GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Pseudomonas simiae WCS417

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate GFF1263 PS417_06415 ABC transporter substrate-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3431
         (257 letters)



>FitnessBrowser__WCS417:GFF1263
          Length = 259

 Score =  204 bits (519), Expect = 1e-57
 Identities = 107/251 (42%), Positives = 158/251 (62%), Gaps = 5/251 (1%)

Query: 2   KKLVLLGALALSVLSLPTFADE-KPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60
           K L+ L ALAL + +  T A E K L+ G++ +Y PF SKA DGS+VGFD D+GNA+C E
Sbjct: 3   KALLTLSALALCMAAGSTLAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAE 62

Query: 61  MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGT 120
           +KVKC WVE +FDG+IP LK  K D ++SSM++T  R+K++DF+++ ++ P  LV K G 
Sbjct: 63  LKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPVREKAIDFSSELFSGPTSLVFKKGA 122

Query: 121 AVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180
             S     LKGK++G ++G+I E +A+ VL   G   K Y +Q+++Y D+ +GRLD +V 
Sbjct: 123 GYS-TPESLKGKSVGYEQGTIQEAYAKAVLDKAGVTTKAYANQDQVYADLTSGRLDASVQ 181

Query: 181 DATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGDA-LKDKINTAIAAIREN 239
           D    + GFLK+ AG G+     A  D         I ++KG+  LK  ++  I A+ ++
Sbjct: 182 DMLQAELGFLKSPAGAGYEV--SAAIDDPLLPSKTAIGIKKGNTELKTLLDKGIKALHDD 239

Query: 240 GKYKQIQDKYF 250
           G Y  IQ K+F
Sbjct: 240 GTYATIQKKHF 250


Lambda     K      H
   0.318    0.138    0.394 

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: 204
Number of extensions: 13
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: 257
Length of database: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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: 47 (22.7 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