GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Pseudomonas putida KT2440

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Putida:PP_0411
          Length = 374

 Score =  226 bits (577), Expect = 7e-64
 Identities = 126/294 (42%), Positives = 176/294 (59%), Gaps = 12/294 (4%)

Query: 7   QALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGT 66
           + + K Y G   ++  L+L I  GEF+ LLGPSG GK+T L M+AG E  + G +++GG 
Sbjct: 18  RGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGR 77

Query: 67  VVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEA 126
            +N++P  +R++ MVFQNYAL+PHM+V +N+AF L        +I  RV+ V  ++ L+A
Sbjct: 78  SINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDA 137

Query: 127 LLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRT 186
             +R P  +SGGQQQR A+ARA++  P + L DEPL  LD +LR  ++ +IK +HQRL  
Sbjct: 138 FAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLGV 197

Query: 187 TTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGT 246
           T VYVTHDQ EA+T++DRV +   G I Q   P  LY  P N F A FIG    N +SGT
Sbjct: 198 TVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIG--ENNRISGT 255

Query: 247 VQRQDGQLFIETAHQRWALTGERFSRL-----RHAMAVKLAVRPDHVRIAGERE 295
           +   DG+       Q     GER   L     +    V L++RP+ VR+ G  E
Sbjct: 256 LLASDGK-----RCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRLNGHSE 304


Lambda     K      H
   0.321    0.137    0.403 

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: 378
Number of extensions: 16
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: 406
Length of database: 374
Length adjustment: 30
Effective length of query: 376
Effective length of database: 344
Effective search space:   129344
Effective search space used:   129344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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