GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Azospirillum brasilense Sp245

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS08245 AZOBR_RS08245 branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__azobra:AZOBR_RS08245
          Length = 294

 Score =  364 bits (935), Expect = e-105
 Identities = 178/271 (65%), Positives = 220/271 (81%)

Query: 6   TNTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYK 65
           T +M+   LL VEHL+M+FGGL+A+ND SF A  G+ITA+IGPNGAGKTT+FNCITGFY 
Sbjct: 3   TQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYT 62

Query: 66  PTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLM 125
           PT+G +T     GK++LLER+P +RI+++A VARTFQNIRLF G++VLENL+VAQHNKL+
Sbjct: 63  PTVGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLI 122

Query: 126 KASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARA 185
           +ASG++I GL+G+  Y R   EA++LA++WL++  L++ AD  AG+LPYGAQRRLEIARA
Sbjct: 123 RASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARA 182

Query: 186 MCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVL 245
           MCT P +LCLDEPAAGLNPRES  L  LL  IR E    +LLIEHDMSVVM ISDHVVVL
Sbjct: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242

Query: 246 EYGQKISDGTPDHVKNDPRVIAAYLGVEDEE 276
           +YG+KISDG P  VKNDP VI AYLG E++E
Sbjct: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEEEDE 273


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: 286
Number of extensions: 4
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: 292
Length of database: 294
Length adjustment: 26
Effective length of query: 266
Effective length of database: 268
Effective search space:    71288
Effective search space used:    71288
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.

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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