GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcrC in Pseudomonas fluorescens GW456-L13

Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate PfGW456L13_3926 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs

Query= SwissProt::O33818
         (161 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3926
          Length = 179

 Score = 98.2 bits (243), Expect = 6e-26
 Identities = 61/156 (39%), Positives = 90/156 (57%), Gaps = 18/156 (11%)

Query: 5   LRLTLNGRAREDL-VPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPRLA--- 60
           L+LTLNG++   + +PD++ ++DYL E   LTG++ GC  G C AC V+VD+    +   
Sbjct: 6   LQLTLNGQSVGPVDIPDDLPMIDYLHEYKNLTGSRLGCGQGICHACVVIVDNPDGTSEEV 65

Query: 61  --CSTLAHQVAGKKVETVESLAT---QGTLSKL---QAAFHEKLGTQCGFCTPGMIMASE 112
             C T AH   GKKV T+E  AT   QG +++L   Q  F ++   QC +C PG + A+ 
Sbjct: 66  RTCITGAHYFEGKKVRTIEGHATCDEQGKVTELNPIQQRFVDEFAFQCSYCAPGFVNAAT 125

Query: 113 AL---LRKNP---SPSRDEIKAALAGNLCRCTGYVR 142
            L   L++ P   S     I+ +L  ++CRCTGYVR
Sbjct: 126 VLVEKLQRQPIVKSQLEKVIEDSLGHHICRCTGYVR 161


Lambda     K      H
   0.318    0.132    0.389 

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: 110
Number of extensions: 7
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: 161
Length of database: 179
Length adjustment: 18
Effective length of query: 143
Effective length of database: 161
Effective search space:    23023
Effective search space used:    23023
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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