GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23200
          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.

Links

Downloads

Related tools

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