GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Desulfovibrio vulgaris Miyazaki F

Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate 8499876 DvMF_0641 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)

Query= metacyc::MONOMER-14378
         (158 letters)



>FitnessBrowser__Miya:8499876
          Length = 905

 Score =  122 bits (307), Expect = 1e-32
 Identities = 67/146 (45%), Positives = 88/146 (60%), Gaps = 3/146 (2%)

Query: 9   VNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTLAHSV 68
           VNG PR   V   A L D LR+ L LTG K GC  G+CGAC+V++DG+   +C      +
Sbjct: 8   VNGIPRNLVVDPEATLADVLREQLLLTGVKVGCGEGQCGACSVILDGKVVRSCAYKMRRL 67

Query: 69  A-GHSIETIEGLSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSRDEIR 127
             G S+ TIEG+     L  LQ A+  H G+QCGFCTPG I++A  LL  N  PSRD++R
Sbjct: 68  PDGASVTTIEGVGSPDCLHPLQLAWTAHGGAQCGFCTPGFIVSARQLLEENKSPSRDDVR 127

Query: 128 AALA--GNLCRCTGYVKIIESVEAAA 151
                  N+CRCTGY  ++++V  AA
Sbjct: 128 DWFQKHRNVCRCTGYKPLVDAVMDAA 153


Lambda     K      H
   0.320    0.135    0.412 

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: 371
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: 158
Length of database: 905
Length adjustment: 30
Effective length of query: 128
Effective length of database: 875
Effective search space:   112000
Effective search space used:   112000
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 (21.8 bits)
S2: 49 (23.5 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