GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iorB in Desulfovibrio vulgaris Hildenborough

Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate 207420 DVU1950 indolepyruvate ferredoxin oxidoreductase, beta subunit, putative

Query= BRENDA::O07836
         (202 letters)



>lcl|MicrobesOnline__882:207420 DVU1950 indolepyruvate ferredoxin
           oxidoreductase, beta subunit, putative
          Length = 198

 Score =  146 bits (368), Expect = 3e-40
 Identities = 84/198 (42%), Positives = 117/198 (59%), Gaps = 2/198 (1%)

Query: 1   MKEYNIVITGVGGQGILTAANLLGWAALRAGYKVRVGEVHGMSQRFGSVIAYVRFGEDVY 60
           M    I +TGVGGQG LTA  LL   AL AG +V  GE+HGM+QR G V + V  G    
Sbjct: 1   MSRIRIYMTGVGGQGTLTATTLLARTALDAGCEVVAGEIHGMAQRGGVVESTVLLG-GWQ 59

Query: 61  GAMVPEGKADVILSFEPVEALRYINYLKKGGLVFTNARPIPPVQVSMGLATYPTLDEMKK 120
              +  G+AD++L FEP+E LR + YL  GG V +NA  +PPV VSMG  +YP LD +++
Sbjct: 60  SPKLSHGEADIVLGFEPLETLRGLPYLTAGGAVLSNAETLPPVGVSMGRESYPCLDGIRE 119

Query: 121 IVEEDFGGKFMAFDAEKLAMEAGNIVTTNVVLIGALSQTPGFPLSEEQIKEVIRISVPPK 180
            V     G+        L ++AG++ + N VL+GAL  T   P   + ++  IR  + PK
Sbjct: 120 KV-TGCSGRAWFLPCRTLGLKAGSVQSGNSVLLGALCATGLLPFGVDALEAAIRRHLAPK 178

Query: 181 TIDVNMRAFELGVKAAKE 198
            +D+N+RA ELGV+A  +
Sbjct: 179 LVDMNLRAVELGVQAVAD 196


Lambda     K      H
   0.320    0.139    0.394 

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: 122
Number of extensions: 5
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: 202
Length of database: 198
Length adjustment: 21
Effective length of query: 181
Effective length of database: 177
Effective search space:    32037
Effective search space used:    32037
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: 45 (21.9 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 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, the preprint on GapMind for carbon sources, 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