GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Rhizobium etli CFN 42

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_011428126.1 RHE_RS25445 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>NCBI__GCF_000092045.1:WP_011428126.1
          Length = 395

 Score =  217 bits (552), Expect = 5e-61
 Identities = 134/373 (35%), Positives = 194/373 (52%), Gaps = 5/373 (1%)

Query: 5   LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64
           LT +++M++D A  +A++ LAP V +  +    D  +  +MGE G  G     EYGG GL
Sbjct: 20  LTNEERMVQDTAHAYAQQKLAPRVLDAFRNEKTDPAIFREMGELGLLGPTISPEYGGAGL 79

Query: 65  DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124
              +Y L   E+ +VD G    +S   SL   PI  FG+  QKQKYL  +A G  +G FG
Sbjct: 80  GYTAYGLIAREVERVDSGYRSMMSVQSSLVMVPIETFGSAAQKQKYLPKLATGEWIGCFG 139

Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184
           LTEP  G+D  +  T A      Y L GSK +I+N   AD +VV+A T+       I  F
Sbjct: 140 LTEPDHGSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADVFVVWAKTEDGL----IRGF 195

Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244
           ILEKG  G     I  K+G   SIT E++ +   VP+ENLL     G K     L+  R 
Sbjct: 196 ILEKGWKGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLL-PGVTGLKGPFTCLNSARF 254

Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304
           G+A  ALG AE   A A +Y  ER+QFGR ++  Q +Q  +ADMA +I            
Sbjct: 255 GIAWGALGAAEDCYARARQYVLERKQFGRPLAANQLIQKKLADMAAEIALGLQGCLRLGR 314

Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364
           +K EG P  E  ++ K  +   A+E+   A  + GG G + ++   R++ N ++   YEG
Sbjct: 315 MKEEGHPPVELTSILKRNSCGKALEMARAARDMLGGNGISDEFGIARHLVNLEVVNTYEG 374

Query: 365 TNQVMRIVTSRAL 377
           T+ +  ++  R++
Sbjct: 375 THDIHALIIGRSI 387


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: 350
Number of extensions: 15
Number of successful extensions: 3
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: 395
Length adjustment: 30
Effective length of query: 353
Effective length of database: 365
Effective search space:   128845
Effective search space used:   128845
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