Align alcohol dehydrogenase (quinone) (EC 1.1.5.5) (characterized)
to candidate H281DRAFT_01296 H281DRAFT_01296 PQQ-dependent dehydrogenase, methanol/ethanol family
Query= BRENDA::Q44002 (739 letters) >FitnessBrowser__Burk376:H281DRAFT_01296 Length = 605 Score = 284 bits (727), Expect = 8e-81 Identities = 195/585 (33%), Positives = 280/585 (47%), Gaps = 58/585 (9%) Query: 26 ISGYATMASADDGQGATGEAIIHADDH-------PGNWMTYGRTYSEQRYSPLDQINRSN 78 + G A +ASA A + AD P NW Y+ RYSPL QIN +N Sbjct: 7 VLGLAILASA-----AMSSIVAQADSQLDGLMKSPSNWAAQAGDYANHRYSPLKQINENN 61 Query: 79 VGNLKLAWYLDLDTNRGQEGTPLVIDGVMYATTNW-SMMKAVDAATGKLLWSYDPRVPGN 137 VG L++AW + RG EG PLVI MY + + + + A++ LW Y P+ + Sbjct: 62 VGKLQVAWTMSTGVLRGHEGAPLVIGDTMYIHSPFPNKVIAINLKDQTFLWQYQPKQDDS 121 Query: 138 IADKGCCDTVNRGAAYWNGKVYFGTFDGRLIALDAKTGKLVWSVNTIPPEAELGKQRS-Y 196 + CCDTVNRG AY +GK++ D +L+AL+AKTG +VW+ A+ G ++ Sbjct: 122 VVSVMCCDTVNRGLAYGDGKIFLQQADTKLVALNAKTGDVVWT-------AQNGNSKAGE 174 Query: 197 TVDGAPRIAKGRVIIGNGGSEFGARGFVTAFDAETGKVDWRFFTAPNPKN---EPDHTAS 253 T AP + +V+ G G EFG RG + A+D +TGK W ++ K+ +PD T + Sbjct: 175 TNTNAPHVFGDKVLTGISGGEFGVRGRLIAYDIKTGKPAWTAYSTGPDKDMLMDPDKTMT 234 Query: 254 DS------VLMNKAYQTWSPTGAWTRQGGGGTVWDSIVYDPVADLVYLGVGNGSPWNYKY 307 + V + + ++W W + GGGT W +DP +LVY G GN WN Sbjct: 235 YADGKMVPVGADSSLKSWK-GDQW--KLGGGTTWGWYAWDPKLNLVYYGTGNPGTWNPTQ 291 Query: 308 RSEGKGDNLFLGSIVALKPETGEYVWHFQETPMDQWDFTSVQQIMTLDLPINGETRHVIV 367 R GDN + SI+A TG W +Q TP D+WD+ V +++ DL I+G+ IV Sbjct: 292 R---PGDNKWSMSIMARDLNTGMAKWVYQMTPHDEWDYDGVNEMILSDLTIDGKKVPAIV 348 Query: 368 HAPKNGFFYIIDAKTGEFISGKNY-VYVNWASGLDPKTGRPIYNPDALYTLTGKEW--YG 424 H +NGF Y ++ ++G+ + + + VNWA +D K+G+PI N G + G Sbjct: 349 HFDRNGFGYTLNRESGQLLVAQKFDPAVNWADSVDLKSGKPIRNAAYSTQAAGSDHNVKG 408 Query: 425 I-PGDLGGHNFAAMAFSPKTGLVYIPAQQVPFLY----TNQVGGFTPHPDSWNLGLDMNK 479 I P LG + A+ P + L +P V Y + V G P+ +G ++ Sbjct: 409 ICPAALGSKDQQPAAYDPNSSLFLVPTNHVCMDYEPFDVDYVSG-QPY-----VGATLSM 462 Query: 480 VGIPDSPEAKQAFVKDLKGWIVAWDPQKQAEAWRVDHKGPWNGGILATGGDLLFQGLANG 539 P+ A G +AWD K W K G LAT G + F G G Sbjct: 463 YPGPNENNA--------MGNFIAWDAAKGKIVWSKPEKFSVWSGALATAGGIAFYGTLEG 514 Query: 540 EFHAYDATNGSDLFHFAADSGIIAPPVTYLANGKQYVAVEVGWGG 584 A +G +L+ F SGII TY GKQYV V G GG Sbjct: 515 YLKAVRIKDGKELWRFKTPSGIIGNVFTYQYQGKQYVGVYSGIGG 559 Lambda K H 0.318 0.137 0.440 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: 1749 Number of extensions: 144 Number of successful extensions: 14 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: 739 Length of database: 605 Length adjustment: 38 Effective length of query: 701 Effective length of database: 567 Effective search space: 397467 Effective search space used: 397467 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: 54 (25.4 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