GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02015 BPHYT_RS02015 MFS
           transporter
          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.

Links

Downloads

Related tools

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, 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