Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate 8499838 DvMF_0603 2-oxoglutarate ferredoxin oxidoreductase subunit alpha (RefSeq)
Query= SwissProt::P72578 (632 letters) >FitnessBrowser__Miya:8499838 Length = 382 Score = 155 bits (392), Expect = 3e-42 Identities = 120/400 (30%), Positives = 205/400 (51%), Gaps = 38/400 (9%) Query: 225 KERRRFWLDGNTAVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKG 284 ++RR + GN AVA G + G F + YPITP S E + + A++ L+ED Sbjct: 8 RKRRELFALGNEAVAEGALLAGCSFYAGYPITP-STEIMEVMANRLPLIEDG-------- 58 Query: 285 TIVVVQAEDELAAINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIR 344 V +Q EDE+A++ IGA+L G +A TATSGPGF+LM E +G+A M E P+V+ +R Sbjct: 59 --VFIQMEDEIASMGATIGASLAGRKAMTATSGPGFALMQEHIGYACMVEAPLVVVNVMR 116 Query: 345 GGPSTGLPTRTAQSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIH 404 GGPSTGLPT AQ+D+ + HG+ P IVL++ + E + + A N AEKY+TPVI Sbjct: 117 GGPSTGLPTSPAQADVQMARWGTHGDHPIIVLSASNVQECLEMTVTAFNFAEKYRTPVIL 176 Query: 405 LVEKTLANSYS--TIPYEELELDKLKAERGKIVESGDISYKRFKFTEDGISPRAFLGKA- 461 L+++ A++ T+P + E++ L + +K + T G+ A +G Sbjct: 177 LLDEVTAHTREKITVPDPD-EVEILSRVEPTVPPEW---FKPYADTARGVPAMAPIGSGY 232 Query: 462 TMYYTGDEHNEEGHISE--DVVNRTMM-----YEKRMKKLEVADKEIPEESRVKI--YGD 512 + TG H+ G+ ++ D V M+ ++ ++++D+ + +++ V + YG Sbjct: 233 RTHVTGLTHDVMGYPTQRPDEVKDAMLRLFRKIDQYYGDIQMSDEYMLDDAEVAVVAYGS 292 Query: 513 L-NSRNLIITWGSPTGVLRDILEESNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEG 571 + S +L + G LL ++ PFP+ V KL ++ E Sbjct: 293 VARSAHLAVEQARERGAKAG----------LLTLKTLFPFPRPAVEKLTHRCHTVVVPEM 342 Query: 572 NYLAQTSLLVKMYTGKDVTNSILKWNGRPFLRDELEEALI 611 N + + ++ G+ +I + +G+ E+ +A++ Sbjct: 343 NMGQMSREVKRVNNGRTKVRTINRVDGQIITPSEILKAIL 382 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: 479 Number of extensions: 19 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