Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta; Short=OFOR1; EC 1.2.7.11 (characterized, see rationale)
to candidate 207020 DVU1570 pyruvate ferredoxin oxidoreductase, beta subunit
Query= uniprot:OFOB1_SULTO (305 letters) >MicrobesOnline__882:207020 Length = 284 Score = 214 bits (546), Expect = 1e-60 Identities = 111/258 (43%), Positives = 164/258 (63%), Gaps = 14/258 (5%) Query: 11 WCPGCGNFGILNAEQQAIVELGVDTKNVVVVSGIGCSGKIPHFFRTPISGVHTLHGRAIA 70 WCPGCGN I+ A +QAIV LG++ V VSGIG + K PH+ R ++G + LHGR++ Sbjct: 15 WCPGCGNHDIMKALRQAIVGLGLEAHKVAHVSGIGQAAKAPHYIR--LNGFNGLHGRSLP 72 Query: 71 FATGIKLSNPDLVVIVNGGDGDLLGIGAGHFVAAGRRNVDMVVILHDNGVYGLTKGQASP 130 A I+L N +L VI GDG G G HF+AA RRNVDM +++HDN +YGLTKGQASP Sbjct: 73 PAQAIRLCNSELTVIAQSGDGCNYGEGGNHFLAAIRRNVDMTLLVHDNQIYGLTKGQASP 132 Query: 131 TLKRGEKPKSLPRPNINDAVNPIALAISSGYTFVARGYAYDVKHLKELIKSAIKHKGLAL 190 T G+ KS P + NP+A+A++ FVAR ++ +V+HL+ +I++A++H+G +L Sbjct: 133 TTGEGQVTKSQPGGVTSAPFNPVAVAVAMRCGFVARSFSGNVEHLQAMIEAAVRHRGFSL 192 Query: 191 IDVLQPCPTYNDINTKEWYDKRIYKLDTLPDWDPVVKKPEEVNEKIKRAIDKSLEWGDRI 250 +D+ PC ++N +NT WY +R ++D D P + N ++ A +GD + Sbjct: 193 VDIFSPCVSFNKVNTFGWYRQRCREIDASHD-------PTDWNAAMRIAD----TFGDVL 241 Query: 251 PIGIFYQNELVPSYEERI 268 PIG+ Y+NE P +ER+ Sbjct: 242 PIGVIYRNER-PPLDERV 258 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: 215 Number of extensions: 11 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: 305 Length of database: 284 Length adjustment: 26 Effective length of query: 279 Effective length of database: 258 Effective search space: 71982 Effective search space used: 71982 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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