Document:

EX-4.3

 Exhibit 4.3 

THIRD SUPPLEMENTAL INDENTURE 

(TO CONVERTIBLE INDENTURE) 

THIS THIRD SUPPLEMENTAL INDENTURE (this “Third Supplemental Indenture”) is dated as of January 29, 2013, and has
been entered into by and between Horizon Lines, Inc., a Delaware corporation, having its principal office at 4046 Colony Road, Suite 200, Charlotte, North Carolina 28211 (the “Company”), the guarantors listed on the signature pages
hereto (the “Guarantors”) and U.S. Bank National Association, as trustee (the “Trustee”) and collateral agent. 

RECITALS 
 WHEREAS,
the Company, the Guarantors and the Trustee previously entered into that certain indenture dated as of October 5, 2011 (as supplemented by that certain first supplemental indenture dated as of April 9, 2012 and that certain second
supplemental indenture dated as of May 3, 2012, the “Indenture”), providing for the issuance of the Company’s 6.00% Series A Convertible Senior Secured Notes due 2017 (the “Series A Notes”) and 6.00%
Series B Mandatorily Convertible Senior Secured Notes (together with the Series A Notes, the “Notes”);  

WHEREAS, Section 11.01 of the Indenture provides that the Company may conform the provisions of the Indenture, the Note
Guarantees, the Security Documents or the Notes to any provision of the section entitled “Description of the New Notes” as set forth in the Registration Statement on Form S-4, File No. 333-176520, dated as of August 26, 2011,
including the prospectus that forms a part thereof, as amended, without the consent of the Noteholders; 
 WHEREAS, the
Company desires to amend certain provisions of the Indenture, as set forth in Article I of this Third Supplemental Indenture; and 

WHEREAS, all acts and requirements necessary to make this Third Supplemental Indenture the legal, valid and binding obligation of the
Company and the Guarantors have been done. 
 AGREEMENT 

NOW, THEREFORE, in consideration of the premises and the covenants and agreements contained herein, and for other good and
valuable consideration the receipt of which is hereby acknowledged, and for the equal and proportionate benefit of the Holders of the Notes, the Company and the Trustee hereby agree as follows: 

ARTICLE I 
 AMENDMENTS
TO INDENTURE 
 Section 1.01 Amendment to Section 4.12 of the Indenture. The second sentence of clause
(e) of Section 4.12 of the Indenture is hereby amended and restated in its entirety to read as follows: 
 In
addition, any Net Proceeds received by the Company or its Restricted Subsidiaries in excess of $60.0 million in the aggregate after the Issue Date that are not applied under Section 4.12(b)(4) (in the case of Net Proceeds in respect of Notes
Priority Collateral) or under Section 4.12(c)(1) (in the case of other Net Proceeds) shall be deemed to be Excess Proceeds, to the extent not applied to such permanent repayment, prepayment, repurchase or other retirement for value within 60
days after receipt thereof (which time period shall be extended during the pendency of any offers using such Net Proceeds that are required to be conducted by the “Asset Sale” or similar provisions of any Senior Lien Debt or an ABL
Facility). 

 ARTICLE II 

MISCELLANEOUS 

Section 2.01 Instruments To Be Read Together. This Third Supplemental Indenture is executed as and shall constitute an
indenture supplemental to and in implementation of the Indenture, and the Indenture and this Third Supplemental Indenture shall henceforth be read together. This Third Supplemental Indenture shall form a part of the Indenture for all purposes, and
every Holder of Notes shall be bound hereby and thereby. 
 Section 2.02 Confirmation. The Indenture as amended
and supplemented by this Third Supplemental Indenture is in all respects confirmed and preserved. 
 Section 2.03
Terms Defined. Capitalized terms used in this Third Supplemental Indenture and not otherwise defined herein shall have the meanings assigned to such terms in the Indenture. 

Section 2.04 Trust Indenture Act Controls. If any provision of this Third Supplemental Indenture limits, qualifies or
conflicts with another provision that is required to be included in this Third Supplemental Indenture or the Indenture by the Trust Indenture Act of 1939, as amended, as in force at the date that this Third Supplemental Indenture is executed, the
provisions required by the Trust Indenture Act of 1939 shall control. 
 Section 2.05 Headings. The headings of
the Articles and Sections of this Third Supplemental Indenture have been inserted for convenience of reference only, and are not to be considered a part hereof and shall in no way modify or restrict any of the terms and provisions hereof.

 Section 2.06 Governing Law. The internal law of the State of New York shall govern this Third Supplemental
Indenture without giving effect to applicable principles of conflicts of law to the extent that the application of the laws of another jurisdiction would be required thereby. 

Section 2.07 Counterparts. This Third Supplemental Indenture may be executed in any number of counterparts, each of which
so executed shall be deemed to be an original, but all such counterparts shall together constitute but one and the same instrument. 

Section 2.08 Effectiveness; Termination. The provisions of this Third Supplemental Indenture will become effective
immediately upon its execution by the Trustee in accordance with the provisions of Section 11.03 of the Indenture; provided, that the amendments to the Indenture set forth in Section 1.01 of this Third Supplemental Indenture shall become
operative as specified in Section 1.01 hereof.  
 Section 2.09 Acceptance by Trustee. The Trustee accepts
the amendments to the Indenture effected by this Third Supplemental Indenture and agrees to execute the trusts created by the Indenture as hereby amended, but only upon the terms and conditions set forth in the Indenture. 

Section 2.10 Responsibility of Trustee. The recitals contained herein shall be taken as the statements of the Company, and the
Trustee assumes no responsibility for their correctness. The Trustee makes no representations as to the validity or sufficiency of this Third Supplemental Indenture. 

  
 2 

 IN WITNESS WHEREOF, the parties hereto have caused this Third Supplemental Indenture to be
duly executed, all as of the date first written above. 
  

			
	HORIZON LINES, INC.
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Senior Vice President, General Counsel and Secretary
	
	HORIZON LINES, LLC
	HORIZON LINES HOLDING CORP.
	HAWAII STEVEDORES, INC.
	HORIZON LINES OF PUERTO RICO, INC.
	HORIZON LINES OF ALASKA, LLC
	HORIZON LINES OF GUAM, LLC
	HORIZON LINES VESSELS, LLC
	H-L DISTRIBUTION SERVICE, LLC
	HORIZON LOGISTICS, LLC
	AERO LOGISTICS, LLC
	SEA-LOGIX, LLC
	HORIZON SERVICES GROUP, LLC
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Secretary

 [Signature Page to Third Supplemental Indenture (Convertible Indenture)] 

 
			
	U.S. BANK NATIONAL ASSOCIATION,
	as Trustee and Collateral Agent
		
	By:	 	 /s/ K. Wendy Kumar

		
	Name:	 	 K. Wendy Kumar

		
	Title:	 	 Vice President

 [Signature Page to Third Supplemental Indenture (Convertible Indenture)]EX-4.1

 Exhibit 4.1 

FIRST AMENDMENT TO 

WARRANT TO PURCHASE STOCK 

This First Amendment to Warrant to Purchase Stock (this “Amendment”) is made as of the 18th day of July, 2013 by and between diaDexus, Inc., a Delaware corporation (the “Company”), and Comerica Ventures Incorporated, a California Corporation, the holder of the Warrant (as
hereinafter defined) (the “Holder”). 
 A. The Holder is the holder of that certain Warrant to
Purchase Stock dated September 23, 2011 (the “Warrant”) by assignment from its affiliate, Comerica Bank, a Texas banking association; 

B. The Holder and the Company wish to amend the Warrant in order to modify the method in which the Warrant may be exercised by the Holder; and

 C. Capitalized terms not otherwise defined herein shall have the respective meanings ascribed thereto in the Warrant. 

NOW, THEREFORE, in consideration of the mutual covenants set forth herein and other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, the parties mutually agree as follows: 
 1. Amendment.
Section 1.1 of the Warrant is hereby amended and restated in its entirety to read as follows: 
 “Method of Exercise. Holder
may exercise this Warrant by a duly executed Notice of Exercise in substantially the form attached as Appendix I to the principal office of the Company (or such other appropriate location as Holder is so instructed by the Company). Payment of the
aggregate Warrant Price for the Shares being purchased shall be made, at the option of the Holder, by the following methods: (i) by delivery to the Company of a check, wire transfer (to an account designated by the Company) or other form of
payment acceptable to the Company; (ii) by instructing the Company to withhold a number of Shares then issuable upon exercise of this Warrant with an aggregate Fair Market Value as of the date of delivery of the Notice of Exercise equal to such
aggregate Warrant Price; or (iii) any combination of the foregoing. In the event of any withholding of Shares pursuant to clause (ii) or (iii) above where the number of Shares whose value is equal to the aggregate Warrant Price for
the Shares being purchased is not a whole number, the number of Shares withheld by or surrendered to the Company shall be rounded up to the nearest whole Share and the Company shall make a cash payment to the Holder (by delivery of a check or by
wire transfer of immediately available funds) based on the incremental fraction of a Share 

 
being so withheld by or surrendered to the Company in an amount equal to the product of (x) such incremental fraction of a Share being so withheld or surrendered multiplied by (y) the
Fair Market Value per Share as of the date of delivery of the Notice of Exercise. 
 For the purpose of this Warrant, “Fair Market
Value” means, as of any particular date: (a) the volume weighted average of the closing sales prices of the Common Stock for such day on all domestic securities exchanges on which the Common Stock may at the time be listed; (b) if
there have been no sales of the Common Stock on any such exchange on any such day, the average of the highest bid and lowest asked prices for the Common Stock on all such exchanges at the end of such day; (c) if on any such day the Common Stock
is not listed on a domestic securities exchange, the closing sales price of the Common Stock as quoted on the Nasdaq Stock Market, Inc. (“Nasdaq”), the National Association of Securities Dealers, Inc. OTC Bulletin Board (“OTC Bulletin
Board”) or similar quotation system or association for such day; or (d) if there have been no sales of the Common Stock on Nasdaq, the OTC Bulletin Board or similar quotation system or association on such day, the average of the highest
bid and lowest asked prices for the Common Stock quoted on Nasdaq, the OTC Bulletin Board or similar quotation system or association at the end of such day. If at any time the Common Stock is not listed on any domestic securities exchange or quoted
on Nasdaq, the OTC Bulletin Board or similar quotation system or association, the “Fair Market Value” of the Common Stock shall be the fair market value per share as determined jointly by the Company’s board of directors and the
Holder. 
 2. No Other Amendments. Except as amended hereby, the Warrant remains in full force and effect in accordance with its
original terms. 
 3. Miscellaneous. 

a. Severability. If one or more provisions of this Amendment are held to be unenforceable under applicable law, such provision shall be
excluded from this Amendment and the balance of the Amendment shall be interpreted as if such provision were so excluded and shall be enforceable in accordance with its terms. 

b. Counterparts. This Amendment may be executed in two or more counterparts, each of which shall be deemed an original, but all of
which together shall constitute one and the same instrument. 
 c. Entire Agreement. The Warrant, as amended by this Amendment,
constitutes the entire agreement of the parties with regard to the subject matter hereof and supersedes any prior oral or written agreements or understandings. 

  
 2 

 d. Governing Law. This Amendment shall be governed by and construed in accordance with the
laws of the State of California, without regard to the conflicts of law provisions of the State of California or any other state. 

[Signature Page Follows] 

  
 3 

 IN WITNESS WHEREOF, the parties have executed this First Amendment to Warrant to Purchase Stock
as of the date first above written. 
  

					
	 THE COMPANY:
  

diaDexus, Inc.

		
	By: 	 	/s/ Jean Viret
		 	Name: 	 	Jean Viret
		 	Title:	 	Chief Financial Officer
	
	 HOLDER:
  

Comerica Ventures Incorporated

		
	By: 	 	 
		 	Name: 	 	
		 	Title:	 	

  

SIGNATURE PAGE TO FIRST AMENDMENT TO
WARRANT TO PURCHASE STOCK 

 IN WITNESS WHEREOF, the parties have executed this First Amendment to Warrant to Purchase Stock
as of the date first above written. 
  

					
	 THE COMPANY:
  

diaDexus, Inc.

		
	By: 	 	 
		 	Name: 	 	
		 	Title:	 	
	
	 HOLDER:
  

Comerica Ventures Incorporated

		
	By: 	 	/s/ LaReeda Rentie
		 	Name: 	 	LaReeda Rentie
		 	Title:	 	Assistant Vice President

  

SIGNATURE PAGE TO FIRST AMENDMENT TO
WARRANT TO PURCHASE STOCK

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