GapMind for catabolism of small carbon sources

 

Alignments for a candidate for crr in Sphingomonas koreensis DSMZ 15582

Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate Ga0059261_1646 Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

Query= SwissProt::P0A283
         (169 letters)



>FitnessBrowser__Korea:Ga0059261_1646
          Length = 830

 Score =  113 bits (283), Expect = 7e-30
 Identities = 52/123 (42%), Positives = 78/123 (63%)

Query: 23  IVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIES 82
           I +PL G    ++ VPD VFA++++GDG+AI+P  + + AP DG +  + E  HA S+ S
Sbjct: 5   ITSPLRGWAAPLDSVPDPVFAQRMMGDGVAIQPLADTVCAPFDGEVVTLHEAGHAVSLRS 64

Query: 83  DSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTPVVIS 142
           D G E+ +H G+DTV LKG GF  +   G  V  GDP+I FD+  +   A S +TPV+++
Sbjct: 65  DEGAEVLIHIGLDTVGLKGRGFTPLVAPGATVARGDPLIRFDMDAVALGATSLITPVIVT 124

Query: 143 NMD 145
           N +
Sbjct: 125 NAE 127


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: 323
Number of extensions: 13
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: 830
Length adjustment: 29
Effective length of query: 140
Effective length of database: 801
Effective search space:   112140
Effective search space used:   112140
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: 49 (23.5 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