Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate 8499411 DvMF_0184 pyruvate flavodoxin/ferredoxin oxidoreductase domain protein (RefSeq)
Query= SwissProt::P72578 (632 letters) >FitnessBrowser__Miya:8499411 Length = 563 Score = 257 bits (656), Expect = 1e-72 Identities = 188/624 (30%), Positives = 302/624 (48%), Gaps = 89/624 (14%) Query: 6 VIGGAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNTQK 65 VIGG G G+ T + A+ +GY + +++Y S ++GGH+ +S+ + D + + + Sbjct: 9 VIGGEAGQGLVTIGQMLTKALIRSGYEVVVSQDYMSRVRGGHNTYSIRVHDAPIAAPAEA 68 Query: 66 IDILVSFDAETVFQHFYDVKD--ILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGYE 123 +D+LV+ + ETV H +++ D I+I + ++PE Sbjct: 69 MDVLVALNQETVSLHKHELADGGIVILD-----------DGLDPE--------------- 102 Query: 124 TTVKGALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLDV 183 +PV + ++A + E N+ + + LLG+D Sbjct: 103 -------------GTKAVPVPFKDVAPRPIFE------------NVAALGVLGSLLGVDR 137 Query: 184 NYLIEAINSTF--KQDLYRKMNELAVKDSYDIVESRYN----LKPSSKERRRFWLDGNTA 237 + + TF K D N + D++ E+ L + R L GN A Sbjct: 138 PTMEGLVRETFGKKGDEVVGQNMKVLDDAWKWAEAHRASCAALPAPKGPKGRMMLHGNEA 197 Query: 238 VAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELAA 297 +A+G + GV+F S+YP+TPA+ + ++ IT +K G +VV QAEDE+AA Sbjct: 198 IALGALAAGVKFCSFYPMTPATS-----------VAQELITKGRKLG-VVVEQAEDEIAA 245 Query: 298 INMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTAQ 357 INM +GA G +A TSG GF+LM EG+ AG+ E PVVI R GP+TGLPTRT Q Sbjct: 246 INMGLGATYAGAKALVPTSGGGFALMTEGVSLAGVMEAPVVIVLAQRPGPATGLPTRTEQ 305 Query: 358 SDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLANSY-ST 416 +DL ++AGHGEFP+ +LA + F A +L E++QTPV L ++ L++SY + Sbjct: 306 ADLNLALYAGHGEFPRAILAPATIEDCFHLTHAAFDLTERFQTPVFVLTDQYLSDSYRAV 365 Query: 417 IPYEELELDKLKAERGKIVESGD----ISYKRFKFTEDGISPRAFLGKATMYYTGD--EH 470 +P+ +LD L G YKR++ TE G+SPR G D EH Sbjct: 366 VPF---DLDALPPVAEPDFGPGGGPKFKRYKRYELTESGVSPRKVPGFTETLVLADCHEH 422 Query: 471 NEEGHISEDVVNRTMMYEKRMKKLE-VADKEIPEESRVKIYGDLNSRNLIITWGS---PT 526 E+G+I+ED R M +KR++K E + IP ++ GD L++ WGS P Sbjct: 423 TEQGNITEDPDLRNAMNDKRLRKGEGLRALCIPP----RVSGDARPDLLLVCWGSSEGPV 478 Query: 527 GVLRDILEESNFDFTLLQIRMFSPFPKNLVSKLMEGRDKIITVEGNYLAQTSLLVKMYTG 586 ++L ++ P ++ +++ VEGN Q + L++ TG Sbjct: 479 AEAAELLRARGRSVGVMSFTQVWPLDPAQFLPALQAAKEVVCVEGNATGQFARLLRQETG 538 Query: 587 KDVTNSILKWNGRPFLRDELEEAL 610 +V+ ++L+++GR F + L E L Sbjct: 539 FEVSRTLLRYDGRIFTPNWLAERL 562 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: 769 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 632 Length of database: 563 Length adjustment: 37 Effective length of query: 595 Effective length of database: 526 Effective search space: 312970 Effective search space used: 312970 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: 53 (25.0 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