GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Sinorhizobium meliloti 1021

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate SMc01949 SMc01949 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__Smeli:SMc01949
          Length = 295

 Score =  374 bits (961), Expect = e-108
 Identities = 183/271 (67%), Positives = 221/271 (81%)

Query: 3   TQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYT 62
           T +MT  P+L VE L+MRFGGL+A+ND SF A  GEITA+IGPNGAGKTT+FNCITGFY 
Sbjct: 5   TDTMTKDPILKVERLSMRFGGLMAINDFSFEAERGEITALIGPNGAGKTTVFNCITGFYK 64

Query: 63  PTVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLI 122
           PT+G +T+R   G EFLLER+P + I++KA VARTFQNIR+F G++VLENL+VAQHNKL+
Sbjct: 65  PTMGMITMRQKSGAEFLLERLPDFEITKKAKVARTFQNIRMFSGLTVLENLLVAQHNKLM 124

Query: 123 RASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARA 182
           RASG++I GL G P+Y    RE+++LA++WL++  L E AD  AG+LPYGAQRRLEIARA
Sbjct: 125 RASGYTILGLFGFPAYREASRESIELARHWLEKASLTERADDPAGDLPYGAQRRLEIARA 184

Query: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242
           MCT P +LCLDEPAAGLNPRES  L  LL  IR +    +LLIEHDMSVVM ISDHVVVL
Sbjct: 185 MCTGPELLCLDEPAAGLNPRESLALNALLQEIRRDTGTSILLIEHDMSVVMEISDHVVVL 244

Query: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEEEDE 273
           +YG+KISDG+P FVKNDP VI AYLG E++E
Sbjct: 245 EYGQKISDGNPDFVKNDPRVIAAYLGVEDEE 275


Lambda     K      H
   0.319    0.137    0.397 

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: 279
Number of extensions: 2
Number of successful extensions: 1
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: 294
Length of database: 295
Length adjustment: 26
Effective length of query: 268
Effective length of database: 269
Effective search space:    72092
Effective search space used:    72092
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: 48 (23.1 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