Align 2-oxoacid oxidoreductase (ferredoxin) (subunit 2/2) (EC 1.2.7.11) (characterized)
to candidate 8499411 DvMF_0184 pyruvate flavodoxin/ferredoxin oxidoreductase domain protein (RefSeq)
Query= BRENDA::Q4J6I9 (621 letters) >FitnessBrowser__Miya:8499411 Length = 563 Score = 253 bits (645), Expect = 2e-71 Identities = 184/614 (29%), Positives = 294/614 (47%), Gaps = 86/614 (14%) Query: 1 MIGGPQGLGVDTSANVFSNAIARAGYYLFGNREYYSNIKGRHSYFEVVFDEKPVRSISSY 60 +IGG G G+ T + + A+ R+GY + +++Y S ++G H+ + + + P+ + + Sbjct: 9 VIGGEAGQGLVTIGQMLTKALIRSGYEVVVSQDYMSRVRGGHNTYSIRVHDAPIAAPAEA 68 Query: 61 TNILATFDAETLFQHFTEVTDFVIYGTDYATTNIDMVKSMEPEMAEQIKQLLSENKMGYT 120 ++L + ET+ H E+ D I D ++PE Sbjct: 69 MDVLVALNQETVSLHKHELADGGIVILD---------DGLDPE----------------- 102 Query: 121 IKDVITYLKNKGIKVIELDYLDILKKIAAELKVQVSVVERAKNMAAVGASIGLLGLPFDI 180 G K + + + D+ + E N+AA+G LLG+ Sbjct: 103 -----------GTKAVPVPFKDVAPRPIFE------------NVAALGVLGSLLGVDRPT 139 Query: 181 LENTISSIF--RNDLFVKMNVMAAKIGYNTVN----NTYHLEVINNVKPRIQIDGNTIAA 234 +E + F + D V N+ + + L K R+ + GN A Sbjct: 140 MEGLVRETFGKKGDEVVGQNMKVLDDAWKWAEAHRASCAALPAPKGPKGRMMLHGNEAIA 199 Query: 235 MGKIAGGLRFQSYYPITPASDESVYIEANQNVDMIVEGNELRKGGVVVVQAEDELAAINM 294 +G +A G++F S+YP+TPA+ + ++I +G RK GVVV QAEDE+AAINM Sbjct: 200 LGALAAGVKFCSFYPMTPATSVAQ--------ELITKG---RKLGVVVEQAEDEIAAINM 248 Query: 295 AIGAALTGARTSTATSGPGFSLMAEGLSWAGMNEVPVVVTYYMRGAPSTGLPTRSGQADL 354 +GA GA+ TSG GF+LM EG+S AG+ E PVV+ R P+TGLPTR+ QADL Sbjct: 249 GLGATYAGAKALVPTSGGGFALMTEGVSLAGVMEAPVVIVLAQRPGPATGLPTRTEQADL 308 Query: 355 KFALNAGHGEFPRIVIASGDHHEIFWDSIWALNLAERYQTPVIHIIEKALANAYSLI--- 411 AL AGHGEFPR ++A + F + A +L ER+QTPV + ++ L+++Y + Sbjct: 309 NLALYAGHGEFPRAILAPATIEDCFHLTHAAFDLTERFQTPVFVLTDQYLSDSYRAVVPF 368 Query: 412 DEDSIKGQIKIDRGKLVKQVGDRFNRFQPSDDGISPRVFLGQSSIFYTGD--EHNEEGHI 469 D D++ + D G R+ R++ ++ G+SPR G + D EH E+G+I Sbjct: 369 DLDALPPVAEPDFGPGGGPKFKRYKRYELTESGVSPRKVPGFTETLVLADCHEHTEQGNI 428 Query: 470 TENSLNRTKMHEKRMKKLETADNEIPEELRV-----NVVGDA--DIVLITWGSPKGAILD 522 TE+ R M++KR++K E LR V GDA D++L+ WGS +G + + Sbjct: 429 TEDPDLRNAMNDKRLRK--------GEGLRALCIPPRVSGDARPDLLLVCWGSSEGPVAE 480 Query: 523 AMSELEKDGIKTMMVQVKMFNPYPTKLVKKLLEGKSKIVAVENNYQAQGAEVLAEKTGIF 582 A L G ++ P L+ ++V VE N Q A +L ++TG Sbjct: 481 AAELLRARGRSVGVMSFTQVWPLDPAQFLPALQAAKEVVCVEGNATGQFARLLRQETGFE 540 Query: 583 ATNYVLKWSGRPIT 596 + +L++ GR T Sbjct: 541 VSRTLLRYDGRIFT 554 Lambda K H 0.316 0.134 0.377 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: 760 Number of extensions: 38 Number of successful extensions: 5 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: 621 Length of database: 563 Length adjustment: 37 Effective length of query: 584 Effective length of database: 526 Effective search space: 307184 Effective search space used: 307184 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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