Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate 349957 BT0429 indolepyruvate oxidoreductase subunit iorB (NCBI ptt file)
Query= BRENDA::O07836 (202 letters) >FitnessBrowser__Btheta:349957 Length = 194 Score = 109 bits (272), Expect = 4e-29 Identities = 66/200 (33%), Positives = 115/200 (57%), Gaps = 14/200 (7%) Query: 5 NIVITGVGGQGILTAANLLGWAALRAGYKVRVGEVHGMSQRFGSVIAYVRFGE-DVYGAM 63 +I+++GVGGQGIL+ A ++G AAL+ G ++ EVHGMSQR G V + +R + + + Sbjct: 4 DIILSGVGGQGILSIATVIGKAALKEGLYMKQAEVHGMSQRGGDVQSNLRISDKPIASDL 63 Query: 64 VPEGKADVILSFEPVEALRYINYLKKGGLVFTNARPIPPVQVSMGLATYPTLDEMKKIVE 123 +P GK D+I+S EP+E LRY+ YL G + TN P + + YP +E K + E Sbjct: 64 IPSGKCDLIISLEPMEGLRYLPYLSPEGWLVTNETPF------VNIPNYP--EEDKVMAE 115 Query: 124 EDFGGKFMAFDAEKLAMEAGNIVTTNVVLIGALSQTPGFPLSEEQIKEVIR---ISVPPK 180 + + + +K+A E G+ N+VL+GA P + E++++ IR + Sbjct: 116 INKLPHKIVLNVDKVAKEVGSARVANIVLLGA--TIPFLGIDYEKVQDSIREIFLRKGEA 173 Query: 181 TIDVNMRAFELGVKAAKEML 200 +++N++A G + A++++ Sbjct: 174 IVEMNLKALAAGKEIAEKLM 193 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: 110 Number of extensions: 4 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: 194 Length adjustment: 20 Effective length of query: 182 Effective length of database: 174 Effective search space: 31668 Effective search space used: 31668 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 Apr 09 2024. 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