Align 2-oxoacid:ferredoxin oxidoreductase subunit beta; OFOR; EC 1.2.7.11 (characterized)
to candidate 208875 DVU3348 pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit, putative
Query= SwissProt::P72579 (305 letters) >MicrobesOnline__882:208875 Length = 260 Score = 95.1 bits (235), Expect = 2e-24 Identities = 64/201 (31%), Positives = 95/201 (47%), Gaps = 15/201 (7%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 +CPGC + + + E+GV ++ + VS IGCS I ++ + V HGRA A Sbjct: 27 YCPGCHHGVAHRLVAEVLTEMGV-AEDTICVSSIGCSVFIYNYLA--VDTVEAPHGRAPA 83 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 ATG+K + D +V GDGDL IG + A R M ++ +N VYG+T GQ +P Sbjct: 84 VATGVKRARKDKIVFAYQGDGDLASIGLAEIMHAANRGERMTIVFVNNTVYGMTGGQMAP 143 Query: 131 TLKRGEKPKSLPRPNINDAVN-PIALAI----SSGYTFVARGYAYDVKHLKELIKSAIK- 184 T G+K + P D P+ +A G + AR VKH++ K+ K Sbjct: 144 TTLVGQKTTTCPSGRCRDTEGLPMKMAEIIAGLGGVAYSARVSLDSVKHIRAAKKALRKA 203 Query: 185 ------HKGLALIDVLQPCPT 199 G +++L CPT Sbjct: 204 FDVQQNDLGFGFVEMLSACPT 224 Lambda K H 0.318 0.139 0.424 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: 162 Number of extensions: 7 Number of successful extensions: 2 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: 260 Length adjustment: 26 Effective length of query: 279 Effective length of database: 234 Effective search space: 65286 Effective search space used: 65286 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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