Alignments for a candidate for acs in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dokdonella koreensis DS-123

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate WP_067644159.1 I596_RS03300 propionate--CoA ligase

Query= curated2:O93730
         (670 letters)



>NCBI__GCF_001632775.1:WP_067644159.1
          Length = 631

 Score =  489 bits (1259), Expect = e-142
 Identities = 263/634 (41%), Positives = 395/634 (62%), Gaps = 17/634 (2%)

Query: 33  YFKFHRQTVENLESFWESVAKELEWFKPWDKVLDASNPPFYKWFVGGRLNLSYLAVDRHV 92
           Y   +RQ++E+ E FW   A+ ++W  P  ++L+ ++PPF +WF GG  NL + AVDRH+
Sbjct: 3   YEDVYRQSIEDPEGFWAEQARAIDWHVPPQRILEYTDPPFRRWFAGGLTNLCHNAVDRHL 62

Query: 93  KTWRKNKLAIEWEGEPVDENGYPTDRRKLTYYDLYREVNRVAYMLKQNFGVKKGDKITLY 152
              R ++LA+      V  +      RK++Y  L+REVN  A  LK + GV +GD++ +Y
Sbjct: 63  AA-RGDQLAL------VAVSSETGTTRKISYRQLHREVNTFAAALK-SLGVGRGDRVVVY 114

Query: 153 LPMVPELPITMLAAWRIGAITSVVFSGFSADALAERINDSQSRIVITADGFWRRGRVVRL 212
           +P + E    MLA  RIGA+ SVVF GF+A  LA RI+D++ +++I AD   R GRV+  
Sbjct: 115 MPNMAEAVFAMLACARIGAVHSVVFGGFAAHNLALRIDDAKPKLLIAADAGMRGGRVIPY 174

Query: 213 KEVVDAALEKATGVESVIVLPRLGLKDVPM-TEGRDYWWNKLMQGIPPNAYIEPEPVESE 271
           K +VD AL  A      +++   GL   P   +GRD  +  L      +A +  E +ES 
Sbjct: 175 KPLVDQALAAAVSPPPHVLIVSRGLDPDPAWVQGRDVDYAPLRARYE-DAEVPVEWLESN 233

Query: 272 HPSFILYTSGTTGKPKGIVHDTGGWAVHVYATMKWVFDIRDDDIFWCTADIGWVTGHSYV 331
            PS++LYTSGTTGKPKG+  D GG+AV +  +M+ V+D+    + + T+D+GW  GHSY 
Sbjct: 234 EPSYLLYTSGTTGKPKGVQRDVGGYAVAMALSMRAVYDVGPGQVMFSTSDVGWAVGHSYN 293

Query: 332 VLGPLLMGATEVIYEGAPDYPQPDRWWSIIERYGVTIFYTSPTAIRMFMRYGEEWPRKHD 391
           V GPL++GAT ++YEG P  P P  WW +   YGV   ++SPT IR+  +    W +KHD
Sbjct: 294 VYGPLIVGATSLLYEGLPTNPDPGIWWKLCADYGVRTMFSSPTGIRVLKKQDGAWLKKHD 353

Query: 392 LSTLRIIHSVGEPINPEAWRWAYRVLGNEKVAFGSTWWMTETGGIVISHAPGLYLVPMKP 451
           L+ L+ +   GEP++    +W    LG   +     +W TETG  V++  PGL L P+K 
Sbjct: 354 LTALKWLFLAGEPLDEPTAQWISDGLGKPII---DNYWQTETGWPVLTLLPGLDLKPVKF 410

Query: 452 GTNGPPLPGFEVDVVDE-NGNPAPPGVKGYLVIKKPW-PGMLHGIWGDPERYIKTYWSRF 509
           G+ G P  G+++ V+DE  G  A  G KG LVI+ P  PG +  +W D +R++ +Y+S F
Sbjct: 411 GSPGLPNLGYKLRVIDEVTGADAAAGQKGVLVIEPPLPPGCMTTVWNDDQRFLSSYFSHF 470

Query: 510 PGMFYAG-DYAIKDKDGYIWVLGRADEVIKVAGHRLGTYELESALISHPAVAESAVVGVP 568
             + Y+  D+A++D+DGY ++LGR D+VI VAGHRLGT E+E ++ +HP+VAE+AVVGV 
Sbjct: 471 KELLYSSLDWAVRDEDGYTFILGRTDDVINVAGHRLGTREIEESVATHPSVAEAAVVGVH 530

Query: 569 DAIKGEVPIAFVVLKQGVAPSDE-LRKELREHVRRTIGPIAEPAQIFFVTKLPKTRSGKI 627
           DA+KG+VP+ F  L+Q  A + E     + + V   +G +A PA+++ V  LPKTRSGK+
Sbjct: 531 DALKGQVPVVFATLRQATADTPESAASGMLQCVVDQLGGVARPARVYVVNALPKTRSGKL 590

Query: 628 MRRLLKAVATGAPLGDVTTLEDETSVEEAKRAYE 661
           +RR L+A+A     GD++TL+D  +++E +RA E
Sbjct: 591 LRRSLQALAEDRDPGDLSTLDDPGALDECRRALE 624


Lambda     K      H
   0.319    0.138    0.440 

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: 1331
Number of extensions: 78
Number of successful extensions: 9
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: 670
Length of database: 631
Length adjustment: 38
Effective length of query: 632
Effective length of database: 593
Effective search space:   374776
Effective search space used:   374776
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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