Align 2-oxoacid:ferredoxin oxidoreductase subunit alpha; OFOR; EC 1.2.7.11 (characterized)
to candidate 207019 DVU1569 pyruvate ferredoxin oxidoreductase, alpha subunit
Query= SwissProt::P72578 (632 letters) >MicrobesOnline__882:207019 Length = 578 Score = 231 bits (590), Expect = 5e-65 Identities = 179/614 (29%), Positives = 295/614 (48%), Gaps = 85/614 (13%) Query: 4 SWVIGGAQGTGIDTAANIFGNAVASAGYYIYGNREYYSNIKGGHSYFSLTISDKRVRSNT 63 S VIGG G G+ T ++ + +GY + + Y S ++GGH+ +++ + V + T Sbjct: 7 SIVIGGEAGQGLVTIGDMLVRTLIRSGYGVLVAQHYMSRVRGGHNTYNIRVGAGDVLAPT 66 Query: 64 QKIDILVSFDAETVFQHFYDVKD-ILIYNKAVETTKIDAVQSMEPELAERIKDFLTKQGY 122 + +LV+ D TV + + D +LI ++ ++ ++A++ LA R Sbjct: 67 DDVHVLVALDQRTVTEQGPRLGDGLLILDERLDPGSLNALRVPFAALAGR---------- 116 Query: 123 ETTVKGALEYASKNNVTLIPVNYDEIAKKVADEMKVPLSVTERVKNIVGITISYKLLGLD 182 PL +NI + + LLGL+ Sbjct: 117 ------------------------------------PL-----YENIAALGVLAALLGLE 135 Query: 183 ---VNYLI-EAINSTFKQDLYRKMN--ELAVKDSYDIVESRYNLKPSSKERRRFWLDGNT 236 V+ L+ EA + + R + E A + + D + L R L GN Sbjct: 136 RAPVDRLVGEAFHKKGDDVITRNLEVLEAAWRWASDHRAASEPLSAPEGPTGRMMLQGNE 195 Query: 237 AVAIGKIYGGVRFQSYYPITPASDESVYIEAHQDVLMEDPITGDKKKGTIVVVQAEDELA 296 A+A+G + GV+F ++YP+TPA+ + + H + + +VV QAEDE+A Sbjct: 196 AIALGALAAGVKFCAFYPMTPATSVAQNLILHAERM------------GVVVEQAEDEIA 243 Query: 297 AINMAIGAALTGVRAATATSGPGFSLMVEGLGWAGMNEVPVVITYYIRGGPSTGLPTRTA 356 A+NM +GA+ G RA TSG GF+LM EG+ AG+ E PVVI R GP+TGLPTRT Sbjct: 244 AMNMVLGASYAGARALVPTSGGGFALMTEGVSLAGVMEQPVVIVLAQRPGPATGLPTRTE 303 Query: 357 QSDLIFPIFAGHGEFPKIVLASGDHAEAFKDAIWALNLAEKYQTPVIHLVEKTLANSYST 416 Q+DL ++AGHGEFP+++ A + F A +LAE++Q P L ++ LA+SY Sbjct: 304 QADLDLALYAGHGEFPRVIFAPATPEDCFHLTYAAFDLAERFQIPAFVLTDQYLADSYRP 363 Query: 417 IPYEELELDKLKAERGKIVESGDIS--YKRFKFTEDGISPRAFLGKATMYYTGD--EHNE 472 + +L+ AE + G YKR++ T+ GISPR G + D EH E Sbjct: 364 VAPFDLDALPPLAEPDFSTDKGPEGDRYKRYELTKSGISPRRIPGFSKSLVLADCHEHTE 423 Query: 473 EGHISEDVVNRTMMYEKRMKKLE-VADKEIPEESRVKIYGDLNSRNLIITWGSPTGVLRD 531 +G+I+ED R M +KR++K + + +P + +GD L+ WGS G + + Sbjct: 424 QGYITEDAGLRIAMSDKRLRKGDGLRSMALPP----RCFGDEAPDLLLACWGSSEGAVVE 479 Query: 532 ILEESNFDFTLLQIRMFSPF----PKNLVSKLMEGRDKIITVEGNYLAQTSLLVKMYTGK 587 + + + F+ P +S+ E +++ +EGN + Q S L+++ G Sbjct: 480 AAQRLRARGRKVGVLSFTQVWPLEPSQFLSRCGEA-SEVVCIEGNAIGQFSRLLRL-GGV 537 Query: 588 DVTNSILKWNGRPF 601 V ++L+++GRPF Sbjct: 538 TVGRTLLRYDGRPF 551 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: 816 Number of extensions: 35 Number of successful extensions: 6 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: 578 Length adjustment: 37 Effective length of query: 595 Effective length of database: 541 Effective search space: 321895 Effective search space used: 321895 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