GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:15923
          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.

Links

Downloads

Related tools

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