GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Pseudomonas simiae WCS417

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 GFF2713 PS417_13840 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>FitnessBrowser__WCS417:GFF2713
          Length = 383

 Score =  342 bits (877), Expect = 1e-98
 Identities = 177/376 (47%), Positives = 248/376 (65%)

Query: 2   DFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGG 61
           D   TE+Q MI+DMA +FA   +AP  +  +KA   D  L+ KMGE G  G+  PEE+GG
Sbjct: 3   DIEYTEEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGG 62

Query: 62  MGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVG 121
             +D ++Y LAVEE+S  D  TG  +S + S+   PI  +GTE QKQ +LA +A G  +G
Sbjct: 63  TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIG 122

Query: 122 AFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGI 181
            F LTEP AG++A   +T A L+   +++ G+K F++NGK A   +VFA+TD   G  GI
Sbjct: 123 CFCLTEPQAGSEAHNLRTRAELRDGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKGI 182

Query: 182 SAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDG 241
           SAF++    PGF   + E KMG   S T  +    C VP+ NLLG+ G+G  IA+  L+G
Sbjct: 183 SAFLVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLEG 242

Query: 242 GRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYH 301
           GRIG+AAQALGIA  A  AA+ Y+++R QF ++I + Q++  ++ADM T++ AAR L+ H
Sbjct: 243 GRIGIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLILH 302

Query: 302 AAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQI 361
           AA L++ GKP    A+ AK FAS++A +V + A+QI GGYGY  DYP ERY R+A+ITQI
Sbjct: 303 AARLRSAGKPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQI 362

Query: 362 YEGTNQVMRIVTSRAL 377
           YEGT+++ R+V +R L
Sbjct: 363 YEGTSEIQRMVIAREL 378


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: 316
Number of extensions: 8
Number of successful extensions: 1
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: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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 Sep 17 2021. 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