GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Kocuria flava HO-9041

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_083529298.1 AS188_RS06770 ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>NCBI__GCF_001482365.1:WP_083529298.1
          Length = 366

 Score =  134 bits (337), Expect = 4e-36
 Identities = 110/343 (32%), Positives = 173/343 (50%), Gaps = 23/343 (6%)

Query: 8   PAASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQAS 67
           P A+  A     T G L        +G L   V++ + F++   +    Q++S +   AS
Sbjct: 24  PTAAAPADERVQTRGLLGALLARPEIGALVGAVVVGLFFAIAAPSITQAQSISTVLYGAS 83

Query: 68  INMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGM-LSVPAALLCGLLFGI 126
              ++  G++ +++ G  DLS G  +  SA+ A L S    L + + V  ALL  L  G+
Sbjct: 84  TIGIMVVGVSLLMIGGEFDLSTGVAVISSALTASLFSWYFGLNVWVGVAVALLTSLAIGL 143

Query: 127 VNGALVAFMKLPPFIVTLGTLTAVRGL----ARLVGNDSTIYNPDI----GFA-----FI 173
           VNG L+   KLP FIVTL T   + GL     RL+G   ++ +P I    GFA     F 
Sbjct: 144 VNGVLLMRTKLPSFIVTLATFLMLTGLNLALTRLIGG--SVSSPSISGMDGFAAAKAVFA 201

Query: 174 GNGEVLGVPWLVIIAF--AVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLF 231
            + EV GV   + + +  A+VA++ FVL +T +G  I+AVGG+ +AAR  G+ V    + 
Sbjct: 202 SSVEVGGVSIRITVFYWIALVAIASFVLLKTRIGNWIFAVGGDPDAARAVGVPVARTKIG 261

Query: 232 VYAVSGLLAGLGGVMSSARLYAANGLQLGQSY--ELDAIAAVILGGTSFVGGTGSIVGTL 289
           ++   GL A L G+ +   L+A + +Q G+    E   I   ++GG    GG GS +G  
Sbjct: 262 LFMGVGLCAWLVGMHN---LFAFDSVQSGEGVGNEFLYIIGAVIGGCLLTGGFGSAIGGA 318

Query: 290 VGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332
           +GALI  + S G+V    +  W     GL+++ A  ++ Y RK
Sbjct: 319 IGALIFGIASRGIVYAEWNPDWFKFFLGLMLLLATIVNMYVRK 361


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: 393
Number of extensions: 22
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: 366
Length adjustment: 29
Effective length of query: 308
Effective length of database: 337
Effective search space:   103796
Effective search space used:   103796
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 24 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