GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Shewanella loihica PV-4

Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate 5210999 Shew_3425 2-deoxyglucose-6-phosphatase (RefSeq)

Query= SwissProt::O06995
         (226 letters)



>FitnessBrowser__PV4:5210999
          Length = 223

 Score = 80.5 bits (197), Expect = 2e-20
 Identities = 58/189 (30%), Positives = 96/189 (50%), Gaps = 10/189 (5%)

Query: 1   MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60
           + AVIFD+DGV+ D+      A   +  Q+ +P      E+  G+  ++ +E    +   
Sbjct: 6   LAAVIFDMDGVLIDSEPSWQAAEYKVLSQLGLPISLSDTEQTTGLRIDQVVE--YWYRRH 63

Query: 61  ETK-YTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSSRNA 119
             K Y NA   E +       Q+    L+  +++ G+   L   K   +K+GLA+SS   
Sbjct: 64  PWKGYDNAATAEAIVT-----QVAGEILSHGEVMSGVKEALEACKQRGLKLGLATSSPTL 118

Query: 120 --PKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGISA 177
               ++++LAI + F AIV    LA GKP P+++L  A  L V+P+ C A+ED+  G+ A
Sbjct: 119 LIDAVMQKLAIRELFDAIVSAEALALGKPHPEVYLNCAKALGVTPSQCLAVEDSFNGLIA 178

Query: 178 IKSAGMFAV 186
            ++A M  V
Sbjct: 179 ARAANMHTV 187


Lambda     K      H
   0.319    0.136    0.390 

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: 106
Number of extensions: 5
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: 226
Length of database: 223
Length adjustment: 22
Effective length of query: 204
Effective length of database: 201
Effective search space:    41004
Effective search space used:    41004
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 (21.7 bits)
S2: 46 (22.3 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