GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iorB in Burkholderia phytofirmans PsJN

Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate BPHYT_RS02015 BPHYT_RS02015 MFS transporter

Query= BRENDA::Q6LZB5
         (188 letters)



>FitnessBrowser__BFirm:BPHYT_RS02015
          Length = 1195

 Score = 50.8 bits (120), Expect = 9e-11
 Identities = 34/110 (30%), Positives = 57/110 (51%), Gaps = 8/110 (7%)

Query: 2   NIVIAAVGGQGAVLASKILGTLAQNLGKDVKVSEVHGMSQRGGSVVAYVKFG---EKVYS 58
           +I++  VGG G V    ++   A   GK   V +  G +Q+GGSV+++V+F    E +  
Sbjct: 732 DILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWLNQ 791

Query: 59  PVVEKGTADIVLAFEMLEGARYVDYLKE----NGKLVVNTQKIDPMPVIT 104
             ++   AD++LA +M+ GA   D L+       ++VVNT  I     +T
Sbjct: 792 VRIDTQQADVLLACDMVVGAS-ADALQTVRHGRTRIVVNTHAIPNATFVT 840


Lambda     K      H
   0.315    0.135    0.370 

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: 461
Number of extensions: 24
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: 188
Length of database: 1195
Length adjustment: 33
Effective length of query: 155
Effective length of database: 1162
Effective search space:   180110
Effective search space used:   180110
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: 51 (24.3 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