GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas putida KT2440

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Putida:PP_0411
          Length = 374

 Score =  240 bits (612), Expect = 5e-68
 Identities = 134/291 (46%), Positives = 181/291 (62%), Gaps = 7/291 (2%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           +  R V K+Y  G    +K++ L I++GEFL L+GPSG GK+T +  +AG ET T G I 
Sbjct: 15  VSFRGVQKSYD-GESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQ 73

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           +G + ++ + P  RDI MVFQ+YAL+P M+V EN+ F L +R + + DI   V RV  ++
Sbjct: 74  LGGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMV 133

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           Q++    R PGQLSGGQQQRVA+ RAL   P++ L DEPL  LD +LR  M+ E+K +HQ
Sbjct: 134 QLDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQ 193

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
           RL  T VYVTHDQ EA+T+ D+VAV   G IQQ   P+ +Y  P N FVA+FIG    N 
Sbjct: 194 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGE--NNR 251

Query: 244 VPLRLQRKDG-RLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIML 293
           +   L   DG R    L  G+    LA+N  +AG     V L +RPE++ L
Sbjct: 252 ISGTLLASDGKRCQVQLPRGERVEALAVNVGQAG---EPVTLSIRPERVRL 299


Lambda     K      H
   0.318    0.135    0.382 

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: 354
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: 386
Length of database: 374
Length adjustment: 30
Effective length of query: 356
Effective length of database: 344
Effective search space:   122464
Effective search space used:   122464
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: 41 (21.7 bits)
S2: 50 (23.9 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