Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate Ac3H11_3427 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3427 Length = 1243 Score = 216 bits (551), Expect = 3e-60 Identities = 145/393 (36%), Positives = 206/393 (52%), Gaps = 31/393 (7%) Query: 34 IKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFD 93 I++G +A GDC CHT+ G GG +++TP G IY+TN+TPD GIG ++F F Sbjct: 852 IERGRLLAAAGDCAVCHTAPGGTPNTGGRAMETPFGKIYTTNLTPDAETGIGQWSFSAFQ 911 Query: 94 EAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHP-TDISWPMS 152 A+R G+ + G LYPA PY SFA+M+ DD+ ALYAY M AQP + P T++++P S Sbjct: 912 RAMREGISQGGKHLYPAFPYTSFAKMSDDDLTALYAYLM--AQPAVRAEVPKTELTFPFS 969 Query: 153 MRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDA 212 +R ++ W ++F A F P P E RG YLV G GHCGACHTPR AL A Sbjct: 970 VRPLMAGWNALFHDA-TPFKPDPTRPPEWNRGAYLVQGVGHCGACHTPR------NALGA 1022 Query: 213 S-GGPDFLGGGGVIDNWIAPSLRNDPVLGLGR----WSDEDLFLFLKSGRT-DHSAAFGG 266 GG FL G +ID W AP+L GL + W+ + L+ +L+ G + H +A G Sbjct: 1023 ELGGAAFL-SGAMIDGWEAPAL-----TGLSKAPVPWTADALYGYLRHGHSPQHGSASGP 1076 Query: 267 MADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQ--MLDSNNISGNAG- 323 MA VV + D D+ AM Y+ S A S AQ + + ++ G Sbjct: 1077 MAPVVR-ELAHLPDDDIRAMASYLASFTAAEAATQPVSDPQQRAQTAVAQAAALAPQPGQ 1135 Query: 324 -AKTYVDQCAICHRN-DGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPS 381 + + CA CH + DG + + PLA N + SD P ++ ++V G P A Sbjct: 1136 AQRLFDGACAACHHDGDGPKLLGVNVPLALNSNLHSDRPDNLLQVIVHGIREPA---ARD 1192 Query: 382 AVAMPDYKNILSDQQIADVVNFIRSAWGNRAPA 414 MP + + LSD QI ++ ++R + PA Sbjct: 1193 IGFMPGFGHALSDAQITELAGYMRQRYAPGRPA 1225 Lambda K H 0.318 0.135 0.430 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: 1734 Number of extensions: 110 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 1243 Length adjustment: 40 Effective length of query: 432 Effective length of database: 1203 Effective search space: 519696 Effective search space used: 519696 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: 55 (25.8 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