GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Escherichia coli BW25113

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)

Query= SwissProt::P39062
         (572 letters)



>lcl|FitnessBrowser__Keio:15923 b1805 acyl-CoA synthase (NCBI)
          Length = 561

 Score =  162 bits (409), Expect = 4e-44
 Identities = 139/522 (26%), Positives = 237/522 (45%), Gaps = 55/522 (10%)

Query: 72  EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131
           E  TF++++E S      L++   ++KGDRV + MP   +    + G ++ G I   +  
Sbjct: 47  EVMTFRKLEERSRAFAAYLQQGLGLKKGDRVALMMPNLLQYPVALFGILRAGMIVVNVNP 106

Query: 132 AFMEGAVKDRLENSEAKVVVTTPEL---LERIPVDKLPHLQHVFVVGGEAESGT---NII 185
            +    ++ +L +S A  +V        LE++ VDK   +QHV +     +  T    ++
Sbjct: 107 LYTPRELEHQLNDSGASAIVIVSNFAHTLEKV-VDKTA-VQHVILTRMGDQLSTAKGTVV 164

Query: 186 NYD-------------------EAAKQESTRLDIEWMD--KKDGFLLHYTSGSTGTPKGV 224
           N+                     +A     R+     +   +D   L YT G+TG  KG 
Sbjct: 165 NFVVKYIKRLVPKYHLPDAISFRSALHNGYRMQYVKPELVPEDLAFLQYTGGTTGVAKGA 224

Query: 225 LHVHEAMIQQYQTGKWVLDLKEEDIYWCTADPGW---VTGT-VYGIFAPWLNGATNVIVG 280
           +  H  M+   +        +    Y     PG    VT   +Y IFA  +N    + +G
Sbjct: 225 MLTHRNMLANLE--------QVNATYGPLLHPGKELVVTALPLYHIFALTINCLLFIELG 276

Query: 281 GR----FSPESWYGTIEQLGVNVWYSAPTAFRMLMGA--GDEMAAKYDLTSLRHVLSVGE 334
           G+     +P    G +++L     ++A T    L  A   ++   + D +SL      G 
Sbjct: 277 GQNLLITNPRDIPGLVKELA-KYPFTAITGVNTLFNALLNNKEFQQLDFSSLHLSAGGGM 335

Query: 335 PLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQ 394
           P+   V     K+  + + + + +TE    +  N   +D   GS+G P+P  EA +VD+ 
Sbjct: 336 PVQQVVAERWVKLTGQYLLEGYGLTECAPLVSVNPYDIDYHSGSIGLPVPSTEAKLVDDD 395

Query: 395 GNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQG 454
            NE+PP + G L +K   P +M   W  P+  +   +  GW  +GD A MDEEG+     
Sbjct: 396 DNEVPPGQPGELCVKG--PQVMLGYWQRPDATDE-IIKNGWLHTGDIAVMDEEGFLRIVD 452

Query: 455 RVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDK 514
           R  D+I+ SG  V P E+E  +++HP + E   +G P    GE +K F+  +   +PS  
Sbjct: 453 RKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVGVPSGSSGEAVKIFVVKK---DPS-L 508

Query: 515 LKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556
            +E +  F ++ L  +  P+ +EF+D+LPK+  GKI+RR L+
Sbjct: 509 TEESLVTFCRRQLTGYKVPKLVEFRDELPKSNVGKILRRELR 550


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: 797
Number of extensions: 50
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 572
Length of database: 561
Length adjustment: 36
Effective length of query: 536
Effective length of database: 525
Effective search space:   281400
Effective search space used:   281400
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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