GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEIIA in Escherichia coli BW25113

Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate 17782 b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= uniprot:P50829
         (168 letters)



>FitnessBrowser__Keio:17782
          Length = 625

 Score =  119 bits (297), Expect = 1e-31
 Identities = 63/171 (36%), Positives = 95/171 (55%), Gaps = 7/171 (4%)

Query: 3   KKLFGMGKIQEKVTEEV-------IYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSG 55
           K+    G  QEK  E +       I SP  G ++ L  V D  F+  ++G+GIA+ PS G
Sbjct: 455 KRQPAQGAPQEKTPEVITPPEQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVG 514

Query: 56  EIVSPAEGEVIQIFHTKHAVGIRTRSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGD 115
           E+ SP  G +  +F T HA+GI +  G+E+LIHVG++TV ++G+ F+AH+  GDKV  GD
Sbjct: 515 EVRSPVAGRIASLFATLHAIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGD 574

Query: 116 PLITCDLELIKEKASSTVIPIVIMNGEAVGSMVSAGEKAARKGESKLFTIK 166
            LI+ D+  I+E       P++I N +    ++  G      GE  L  I+
Sbjct: 575 RLISFDIPAIREAGFDLTTPVLISNSDDFTDVLPHGTAQISAGEPLLSIIR 625


Lambda     K      H
   0.314    0.134    0.365 

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: 255
Number of extensions: 14
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: 168
Length of database: 625
Length adjustment: 27
Effective length of query: 141
Effective length of database: 598
Effective search space:    84318
Effective search space used:    84318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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