GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatP in Acidovorax sp. GW101-3H11

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2880
          Length = 350

 Score =  186 bits (471), Expect = 1e-51
 Identities = 113/302 (37%), Positives = 171/302 (56%), Gaps = 8/302 (2%)

Query: 29  ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88
           ++ L+LL       N  F T  N +N+L+  +  GIIAVGM FVI+ GGID++VGS+ A 
Sbjct: 44  VIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAAL 103

Query: 89  ASIAAAYVVTA---VVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGM 145
            + +    + A   V+G   A  ++ +L++ ++G   G V G  +T   +  FIVTLG +
Sbjct: 104 IAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTL 163

Query: 146 TVWRGATLLLNDGGPIS---GFNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRY 202
            ++R      ++GG I+     +D Y       +L +P+PV IF LVA  G V L  T Y
Sbjct: 164 GIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVILNRTAY 223

Query: 203 GRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYEL 262
           GR V A+G N + A+ + V+V  I    Y ++G   G++  L   RLGSA    G  +EL
Sbjct: 224 GRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLWEL 283

Query: 263 RVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTS-YVQQVVIGLIIVAAV 321
             IA+V++GG  L GG+G + GTV+GA+L+ V+SN L +  + S Y+   V G +I+ AV
Sbjct: 284 EAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVII-AV 342

Query: 322 AF 323
           AF
Sbjct: 343 AF 344


Lambda     K      H
   0.325    0.140    0.413 

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: 296
Number of extensions: 25
Number of successful extensions: 4
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: 332
Length of database: 350
Length adjustment: 28
Effective length of query: 304
Effective length of database: 322
Effective search space:    97888
Effective search space used:    97888
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: 40 (21.6 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