GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas simiae WCS417

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3281 PS417_16795 ABC transporter

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__WCS417:GFF3281
          Length = 257

 Score =  196 bits (497), Expect = 6e-55
 Identities = 112/260 (43%), Positives = 154/260 (59%), Gaps = 11/260 (4%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +L+V  +S+ F G+ AIN  SFE  RG+I ALIGPNGAGK+++ N + G Y+   G I F
Sbjct: 5   ILQVRDISLSFKGIKAINALSFEVARGEICALIGPNGAGKSSLLNVLNGVYRFDAGEIVF 64

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
             +        R+      +   + RTFQN  LF  ++VL+N+L      +  +     L
Sbjct: 65  EDQH-----FHRIDPLGAARRG-IGRTFQNNALFKKMSVLDNILTGLSRHMRSSVIEQAL 118

Query: 134 GLIGVGPYKREAAEAIEL-ARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192
           GL    P  R  AEA  L A+  LE  +L    D   G+L YG Q+R+E+ RA+  GP L
Sbjct: 119 GL----PRARREAEAFRLRAQGILEFLELQAHRDVLVGNLSYGLQKRVELGRALIAGPSL 174

Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252
           L LDEP AG+N  E   +   +  +  + GT+++LIEHDM VVM +SDHVVVL+YG+K+ 
Sbjct: 175 LLLDEPMAGMNAEEKQEMARFVADVNRDLGTTVVLIEHDMGVVMGLSDHVVVLDYGRKVG 234

Query: 253 DGTPDHVKNDPRVIAAYLGV 272
           DGTP  V+ +P VIAAYLGV
Sbjct: 235 DGTPADVQANPEVIAAYLGV 254


Lambda     K      H
   0.318    0.136    0.386 

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: 182
Number of extensions: 6
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: 292
Length of database: 257
Length adjustment: 25
Effective length of query: 267
Effective length of database: 232
Effective search space:    61944
Effective search space used:    61944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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