GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntEIID in Escherichia coli BW25113

Align PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate 15937 b1819 mannose-specific enzyme IID component of PTS (NCBI)

Query= TCDB::Q82ZC6
         (290 letters)



>FitnessBrowser__Keio:15937
          Length = 283

 Score =  125 bits (313), Expect = 1e-33
 Identities = 89/266 (33%), Positives = 135/266 (50%), Gaps = 15/266 (5%)

Query: 8   VVPKTTNLAPEEITNKDVTKAYLRWHFANEIPHSFERYLAPSLLYAMMPLLKKLY-KDDE 66
           +V  T     +++T  D+   +LR +       +FER  A    ++M+P +++LY +++E
Sbjct: 1   MVDTTQTTTEKKLTQSDIRGVFLRSNLFQG-SWNFERMQALGFCFSMVPAIRRLYPENNE 59

Query: 67  QLKAAYMRQLLFFNTQLSWGGGVITGLMASMEQERAKEEHEGREIMMQDDLMYNTKAGLM 126
             K A  R L FFNTQ  +    I G+  ++E++RA     G EI   D  +   K GLM
Sbjct: 60  ARKQAIRRHLEFFNTQ-PFVAAPILGVTLALEEQRAN----GAEI--DDGAINGIKVGLM 112

Query: 127 GALAGIGDAIDSGTVQYIFIAIAVPWAQQGSALGAIFPFVAFALYQVLLGVFFARQSFKM 186
           G LAG+GD I  GTV+ +F A+    A  GS LG +  F+ F L ++    +     +  
Sbjct: 113 GPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSK 172

Query: 187 GRNATGLMQSAGIQKAIEMLSVLGLFMMGILAGNYVKVSSTLQFK----LSGREFV--VQ 240
           G +    M    +QK  E  S+LGLF+MG L   +  V+  L        +G+E V  VQ
Sbjct: 173 GIDIVKDMGGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQ 232

Query: 241 DILDQIVPGLLPLAVVMGVYWFYTKK 266
            ILDQ++PGL+PL +     W   KK
Sbjct: 233 TILDQLMPGLVPLLLTFACMWLLRKK 258


Lambda     K      H
   0.324    0.138    0.402 

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: 228
Number of extensions: 13
Number of successful extensions: 3
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: 290
Length of database: 283
Length adjustment: 26
Effective length of query: 264
Effective length of database: 257
Effective search space:    67848
Effective search space used:    67848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 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