GapMind for catabolism of small carbon sources


Alignments for a candidate for gcvH in Pseudomonas stutzeri RCH2

Align Glycine cleavage system H protein (characterized)
to candidate GFF4052 Psest_4125 Glycine cleavage system H protein (lipoate-binding)

Query= SwissProt::P0A6T9
         (129 letters)

          Length = 154

 Score = 82.8 bits (203), Expect = 2e-21
 Identities = 40/106 (37%), Positives = 62/106 (58%), Gaps = 1/106 (0%)

           P  L+Y+ EH  WLR+E DG+ T+G+T +   L G +       VGA +       V E 

            KAAS   +P++GE++AVN+AL + P L+N + Y  GW+ +++  D

Lambda     K      H
   0.308    0.127    0.354 

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: 58
Number of extensions: 3
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: 129
Length of database: 154
Length adjustment: 15
Effective length of query: 114
Effective length of database: 139
Effective search space:    15846
Effective search space used:    15846
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 42 (20.8 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