Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; Short=OFOR2; EC 1.2.7.11 (characterized, see rationale)
to candidate 207019 DVU1569 pyruvate ferredoxin oxidoreductase, alpha subunit
Query= uniprot:OFOA2_AERPE (642 letters) >MicrobesOnline__882:207019 Length = 578 Score = 229 bits (584), Expect = 3e-64 Identities = 189/621 (30%), Positives = 294/621 (47%), Gaps = 87/621 (14%) Query: 5 SLIIGGPQGGGIESAGQIAIKSMVLLGYEVLGSREYHSNIMGAHSYYHLRVQQHRPRSLK 64 S++IGG G G+ + G + +++++ GY VL ++ Y S + G H+ Y++RV + Sbjct: 7 SIVIGGEAGQGLVTIGDMLVRTLIRSGYGVLVAQHYMSRVRGGHNTYNIRVGAGDVLAPT 66 Query: 65 LPVDGVLALDAESVFTHFRDVRPGGILVYDPGTKSTRVDAIQ-PMAGPLKKRLKSLFDSR 123 V ++ALD +V T G+L+ D ++A++ P A Sbjct: 67 DDVHVLVALDQRTV-TEQGPRLGDGLLILDERLDPGSLNALRVPFAA------------- 112 Query: 124 GMQPVVESAVKLAEEAGARIVGLPLKEMLKTLSERTGAPVARVSRALNTLGLASMLYMLG 183 + G PL E N L + +LG Sbjct: 113 -------------------LAGRPLYE--------------------NIAALGVLAALLG 133 Query: 184 VPVEYIEKAISLQFAGK-EKVINMNVEAVRIAVDYVRE--AFGEPESRLPPGPRRGQTMM 240 + +++ + F K + VI N+E + A + + A EP S P GP M Sbjct: 134 LERAPVDRLVGEAFHKKGDDVITRNLEVLEAAWRWASDHRAASEPLSA-PEGPTG---RM 189 Query: 241 VATGNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDKIAVAI 300 + GN+ +A+G + G+ +YP+TP++ A + H AE++G V + Sbjct: 190 MLQGNEAIALGALAAGVKFCAFYPMTPATSVAQNLILH---------AERMG-----VVV 235 Query: 301 VQMEDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPS 360 Q EDE+A++N VLGA+ AGARA TSG GF+LM E VSLA E PVV+ L R GP+ Sbjct: 236 EQAEDEIAAMNMVLGASYAGARALVPTSGGGFALMTEGVSLAGVMEQPVVIVLAQRPGPA 295 Query: 361 TGMPTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHLLDK 420 TG+PTRT Q DL ++++GHG+ P+++ A + F+ AF+ AE FQ P L D+ Sbjct: 296 TGLPTRTEQADLDLALYAGHGEFPRVIFAPATPEDCFHLTYAAFDLAERFQIPAFVLTDQ 355 Query: 421 YLASSMVSLAREDLDPSKVPITRGKLLDNPPAD--YRRYEVVEDGISPRARLG-SATMVI 477 YLA S +A DLD D P Y+RYE+ + GISPR G S ++V+ Sbjct: 356 YLADSYRPVAPFDLDALPPLAEPDFSTDKGPEGDRYKRYELTKSGISPRRIPGFSKSLVL 415 Query: 478 TGL-EHDEYGYATEDPVMREIMMFKRERKFKVIEE-RIPDEEKAVLHGDSEASVALVSFG 535 EH E GY TED +R M KR RK + +P GD + L +G Sbjct: 416 ADCHEHTEQGYITEDAGLRIAMSDKRLRKGDGLRSMALPPR----CFGDEAPDLLLACWG 471 Query: 536 STKQPILEALEMLRDEGVRARFAQVRLLYPF-PGRLVEEMLEGVEKVIMVEQNLLGQLAM 594 S++ ++EA + LR G + ++P P + + E E V+ +E N +GQ + Sbjct: 472 SSEGAVVEAAQRLRARGRKVGVLSFTQVWPLEPSQFLSRCGEASE-VVCIEGNAIGQFSR 530 Query: 595 LLRAHTSIKPDSSIVKINGRP 615 LLR + ++++ +GRP Sbjct: 531 LLRL-GGVTVGRTLLRYDGRP 550 Lambda K H 0.318 0.135 0.380 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: 841 Number of extensions: 43 Number of successful extensions: 9 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: 642 Length of database: 578 Length adjustment: 37 Effective length of query: 605 Effective length of database: 541 Effective search space: 327305 Effective search space used: 327305 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: 53 (25.0 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