GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12055 in Pseudomonas fluorescens FW300-N2C3

Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate AO356_23200 AO356_23200 rhizopine-binding protein

Query= uniprot:A0A1N7UEK0
         (335 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23200 AO356_23200
           rhizopine-binding protein
          Length = 308

 Score =  169 bits (427), Expect = 1e-46
 Identities = 103/303 (33%), Positives = 166/303 (54%), Gaps = 21/303 (6%)

Query: 6   TLAATAALSLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEH-----PAVKDGT 60
           T  A+ ALSL+  S A  AD    K+G ++     QF   W+  L+E       ++ DG 
Sbjct: 5   TRIASLALSLMLTSGAALAD---LKIGVSM----SQFDDTWLTYLRESMDKKAKSLPDG- 56

Query: 61  VQLTVFDGNYDALTQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTK 120
           V L   D   D + Q +Q+E+ ++Q+ DA++  P+DT A     KAA++  + ++  N +
Sbjct: 57  VTLQFEDARSDVVKQLSQVESFISQKVDALIVNPVDTAATQRITKAAVAAGIPLVYVNRR 116

Query: 121 VADASVPY----VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEV 176
             D  +P     V +DD+E GR+Q Q + +K+ GKGN+VI+ G +  ++  +R KG  +V
Sbjct: 117 PDDPKLPEGVVTVASDDLEAGRMQMQYLAEKMGGKGNIVILLGDLANNSTANRTKGVKDV 176

Query: 177 LGKHPDIKIIEKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGL 236
           L K+P IKI +++T  W R + + L  DWL    +    V+A ND+MA+GA  ALK  G 
Sbjct: 177 LAKYPGIKIEQEQTGIWLRDKGMTLVNDWL-TQGREFQAVVANNDEMAIGAAMALKQAGT 235

Query: 237 TSKDVPVTSIDGMPDAIQAAKKDEV-TTFLQDAQAQSQGALDVALRALAGKDYKPQSVIW 295
               V +  +DG PD + A KK E+  +  QDA+ Q+ G++D A++ +  K    +  +W
Sbjct: 236 EKGSVLIAGVDGTPDGLNAIKKGEMAVSVFQDAKGQADGSIDTAVKMV--KKQPVEQAVW 293

Query: 296 ERY 298
             Y
Sbjct: 294 VPY 296


Lambda     K      H
   0.314    0.130    0.373 

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: 249
Number of extensions: 15
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: 335
Length of database: 308
Length adjustment: 28
Effective length of query: 307
Effective length of database: 280
Effective search space:    85960
Effective search space used:    85960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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 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