GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Phaeobacter inhibens BS107

Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate GFF2055 PGA1_c20880 molybdenum hydroxylase family protein, small subunit

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



>FitnessBrowser__Phaeo:GFF2055
          Length = 161

 Score =  161 bits (407), Expect = 5e-45
 Identities = 81/154 (52%), Positives = 105/154 (68%), Gaps = 2/154 (1%)

Query: 5   LTLSVNGRPREDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLVDGQPRLACCTL 64
           +T++VNGR     V G  LL  +LR+ LGLTGT  GCD  +CGAC V VDG+   AC  L
Sbjct: 4   VTMTVNGRTASGEVEGRTLLSGFLREELGLTGTHVGCDTSQCGACVVHVDGKAVKACTML 63

Query: 65  AHSVAGHSIETIEG-LSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQPSR 123
           A    G  + TIEG  + +G L+ +Q+AF +H G QCGFCTPGM+M+A ALL+ NP+PS 
Sbjct: 64  AAEADGADVATIEGQAAPDGTLNTIQQAFQDHHGLQCGFCTPGMVMSAAALLKDNPKPSE 123

Query: 124 DEIRAALAGNLCRCTGYVKIIESVEAAACGSEVS 157
            EIR  L GNLCRCTGY  I++++ AA+ G +VS
Sbjct: 124 QEIREYLEGNLCRCTGYHNIVKAIMAAS-GQDVS 156


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: 147
Number of extensions: 12
Number of successful extensions: 2
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: 161
Length adjustment: 17
Effective length of query: 141
Effective length of database: 144
Effective search space:    20304
Effective search space used:    20304
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: 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