GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Azospirillum brasilense Sp245

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS00060 AZOBR_RS00060 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__azobra:AZOBR_RS00060
          Length = 357

 Score =  325 bits (832), Expect = 2e-93
 Identities = 184/373 (49%), Positives = 237/373 (63%), Gaps = 25/373 (6%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA + L+ V K Y     G + A++ I + + DGEFLVL+GPSGCGKST LRM+AGLE++
Sbjct: 1   MATVDLNQVRKSY-----GAVEAIKGIDISVADGEFLVLLGPSGCGKSTLLRMVAGLESI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T GE+ +  RV+NG+  +DRDIAMVFQ+YALYPH SV  NM++GL+   GLP  EI+ RV
Sbjct: 56  TGGEIAIGGRVVNGLEPKDRDIAMVFQNYALYPHMSVFDNMAYGLK-IRGLPKAEIQARV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
            +  ++L ++  LDR+P QLSGGQ+QRVA+GRAIVR+P  FL DEPLSNLDAKLR +MR 
Sbjct: 115 AKAAEILELNRFLDRRPSQLSGGQRQRVAMGRAIVREPAAFLFDEPLSNLDAKLRTQMRV 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E++RLQ  LG+T++YVTHDQ EAMT+ DR+ V++ G  +QVGTPL+ Y RP +LFVAGFI
Sbjct: 175 EIKRLQDRLGITSLYVTHDQVEAMTLADRILVMNHGVAEQVGTPLEVYQRPASLFVAGFI 234

Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGAT-------RDQLGGASGLTLGIRPEDVTVGE 293
           G P MN+ D       F G G    L G T       R  + G   + LG+RPE + V  
Sbjct: 235 GSPPMNVLDA-----RFDGAGQAVALPGGTAFLLPRPRPDMAGRP-VKLGVRPEHLAV-- 286

Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353
              G       V  VE  G +  V+ R  DG+          G      G+   V  P D
Sbjct: 287 -TPGHGPLIVTVDXVEALGADTVVYGRLPDGE---GMVVRVAGLPFCREGETLRVGAPPD 342

Query: 354 AIHLFDGETGDAL 366
           A+HLFD ETG  L
Sbjct: 343 ALHLFDAETGRRL 355


Lambda     K      H
   0.316    0.136    0.384 

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: 440
Number of extensions: 28
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: 383
Length of database: 357
Length adjustment: 30
Effective length of query: 353
Effective length of database: 327
Effective search space:   115431
Effective search space used:   115431
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: 42 (22.0 bits)
S2: 49 (23.5 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