GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Crocosphaera subtropica ATCC 51142

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_198019416.1 CCE_RS05895 SDR family oxidoreductase

Query= BRENDA::Q84X96
         (319 letters)



>NCBI__GCF_000017845.1:WP_198019416.1
          Length = 259

 Score = 85.9 bits (211), Expect = 1e-21
 Identities = 61/180 (33%), Positives = 100/180 (55%), Gaps = 13/180 (7%)

Query: 54  AIITGPTDGIGKAFAFQLAQKGLNLVLVARNPDKLKDVSDSIQAKYSNTQIKTVVMDFSG 113
           A+ITG + GIG+AFA +LA +  NL+L+AR+ DKL  ++  ++ K ++  +K +V D + 
Sbjct: 4   ALITGASSGIGQAFAEELATRQTNLILIARSQDKLYRLAKHLREK-TSIDVKVMVQDLTE 62

Query: 114 DIDGGVRRIKEAIE--GLEVGILINNAGVSYPYAKY--FHEVDEEMLGNLIKINVEGTTK 169
              G  +++ + ++  GL V +LINNAG    +  Y  F+E D      +I++NV    +
Sbjct: 63  PQAG--QKVYDWVQNKGLSVDLLINNAG----FGDYGLFYERDLSRQLAMIQLNVTVLVE 116

Query: 170 VTQAVLVNMLKRKRGAIVNMGSGAAALIPSYPFYSVYAGAKTYVDQFSRCLHVEYKKSGI 229
           +T   L  M +R  G+I+N+ S A        + S+YA  K +V  F+  L  E K  GI
Sbjct: 117 LTHLFLSQMQQRGEGSIINVSSIAG--FQPLAYMSLYAATKAFVLSFTEALWAENKDKGI 174


Lambda     K      H
   0.322    0.138    0.405 

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: 142
Number of extensions: 9
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: 319
Length of database: 259
Length adjustment: 26
Effective length of query: 293
Effective length of database: 233
Effective search space:    68269
Effective search space used:    68269
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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