GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pseudomonas fluorescens GW456-L13

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate PfGW456L13_85 Urea ABC transporter, ATPase protein UrtE

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_85
          Length = 232

 Score =  168 bits (426), Expect = 7e-47
 Identities = 93/224 (41%), Positives = 136/224 (60%), Gaps = 2/224 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML+V  +H +YG    L+G+  ++  GE+  L+G NG GK+TLL  + G   A+ G + +
Sbjct: 1   MLQVEKLHQYYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAKEGAVNW 60

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELER-VLTL 119
           EG+ IT    ++ V  GIA  P+GR IF R++V ENL MG ++  PGS A E+   +  L
Sbjct: 61  EGKPITAFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMG-LSRFPGSEAKEVPAFIYEL 119

Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179
           FP L +   +R G +SGG+QQ LAIGRAL S+PRLL+LDEP+ G+ P V+K+I   +K +
Sbjct: 120 FPVLLQMKQRRGGDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAVIKKL 179

Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLA 223
                M + +VEQ    A +LA +  VM  G++   G G  + A
Sbjct: 180 AARGDMAILLVEQFYDFAAELADQYLVMSRGEIVQQGRGENMEA 223


Lambda     K      H
   0.320    0.136    0.377 

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: 152
Number of extensions: 7
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: 236
Length of database: 232
Length adjustment: 23
Effective length of query: 213
Effective length of database: 209
Effective search space:    44517
Effective search space used:    44517
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: 46 (22.3 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