GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Burkholderia phytofirmans PsJN

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate BPHYT_RS15595 BPHYT_RS15595 ABC transporter

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__BFirm:BPHYT_RS15595
          Length = 257

 Score =  215 bits (548), Expect = 7e-61
 Identities = 122/257 (47%), Positives = 167/257 (64%), Gaps = 10/257 (3%)

Query: 12  LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71
           L+V+ +  RFGGL A+++V     +G+I  +IGPNGAGKTT FN ITG YTP  G   L 
Sbjct: 7   LSVKGVNKRFGGLQALSEVGLEIKSGQIYGLIGPNGAGKTTFFNVITGLYTPDSGEFKL- 65

Query: 72  HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131
             DG+ +    +  Y+++ KA +ARTFQNIRLFGGM+ LEN++V +H   +R     I  
Sbjct: 66  --DGENYTPTAV--YQVA-KAGIARTFQNIRLFGGMTALENVMVGRH---VRTKHGLIGA 117

Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191
           +   P+  + ERE  + A   L+ V + ++AD+ + NL YG QRRLEIARA+ T+P +L 
Sbjct: 118 VFQTPAERKEEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALATDPKLLA 177

Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251
           LDEPAAG+N  E  EL  LL  IR + K  +LLIEHD+ +VM + + + VLDYG+ I+ G
Sbjct: 178 LDEPAAGMNATEKVELTKLLDKIRADGKT-ILLIEHDVKLVMGLCNQMTVLDYGKVIAQG 236

Query: 252 DPAFVKNDPAVIRAYLG 268
            P  V+ DP VI AYLG
Sbjct: 237 LPQDVQKDPKVIEAYLG 253


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: 221
Number of extensions: 12
Number of successful extensions: 4
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: 257
Length adjustment: 25
Effective length of query: 269
Effective length of database: 232
Effective search space:    62408
Effective search space used:    62408
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: 47 (22.7 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