Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate 349958 BT0430 indolepyruvate oxidoreductase subunit iorA (NCBI ptt file)
Query= BRENDA::Q6LZB6 (578 letters) >FitnessBrowser__Btheta:349958 Length = 530 Score = 362 bits (929), Expect = e-104 Identities = 214/534 (40%), Positives = 313/534 (58%), Gaps = 40/534 (7%) Query: 2 KKLMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYP-----EINSEWSVNEKVAL 56 K+L+LG+EA+A+ A +AG+ AYPGTPSTEITE+I P I++ W NEK A+ Sbjct: 3 KQLLLGDEAIAQAALDAGLSGVYAYPGTPSTEITEYIQMAPITTEQNIHNRWCANEKTAM 62 Query: 57 EVAIGSAIAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDT 116 E A+G + G R +V MKHVG+NVAAD + A TG+ GL++I ADDPSMHSSQNEQD+ Sbjct: 63 EAALGMSFVGKRALVCMKHVGMNVAADCFVNSAITGVKGGLIVIAADDPSMHSSQNEQDS 122 Query: 117 RYYGIFSKIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEEKEK 176 R+YG FS IP+ EPS+ QE D V G E SEK P+++R+ TR++HS+S VE +E++ Sbjct: 123 RFYGDFSLIPMYEPSNQQEAYDMVYNGFEFSEKTGEPILMRMVTRLAHSRSGVERKEQKP 182 Query: 177 IELKPYDYNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNK-IEYANKKIGIITSG 235 + +P +++ P NA+KR + R E ++ S NK I+ NKK+GI+ G Sbjct: 183 QNSISFSEDPRQFILLPGNARKRYKVLLARQDEFIKASEESPYNKYIDGPNKKLGIVACG 242 Query: 236 VAYNYAKEAVSDA---SFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIR--- 289 + YNY E + LK G YPLP++++ + V++CD++ V E+ +P E+ ++ Sbjct: 243 IGYNYLMENYPEGCEYPVLKIG-QYPLPKKQLLQLVESCDEILVLEDGQPFVEKHLKGYL 301 Query: 290 SMGLNVIGK--EIFPIVGELSSEIIRNALLNESKIVIEKIEDLPQRPPVLCPGCHHRGPF 347 +G+ V G+ GEL+ + + A+ E+K + RPP LC GC HR + Sbjct: 302 GIGIKVKGRLDGTLSQDGELNPDSVARAVGKENKSEFGVPSVVEMRPPALCEGCGHRDMY 361 Query: 348 YVLKKL------KLHVAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAK 401 L ++ V DIGCYTLG P NAI++ + MGASI MA G A G Sbjct: 362 ITLTEVLKEEYPSHKVFSDIGCYTLGANAPFNAINSCVDMGASITMAKG--AADGG--LH 417 Query: 402 KSVAVIGDSTFWHSGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTN 461 SVAVIGDSTF HSG+TGL+D V + ++I DN TAMTG Q++ TG+ Sbjct: 418 PSVAVIGDSTFTHSGMTGLLDCVNENANVVIVISDNETTAMTGGQDSAGTGR-------- 469 Query: 462 QIDFEALGRSIGIN----RICVVDAYDLKALEETIKEEVNAEEPSLIITKRPCV 511 E++ +G++ R+ V + + + + I+EE+ S+II +R C+ Sbjct: 470 ---IESICIGLGVDPAHIRVVVPLKKNHEEMRQIIREEIEYNGVSVIIPRRECI 520 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: 826 Number of extensions: 44 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 578 Length of database: 530 Length adjustment: 36 Effective length of query: 542 Effective length of database: 494 Effective search space: 267748 Effective search space used: 267748 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 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