GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araWsh in Pseudomonas fluorescens FW300-N1B4

Align Inner-membrane translocator (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:A0KWY6
         (405 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Ribose ABC transport
           system, permease protein RbsC (TC 3.A.1.2.1)
          Length = 325

 Score =  134 bits (337), Expect = 4e-36
 Identities = 95/321 (29%), Positives = 161/321 (50%), Gaps = 10/321 (3%)

Query: 52  QAGKSTSMGRYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLS 111
           ++G    +G YL   LA ++L +  LF   S   +SY       +   + N+   + +L+
Sbjct: 10  RSGNFYGLGTYLG--LAGALLAMVALFSVLSSHFLSYD------TFSTLANQIPDLMVLA 61

Query: 112 IGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLV 171
           +GM+ V+  GGIDLSVG+V+A+A +  +  +L    S++     G+ V  LAG I G + 
Sbjct: 62  VGMTFVLIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSIT 121

Query: 172 SFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGML 231
               I   + +L ++   RG+A  +  G    +    FA +      G+     I + ++
Sbjct: 122 VAWRIPSFIVSLGVLEMARGLAYQMT-GSRTAYIGDAFAWLSNPIAFGISPSFIIALLII 180

Query: 232 TFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQ 291
             +Q +L +T  G ++  +G N +A R  GIN K  K+  + + GL A +A +   + ++
Sbjct: 181 FIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLE 240

Query: 292 GSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFN 351
            +D  NAG  LEL  + AVVIGG +L GGR S+I +  G LII  LA  +   G      
Sbjct: 241 AADP-NAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTK 299

Query: 352 LLIKAIVILTVLLLQSAKFRR 372
            +I   VI+  ++L + + +R
Sbjct: 300 RIITGAVIVVAVVLDTYRSQR 320


Lambda     K      H
   0.323    0.136    0.379 

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: 311
Number of extensions: 18
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: 405
Length of database: 325
Length adjustment: 29
Effective length of query: 376
Effective length of database: 296
Effective search space:   111296
Effective search space used:   111296
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 (22.0 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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