GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Desulfacinum infernum DSM 9756

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate WP_073037063.1 BUB04_RS03730 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>NCBI__GCF_900129305.1:WP_073037063.1
          Length = 382

 Score =  410 bits (1055), Expect = e-119
 Identities = 202/379 (53%), Positives = 275/379 (72%), Gaps = 1/379 (0%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           M F LTE+Q+MI+DMA +FAE+ +AP   E D+ H    +++ KMGE G  GI  P EYG
Sbjct: 1   MHFELTEEQRMIQDMARKFAEREIAPVAAELDRTHKHPEEIVKKMGELGLMGITIPPEYG 60

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
           G G+D +SY+LA+ E+SK     G+ +S   SL   P+Y +GTEEQKQ++L P+A G ++
Sbjct: 61  GAGMDYVSYVLAMIEISKACASCGVIMSVCNSLYNFPVYTYGTEEQKQQFLTPVASGEYL 120

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180
           G +GLTE  AG+D +  +TTAVL G+++++NG K FITNG  A   V+ A+TDK +G  G
Sbjct: 121 GCYGLTEAGAGSDPAKMRTTAVLDGNEWVINGEKKFITNGNVARYCVLAAVTDKEKGYKG 180

Query: 181 ISAFILE-KGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETL 239
           IS+F+++    PGF+ G++E+K+G + S TAELIFED  +PKENLLGKEGEGFK  + TL
Sbjct: 181 ISSFLVDLHNTPGFKVGRVEEKLGINASGTAELIFEDARIPKENLLGKEGEGFKQMLTTL 240

Query: 240 DGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLV 299
           DGGRIG+A+QA+GI    L  A++Y+K REQFGR I+ FQA+Q+ +AD+AT+++AA  L 
Sbjct: 241 DGGRIGIASQAIGIGRAVLEEAIEYAKTREQFGRPIASFQAIQWKLADIATQLDAAELLT 300

Query: 300 YHAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359
             AA L+  G+ Y + AAMAK FASD AM    + VQI GGYGY  +YP ER+MR+AKIT
Sbjct: 301 LRAAWLEQNGRGYEKEAAMAKLFASDTAMWAAVEGVQILGGYGYCKEYPMERHMRDAKIT 360

Query: 360 QIYEGTNQVMRIVTSRALL 378
           QIYEGTN++MR+V SR +L
Sbjct: 361 QIYEGTNEIMRLVISRNIL 379


Lambda     K      H
   0.318    0.134    0.379 

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: 427
Number of extensions: 13
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: 383
Length of database: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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: 50 (23.9 bits)

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

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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:

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