Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate GFF3098 PS417_15850 alcohol dehydrogenase
Query= SwissProt::Q0KDL6 (366 letters) >FitnessBrowser__WCS417:GFF3098 Length = 357 Score = 516 bits (1329), Expect = e-151 Identities = 260/363 (71%), Positives = 296/363 (81%), Gaps = 7/363 (1%) Query: 3 AMMKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGH 62 A MKAA+FVE RI L DKPIP++GP DAL+RITTTTICGTDVHIL+GEYPVAKGLT+GH Sbjct: 2 ATMKAAIFVEKNRIVLEDKPIPEVGPLDALIRITTTTICGTDVHILRGEYPVAKGLTIGH 61 Query: 63 EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYK 122 EPVGIIE+LGS V G+ EGQRVIAGAI P+ SYA G ASQDG HG++ Sbjct: 62 EPVGIIERLGSQVRGFVEGQRVIAGAITPSGQSYACLCGCASQDGPDTR-------HGFR 114 Query: 123 ATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIR 182 AT GW+FGN+IDG QAEYVLVPDA ANL PIPDGL+DEQVLMCPDIMSTGF GAE I Sbjct: 115 ATGGWKFGNIIDGCQAEYVLVPDALANLCPIPDGLSDEQVLMCPDIMSTGFSGAERGEIN 174 Query: 183 IGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVD 242 IGDTVAVFA GPIGLCA AGARL GATTII +D R+ +AR++GA V+NF+ +VV+ Sbjct: 175 IGDTVAVFALGPIGLCAVAGARLKGATTIIGVDAVAQRMSVARQLGATHVVNFKEANVVE 234 Query: 243 EVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGD 302 ++M LT GRGVD SIEALGTQ TFE +LRVL+PGG LSSLGVYSSDL IPL AFAAGLGD Sbjct: 235 QIMALTDGRGVDVSIEALGTQGTFESALRVLRPGGRLSSLGVYSSDLRIPLDAFAAGLGD 294 Query: 303 HKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIA 362 + I T LCPGGKERMRRL+ V++SG VDL LVTH ++LDDI AAY+LFANQRDGV+K+A Sbjct: 295 YSIVTTLCPGGKERMRRLMAVVQSGAVDLSPLVTHHFKLDDIEAAYELFANQRDGVMKVA 354 Query: 363 IKP 365 I P Sbjct: 355 ITP 357 Lambda K H 0.320 0.138 0.408 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: 547 Number of extensions: 19 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: 366 Length of database: 357 Length adjustment: 29 Effective length of query: 337 Effective length of database: 328 Effective search space: 110536 Effective search space used: 110536 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: 49 (23.5 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