GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc01949 SMc01949 high-affinity
           branched-chain amino acid ABC transporter ATP-binding
           protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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