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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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