Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate WP_043744857.1 AMB_RS16330 indolepyruvate oxidoreductase
Query= BRENDA::Q6LZB5 (188 letters) >NCBI__GCF_000009985.1:WP_043744857.1 Length = 206 Score = 130 bits (326), Expect = 2e-35 Identities = 73/188 (38%), Positives = 108/188 (57%), Gaps = 3/188 (1%) Query: 2 NIVIAAVGGQGAVLASKILGTLAQNLGKDVKVSEVHGMSQRGGSVVAYVKFGEKVYSPVV 61 NI++ GGQG + A++IL A G D K SEV GM+QRGG V ++V+FG++V+SPV+ Sbjct: 7 NILVCGTGGQGVMTAAEILSQAAMARGLDCKKSEVAGMAQRGGVVTSHVRFGKRVWSPVI 66 Query: 62 EKGTADIVLAFEMLEGARYVDYLKENGKLVVNTQKIDPMPVITGDVKYPSDLNEKFEKLN 121 GTADI++AFE+ EG+R+ D L+ G +VNT ++ P V G KYP D + Sbjct: 67 TPGTADILVAFEVAEGSRWADMLRPGGVAMVNTIRLVPPVVSAGLFKYPDDPVAQMRAAG 126 Query: 122 IGYVPVDALSIAKNAGTLKAVNVALIGVLAKNSNIKKEEWIKAIKDTVPEK---FLELNL 178 + DA +IA+ G L+ +N ++G +A E + I E+ +E+N Sbjct: 127 VTVYDFDAGAIARELGDLRLINTIMLGAIADYLPFPAAELEEQIVGRFRERKPAMVEVNQ 186 Query: 179 KAFEMGYD 186 KAF G D Sbjct: 187 KAFAAGRD 194 Lambda K H 0.315 0.135 0.370 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: 88 Number of extensions: 3 Number of successful extensions: 1 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: 188 Length of database: 206 Length adjustment: 20 Effective length of query: 168 Effective length of database: 186 Effective search space: 31248 Effective search space used: 31248 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: 42 (22.0 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