GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofob in Desulfovibrio vulgaris Miyazaki F

Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta; Short=OFOR1; EC 1.2.7.11 (characterized, see rationale)
to candidate 8501323 DvMF_2056 thiamine pyrophosphate protein domain protein TPP-binding (RefSeq)

Query= uniprot:OFOB1_SULTO
         (305 letters)



>FitnessBrowser__Miya:8501323
          Length = 263

 Score = 89.0 bits (219), Expect = 1e-22
 Identities = 62/201 (30%), Positives = 93/201 (46%), Gaps = 15/201 (7%)

Query: 11  WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70
           +CPGC +        + + E+GV   + + V+ IGCS  I ++    +  V   HGRA A
Sbjct: 30  YCPGCHHGIAHRLVAEVLEEMGV-VDDTICVASIGCSVFIYNYLA--VDSVEAPHGRAPA 86

Query: 71  FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130
            ATG+K    D +V    GDGDL  IG    + A  R   + ++  +N VYG+T GQ +P
Sbjct: 87  VATGVKRGRTDKIVFTYQGDGDLASIGLAEVMHAANRGERITIVFVNNTVYGMTGGQMAP 146

Query: 131 TLKRGEKPKSLPRPNINDAVN-PIALAI----SSGYTFVARGYAYDVKHLKELIKSAIK- 184
           T   G+K  + P     D    PI +A       G  + AR     VK+++   K+  K 
Sbjct: 147 TTLIGQKTTTCPGGRCRDREGMPIRMAEIIAGLGGVAYSARASLDSVKNIRAAKKAVRKA 206

Query: 185 ------HKGLALIDVLQPCPT 199
                   G   +++L  CPT
Sbjct: 207 FDVQQQGLGFGFVELLSGCPT 227


Lambda     K      H
   0.318    0.139    0.425 

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: 177
Number of extensions: 11
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: 305
Length of database: 263
Length adjustment: 26
Effective length of query: 279
Effective length of database: 237
Effective search space:    66123
Effective search space used:    66123
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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