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_035237353.1 Q366_RS06190 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_000745975.1:WP_035237353.1
          Length = 584

 Score =  545 bits (1404), Expect = e-159
 Identities = 283/565 (50%), Positives = 386/565 (68%), Gaps = 17/565 (3%)

Query: 2   VTVQDFFRKFIEFQN----SPNEKSLQEIVKLVGQLDL-RRFNWVRDVFEDIHVKERGSK 56
           +T++ F+++ +        +  E   Q   K +   +L + FNW +++FEDIHVKER  +
Sbjct: 1   MTLKRFYKEVMALNGIQDMAQREIEAQTFFKRLNSAELPQTFNWAQEIFEDIHVKERPDQ 60

Query: 57  TALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLAV 116
            ALIW D++T E+ + +Y +L+   N+VL+ LRK G++KGD +Y++T + P  W    A 
Sbjct: 61  LALIWADLHTDEQEQYTYTQLAENGNKVLNFLRKQGVEKGDNLYMLTPIVPQTWFASFAA 120

Query: 117 IKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEAL---GSLKVEKFLIDG 173
           IKGGFV VP+AT +T  E+++RF    P  +I+    A ++++AL   G +   K ++ G
Sbjct: 121 IKGGFVAVPTATTMTEREIQFRFEAYPPDVVIALESLADLVDDALAKAGCIPKAKIIL-G 179

Query: 174 KRETWNS---LEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSITTAS 230
            ++ W S   + +ES  A P   + EDV+  +FTSGTTG+PKRV H+AVSYP+G ++TA 
Sbjct: 180 AKQGWTSYPEIAEESPIASPATIKSEDVLFCFFTSGTTGLPKRVGHSAVSYPLGHMSTAV 239

Query: 231 IVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVENLGVT 290
            +G+    +H NLSA GWAK+AWSSFFSP  VG T  G N+   LD ++YL  V    + 
Sbjct: 240 TIGLEPGGIHHNLSAPGWAKWAWSSFFSPFNVGGTATGFNFTA-LDIKKYLSFVAKYKIN 298

Query: 291 SFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQTET 350
           SFCAPPTAWR F+ LDL  + F  L+  +SAGEPLNPEVI  W++     IRDFYGQTE 
Sbjct: 299 SFCAPPTAWRAFVGLDLAAYDFSNLKYSLSAGEPLNPEVIDQWREATGTEIRDFYGQTEA 358

Query: 351 TAMVGNFPFL--KVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKL-NPRPIGLF 407
           T M+GN P++  K++ GS G P  +YDI L DDEGK+IT+P   GHI ++L N R IGLF
Sbjct: 359 TCMIGNPPWMEGKMRLGSFGYPSSMYDIMLSDDEGKQITEPDTTGHIVIRLSNWRAIGLF 418

Query: 408 LGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALL 466
             Y  +E K  E+F+ G Y+TGDKA FD++GY++FVGR DDVIK+SDYRVGPFEVESAL+
Sbjct: 419 QEYIGNEAKTAEAFKHGLYFTGDKATFDKDGYWWFVGRSDDVIKSSDYRVGPFEVESALI 478

Query: 467 EHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRIIE 526
           EHPAV E AVVGVPD  R QLVKA+++L  G  PS+ELA E+ +    +L+ +K+PRIIE
Sbjct: 479 EHPAVMETAVVGVPDPKRHQLVKAFVILVPGQKPSRELALELFKHTIDVLAKFKIPRIIE 538

Query: 527 FVDELPKTISGKIRRVELRKREEEK 551
           FV+ELPKTISGKIRR+ELR+ EE K
Sbjct: 539 FVEELPKTISGKIRRIELRENEESK 563


Lambda     K      H
   0.318    0.137    0.402 

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: 874
Number of extensions: 36
Number of successful extensions: 5
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: 564
Length of database: 584
Length adjustment: 36
Effective length of query: 528
Effective length of database: 548
Effective search space:   289344
Effective search space used:   289344
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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