-binding ligands via metaldetector v <dig>  analysis.
these metal-binding residues resemble those of sco <dig> proteins which similarly contain two cys and a his residues at their metal-binding sites  <cit> .
hence, there is a possibility that the conserved cys- <dig>  cys- <dig> and his- <dig> residues of bleg1_ <dig> form the metal binding site of bleg1_ <dig>  further analysis on the sequence of bleg1_ <dig> revealed that the protein also possessed cxxxc and dxxxd motifs, which are very well preserved in all eukaryotic and prokaryotic sco proteins  <cit> .
both of the conserved cys in the cxxxc motif of bleg1_ <dig> are made up of cys- <dig> and cys- <dig> respectively while the conserved asp in the dxxxd motif are made up of asp- <dig> and asp- <dig> respectively .
the conserved asp residues of the motif have been implicated in copper ion binding during cua assembly  <cit> .
since the results above highlight the possibility of hp bleg1_ <dig> to be a sco <dig> protein, a genome search for the sequence encoding the well-documented redox partner of sco <dig>  coxii  <cit>  was performed.
according to  <cit> , 82% of regular prokaryotic genomes possessed the same number of sco and coxii genes or the absence of both.
based on blastp result of bleg1_ <dig>  there were  <dig> hps which exhibited 40-50% of sequence similarity to bleg1_ <dig>  originating from b. halodurans, b. clausii ksm-k <dig> and b. pseudofirmus of <dig> .
search for coxii from the genomes of these microorganisms revealed that coxii was present in these microorganisms with the accession number of np_ <dig> , yp_ <dig>  and yp_ <dig>  respectively.
this suggested a correlation between these genes and highlights the possible presence of the coxii gene in the genome of b. lehensis g <dig>  the genome search led to the retrieval of bleg1_ <dig> sequence whereby blastp analysis on this  <dig> amino acids protein showed 80% identity to coxii of b. clausii ksm- <dig>  scanprosite analysis showed the presence of cox2_cua  domain in bleg1_ <dig> spanning from amino acid number 125– <dig>  three conserved amino acid residues namely cys- <dig>  cys- <dig> and his- <dig> were identified to be metal-binding ligands.
in addition to these residues, metal detector v <dig>  program predicted cys- <dig>  cys- <dig> and his- <dig> to be metal-binding ligands as well.
clustalw alignment of bleg1_ <dig> showed that its predicted metal-binding residues, cys- <dig>  cys- <dig> and his- <dig> are very well aligned with those of coxii sequences from other organisms such as thermus thermophiles, bos taurus and paracoccus denitrificans .
this result strengthens the prediction that bleg1_ <dig> is indeed a coxii protein and that the sets of conserved residues are indeed metal-binding ligands, similar with reported metal-binding ligands of other coxii proteins  <cit> .
further probing on bleg1_ <dig> using consurf indicated that several hydrophobic residues such as val- <dig>  ser- <dig>  phe- <dig>  trp- <dig> and pro- <dig> were found to be highly conserved as well .
such hydrophobic residues have been highlighted to play an important role in the hydrophobic interaction with sco protein  <cit> .
homology modeling of bleg1_ <dig> and bleg1_2337
potential templates for homology modeling of both bleg1_ <dig> and bleg1_ <dig> were retrieved using psi-blast  <cit>  search against pdb.
four templates were obtained for hp bleg1_ <dig>  alignment of these sequences with bleg1_ <dig> showed that cys- <dig>  cys- <dig> of the cxxxc motif, his- <dig>  asp- <dig> and asp- <dig> of the dxxxd motif of the hp aligned perfectly with all of the potential templates .
1xzo, chain a, which is a crystal structure of a disulfide switch in b. subtilis sco  and a well-studied member of the sco family of cox assembly proteins  <cit>  was selected as the template for homology modeling as it possessed the highest sequence similarity to bleg1_ <dig> with 39% identity and lower e-value of 5e- <dig> compared to other templates .
in addition to this, parsimony phylogenetic analysis from phylip also revealed that 1xzo is closely related to bleg1_ <dig> ), lending further credence for it to be used as the template for bleg1_ <dig> model generation.
as for bleg1_ <dig>  six templates were obtained and alignment of their sequences with bleg1_ <dig> showed that highly the conserved residues, cys- <dig>   <dig> and his- <dig> as well as the hydrophobic residues mentioned above were very well aligned.
2yev chain b, which is a crystal structure of caa3-type cytochrome oxidase thermus thermophilus hb <dig>  <cit>  was selected as the template for homology modeling of bleg1_ <dig> as it has the highest sequence identity of 37% and low e-value of 4e- <dig> when compared to other templates.
phylogenetic analysis from phylip also revealed that 2yev chain b is closely related to bleg1_ <dig> ).
the best built models for bleg1_ <dig> and bleg1_ <dig>  & ) have the lowest dope values and ga  <dig> scores of one, suggesting that the developed models resemble the native structure and hence reliable.
further supporting results from the superimposition of all cα atoms of both developed models and templates gave forth low rmsd of less than  <dig>  Å, suggesting that the built models are indeed reliable.
bleg1_ <dig> and bleg1_ <dig> model refinement and validation
refinement of the built models using foldx in yasara resulted in minimization of the free energy of bleg1_ <dig> from  <dig>  kcal/mol to  <dig>  kcal/mol and from  <dig>  kcal/mol to  <dig>  kcal/mol for bleg1_ <dig>
evaluations on the quality of the refined protein structures using errat  <cit>  indicated that  <dig> % of the amino acids of the refined bleg1_ <dig> model were located in the acceptable region within 95% confidence limit, as opposed to only  <dig> % before refinement.
as for refined bleg1_ <dig> model,  <dig> % of its amino acids were located in the acceptable region within the 95% confidence limit, as opposed to only  <dig> % before refinement.
these indicated that the refined protein models for bleg1_ <dig> and bleg1_ <dig>  & ) were precise and reliable since the frequencies of atom randomizations were low.
further supporting results from procheck ramachandran analysis on refined bleg1_ <dig> model revealed that  <dig> % of the residues were located in favored region,  <dig> % in additional allowed region,  <dig> % and  <dig> % in generously allowed and disallowed regions respectively.
as for bleg1_ <dig> refined model,  <dig> % of the residues were located in favored region,  <dig> % in additional allowed region and 2% were located in generously allowed region.
overall, both errat and procheck evaluations further reaffirmed that both of the predicted protein models were reliable.
probing the structures of bleg1_ <dig> and bleg1_2337
overall, the built model for hp bleg1_ <dig> showed that it adopted a global topology unique to thioredoxin -like superfamily of proteins including sco proteins whereby four β-sheets  are flanked by three α-helices  at the core of the structure ).
this is similar to trx-like superfamily members which have a characteristic, common core βαβαββ secondary structural pattern with different insertions of secondary structural elements to distinguish the various structural families such as thioltransferases, glutaredoxins, bacterial arsenate reductases and disulfide bond isomerases.
they are in general involved in cellular thiol-redox reactions to maintain the reduction and oxidation of proteins or certain small molecules  <cit> .
other than this core structure, bleg1_ <dig> also consisted three flanking β-sheets , a  <dig> –helix at the n-terminus and a hairpin formed by β <dig> and β <dig>  which are the additional secondary structure elements only present in sco proteins  <cit> .
other similarities between include the presence of a transmembrane region in the n-terminal of bleg1_ <dig> in which an external loop comprising of  <dig> amino acids at the n-terminus could be observed ).
sigcleave analysis from emboss  <cit>  revealed that the amino acids from leu- <dig> to cys- <dig> in this loop were predicted to be a signal peptide, which can be subjected to cleavage to give forth the mature protein.
previous study has shown that in the sco protein of b. subtilis,  the first  <dig> amino acids are located in the transmembrane and cys- <dig> is the signal peptidase ii recognition site.
to this cleaved site a diacyl glycerol moiety will be attached to the protein and the post-translationally modified protein will subsequently be able to anchor to the membrane through the attached lipid by covalent bond  <cit> .
this in turn highlights that cys- <dig> in hp bleg1_ <dig> is most probably a cleavage recognition site similar to the one found in bssco for processing of the native sco protein before it can be partially integrated into the membrane.
unique to bleg1_ <dig> however, there is an α-helix  near loop  <dig> and a β-strand  that are parallel with β <dig> and β <dig> ), which are not present in trx.
in addition to this, the location of the metal-binding ligands in bleg1_ <dig> is different from the solution structure of bssco.
for instance, in the predicted model of bleg1_ <dig>  both metal-binding cys- <dig> and cys- <dig> residues were located in loop  <dig>  while his- <dig> was positioned in loop  <dig>  ).
in bssco on the other hand, its metal-binding residues, namely cys- <dig> and cys- <dig>  were located in loop  <dig> and the conserved his- <dig> was located in loop  <dig>  <cit> .
looking closely at the predicted metal-binding cavity of bleg1_ <dig>  it featured the highly conserved cys- <dig>  cys- <dig>  and his- <dig> residues.
these residues which are strictly preserved in all sco proteins have been implicated to be responsible in copper-binding and redox reaction  <cit> .
in proximity to the cxxxc motif, a hydrophobic groove which is formed by phe- <dig>   <dig>  ala- <dig>  val- <dig>  met- <dig>   <dig> and pro- <dig> was observed ).
besides this, another hydrophobic groove formed by the his-ligand loop consisting of val- <dig>  pro- <dig>   <dig>  ala- <dig>  gly- <dig>  ile- <dig>   <dig>  and phe- <dig> was also observed ).
both of the hydrophobic grooves formed a hydrophobic pocket which may allow proteins and small molecules such as copper ion to be accommodated  <cit> .
according to balatri et al.,  <dig>  <cit> , the interaction of hydrophobic residues within the protein are essential in the metallated state of sco, because it is able to stabilize the metal-ligand region of the protein, which are located far apart from each other within the two hydrophobic grooves, by coordinating the metal-ligand geometry.
based on the sco <dig> protein crystal structures from b. subtilis <cit> , yeast  <cit>  and human  <cit>  the distances between the n atoms of his residues and the s atom of cysteine pair are in the range of 10–19 Å. in the case of bleg1_ <dig>  the distance between nϵ <dig> of his- <dig> and s of cys- <dig> was ~ <dig>  Å, while the distance between nδ <dig> of his- <dig> and s of cys- <dig> was ~ <dig>  Å ), similar to the range noted above for the respective sco <dig> proteins from b. subtilis, yeast and human.
these distances are considered far for metal-ligand interaction in the apo-form state of the predicted sco protein.
it has been proposed by balatri et al.,  <dig>  <cit>  that the hydrophobic residues in the hydrophobic grooves of bleg1_ <dig> might be responsible in regulating the appropriate geometric coordination for metal-ligand interaction to occur.
according to andruzzi et al.
<cit> , the oxidized bssco was coordinated to cu by a distorted tetragonal square planar, in which the cys- <dig>  cys- <dig> and his- <dig> are ligated equatorially and water was ligated axially to the cu respectively.
hence, cys- <dig>  cys- <dig> and his- <dig> of the predicted sco of bleg1_ <dig> was proposed to coordinate the copper through square planar geometry.
based on these observations, we propose that this particular hp is potentially a sco protein with an ability to bind and chaperone copper to the cua site in coxii.
interaction between bleg1_ <dig> and putative coxii redox protein, bleg1_ <dig> and their possible mechanism of action
to test the above hypothesis, hp bleg1_ <dig> was docked to its predicted redox partner, bleg1_ <dig>  a putative coxii protein to investigate possible interaction between these two proteins.
docking results showed that bleg1_ <dig> was indeed able to interact with bleg1_ <dig> with lowest energy of − <dig>  kj/mol.
from the results, bleg1_ <dig> could be seen embracing bleg1_ <dig> with an extended arm ).
refinement of the docked protein complex successfully decreased the potential energy from − <dig>  kj/mol to − <dig>  kj/mol signifying favorable protein conformation.
inspecting the interface of both interacting proteins, bleg1_ <dig> possessed a set of acidic residues such as asp- <dig>   <dig>   <dig> and  <dig>  glu- <dig>   <dig> and  <dig> on its surface ).
this observation lends support to protparam analysis which revealed that bleg1_ <dig> has an acidic pi of  <dig> , indicating this hp has abundant number of acidic residues.
its putative cox partner, bleg1_ <dig>  on the other hand, possessed a set of positively charged, basic residues on its surface such as lys- <dig>   <dig>   <dig> ,  <dig> and  <dig>  arg- <dig>   <dig> and  <dig> and his- <dig> ), which gave the protein a basic pi value of  <dig>  according to protparam analysis.
the presence of these oppositely charged residues on the respective proteins undoubtedly facilitated ionic interaction between the two macromolecules.
such ionic interaction between sco and cox proteins has been similarly observed and was proposed to generate a charged-mediated sco-apo-cua located in the cox protein which will allow copper exchange to occur  <cit> .
based on the mechanism proposed for bssco protein, for copper to be bound and later transferred from sco to cox, both of the conserved cysteine residues in the cxxxc motif of bssco will be firstly reduced to di-thiol state via formation of sh-sh bond.
this will result in a reduced bssco protein that is able to strongly interact with cu ion to form bssco-cu complex.
from the bssco-cu complex, the metal ion will then be transferred to its intended target i.e.
apo-subunit ii of cox via association of both of the proteins .
in this process, the histidine residue was postulated to play an important role in this second phase of copper coordination by regulating the structural dynamism of bacterial sco  <cit> .
during association of both of the proteins, apart from metal ion transfer, an oxidation-reduction  process also takes place via electron transfer  <cit> .
during interaction of the proteins, bssco will undergo oxidation by releasing electrons which will be subsequently delivered to the binuclear cua site of coxii.
consequently, the received electrons in the cua site of coxii which made up of cys- <dig>   <dig> and his- <dig> will reduce fe to fe or cu to cu  <cit> .
the di-thiol state of bssco is vital in this electron transfer process and maintaining the redox state of the partner.
in the case of bleg1_ <dig>  it is therefore highly possible that it may possess redox properties by potentially acting as a thiol disulfide oxidoreductase.
similar to bssco, both the conserved cys- <dig> and cys- <dig> in bleg1_ <dig> may also form the sh-sh bond and give forth the di-thiol state of the protein.
from this point onwards, bleg1_ <dig> hp may be able to undergo oxidation to release electrons which are subsequently delivered to the binuclear cua site of reduced coxii of bleg1_ <dig> which were made up of cys- <dig>   <dig> and his- <dig> and cys- <dig>   <dig> and his- <dig> , to reduce the respective metal ion at the site.
this postulation is further supported by the presence of hydrophobic grooves in hp bleg1_ <dig> which form an extensive uncharged surface surrounding the active disulfide bond formed by cys- <dig>  cys- <dig> and his- <dig> encompassed in a solvent exposed environment which might facilitate the electron transfer process, similar to the features observed in bssco  <cit> .
it is worthy to note that other than binding metal ions, the conserved cys pair and his-ligand loops of sco proteins are important for sco to interact with other proteins as well  <cit> .
this feature was clearly observed in our docking results where these residues of hp bleg1_ <dig> are shown to interact with putative coxii  via hydrophobic interaction, stabilized by uncharged surface features surrounding the hydrophobic pocket between loop  <dig> and loop  <dig> ).
in the cysteine pair loop , it possessed uncharged polar residues such as thr- <dig>   <dig>   <dig> and  <dig> and asn- <dig>  while, thr- <dig>   <dig> and ser- <dig> were located in the his-ligand loop .
similarly in its redox partner, the putative coxii , crucial hydrophobic residues such as val- <dig> and  <dig>  gly- <dig>  trp- <dig> and  <dig>  ile- <dig>  pro- <dig> and  <dig>  leu- <dig>  phe- <dig> and  <dig>  thr- <dig>  ser- <dig> and pro <dig> may have contributed to the interaction of both proteins ), in accordance to other similarly reported study  <cit> .
all of these residues are crucial in maintaining the intactness of sco-cua protein complex for electron transfer  <cit> .
structural and functional comparison of sco proteins
comparing the sequences of the predicted sco bleg1_ <dig>  bssco , human sco <dig>  and yeast sco <dig> , these proteins share many conserved residues regardless of their taxonomic and sequence differences .
superimposition of predicted protein model of bleg1_ <dig> with the 3d structure of bssco showed that they are highly similar with rmsd value of  <dig>  Å ).
interestingly, superimposition of predicted protein model of bleg1_ <dig> with the 3d structures of human and yeast sco <dig> showed that their structures are comparatively similar as well even at rmsd values of  <dig>  Å and  <dig>  Å respectively ).
it is important to note that bleg1_ <dig>  bssco and sco <dig> of yeast contain the same number of β-sheets and α-helices i.e.
eight and four respectively.
the 3d structure of human sco <dig> , however, contained only six β-sheets.
the two additional β sheets in bleg1_ <dig> are β <dig> and β <dig>  which forms the hairpin structure located before the 310- helix at the n-terminus.
in addition, although bleg1_ <dig> shares relatively low sequence identity to bssco , human sco <dig>   and yeast sco <dig> , the predicted metal-binding residues of bleg1_ <dig> i.e.
cys- <dig>  cys- <dig> and his- <dig>  were located at flexible active loops  similar to other sco proteins across biological taxa.
it is indeed interesting to note that despite their remarkable structural similarity, sco proteins are rather diverse in function.
in eukaryotes, sco proteins are involved in the assembly of the cua cofactor of mitochondrial cytochrome c oxidase, redox signaling and regulation of copper homeostasis  <cit> .
in prokaryotes, sco proteins are more promiscuous in functions.
while some are required for cox biosynthesis, others have been implicated in different processes such as copper delivery to other enzymes and protection against oxidative stress  <cit> .
more investigations as to the physiological function and mechanism of sco proteins will be useful in determining its exact role and importance in the system biology of an organism.
CONCLUSIONS
in this study, genome mining of hypothetical protein sequences of b. lehensis g <dig> alkaliphile led to the discovery of bleg1_ <dig> which showed the presence of a trx-like domain linked to sco protein.
showing only 35% of similarity to bssco, the prokaryotic model of sco, the 3-d model of bleg1_ <dig> was built by homology modeling.
the built protein model showed good preservation of the βαβαββ core structure , three flanking β-sheets, a  <dig> –helix at the n-terminus and a hairpin .
unique to bleg1_ <dig>  there is an α-helix  near loop  <dig> and a β-strand  that are parallel with β <dig> and β <dig>  which are not present in trx.
another distinct feature of bleg1_ <dig> compared to bssco is the difference in the location of the metal-binding ligands in bleg1_ <dig>  docking simulations interestingly provided a view of bleg1_ <dig> in association with its putative coxii redox partner, bleg1_ <dig>  where the latter can be seen to hold its partner in an embrace, facilitated via hydrophobic and ionic interaction between the two proteins.
although bleg1_ <dig> shares relatively low sequence homology to bssco, interestingly, it is structurally similar to the protein as well as other sco proteins across biological taxa.
this observation highlights that despite its varying functions in prokaryotes and eukaryotes, sco proteins are structurally well preserved.
based on all the results obtained, we hereby propose that hp bleg1_ <dig> of b. lehensis g <dig> is a sco protein which is able to interact with coxii, its redox partner.
hence, it is highly possible that hp bleg1_ <dig> may possess metallochaperone and disulfide redox functions similar to other documented bacterial sco proteins.
it is hoped that the predicted structure and function of bleg1_ <dig> from the hypothetical protein dataset of b. lehensis g <dig> will help to spur the search for other physiologically relevant proteins among the so-called “orphan” proteins of any given organism as well as direct future biological studies in improving our understanding of cox complex assembly process.
competing interests
the authors declare that they have no competing interests.
authors’ contributions
tsh carried out bioinformatics analyses and clustering of all the hypothetical proteins, homology modelling and protein docking in this study.
tsh and ymn drafted the manuscript.
abs, mbar, rak, altc, amam, nmm revised and proofread the manuscript.
ymn conceived the study and participated in its design and coordination together with abs, mbar.
rak, altc, amam gave technical advice to the study.
all authors read and approved the final manuscript.

 hypothetical proteins are generally known as proteins of unknown structures and functions. they constitute approximately 25% of any sequenced genome even in simple, model organisms such as escherichia coli, bacillus subtilis and saccharomyces cerevisiae. annotating their biological function has remained a challenge due to their low sequence and structural homology to other known proteins. this in turn creates difficulties in attempts to understand a biological system as a whole due to the information gaps posed by these “orphan” proteins. therefore, efforts in trying to unravel their structures and functions are crucial in filling these information gaps for any particular system and hence, should be encouraged. to deepen our understanding on these proteins, in silico methods of analysis are the most time and cost effective in generating a wealth of reliable and useful information on hps ranging from their localization, properties to their possible structures and functions. it also provides a quick means to preliminary screen and chooses potential hps for subsequent downstream in vitro and in vivo experiments, particularly to initiate structural genomic projects in the future. with the wealth of information which can be generated using the in silico approach, this present study highlights the utilization of various in silico tools and methods to functionally predict and cluster all hps present in the complete genome of a locally isolated alkaliphile, bacillus lehensis g with the purpose of establishing a platform to mine and later select specific hps to be studied further in greater detail. whilst the genome of this alkaliphile has been completely sequenced, the structural and functional omics of this extremophile is not well characterised, particularly its hps. hence, our attempt at firstly predicting their functions and clustering them accordingly will serve as a platform in mining and selecting specific hps to be studied further in greater detail. stemming from this effort, our attention was led to a particular hp, bleg1_ in the metalloprotein category of the cluster. this hp contained a sco domain of the thioredoxin superfamily and showed up to 50% of sequence identity to other bacterial hps and 47% to bacterial sco proteins. it is important to note that sco proteins are present in both prokaryotic and eukaryotic organisms and are required for the proper assembly of cytochrome c oxidase, a terminal enzyme in the respiratory chain. sco was suggested to be involved in the delivery of copper ion to cox complex –. to date, the only bacterial sco protein which was structurally studied and analysed at length is from bacillus subtilis while its eukaryotic counterpart is from yeast, human and plant. sco proteins have garnered importance in recent years due to their roles in the correct assembly of the copper center of cox subunit ii. improper assembly of cox has been reported to cause fatal infantile encephalopathy due to mutations in sco and sco genes in humans. due to the physiological relevance of sco proteins, we embarked on the task of building the structure of hp bleg1_ of b. lehensis g via homology modelling to investigate the structural similarities and differences between this protein with sco protein from b. subtilis, yeast and human. as sco was suggested to be involved in the delivery of copper ion to cox complex, specifically coxii –, we subsequently mined the genome of b. lehensis g for the sequence encoding coxii by performing a blastp search. as a result, bleg1_ was retrieved and its structure was built via homology modelling. docking of both hp bleg1_ and bleg1_ models was performed to investigate their possible interaction. based on the results obtained, the possible structure, function and mechanism of hp bleg1_ from b. lehensis g are duly discussed. lastly, the structure of hp bleg1_ of b. lehensis g was compared to other sco proteins to highlight its similarity and distinctness. methods domain and sequence similarity analysis of hps of b. lehensis g1: development of an hp cluster all sequences encoding hps in the genome of b. lehensis g were firstly subjected to interproscan and conserved domain search analyses to detect possible functional domains within the sequences. sequence similarity of all the hps with other proteins in the database was investigated also using blastp. based on the predicted functional domains and sequence similarity, an hp cluster was built to categorize the proteins accordingly. a scan on hps which showed acceptable similarity to other proteins with low e-value was carried out and the potential candidate was chosen for further analyses and structure prediction. sequence analysis of selected hp and putative cytochrome c oxidase subunit ii, coxii from the above scan, a particular hp in the metal-binding group of proteins encoded by bleg1_ gene was chosen for further analyses based on the presence of the conserved copper chaperone sco domain related to trx-like superfamily. firstly, the possible presence of consensus amino acids pattern in bleg1_ sequence was identified using scanprosite. important and metal-binding residues were subsequently identified using consurf and metaldetector v respectively. the physicochemical aspect of the protein such as its theoretical pi value was investigated using protparam. sigcleave from emboss was used to investigate the possible presence of signal peptide in bleg1_ while the evolutionary relatedness of the protein with other known proteins was investigated using phylip. subsequently, a genome-wide scan for bleg1_ redox partner i.e. cytochrome c oxidase subunit ii, was performed. as a result, bleg1_ a putative coxii protein was identified from the genome sequence of b. lehensis g further analyses similar to the ones mentioned above were performed on bleg1_ homology modeling of hp bleg1_ and bleg1_2337 psi-blast search against protein data bank was performed to retrieve potential templates for bleg1_ and bleg1_ model construction. subsequently, multiple sequence alignment of the templates with the query sequences was performed using clustalw to determine the degree of similarity and conservation of specific motifs and amino acids in the sequences. 3d models of both proteins were developed via homology modeling using modeller 9v. the best built models for bleg1_ and bleg1_ were chosen based on their lowest discrete optimized protein energy values and ga score of one, which signify that the models resemble the native structure and hence, reliable. the generated models were visualized by pymol. to aid assessment and ease discussion on the models, a color gradient scheme representing different levels of hydrophobicity of the amino acid side chains were utilized. further confirmation on the validity of the models was made based on their root mean square deviation calculated by superimposing them with their respective templates using chimera uscf.. model refinement and validation refinement of the built models was performed using foldx to remove van der waals clashes and bad contacts of amino acid side chains. subsequently, structural evaluation and stereochemical analyses of the refined models were performed using errat which sets a 95% confidence limit being the cut-off value to evaluate any incorrect residues present in the protein structure based on the average of six atomic interactions in the protein i.e. ƒ, ƒ, ƒ, ƒ, ƒ and ƒ. further supporting analysis to evaluate the models was performed using procheck ramachandran plot. docking of bleg1_ and bleg1_ models and energy minimization of protein complex both of the models were docked by using cluspro v to predict protein interaction. subsequently, the docked protein complex was refined using amber force in yasara.  domain and sequence similarity analyses and clustering of hps of b. lehensis g1 based on the bleg1db v complete genome of the locally isolated alkaliphilic b. lehensis g, the mbp genome consisted of predicted genes, in which of them encode proteins with putative functions while of them encode uncharacterized, hypothetical proteins. interproscan analysis on all the hps revealed that % of them were predicted with functions, while % were of unknown functions and hence categorized as unknown proteins. in the category of proteins with predicted functions, majority of the hps were signal peptides, in which of them were transmembrane peptides. other than these signal peptides, there were other transmembrane proteins as well. the second most abundant type of hps was predicted to have enzymatic functions. the remaining numbers of hps were predicted to be regulatory proteins, metal-binding proteins and antibiotic-related. bleg1_ and bleg1_ sequence analyses within the pool of metal-binding proteins, hp bleg1_ which consists of amino acids was discovered to possess a copper chaperone sco domain related to trx-like superfamily from both interproscan and ncbi-cdd analyses. sequence similarity analysis of the hp using blastp indicated that bleg1_ is similar to hps of other bacillus species with 40-50% identities. additionally in the top hits of the blastp analysis, results also indicated that bleg1_ shared similarity to electron transport protein sco of various microorganisms. sco1/senc protein from planococcus antarcticus dsm has the highest identity of 47% while the model sco protein from b. subtilis surprisingly shared only 35% identity with bleg1_. further analysis on bleg1_ using scanprosite revealed that amino acids 31– matched a thioredoxin_ consensus pattern with total score of apart from this, analysis on the degree of amino acids conservation in bleg1_ using consurf revealed that cys- cys- and his- were highly conserved and similar to the ones in the top hits from the uniref database of the consurf program. the hits include the assembly factor of copper ii site of cox in b. atrophaeus sco protein homolog from b. subtilis and putative uncharacterized protein from b. clausii ksm- in addition to this, these residues were also identified as potential metal-binding ligands via metaldetector v analysis. these metal-binding residues resemble those of sco proteins which similarly contain two cys and a his residues at their metal-binding sites. hence, there is a possibility that the conserved cys- cys- and his- residues of bleg1_ form the metal binding site of bleg1_ further analysis on the sequence of bleg1_ revealed that the protein also possessed cxxxc and dxxxd motifs, which are very well preserved in all eukaryotic and prokaryotic sco proteins. both of the conserved cys in the cxxxc motif of bleg1_ are made up of cys- and cys- respectively while the conserved asp in the dxxxd motif are made up of asp- and asp- respectively. the conserved asp residues of the motif have been implicated in copper ion binding during cua assembly. since the results above highlight the possibility of hp bleg1_ to be a sco protein, a genome search for the sequence encoding the well-documented redox partner of sco coxii was performed. according to, 82% of regular prokaryotic genomes possessed the same number of sco and coxii genes or the absence of both. based on blastp result of bleg1_ there were hps which exhibited 40-50% of sequence similarity to bleg1_ originating from b. halodurans, b. clausii ksm-k and b. pseudofirmus of. search for coxii from the genomes of these microorganisms revealed that coxii was present in these microorganisms with the accession number of np_, yp_ and yp_ respectively. this suggested a correlation between these genes and highlights the possible presence of the coxii gene in the genome of b. lehensis g the genome search led to the retrieval of bleg1_ sequence whereby blastp analysis on this amino acids protein showed 80% identity to coxii of b. clausii ksm- scanprosite analysis showed the presence of cox2_cua domain in bleg1_ spanning from amino acid number 125– three conserved amino acid residues namely cys- cys- and his- were identified to be metal-binding ligands. in addition to these residues, metal detector v program predicted cys- cys- and his- to be metal-binding ligands as well. clustalw alignment of bleg1_ showed that its predicted metal-binding residues, cys- cys- and his- are very well aligned with those of coxii sequences from other organisms such as thermus thermophiles, bos taurus and paracoccus denitrificans. this result strengthens the prediction that bleg1_ is indeed a coxii protein and that the sets of conserved residues are indeed metal-binding ligands, similar with reported metal-binding ligands of other coxii proteins. further probing on bleg1_ using consurf indicated that several hydrophobic residues such as val- ser- phe- trp- and pro- were found to be highly conserved as well. such hydrophobic residues have been highlighted to play an important role in the hydrophobic interaction with sco protein. homology modeling of bleg1_ and bleg1_2337 potential templates for homology modeling of both bleg1_ and bleg1_ were retrieved using psi-blast search against pdb. four templates were obtained for hp bleg1_ alignment of these sequences with bleg1_ showed that cys- cys- of the cxxxc motif, his- asp- and asp- of the dxxxd motif of the hp aligned perfectly with all of the potential templates. 1xzo, chain a, which is a crystal structure of a disulfide switch in b. subtilis sco and a well-studied member of the sco family of cox assembly proteins was selected as the template for homology modeling as it possessed the highest sequence similarity to bleg1_ with 39% identity and lower e-value of 5e- compared to other templates. in addition to this, parsimony phylogenetic analysis from phylip also revealed that 1xzo is closely related to bleg1_ ), lending further credence for it to be used as the template for bleg1_ model generation. as for bleg1_ six templates were obtained and alignment of their sequences with bleg1_ showed that highly the conserved residues, cys- and his- as well as the hydrophobic residues mentioned above were very well aligned. 2yev chain b, which is a crystal structure of caa3-type cytochrome oxidase thermus thermophilus hb was selected as the template for homology modeling of bleg1_ as it has the highest sequence identity of 37% and low e-value of 4e- when compared to other templates. phylogenetic analysis from phylip also revealed that 2yev chain b is closely related to bleg1_ ). the best built models for bleg1_ and bleg1_ & ) have the lowest dope values and ga scores of one, suggesting that the developed models resemble the native structure and hence reliable. further supporting results from the superimposition of all cα atoms of both developed models and templates gave forth low rmsd of less than  Å, suggesting that the built models are indeed reliable. bleg1_ and bleg1_ model refinement and validation refinement of the built models using foldx in yasara resulted in minimization of the free energy of bleg1_ from  kcal/mol to  kcal/mol and from  kcal/mol to  kcal/mol for bleg1_ evaluations on the quality of the refined protein structures using errat indicated that % of the amino acids of the refined bleg1_ model were located in the acceptable region within 95% confidence limit, as opposed to only % before refinement. as for refined bleg1_ model, % of its amino acids were located in the acceptable region within the 95% confidence limit, as opposed to only % before refinement. these indicated that the refined protein models for bleg1_ and bleg1_ & ) were precise and reliable since the frequencies of atom randomizations were low. further supporting results from procheck ramachandran analysis on refined bleg1_ model revealed that % of the residues were located in favored region, % in additional allowed region, % and % in generously allowed and disallowed regions respectively. as for bleg1_ refined model, % of the residues were located in favored region, % in additional allowed region and 2% were located in generously allowed region. overall, both errat and procheck evaluations further reaffirmed that both of the predicted protein models were reliable. probing the structures of bleg1_ and bleg1_2337 overall, the built model for hp bleg1_ showed that it adopted a global topology unique to thioredoxin -like superfamily of proteins including sco proteins whereby four β-sheets are flanked by three α-helices at the core of the structure ). this is similar to trx-like superfamily members which have a characteristic, common core βαβαββ secondary structural pattern with different insertions of secondary structural elements to distinguish the various structural families such as thioltransferases, glutaredoxins, bacterial arsenate reductases and disulfide bond isomerases. they are in general involved in cellular thiol-redox reactions to maintain the reduction and oxidation of proteins or certain small molecules. other than this core structure, bleg1_ also consisted three flanking β-sheets, a –helix at the n-terminus and a hairpin formed by β and β which are the additional secondary structure elements only present in sco proteins. other similarities between include the presence of a transmembrane region in the n-terminal of bleg1_ in which an external loop comprising of amino acids at the n-terminus could be observed ). sigcleave analysis from emboss revealed that the amino acids from leu- to cys- in this loop were predicted to be a signal peptide, which can be subjected to cleavage to give forth the mature protein. previous study has shown that in the sco protein of b. subtilis, the first amino acids are located in the transmembrane and cys- is the signal peptidase ii recognition site. to this cleaved site a diacyl glycerol moiety will be attached to the protein and the post-translationally modified protein will subsequently be able to anchor to the membrane through the attached lipid by covalent bond. this in turn highlights that cys- in hp bleg1_ is most probably a cleavage recognition site similar to the one found in bssco for processing of the native sco protein before it can be partially integrated into the membrane. unique to bleg1_ however, there is an α-helix near loop and a β-strand that are parallel with β and β ), which are not present in trx. in addition to this, the location of the metal-binding ligands in bleg1_ is different from the solution structure of bssco. for instance, in the predicted model of bleg1_ both metal-binding cys- and cys- residues were located in loop while his- was positioned in loop ). in bssco on the other hand, its metal-binding residues, namely cys- and cys- were located in loop and the conserved his- was located in loop. looking closely at the predicted metal-binding cavity of bleg1_ it featured the highly conserved cys- cys- and his- residues. these residues which are strictly preserved in all sco proteins have been implicated to be responsible in copper-binding and redox reaction. in proximity to the cxxxc motif, a hydrophobic groove which is formed by phe- ala- val- met- and pro- was observed ). besides this, another hydrophobic groove formed by the his-ligand loop consisting of val- pro- ala- gly- ile- and phe- was also observed ). both of the hydrophobic grooves formed a hydrophobic pocket which may allow proteins and small molecules such as copper ion to be accommodated. according to balatri et al.,, the interaction of hydrophobic residues within the protein are essential in the metallated state of sco, because it is able to stabilize the metal-ligand region of the protein, which are located far apart from each other within the two hydrophobic grooves, by coordinating the metal-ligand geometry. based on the sco protein crystal structures from b. subtilis, yeast and human the distances between the n atoms of his residues and the s atom of cysteine pair are in the range of 10–19 Å. in the case of bleg1_ the distance between nϵ of his- and s of cys- was ~  Å, while the distance between nδ of his- and s of cys- was ~  Å ), similar to the range noted above for the respective sco proteins from b. subtilis, yeast and human. these distances are considered far for metal-ligand interaction in the apo-form state of the predicted sco protein. it has been proposed by balatri et al., that the hydrophobic residues in the hydrophobic grooves of bleg1_ might be responsible in regulating the appropriate geometric coordination for metal-ligand interaction to occur. according to andruzzi et al., the oxidized bssco was coordinated to cu by a distorted tetragonal square planar, in which the cys- cys- and his- are ligated equatorially and water was ligated axially to the cu respectively. hence, cys- cys- and his- of the predicted sco of bleg1_ was proposed to coordinate the copper through square planar geometry. based on these observations, we propose that this particular hp is potentially a sco protein with an ability to bind and chaperone copper to the cua site in coxii. interaction between bleg1_ and putative coxii redox protein, bleg1_ and their possible mechanism of action to test the above hypothesis, hp bleg1_ was docked to its predicted redox partner, bleg1_ a putative coxii protein to investigate possible interaction between these two proteins. docking results showed that bleg1_ was indeed able to interact with bleg1_ with lowest energy of − kj/mol. from the results, bleg1_ could be seen embracing bleg1_ with an extended arm ). refinement of the docked protein complex successfully decreased the potential energy from − kj/mol to − kj/mol signifying favorable protein conformation. inspecting the interface of both interacting proteins, bleg1_ possessed a set of acidic residues such as asp- and glu- and on its surface ). this observation lends support to protparam analysis which revealed that bleg1_ has an acidic pi of, indicating this hp has abundant number of acidic residues. its putative cox partner, bleg1_ on the other hand, possessed a set of positively charged, basic residues on its surface such as lys-, and arg- and and his- ), which gave the protein a basic pi value of according to protparam analysis. the presence of these oppositely charged residues on the respective proteins undoubtedly facilitated ionic interaction between the two macromolecules. such ionic interaction between sco and cox proteins has been similarly observed and was proposed to generate a charged-mediated sco-apo-cua located in the cox protein which will allow copper exchange to occur. based on the mechanism proposed for bssco protein, for copper to be bound and later transferred from sco to cox, both of the conserved cysteine residues in the cxxxc motif of bssco will be firstly reduced to di-thiol state via formation of sh-sh bond. this will result in a reduced bssco protein that is able to strongly interact with cu ion to form bssco-cu complex. from the bssco-cu complex, the metal ion will then be transferred to its intended target i.e. apo-subunit ii of cox via association of both of the proteins. in this process, the histidine residue was postulated to play an important role in this second phase of copper coordination by regulating the structural dynamism of bacterial sco. during association of both of the proteins, apart from metal ion transfer, an oxidation-reduction process also takes place via electron transfer. during interaction of the proteins, bssco will undergo oxidation by releasing electrons which will be subsequently delivered to the binuclear cua site of coxii. consequently, the received electrons in the cua site of coxii which made up of cys- and his- will reduce fe to fe or cu to cu. the di-thiol state of bssco is vital in this electron transfer process and maintaining the redox state of the partner. in the case of bleg1_ it is therefore highly possible that it may possess redox properties by potentially acting as a thiol disulfide oxidoreductase. similar to bssco, both the conserved cys- and cys- in bleg1_ may also form the sh-sh bond and give forth the di-thiol state of the protein. from this point onwards, bleg1_ hp may be able to undergo oxidation to release electrons which are subsequently delivered to the binuclear cua site of reduced coxii of bleg1_ which were made up of cys- and his- and cys- and his-, to reduce the respective metal ion at the site. this postulation is further supported by the presence of hydrophobic grooves in hp bleg1_ which form an extensive uncharged surface surrounding the active disulfide bond formed by cys- cys- and his- encompassed in a solvent exposed environment which might facilitate the electron transfer process, similar to the features observed in bssco. it is worthy to note that other than binding metal ions, the conserved cys pair and his-ligand loops of sco proteins are important for sco to interact with other proteins as well. this feature was clearly observed in our docking results where these residues of hp bleg1_ are shown to interact with putative coxii via hydrophobic interaction, stabilized by uncharged surface features surrounding the hydrophobic pocket between loop and loop ). in the cysteine pair loop, it possessed uncharged polar residues such as thr- and and asn- while, thr- and ser- were located in the his-ligand loop. similarly in its redox partner, the putative coxii, crucial hydrophobic residues such as val- and gly- trp- and ile- pro- and leu- phe- and thr- ser- and pro may have contributed to the interaction of both proteins ), in accordance to other similarly reported study. all of these residues are crucial in maintaining the intactness of sco-cua protein complex for electron transfer. structural and functional comparison of sco proteins comparing the sequences of the predicted sco bleg1_ bssco, human sco and yeast sco, these proteins share many conserved residues regardless of their taxonomic and sequence differences. superimposition of predicted protein model of bleg1_ with the 3d structure of bssco showed that they are highly similar with rmsd value of  Å ). interestingly, superimposition of predicted protein model of bleg1_ with the 3d structures of human and yeast sco showed that their structures are comparatively similar as well even at rmsd values of  Å and  Å respectively ). it is important to note that bleg1_ bssco and sco of yeast contain the same number of β-sheets and α-helices i.e. eight and four respectively. the 3d structure of human sco, however, contained only six β-sheets. the two additional β sheets in bleg1_ are β and β which forms the hairpin structure located before the 310- helix at the n-terminus. in addition, although bleg1_ shares relatively low sequence identity to bssco, human sco and yeast sco, the predicted metal-binding residues of bleg1_ i.e. cys- cys- and his- were located at flexible active loops similar to other sco proteins across biological taxa. it is indeed interesting to note that despite their remarkable structural similarity, sco proteins are rather diverse in function. in eukaryotes, sco proteins are involved in the assembly of the cua cofactor of mitochondrial cytochrome c oxidase, redox signaling and regulation of copper homeostasis. in prokaryotes, sco proteins are more promiscuous in functions. while some are required for cox biosynthesis, others have been implicated in different processes such as copper delivery to other enzymes and protection against oxidative stress. more investigations as to the physiological function and mechanism of sco proteins will be useful in determining its exact role and importance in the system biology of an organism.  in this study, genome mining of hypothetical protein sequences of b. lehensis g alkaliphile led to the discovery of bleg1_ which showed the presence of a trx-like domain linked to sco protein. showing only 35% of similarity to bssco, the prokaryotic model of sco, the 3-d model of bleg1_ was built by homology modeling. the built protein model showed good preservation of the βαβαββ core structure, three flanking β-sheets, a –helix at the n-terminus and a hairpin. unique to bleg1_ there is an α-helix near loop and a β-strand that are parallel with β and β which are not present in trx. another distinct feature of bleg1_ compared to bssco is the difference in the location of the metal-binding ligands in bleg1_ docking simulations interestingly provided a view of bleg1_ in association with its putative coxii redox partner, bleg1_ where the latter can be seen to hold its partner in an embrace, facilitated via hydrophobic and ionic interaction between the two proteins. although bleg1_ shares relatively low sequence homology to bssco, interestingly, it is structurally similar to the protein as well as other sco proteins across biological taxa. this observation highlights that despite its varying functions in prokaryotes and eukaryotes, sco proteins are structurally well preserved. based on all the results obtained, we hereby propose that hp bleg1_ of b. lehensis g is a sco protein which is able to interact with coxii, its redox partner. hence, it is highly possible that hp bleg1_ may possess metallochaperone and disulfide redox functions similar to other documented bacterial sco proteins. it is hoped that the predicted structure and function of bleg1_ from the hypothetical protein dataset of b. lehensis g will help to spur the search for other physiologically relevant proteins among the so-called “orphan” proteins of any given organism as well as direct future biological studies in improving our understanding of cox complex assembly process. competing interests the authors declare that they have no competing interests. authors’ contributions tsh carried out bioinformatics analyses and clustering of all the hypothetical proteins, homology modelling and protein docking in this study. tsh and ymn drafted the manuscript. abs, mbar, rak, altc, amam, nmm revised and proofread the manuscript. ymn conceived the study and participated in its design and coordination together with abs, mbar. rak, altc, amam gave technical advice to the study. all authors read and approved the final manuscript. 
from the metal-binding group of hps of the cluster, an hp termed bleg1_ was discovered to contain a thioredoxin domain and highly-conserved metal-binding ligands represented by cys cys and his similar to all prokaryotic and eukaryotic sco proteins. the built 3d structure of bleg1_ showed that it shared the βαβαββ core structure of trx-like proteins as well as three flanking β-sheets, a –helix at the n-terminus and a hairpin structure unique to sco proteins. cys- cys- and his- were located at flexible active loops similar to other sco proteins across biological taxa. we propose that hp bleg1_ is a sco protein which is able to interact with coxii, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial sco proteins. although bleg1_ shares relatively low sequence identity to bssco, interestingly, the predicted metal-binding residues of bleg1_ i.e. docking simulations provided an interesting view of bleg1_ in association with its putative cytochrome c oxidase subunit ii redox partner, bleg1_ where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. it is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called “orphan” proteins of any given organism. at least a quarter of any complete genome encodes for hypothetical proteins which are largely non-similar to other known, well-characterized proteins. hypothetical proteinsbleg1_2507scothioredoxincopper bindingredox reactioncytochrome c oxidase all hps of b. lehensis g were grouped according to their predicted functions based on the presence of functional domains in their sequences. the present study highlights the primary effort to classify and cluster hps of bacillus lehensis g alkaliphile to serve as a platform to mine and select specific hp to be studied further in greater detail.
 at least a quarter of any complete genome encodes for hypothetical proteins which are largely non-similar to other known, well-characterized proteins. predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. the present study highlights the primary effort to classify and cluster hps of bacillus lehensis g alkaliphile to serve as a platform to mine and select specific hp to be studied further in greater detail.  all hps of b. lehensis g were grouped according to their predicted functions based on the presence of functional domains in their sequences. from the metal-binding group of hps of the cluster, an hp termed bleg1_ was discovered to contain a thioredoxin domain and highly-conserved metal-binding ligands represented by cys cys and his similar to all prokaryotic and eukaryotic sco proteins. the built 3d structure of bleg1_ showed that it shared the βαβαββ core structure of trx-like proteins as well as three flanking β-sheets, a –helix at the n-terminus and a hairpin structure unique to sco proteins. docking simulations provided an interesting view of bleg1_ in association with its putative cytochrome c oxidase subunit ii redox partner, bleg1_ where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. although bleg1_ shares relatively low sequence identity to bssco, interestingly, the predicted metal-binding residues of bleg1_ i.e. cys- cys- and his- were located at flexible active loops similar to other sco proteins across biological taxa. this highlights structural conservation of sco despite their various functions in prokaryotes and eukaryotes.  we propose that hp bleg1_ is a sco protein which is able to interact with coxii, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial sco proteins. it is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called “orphan” proteins of any given organism. hypothetical proteinsbleg1_2507scothioredoxincopper bindingredox reactioncytochrome c oxidase 