GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvH in Paraburkholderia bryophila 376MFSha3.1

Align Glycine cleavage system H protein (characterized)
to candidate H281DRAFT_02410 H281DRAFT_02410 glycine cleavage system H protein

Query= SwissProt::P0A6T9
         (129 letters)



>FitnessBrowser__Burk376:H281DRAFT_02410
          Length = 126

 Score =  154 bits (388), Expect = 5e-43
 Identities = 73/120 (60%), Positives = 96/120 (80%), Gaps = 1/120 (0%)

Query: 3   NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAE 62
           ++PA+LKY++ HEW+R EADGT TVGIT+HAQE LGD+VF ++ E+G TV+AGD  AV E
Sbjct: 2   SIPADLKYTESHEWVRTEADGTLTVGITDHAQEALGDIVFFEVQELGKTVTAGDTVAVIE 61

Query: 63  SVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAY 122
           SVKAASDIYAPVSGEI+  N A++D+P+ VNS PY   W+FKIK + ++  + L+DA AY
Sbjct: 62  SVKAASDIYAPVSGEIIEANTAVADTPDSVNSAPYE-SWLFKIKPASDAAQDRLIDADAY 120


Lambda     K      H
   0.308    0.127    0.354 

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: 91
Number of extensions: 2
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: 129
Length of database: 126
Length adjustment: 14
Effective length of query: 115
Effective length of database: 112
Effective search space:    12880
Effective search space used:    12880
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: 41 (21.2 bits)
S2: 41 (20.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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