GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iorB in Dechlorosoma suillum PS

Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate Dsui_0094 Dsui_0094 2-oxoacid:ferredoxin oxidoreductase, gamma subunit

Query= BRENDA::Q6LZB5
         (188 letters)



>FitnessBrowser__PS:Dsui_0094
          Length = 205

 Score =  113 bits (283), Expect = 2e-30
 Identities = 67/186 (36%), Positives = 101/186 (54%), Gaps = 3/186 (1%)

Query: 2   NIVIAAVGGQGAVLASKILGTLAQNLGKDVKVSEVHGMSQRGGSVVAYVKFGEKVYSPVV 61
           NI++  +GGQG + A++IL   A  LG DVK +EV GM+QRGG V ++++FG KV SP +
Sbjct: 7   NILVVGIGGQGVMTATEILAEAAIALGHDVKKTEVAGMAQRGGVVSSHLRFGPKVLSPQI 66

Query: 62  EKGTADIVLAFEMLEGARYVDYLKENGKLVVNTQKIDPMPVITGDVKYPSDLNEKFEKLN 121
             GTA ++L FE  E  R+   L   G  ++NT ++ P  V  G   YP+D     +   
Sbjct: 67  TPGTAHVLLGFEAAEAMRWRHMLVPEGIALMNTAQLTPPVVDLGLYDYPADPVGSMKDSG 126

Query: 122 IGYVPVDALSIAKNAGTLKAVNVALIGVLAKNSNIKKEEWIKAIKDTVP---EKFLELNL 178
              V  DA++IAK+ G ++  N  ++G +A +     +  +  I        EK +E N 
Sbjct: 127 CRVVAFDAMAIAKDLGDIRLGNTVMLGAVADHLPFSADILLNCILQRFARKGEKVVEQNR 186

Query: 179 KAFEMG 184
           KAF  G
Sbjct: 187 KAFAAG 192


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: 92
Number of extensions: 2
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: 205
Length adjustment: 20
Effective length of query: 168
Effective length of database: 185
Effective search space:    31080
Effective search space used:    31080
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: 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 (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