GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Stutzerimonas stutzeri A1501

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_011912851.1 PST_RS08590 acyl-CoA dehydrogenase family protein

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000013785.1:WP_011912851.1
          Length = 387

 Score =  201 bits (512), Expect = 2e-56
 Identities = 114/358 (31%), Positives = 203/358 (56%), Gaps = 15/358 (4%)

Query: 16  VSFAENEVKPLATE--------LDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVG 67
           +SF    V+ L  E        +DEE+ FP   V  M +AG +    P+EYGG G     
Sbjct: 9   LSFIREGVRALCAEFPAEYWRRIDEEKGFPEAFVTAMTEAGWLSAMIPEEYGGSGLGLAE 68

Query: 68  YIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGE-KLGAFGLTE 126
             + +EE++R  G +G I     ++  + + + G+EEQK+ +L  LA+GE +L + G+TE
Sbjct: 69  ASVILEEVNRCGGNSGTIHGQMYNM--FTLLRNGSEEQKRYYLPKLANGELRLQSMGVTE 126

Query: 127 PNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMT----DKSKGNKGISA 182
           P  GTD +  +TTAV  GD+Y++NG K++I+     D+ +++A T    +  + ++G+S 
Sbjct: 127 PTTGTDTTKIKTTAVRRGDKYVINGQKVWISRIQHSDLMILLARTTPLAEVQRKSEGMSI 186

Query: 183 FIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGR 242
           F+V+      +    +    +    T+EL F++  IP  +L+G+EG+GF+  +  L+  R
Sbjct: 187 FLVDLREAIGNGLTVQPIANMVNHETNELFFDNLEIPASSLIGEEGKGFRYILDGLNAER 246

Query: 243 IGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAA 302
             IAA+ +G  +  ++++ +Y ++RV FGRP+ + Q  QF +A+  ++++AA  + ++A 
Sbjct: 247 TLIAAECIGDGRWFVEKSAQYARDRVVFGRPIGQNQGVQFPIAEAHIEIEAADLMRWRAC 306

Query: 303 INKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360
              D G+  G  A MAK  AA+ + E     +Q HGG+G+  +Y VER  R+ ++ ++
Sbjct: 307 DEYDAGRNAGAAANMAKYLAAKASWEAANACLQTHGGFGFANEYDVERKFRETRLYQV 364


Lambda     K      H
   0.315    0.133    0.373 

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: 352
Number of extensions: 15
Number of successful extensions: 4
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: 378
Length of database: 387
Length adjustment: 30
Effective length of query: 348
Effective length of database: 357
Effective search space:   124236
Effective search space used:   124236
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: 42 (22.0 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