# CBMDB: A Database for Accessing, Analyzing, and Mining CBM Information
## 3 Results and Discussion
### Application  
To illustrate the application of CBMDB, a known CBM (GenBank accession number: ABN53395.1) was selected for analysis. Firstly, the accession number was used as a search term to collect basic information about the CBM. The search results page showed that the target CBM originates from the strain _Hungateiclostridium thermocellum_ and belongs to the CBM6 family. Amino acid sequences and the position information of the target CBM and the enzyme containing this CBM were also available (Figure 3a). Further, using the Sequence Similarity Search module, a sequence BLAST between the query CBM and subject CBMs was performed. Based on the sequence BLAST results, multiple alignment was then conducted. As shown in Figure 3b,c, ABN53395.1 showed the highest identity scores with three characterized CBMs, including CBM6 from positions 399 to 515 (accession number EFB38194.1, 100.0% identity), CBM6 from positions 393 to 510 (accession number EFL62381.1, 77.8% identity), and CBM6 from positions 2108 to 2221 (accession number QDV75083.1, 60.2% identity) (Figure 3b). The sequence alignment of ABN53395.1 with EFB38194.1, EFL62381.1, and QDV75083.1 revealed two conserved substrate binding residues (Tyr22, Trp84) [23]. The CBM was then analyzed using the Domain Annotationmodule. As shown in Figure 3d, the highest score, c-Evalue, and i-Evalue are 5.3 \(\times\) 10\({}^{-24}\), 1.1 \(\times\) 10\({}^{-20}\), and 74.2 respectively, indicating that the query sequence belongs to CBM6 and that the positions of CBM6 in the query sequence are 402-514. The phylogenetic relationship between the CBM ABN53395.1 and the known CBMs in the database was then evaluated using the Phylogenetic Tree module. The results suggested that ABN53395.1 was clearly clustered into the clade of CBM family 6 in the phylogenetic tree based on the neighbor-joining method of the amino sequences of CBMs, in which the level of sequence similarity between ABN53395.1 and EFL62831.1 was 77.8% (Figure 3e). Finally, the structure information of ABN53395.1 was obtained by the Structure Similarity Search module through the PDB API. The result revealed a typical beta sandwich structure of the CBM6 family [2]. Additionally, the 3D models of the CBMs, such as 2Y8K, 5G56 and 1 UY0, which showed high sequence similarity to the query sequence, were found on this results page (Figure 3f). Figure 3: _Cont._  
CLUSTAL 0(1.2.4) multiple sequence alignment  
AN53395.1*8, CBM_6, Position:399-515 -GGQURPEGVDIEXT-SDTGGGNYNGFISEEELETIIRVRPGTYNSLRVAGIS6--
56  
EFB38194.1*17, CBM_6, Position:399-515 -GGQURPEGVDIEXT-SDTGGGNYNGFISEEELETIIRVRPGTYNSLRVAGIS6--
56  
QUR75083.1*2153, CBM_6, Position:2108-2221 -QAPADALSAGEAVEASGEOFFGOOYYYSASTGGSIEETYNANAADLIMORFNALYSIS
60  
EFLE62381.1*5649, CBM_6, Position:393-510 -KGQURPLEAVDIETET-RADDAGNGNGFIEDEELTTIVWQFPYNALARVASS6--
57  
...*:... **. Another important application of the CBMDB is the examination of unknown proteins with potential CBM functions. Here, the C-Terminus module of an endotype xanthanase (ALX66163.1) from the genus _Microbacterium_ was analyzed as an example. Sequence alignment was run with the Sequence Similarity Search module [24]. The subject \"AMM07675.1#8969, CBM6, Position: 917-1041\" showed the highest amino sequence similarity to the query sequence (30.1% identity) (Figure 4a), suggesting that the unknown C-terminus of the xanthanase might function as a CBM and belong to the CBM6 family. The multiple sequence alignment results showed a low sequence identity of the unknown C-terminus to CBM6 (AMM07675.1, 30.1% identity), CBM4_9 (ADQ44988.1, 26.5% identity), and CBM6 (AYY1313.1, 25.3% identity). However, several conserved substrate binding residues (Tyr and Trp) were still observed (Figure 4b). After structure similarity searches, the 3D model of CBM6 (1W9W) with a 34.9% identity to query sequence was obtained and displayed a typical beta sandwich structure of the CBM6 family [2] (Figure 4c). The phylogenetic results demonstrated that the query protein was clustered into the clade of CBM family 6 (Figure 4d).