Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate 8499844 DvMF_0609 Indolepyruvate ferredoxin oxidoreductase (RefSeq)
Query= BRENDA::O07836 (202 letters) >FitnessBrowser__Miya:8499844 Length = 201 Score = 137 bits (344), Expect = 2e-37 Identities = 80/193 (41%), Positives = 112/193 (58%), Gaps = 8/193 (4%) Query: 6 IVITGVGGQGILTAANLLGWAALRAGYKVRVGEVHGMSQRFGSVIAYVRFGEDVYGAMVP 65 I +TGVGGQG LTA LL AL G +V GE+HGM+QR G V + + G G M P Sbjct: 9 IYLTGVGGQGTLTATTLLARTALDQGLEVTSGEIHGMAQRGGVVESTILLG----GWMSP 64 Query: 66 E---GKADVILSFEPVEALRYINYLKKGGLVFTNARPIPPVQVSMGLATYPTLDEMKKIV 122 + G+AD+IL FEP+E LR + +L GG V +N P+PPV VS G YP ++ ++ V Sbjct: 65 KIGHGEADLILGFEPLETLRGMTHLAAGGSVLSNTEPLPPVGVSTGREAYPEMERIRAKV 124 Query: 123 EEDFGGKFMAFDAEKLAMEAGNIVTTNVVLIGALSQTPGFPLSEEQIKEVIRISVPPKTI 182 E K L ++AG++ N VL+GA + P + ++ IR + PK + Sbjct: 125 -EGCAAKSWFLPCRTLGLQAGSVQAGNSVLLGAACASGLLPFGPDALEAAIRTHLAPKLM 183 Query: 183 DVNMRAFELGVKA 195 D+N+RA ELGV+A Sbjct: 184 DMNLRAVELGVRA 196 Lambda K H 0.320 0.139 0.394 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: 117 Number of extensions: 5 Number of successful extensions: 3 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: 202 Length of database: 201 Length adjustment: 21 Effective length of query: 181 Effective length of database: 180 Effective search space: 32580 Effective search space used: 32580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 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