GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudomonas simiae WCS417

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__WCS417:GFF3462
          Length = 330

 Score =  221 bits (564), Expect = 2e-62
 Identities = 131/315 (41%), Positives = 190/315 (60%), Gaps = 9/315 (2%)

Query: 23  RLTTQERLRALGMLPV--LVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVI 80
           RL     +R+    P   LV++ +   + ++ F    NLS IA+Q SIN ++A GMT VI
Sbjct: 20  RLNLARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVI 79

Query: 81  LTGGIDLSVGSILSISAVVA---MLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKL 137
           LTGGIDLSVG ++++S  +    M+  L P L   ++ A +L G+ FGI NG  VA++ +
Sbjct: 80  LTGGIDLSVGPVMALSGTLTAGLMVAGLPPGL---AIGAGMLIGVAFGIGNGLFVAYLHM 136

Query: 138 PPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWF 197
           PP IVTL T+   RGL  +  +   I      FAF G   + G+   ++I      V++ 
Sbjct: 137 PPIIVTLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYV 196

Query: 198 VLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGL 257
           +L+ T +G  IYA+GGN EA RLSG++     L VY +SGL A + G++ ++RL +    
Sbjct: 197 LLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQP- 255

Query: 258 QLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKG 317
             G S+ELDAIAAV+LGG S  GG G IVGTL+GA+++ VL+NGL +LGVS   Q +IKG
Sbjct: 256 NAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKG 315

Query: 318 LVIIGAVALDSYRRK 332
            +I+ A+ +   R K
Sbjct: 316 GIILLAIFISRQRHK 330


Lambda     K      H
   0.325    0.141    0.409 

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: 327
Number of extensions: 19
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: 337
Length of database: 330
Length adjustment: 28
Effective length of query: 309
Effective length of database: 302
Effective search space:    93318
Effective search space used:    93318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 (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