Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 6938336 Sama_2455 alcohol dehydrogenase II (RefSeq)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__SB2B:6938336 Length = 382 Score = 228 bits (582), Expect = 2e-64 Identities = 133/359 (37%), Positives = 198/359 (55%), Gaps = 5/359 (1%) Query: 4 ARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVH 63 A+ P ++ +G GA+D+ + ++ LG K L++TD LV+IG+ ++ L + G + Sbjct: 3 AKFFIPSVNVLGQGAVDEAIGDIVTLGFKQALIVTDKPLVQIGIAGELVEKLGERGITAV 62 Query: 64 VYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNL 123 V+ V P P E +A D VI +GGGS D AK A++A + GS+ DY Sbjct: 63 VFDGVQPNPTTANVEAGLALLNAHGCDFVISLGGGSPHDCAKGIALVATNGGSIKDY--- 119 Query: 124 TGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLT 181 G K LP + I TT+GT SE+T +++ E K + + +++ DP+L Sbjct: 120 EGVDKSAKPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPILSVNDPELM 179 Query: 182 VSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQAR 241 V P +TAATG+DALTHAVEAYVSV A+P +D A+ AI LI + L +AV G D QAR Sbjct: 180 VKKPAALTAATGMDALTHAVEAYVSVAANPITDACAIKAIELIQQYLERAVKQGQDLQAR 239 Query: 242 IDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRM 301 MA +LAG+AF NA + VHA+A+ LGG + + HG NA+LLPYV Y R+ Sbjct: 240 EQMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPYVQEYNAAVAAARL 299 Query: 302 ADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQ 360 D+ A+G L + E + + ++ V IP+ L G+ E + L +A++ Sbjct: 300 KDVAKAMGVAVDGLDDQEGAKAAISAIKALSKAVNIPENLTVLGVKEEDIPLLADNALK 358 Lambda K H 0.318 0.135 0.381 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: 356 Number of extensions: 14 Number of successful extensions: 3 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: 395 Length of database: 382 Length adjustment: 30 Effective length of query: 365 Effective length of database: 352 Effective search space: 128480 Effective search space used: 128480 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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