GapMind for catabolism of small carbon sources

 

Alignments for a candidate for crr in Collinsella tanakaei YIT 12063

Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_009140205.1 HMPREF9452_RS00875 PTS glucose transporter subunit IIA

Query= SwissProt::P0A283
         (169 letters)



>NCBI__GCF_000225705.1:WP_009140205.1
          Length = 186

 Score = 99.0 bits (245), Expect = 4e-26
 Identities = 48/147 (32%), Positives = 85/147 (57%), Gaps = 3/147 (2%)

Query: 23  IVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIES 82
           I AP+SG +V + ++ D   +  + G G  I P GN + AP +G I     +NH+  + +
Sbjct: 32  IYAPISGVLVELSEIDDDSISSGLFGRGYGIVPVGNVIYAPANGRIAATTVSNHSIGLRT 91

Query: 83  DSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTPVVIS 142
           D+GIEL +H GIDTV+++G+GF R+ E  Q VK G P++ FD   ++      +  V+++
Sbjct: 92  DNGIELIIHVGIDTVKMEGKGFNRLVESEQEVKAGQPILVFDDDAIKAAGYDDVVTVIVT 151

Query: 143 NMDEIKELIKLSG--SVTVGETPVIRI 167
           +   + + +KL G  +    + P+++I
Sbjct: 152 S-PSLLDKVKLVGQSNTLFADHPLVKI 177


Lambda     K      H
   0.315    0.139    0.377 

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: 103
Number of extensions: 4
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: 169
Length of database: 186
Length adjustment: 19
Effective length of query: 150
Effective length of database: 167
Effective search space:    25050
Effective search space used:    25050
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: 42 (21.9 bits)
S2: 44 (21.6 bits)

This GapMind analysis is from Sep 24 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