GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatP in Pseudomonas simiae WCS417

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 GFF2365 PS417_12060 sugar ABC transporter permease

Query= TCDB::B8H230
         (332 letters)



>lcl|FitnessBrowser__WCS417:GFF2365 PS417_12060 sugar ABC
           transporter permease
          Length = 325

 Score =  264 bits (674), Expect = 3e-75
 Identities = 158/324 (48%), Positives = 205/324 (63%), Gaps = 6/324 (1%)

Query: 1   MTAPSSPAPLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVS 60
           M A +  AP+ T  PR  L     +    L  +LL  V   ++E F+T RN ++IL + S
Sbjct: 1   MNAKTITAPV-TAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTS 59

Query: 61  IYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGL 120
           I GI+AVGMT+VIL  GID++VGS+LAFA + +A V T   G      L A+      G 
Sbjct: 60  INGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYG-----LLAAVSAGMFAGA 114

Query: 121 AGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGEILFLP 180
             G V G  V  L +P F+ TLG +++ RG T +LNDG PI+   DAY   G G+I  + 
Sbjct: 115 MLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIG 174

Query: 181 VPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGL 240
           VP++IFA+VA    + LRYT YGR VYAVGGN ++AR SG+ V  +  SVY + G LAGL
Sbjct: 175 VPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGL 234

Query: 241 SGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLV 300
           +G +LSAR  SA   AG  YEL  IA+VVIGG SL+GG+G + GT+ GALLIGV++NGL 
Sbjct: 235 AGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLN 294

Query: 301 MLHVTSYVQQVVIGLIIVAAVAFD 324
           +L V+SY QQV  GLIIV AV  D
Sbjct: 295 LLGVSSYYQQVAKGLIIVFAVLID 318


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: 290
Number of extensions: 12
Number of successful extensions: 2
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: 325
Length adjustment: 28
Effective length of query: 304
Effective length of database: 297
Effective search space:    90288
Effective search space used:    90288
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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