GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Burkholderia phytofirmans PsJN

Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate BPHYT_RS10825 BPHYT_RS10825 (2Fe-2S)-binding protein

Query= metacyc::MONOMER-17403
         (163 letters)



>FitnessBrowser__BFirm:BPHYT_RS10825
          Length = 176

 Score =  143 bits (361), Expect = 1e-39
 Identities = 71/151 (47%), Positives = 96/151 (63%)

Query: 5   MLRRRKRLLGLNVNGRWREDAVTDDMLLVDYLRDIAGLTGVKTGCDGGECGACTVLIDGE 64
           M +  ++ + L +NGR R        LL D++R   G TG   GC+ G CGACTV +DG 
Sbjct: 4   MRQGERQCVTLTLNGRERSGYCEPRELLSDFIRQELGATGTHVGCEHGVCGACTVHVDGV 63

Query: 65  AAPSCLVLAVRCEGRYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLR 124
           A  SCL+LAV+ +GR I+TVEGLA + +L  LQQ F      QCGFCT G++M+    L+
Sbjct: 64  AGRSCLMLAVQADGRRIDTVEGLAPDMQLGDLQQAFQRHHALQCGFCTAGILMSCADYLQ 123

Query: 125 RNPSPTDEEIRTALSGNLCRCTGYAKIVESV 155
           R P P++ ++R  LSG+LCRCTGY  IV +V
Sbjct: 124 RVPDPSEAQVRDMLSGHLCRCTGYTPIVAAV 154


Lambda     K      H
   0.322    0.138    0.425 

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: 145
Number of extensions: 6
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: 163
Length of database: 176
Length adjustment: 18
Effective length of query: 145
Effective length of database: 158
Effective search space:    22910
Effective search space used:    22910
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