Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate 207415 DVU1945 pyruvate ferredoxin oxidoreductase, alpha subunit, putative
Query= SwissProt::P72578 (632 letters) >MicrobesOnline__882:207415 Length = 382 Score = 151 bits (381), Expect = 6e-41 Identities = 124/378 (32%), Positives = 186/378 (49%), Gaps = 43/378 (11%) Query: 220 LKPSSKERRRFWLDGNTAVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITG 279 L+ ++RR + GN AVA G + G F + YPITP S E + + A + MED Sbjct: 3 LQLKRRKRRELFALGNEAVAEGALLAGCTFYAGYPITP-STEIMEVMAARLPRMEDG--- 58 Query: 280 DKKKGTIVVVQAEDELAAINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVI 339 V +Q EDE+A++ AIGA+L G +A TATSGPGFSLM E +G+A M E P+VI Sbjct: 59 -------VFIQMEDEIASMGAAIGASLAGRKAMTATSGPGFSLMQEHIGYACMVEAPLVI 111 Query: 340 TYYIRGGPSTGLPTRTAQSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQ 399 +RGGPSTGLPT AQ D+ + HG+ P IVL++ + E + + A N AEKY+ Sbjct: 112 VNVMRGGPSTGLPTCPAQGDVQMARWGTHGDHPIIVLSASNVQECLEMTVTAFNYAEKYR 171 Query: 400 TPVIHLVEKTLANSYSTI--PYEELELDKLKAERGKIVESGDISYKRFKFTEDGISPRAF 457 TPVI L+++ A++ I P+ E EL+ + + +K + T G+ Sbjct: 172 TPVILLIDEVTAHTREKIIVPHAE-ELEIISRVEPTVPPEW---FKPYADTVRGVPAMPA 227 Query: 458 LGKA-TMYYTGDEHNEEGHISEDVVNRTMMYEKRMKKLEVADKEIPEESRVKIYGDL--- 513 +G M+ TG H+ G+ ++ M + +K++ + YGD+ Sbjct: 228 IGSGYRMHVTGLTHDVMGYPTQRPDEVKDMMLRLFRKID------------QFYGDIQLT 275 Query: 514 ------NSRNLIITWGSPTGVLRDILE---ESNFDFTLLQIRMFSPFPKNLVSKLMEGRD 564 ++ +I +GS +E E LL ++ PFP+ V L R Sbjct: 276 DSFALEDAEVAVIAYGSVARSAHLAVEQARERGAKAGLLTLKTLFPFPRPAVETLAR-RC 334 Query: 565 KIITVEGNYLAQTSLLVK 582 I+ V + Q S VK Sbjct: 335 SILVVPEMNMGQMSREVK 352 Lambda K H 0.316 0.135 0.382 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: 486 Number of extensions: 26 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: 632 Length of database: 382 Length adjustment: 34 Effective length of query: 598 Effective length of database: 348 Effective search space: 208104 Effective search space used: 208104 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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