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 GFF2365 PS417_12060 sugar ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  265 bits (677), Expect = 1e-75
 Identities = 157/327 (48%), Positives = 213/327 (65%), Gaps = 9/327 (2%)

Query: 9   AASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASI 68
           A +  AP+ A    RL     L   G+  V +LLC+  +  +E F  W+N   I +Q SI
Sbjct: 3   AKTITAPVTAAPRNRLRLS--LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSI 60

Query: 69  NMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVN 128
           N +LA GMT+VILT GIDLSVGSIL+ + + + +V+      + +V A +  G + G+VN
Sbjct: 61  NGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVN 120

Query: 129 GALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEV--LGVPWLVI 186
           G +VA + +PPF+ TLG L+  RG+  ++ + S I +    +  +G G++  +GVP   I
Sbjct: 121 GFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVP---I 177

Query: 187 IAFAVVA-VSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGV 245
           I FAVVA + W VLR T  G  +YAVGGN ++AR SGI V  V+  VY VSGLLAGL GV
Sbjct: 178 IIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGV 237

Query: 246 MSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLL 305
           + SAR  +A   Q G SYELDAIAAV++GGTS  GGTGSIVGTL GAL+I V++NGL LL
Sbjct: 238 VLSARTTSALP-QAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLL 296

Query: 306 GVSDIWQYIIKGLVIIGAVALDSYRRK 332
           GVS  +Q + KGL+I+ AV +D +R+K
Sbjct: 297 GVSSYYQQVAKGLIIVFAVLIDVWRKK 323


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: 373
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: 325
Length adjustment: 28
Effective length of query: 309
Effective length of database: 297
Effective search space:    91773
Effective search space used:    91773
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