GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Desulfovibrio vulgaris Hildenborough

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase

Query= BRENDA::D6EQU8
         (658 letters)



>MicrobesOnline__882:408300
          Length = 648

 Score =  231 bits (590), Expect = 6e-65
 Identities = 181/612 (29%), Positives = 284/612 (46%), Gaps = 37/612 (6%)

Query: 55  FWKAVTEWFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHAL--RAAGTRPDEPALLY 112
           FW+   E  ++ +   +  VL D   P  +WFPGA  N   +AL      +     AL++
Sbjct: 49  FWEEAAE--ELEWFRRWDGVLDDSNAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIW 106

Query: 113 VDETHEPAPVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGV 172
             E  +    T+ +L R+V  LA  +R+LGV  GDRV  Y+P +P+ V A+LA A +G V
Sbjct: 107 EGEPGDSRRFTYFDLYREVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAV 166

Query: 173 WTSCAPDFGARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRREL-PTLRA--- 228
            ++    F ARS+ DR +   P +L TVDG+   G+    +    +    L P  RA   
Sbjct: 167 HSTVFGGFSARSLCDRVEDARPTLLLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLH 226

Query: 229 ---VIHIPLLGTEAPDGTLDW--ETLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIV 283
              V+H   L T   DG   W  + +     E + E +  + PL+VLY+SGTTG PK +V
Sbjct: 227 HVVVVHRAHLETPMRDGRDIWYHDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLV 286

Query: 284 QSQGGILVEHLKQLGLHCDLGPGDRFFWYTSTGWMMWNF--LVSGLLTGTTIVLYDGSPG 341
            S GG +V   + +    D+ P D F+     GW+  +   +   L+ GTT VLY+G P 
Sbjct: 287 HSHGGYMVGVHRTMRWVFDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPL 346

Query: 342 FPATDAQWRIAERTGATLFGTSAAYV-MACRKAGVHPARDLDLSAIQCVATTGSPLPPDG 400
           +P     W + ER G T+  T    + M  R   ++PAR  D++ ++ +AT G P+ P+ 
Sbjct: 347 YPEAGRLWSMVERWGVTILYTVPTVIRMLMRFGPLYPARH-DITTLRLLATVGEPISPET 405

Query: 401 FRWLHDEFAAGGA---DLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWD 457
           + W +     G     D W  + +G           +P   +  G +  P  G D+   D
Sbjct: 406 WVWFYRTIGRGRCPVLDTWWQTETG-----MIMVSPLPVSALKPGSVARPLPGVDVDIVD 460

Query: 458 PSGDPL-TDEVGELVVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRG 516
             G P+     G LVV NP P+M    + D +   +   Y++ +PG +  GD       G
Sbjct: 461 GEGAPVPPGRGGLLVVKNPWPAMACGVFGDDEA--FRRLYWERFPGWYCTGDVARRDDDG 518

Query: 517 SVVIHGRSDSTLNRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHL--- 573
            + I GR+D  +   G R+G+A++  A+   P + E  VIG+     G     FV L   
Sbjct: 519 YIWIQGRADDVILIAGHRIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRDT 578

Query: 574 APGATLDDALLDRIKRTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLD 633
              A  + AL   +   +R  L P  V  +V+   G+P   +GK     ++R+L+    +
Sbjct: 579 EEAAAEEQALATSLVGHVRRELGPVAVIRDVVFREGLPRNRSGK----IMRRILRSE--E 632

Query: 634 KAVNPGSIDNLD 645
             V  G +  L+
Sbjct: 633 MGVETGDLSTLE 644


Lambda     K      H
   0.320    0.138    0.442 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1315
Number of extensions: 77
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 658
Length of database: 648
Length adjustment: 38
Effective length of query: 620
Effective length of database: 610
Effective search space:   378200
Effective search space used:   378200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory