Alignments for a candidate for acs in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Marinobacter adhaerens HP15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF944 HP15_923 acetyl-coA synthetase/AMP-(fatty) acid ligase

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__Marino:GFF944
          Length = 549

 Score =  319 bits (817), Expect = 2e-91
 Identities = 204/554 (36%), Positives = 300/554 (54%), Gaps = 26/554 (4%)

Query: 14  NLKNYEETYRHFDWAEAEKHF-SWHETGKLNAAYEAIDRHAESFRKNKVALYYK-DAKRD 71
           +L  Y + Y +FD A  E           LN  +E  D+ A+    ++VALYY+ +   D
Sbjct: 2   SLPEYTDVYNNFDPAALEADILDGRLDSGLNVCHEICDKWADD--PSRVALYYETEDGGD 59

Query: 72  EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131
              TF E+KE S R  N L+  G + KGDRV   +PR+PEL  ++ G ++ GA+  PLF 
Sbjct: 60  GTLTFAELKEASARFANYLKSQG-IGKGDRVAALLPRTPELLIVIAGTLRAGAVYQPLFT 118

Query: 132 AFMEGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVGGEA-ESGTNIINYDE 189
           AF  GA++ R E +  K+VVT PE   ++  V   P      VVG  A E G +I +++E
Sbjct: 119 AFGSGAIEYRFERASTKLVVTNPENYPKLNDVKVCPP-----VVGVNASEIGADIPDFEE 173

Query: 190 AAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDI 249
               +S+  +   +   D FL  +TSG+ G  KGV    +A++  Y   K+ +DL++ D 
Sbjct: 174 TLAAQSSDFEPVMIKGDDPFLQMFTSGTVGKSKGVAVPAKALLAFYVYMKYAIDLQDGDR 233

Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRM 309
           +W  ADPGW  G  Y +  P L G       G F+PES Y  I +  +    +APTA+R+
Sbjct: 234 FWNVADPGWAYGLYYAVVGPLLMGHATHFNPGGFTPESTYDMIRKYKITNLAAAPTAYRL 293

Query: 310 LMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNY 369
           L  A D +  + +   LR   S GEPLNPEV+ W        + D +  TETG    CN+
Sbjct: 294 LK-ANDHVLPEGENLGLRVASSAGEPLNPEVVNWIRNRHYCPVKDHYGQTETG-MTCCNF 351

Query: 370 PCM--DIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT---IWNNPE 424
             +   ++ GSMG   PG +   ++ +   +    +G LA+      + H     W   +
Sbjct: 352 HGLAHPVREGSMGYASPGHKVVALNEKNEVVGEGEVGQLAVDVKASPLFHFDGYTWGEKD 411

Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484
            + +     G+Y++GD       G F F GR DD+I T+G RVGP +VES L+EH A+AE
Sbjct: 412 PFVN-----GYYLTGDMVINHGNGNFSFSGRDDDIITTAGYRVGPADVESTLLEHAAVAE 466

Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEPSDK--LKEEIRLFVKQGLAAHAAPREIEFKDKL 542
           +GV+GKPD  RG IIKA++ ++  +   D+  LK+E++  V++ L+ HA PREIEF D+L
Sbjct: 467 SGVVGKPDEKRGSIIKAYVVIKGDYALGDEQALKDELQELVRRRLSTHAFPREIEFVDEL 526

Query: 543 PKTRSGKIMRRVLK 556
           PKT SGKI R VL+
Sbjct: 527 PKTPSGKIQRFVLR 540


Lambda     K      H
   0.318    0.136    0.425 

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: 899
Number of extensions: 41
Number of successful extensions: 6
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: 572
Length of database: 549
Length adjustment: 36
Effective length of query: 536
Effective length of database: 513
Effective search space:   274968
Effective search space used:   274968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources