Alignments for a candidate for adh in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Desulfobacter vibrioformis DSM 8776

Align Aldehyde dehydrogenase family 7 member B4; Antiquitin-1; Turgor-responsive ALDH; EC 1.2.1.3 (characterized)
to candidate WP_035238996.1 Q366_RS11495 aldehyde dehydrogenase family protein

Query= SwissProt::Q9SYG7
         (508 letters)



>NCBI__GCF_000745975.1:WP_035238996.1
          Length = 519

 Score =  491 bits (1264), Expect = e-143
 Identities = 254/507 (50%), Positives = 348/507 (68%), Gaps = 9/507 (1%)

Query: 9   EFLSEIGLTSHNLGSYVAGK--WQAN-GPLVSTLNPANNQPIAQVVEASLEDYEQGLKAC 65
           + L  +G+ S N G+   G   W    G  + + +P N +PIA V+ A  +DYE  +   
Sbjct: 11  QILDALGIKSVNSGATTGGSKGWLGTKGKELVSCSPINGKPIASVLMAEKKDYEAVMAKA 70

Query: 66  EEAAKIWMQVTAPKRGDIVRQIGDALRSKLDYLGRLLSLEMGKILAEGIGEVQEVIDMCD 125
           + A K +  + AP+RG +VR+IG+ALR     LG L++LE+GKI AEG GEVQE+ID+ D
Sbjct: 71  QAAFKTFRMMPAPRRGQMVREIGNALRENKKALGALIALEVGKIRAEGEGEVQEMIDIAD 130

Query: 126 FAVGLSRQLNGSVIPSERPNHMMLEMWNPLGIVGVITAFNFPCAVLGWNACIALVCGNCV 185
           FA GLSRQL G  + SERP H M E W+PLGIVG+ITAFNFP A   WN+ IA VCG+ +
Sbjct: 131 FATGLSRQLYGLTMHSERPEHRMYEQWHPLGIVGLITAFNFPVAPWSWNSLIACVCGDAI 190

Query: 186 VWKGAPTTPLITIAMTKLVAEVLEKNNLPGAIFTAMCGGAE-IGEAIAKDTRIPLVSFTG 244
           V+K +  +PL +IA+  ++  V++K  + G IF  + G  E +GE +  D RIPL+S TG
Sbjct: 191 VFKPSSKSPLTSIAIQNILGPVVDKYGVQG-IFNMVIGSREDVGEPMLHDPRIPLISATG 249

Query: 245 SSRVGSMVQQTVNARSGKTLLELSGNNAIIVMDDADIQLAARSVLFAAVGTAGQRCTTCR 304
           S+ +G  V + V  R G+TLLEL GNNAIIV +DAD+ +A R+ LF AVGTAGQRCT+ R
Sbjct: 250 STAMGKHVGKVVGGRLGRTLLELGGNNAIIVTEDADMDMAIRATLFGAVGTAGQRCTSTR 309

Query: 305 RLLLHESVYDKVLEQLLTSYKQVKIGNPLEKGTLLGPLHTPESKKNFEKGIEVIKSQGGK 364
           R+++H+SV    +  L+ +YKQVK+GNPL+K TL+GPL    +    E+ ++ +K+ GGK
Sbjct: 310 RIIIHDSVKQAFVNNLVKAYKQVKVGNPLDKDTLMGPLIDQGAVLAMEQALKAVKACGGK 369

Query: 365 ILTGGKAVEGE----GNFVEPTIIEISADAAVVKEELFAPVLYVLKFKSFGEAVAINNSV 420
           +L GG+ V  +    G++V P + E+  D  +V+ E FAP+LY++ +  F +A+ ++N V
Sbjct: 370 LLCGGERVTVDGCDGGHYVRPAVAEVKNDFPIVQSETFAPILYIIAYNDFQQALELHNDV 429

Query: 421 PQGLSSSIFTRNPENIFRWIGPLGSDCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSD 480
           PQGLSS+IFTR+     +++   GSDCGI NVNI T+GAEIGGAFGGEK TGGGRE+GSD
Sbjct: 430 PQGLSSAIFTRSLHYQEKFLSHKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSD 489

Query: 481 SWKQYMRRSTCTINYGNELPLAQGINF 507
           +WK YMRR T TIN+G ELPLAQGI F
Sbjct: 490 AWKAYMRRQTNTINWGKELPLAQGIEF 516


Lambda     K      H
   0.317    0.135    0.398 

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: 741
Number of extensions: 26
Number of successful extensions: 2
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: 508
Length of database: 519
Length adjustment: 35
Effective length of query: 473
Effective length of database: 484
Effective search space:   228932
Effective search space used:   228932
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 (21.6 bits)
S2: 52 (24.6 bits)

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

Downloads

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

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:

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