GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iorB in Desulfovibrio vulgaris Hildenborough

Align Indolepyruvate oxidoreductase subunit IorB; IOR; Indolepyruvate ferredoxin oxidoreductase subunit beta; EC 1.2.7.8 (characterized)
to candidate 209309 DVU0374 pyruvate ferredoxin/flavodoxin oxidoreductase family protein

Query= SwissProt::P80911
         (196 letters)



>MicrobesOnline__882:209309
          Length = 832

 Score = 63.9 bits (154), Expect = 8e-15
 Identities = 59/196 (30%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 5   IYVCGVGGQGIIKTSVIIGEAAMNEGM---NVVMSEIHGMAQRGGAVSTEIRFGDVRGSI 61
           + + GVGGQG +    ++ + A   G    NVV  E HGMAQ GG V +    G V   +
Sbjct: 639 VAIRGVGGQGNLFFGRVLTQLAFLAGYGDTNVVKGETHGMAQMGGPVISTFSCGKVVSPV 698

Query: 62  IPQGEADLVIAFEPLEALRA--LPKMSEDACVIVNTSKIPPFNLIKSPHPYPPLEEIIKT 119
           +  G AD +++ E  E LR   +  +     V++  +++ P+ +  S   YP  + I+ T
Sbjct: 699 LLPGTADCLVSMEMSEVLRPGYVGMLRPGGTVLLADTRVLPYGV--SEDAYPHRDAILGT 756

Query: 120 LEENAGRVRSFNGEKIAVEAGHILS--LNMVMLGA---AAATTGFPLGEETLIESMKNNL 174
           L+     V   +  K A+E G       N+VM+GA    A   GFP   E  +++++N  
Sbjct: 757 LD--GYNVIIIDVLKAALELGDPTGRIANVVMIGALSTLAPFDGFP--AELWLQALRNVS 812

Query: 175 P-PKLMEVNLRAFHEG 189
           P P +   N  AF+ G
Sbjct: 813 PKPAIWTANHAAFNVG 828


Lambda     K      H
   0.317    0.136    0.389 

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: 392
Number of extensions: 22
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: 196
Length of database: 832
Length adjustment: 31
Effective length of query: 165
Effective length of database: 801
Effective search space:   132165
Effective search space used:   132165
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: 41 (21.6 bits)
S2: 50 (23.9 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