Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate 209309 DVU0374 pyruvate ferredoxin/flavodoxin oxidoreductase family protein
Query= BRENDA::Q6LZB6 (578 letters) >MicrobesOnline__882:209309 Length = 832 Score = 222 bits (565), Expect = 5e-62 Identities = 183/600 (30%), Positives = 290/600 (48%), Gaps = 46/600 (7%) Query: 4 LMLGNEAVARGAYEAGVLVATAYPGTPSTEITEH-ISKYPE-INSEWSVNEKVALEVAIG 61 ++ GN A A G +G+ YPGTPSTE+ + +S + I WSV+E VA+ + G Sbjct: 17 VLQGNIAFAAGCVRSGIHAVDGYPGTPSTEVIDKGLSNVQDMIKVGWSVSEAVAVSMGHG 76 Query: 62 SAIAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLII-VADDPSMHSSQNEQDTRYYG 120 ++AG +V+MK GL A DP + A+ + G L+ +A D + S+Q+ D R + Sbjct: 77 HSLAGEDCIVTMKIPGLFQAGDPFSSSAFFTEDRGALVYYLASDFTPSSTQHLVDPRPFI 136 Query: 121 IFSKIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEE------- 173 P+ EP + QE + ++ +IS ++ TPV++ S + HS+ LV L E Sbjct: 137 RSCFTPIFEPRNHQEMHEAAEIAADISRQYKTPVVILASGTLCHSEGLVRLSEIRTRERV 196 Query: 174 KEKIELKPYDYNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNKIEYANKKIGIIT 233 + LK ++ P V+A N K + ER+ L++ + S +N E ++K+G+IT Sbjct: 197 VSSVPLKAFNTLP---VTARRNYDK---VVTERMPALADMVEKSPLNVWERGSRKVGVIT 250 Query: 234 SGVAYNYAKEAV----SDASFLKFGMSYPLPEEKIKEFVQNCD-KVYVFEELEPIFEQKI 288 GV +E D L G + PLP I+EF + + VYV E+ ++++ Sbjct: 251 FGVGEMMVREVKQALGEDIDILSLGFTCPLPMNLIREFHASIEGDVYVVEDGYRYLQEEL 310 Query: 289 RSMGLNVIGKEIFPIVGELSSEIIRNALLNES--KIVIEKIEDLPQRPPVLCPGCHHRGP 346 GL V GK V E I ALL S + LP R P++C GC +R Sbjct: 311 ERAGLAVKGKSPADTVTEWDPAGIA-ALLGYSLKSPAASDVAPLP-RAPMICAGCPYRLF 368 Query: 347 FYVLKKLKLH-----VAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAK 401 ++ +K GDIGC TL F ++A+DT + MGA GF +A + A Sbjct: 369 GETVRSMKKRGKIEACFGDIGCNTLLYF--MDAMDTNVAMGAGEAHRAGFIVA-NPDKAA 425 Query: 402 KSVAVIGDSTFWHSGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTN 461 K ++++GD T HSG+ + ++ ++LDN+ TAMTG Q P++ L+G+ N Sbjct: 426 KCISLLGDGTECHSGMDATRNTIFRHIAGVKVVLDNNWTAMTGGQPGPTSPVNLAGQE-N 484 Query: 462 QIDFEALGRSIGINRICVVDAYDLK----ALEETIKEEVNAEEPSLIITKRPCVLIKGAK 517 D +A ++ G ++ VV+ YD K AL +++ N E ++++T C+ Sbjct: 485 TFDLQASLKAHGA-KVVVVNGYDRKGIRTALTSALEDAANGEFTTMVVT-GVCIRKMPKS 542 Query: 518 FDFKDYKIDPKLCTGCKLCLKAGCPAISFDGKVAKINDSLCVGC----GLCKDLCKFSAI 573 +D LC C C CP IS D + ++LC GC C +C AI Sbjct: 543 AYGTRMTVDADLCKRCGQC--QICPGISADAEGLPSFNNLCSGCVSQNAACGQMCPVHAI 600 Lambda K H 0.317 0.136 0.392 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: 1056 Number of extensions: 69 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: 1 Length of query: 578 Length of database: 832 Length adjustment: 39 Effective length of query: 539 Effective length of database: 793 Effective search space: 427427 Effective search space used: 427427 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: 54 (25.4 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