GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Cupriavidus basilensis 4G11

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS01630 RR42_RS01630 branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Cup4G11:RR42_RS01630
          Length = 307

 Score =  199 bits (505), Expect = 8e-56
 Identities = 106/262 (40%), Positives = 157/262 (59%), Gaps = 13/262 (4%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           D +L ++++S+ FGG+ A+ D SF+ +  +I A+IGPNGAGK+++ N I G Y P  G I
Sbjct: 54  DVILDLQNISLAFGGVKALTDISFDVREHEIRAIIGPNGAGKSSMLNVINGVYHPQQGRI 113

Query: 72  TFNQKSGKQYLLERLPDFRITKEAR--VARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129
            F  +  ++           T  AR  +ARTFQNI LF G+TVL+N++  ++ +      
Sbjct: 114 VFRGEERRK--------MHPTAAARQGIARTFQNIALFKGMTVLDNIMTGRNTRFRSG-- 163

Query: 130 YTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189
             +   +  GP + E  +        ++  ++      P G LPYG Q+R+E+ARA+   
Sbjct: 164 -LLANALWWGPARNEEMQHRRKVEEVIDFLEIQAIRKTPVGRLPYGLQKRVELARALAAE 222

Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249
           P +L LDEP AG+N  E   +   +  +  + GT+I+LIEHDM VVM+ISD VVVL+YG+
Sbjct: 223 PSMLLLDEPMAGMNVEEKQDMCRFILDVNHQFGTTIVLIEHDMGVVMDISDRVVVLDYGK 282

Query: 250 KISDGTPDHVKNDPRVIAAYLG 271
           KI DGTP+ VK +P VI AYLG
Sbjct: 283 KIGDGTPEAVKANPDVIRAYLG 304


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: 213
Number of extensions: 9
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: 307
Length adjustment: 27
Effective length of query: 265
Effective length of database: 280
Effective search space:    74200
Effective search space used:    74200
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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