Align Indolepyruvate oxidoreductase subunit IorB; IOR; Indolepyruvate ferredoxin oxidoreductase subunit beta; EC 1.2.7.8 (characterized)
to candidate WP_028322065.1 H567_RS0115240 pyruvate ferredoxin oxidoreductase
Query= SwissProt::P80911 (196 letters) >NCBI__GCF_000422285.1:WP_028322065.1 Length = 196 Score = 146 bits (369), Expect = 2e-40 Identities = 78/182 (42%), Positives = 115/182 (63%), Gaps = 1/182 (0%) Query: 9 GVGGQGIIKTSVIIGEAAMNEGMNVVMSEIHGMAQRGGAVSTEIRFGDVRGSIIPQGEAD 68 GVGGQG + S ++GEAA+ G+ VV+SEIHGMAQRGG V + + G+V I+ EAD Sbjct: 10 GVGGQGNLLASRLLGEAALAAGIPVVVSEIHGMAQRGGIVESAVLMGNVTSPIVSGAEAD 69 Query: 69 LVIAFEPLEALRALPKMSEDACVIVNTSKIPPFNLIKSPHPYPPLEEIIKTLEENA-GRV 127 ++I FEP+E LRA+ K S D+ VI N S +PPF + YP +EE ++ +++ +V Sbjct: 70 VLIGFEPIETLRAMGKCSADSLVITNLSPLPPFTVSIGQGKYPKVEEALELIQKKVKKKV 129 Query: 128 RSFNGEKIAVEAGHILSLNMVMLGAAAATTGFPLGEETLIESMKNNLPPKLMEVNLRAFH 187 + NG +A EAG+ LSLNMVMLGA + P+ E + +++ + +E N++AF Sbjct: 130 IALNGSALAAEAGNPLSLNMVMLGALIGSGAVPITPEDMKKTIAASTKKAFLESNIKAFD 189 Query: 188 EG 189 G Sbjct: 190 LG 191 Lambda K H 0.317 0.136 0.389 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: 106 Number of extensions: 3 Number of successful extensions: 2 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: 196 Length of database: 196 Length adjustment: 20 Effective length of query: 176 Effective length of database: 176 Effective search space: 30976 Effective search space used: 30976 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 (21.6 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 24 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