GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Cupriavidus basilensis 4G11

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate RR42_RS16960 RR42_RS16960 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__Cup4G11:RR42_RS16960
          Length = 238

 Score =  239 bits (609), Expect = 5e-68
 Identities = 123/233 (52%), Positives = 172/233 (73%), Gaps = 2/233 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           +LK+SG+   YG I+A+KG+D+EI  GE+V+LIGANGAGK+T +  I G      G + +
Sbjct: 5   LLKISGLKVAYGGIQAVKGIDLEIKEGELVTLIGANGAGKTTTMKAITGLQGWAGGDVEY 64

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSIT-AKPGSFANELERVLTL 119
            G+ I  +P+Y L++ G+A  PEGR +F RM++ ENLQMG+ T         +++R+  +
Sbjct: 65  MGKSIKGVPSYTLLKQGLAMVPEGRGVFARMTITENLQMGAYTRTDEAGIKADIDRMFGI 124

Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179
           FPRLKER +Q AGTMSGGEQQMLA+ RALMSQP+LLLLDEPS+GL+P++V +IF+ V+D+
Sbjct: 125 FPRLKERANQLAGTMSGGEQQMLAMARALMSQPKLLLLDEPSMGLSPIMVAKIFEVVRDV 184

Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           +    +TV +VEQNA  AL+ AHRGYVM +G VTMSG   ++L + +VR+AYL
Sbjct: 185 S-ALGVTVLLVEQNARLALQAAHRGYVMESGLVTMSGDAKQMLDDPKVRAAYL 236


Lambda     K      H
   0.320    0.136    0.377 

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: 195
Number of extensions: 10
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: 236
Length of database: 238
Length adjustment: 23
Effective length of query: 213
Effective length of database: 215
Effective search space:    45795
Effective search space used:    45795
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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