GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamG in Synechococcus elongatus PCC 7942

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Synpcc7942_0278 Synpcc7942_0278 bidirectional hydrogenase complex protein HoxE

Query= uniprot:Q39TW4
         (150 letters)



>FitnessBrowser__SynE:Synpcc7942_0278
          Length = 165

 Score =  117 bits (292), Expect = 1e-31
 Identities = 54/131 (41%), Positives = 85/131 (64%)

Query: 5   RIDQIIDKHDGEASSLIQILLDIQSEHNWLPKEALKRVCERLQVPMSRITHIATFYKAFS 64
           R++  I +   +A +LI+IL + QS + +L +E L+ V E+L +P S++  +A+FY  F 
Sbjct: 16  RLELAIKRQAAQADALIEILHEAQSLYGYLDRELLQWVAEQLALPRSKVYGVASFYHLFQ 75

Query: 65  LVPKGRHQVHVCMGTACHVRGAQRVLDTVQEVTGVKSGETDSDLKFSVETVNCLGCCALG 124
           L P GRH+ HVC+GTAC+V+G+Q +LD +    G++ GET +D   S+ TV C+G C + 
Sbjct: 76  LNPSGRHRCHVCLGTACYVKGSQAILDCLIAELGIREGETTNDGSVSLGTVRCVGACGIA 135

Query: 125 PVMEVDGKHHG 135
           PV+  DG   G
Sbjct: 136 PVVVYDGDIQG 146


Lambda     K      H
   0.321    0.135    0.408 

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: 76
Number of extensions: 1
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: 150
Length of database: 165
Length adjustment: 17
Effective length of query: 133
Effective length of database: 148
Effective search space:    19684
Effective search space used:    19684
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: 43 (21.2 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