GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcC in Klebsiella michiganensis M5al

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BWI76_RS07650 BWI76_RS07650 ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07650 BWI76_RS07650 ABC
           transporter permease
          Length = 351

 Score =  219 bits (558), Expect = 8e-62
 Identities = 122/311 (39%), Positives = 192/311 (61%), Gaps = 18/311 (5%)

Query: 39  LVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAV 98
           L+L+   FSV+  NF    NL I+ Q  +I  +LA GMT VILTGGIDLSVG++  I  +
Sbjct: 20  LLLVIAFFSVMVPNFLTTSNLLIMTQHVAITGLLAIGMTLVILTGGIDLSVGAVAGICGM 79

Query: 99  VA--MLVSLMP----QLGMLSVPAALLC----GLLFGIVNGALVAFMKLPPFIVTLGTLT 148
           VA  +L + +P     +   +VP  +LC    G+L G VNGA++    + PFI TLG + 
Sbjct: 80  VAGALLTNGLPLWNGSVIFFNVPEVILCVALFGVLVGFVNGAVITRFGVAPFICTLGMMY 139

Query: 149 AVRGLARLVGNDSTIYN-------PDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRR 201
             RG A L  + ST  N        + GF+ +G+G ++G+   + +    + + +++  +
Sbjct: 140 VARGSALLFNDGSTYPNLNGMEALGNTGFSTLGSGTLMGIYLPIWLMIGFLLLGYWLTTK 199

Query: 202 TVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQ 261
           T LG  IYA+GGN  AARL+G+ +    +FVYA SGL +   G++ +++L  A+ +  G 
Sbjct: 200 TPLGRYIYAIGGNESAARLAGVPIVKAKIFVYAFSGLCSAFVGLIVASQLQTAHPMT-GN 258

Query: 262 SYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVII 321
            +E+DAI A +LGGT+  GG G + G+++GA +I  L++G+V++GVSD WQ +IKG+VI+
Sbjct: 259 MFEMDAIGATVLGGTALAGGRGRVTGSIIGAFVIVFLADGMVMMGVSDFWQMVIKGVVIV 318

Query: 322 GAVALDSYRRK 332
            AV +D +++K
Sbjct: 319 TAVVVDQFQQK 329


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: 411
Number of extensions: 33
Number of successful extensions: 5
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: 351
Length adjustment: 29
Effective length of query: 308
Effective length of database: 322
Effective search space:    99176
Effective search space used:    99176
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 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