Alignments for a candidate for acs in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfobacter vibrioformis DSM 8776

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_035239666.1 Q366_RS13170 acyl--CoA ligase family protein

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_000745975.1:WP_035239666.1
          Length = 536

 Score =  501 bits (1291), Expect = e-146
 Identities = 247/523 (47%), Positives = 344/523 (65%), Gaps = 6/523 (1%)

Query: 19  YSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFI 78
           Y +L+P  FL+R+ K + +KTAV+Y D  +T++ F + V   A+ L   G  R DK++F+
Sbjct: 8   YEILSPTNFLDRSVKVYPEKTAVIYGDKTFTWAGFQERVFRLANGLKACGVGRGDKVAFV 67

Query: 79  SRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKD 138
             N P  LE+ + VP  G  LV IN RLS  EM+YIINHSD+K VV D  +   L +V  
Sbjct: 68  CPNTPPMLEAHYAVPLLGAALVSINIRLSANEMSYIINHSDAKVVVADNEFGKVLSKVVP 127

Query: 139 QIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGT 198
           ++ A    +   D   +      E    Y   +     DP+ +  ++E  ++ L YTSGT
Sbjct: 128 ELTAVKTFVNICDIDDSMPLDGPE----YERFLADSPDDPVSLAIEDEREILALNYTSGT 183

Query: 199 TGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVC 258
           TGLPKGVM+HHRGA+LN++ E+LE ++D +S YLWTLPMFH   W F+WA  A+GAT+VC
Sbjct: 184 TGLPKGVMYHHRGAYLNSLGELLEFKIDRDSKYLWTLPMFHCNGWCFTWAITAMGATHVC 243

Query: 259 LDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATL 318
           L KVD   IYR++    VTH+CAAPT+ + ++ + K N ++ S R+ ++ AGA PAP  +
Sbjct: 244 LRKVDPVEIYRIIADVGVTHLCAAPTILIGMSVFAKENAVQLSRRLEIMTAGAPPAPMVI 303

Query: 319 KAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFE-MDVF 377
           + M+ IG  +   YGLTE +GPHS+C+W+ +WD L    +A +KARQG+PY+  E MDV 
Sbjct: 304 QNMEHIGANITQTYGLTEVFGPHSVCQWQDKWDDLSPMARAGIKARQGVPYIVAEHMDVV 363

Query: 378 DA-NGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIE 436
           DA   +PVP DG T+GE+VMRG+NV LGYYK+ E + E+FR GWFHSGD AV+HPD Y++
Sbjct: 364 DAVTMEPVPRDGTTMGEIVMRGNNVMLGYYKDAEASTEAFRGGWFHSGDLAVMHPDNYVQ 423

Query: 437 IVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKL 496
           I+DR KD+I +GGE +S++ +E  L   P V  VAV   PDEKWGEV  A I  + G   
Sbjct: 424 IMDRKKDIIISGGENISTVEIENVLYAHPDVLEVAVISVPDEKWGEVPKAFILPRAGANP 483

Query: 497 TEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNE 539
              ++I +CKE+LA F+ PK +EFGP+P TATGK+QK+ LR +
Sbjct: 484 DPAQIIAYCKEKLARFKAPKYIEFGPLPKTATGKLQKFKLREK 526


Lambda     K      H
   0.319    0.136    0.411 

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: 779
Number of extensions: 29
Number of successful extensions: 3
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: 549
Length of database: 536
Length adjustment: 35
Effective length of query: 514
Effective length of database: 501
Effective search space:   257514
Effective search space used:   257514
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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)
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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 2024 update 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