Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate RR42_RS24560 RR42_RS24560 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS24560 Length = 389 Score = 250 bits (639), Expect = 4e-71 Identities = 150/356 (42%), Positives = 219/356 (61%), Gaps = 5/356 (1%) Query: 32 KHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETGEKAVAFARDGKFDL 91 + +LV+TD L K G+++ + L G+ V V+ +VV +PP + V AR + DL Sbjct: 37 RSVLVVTDGGLHKAGVLEGAKASLAAAGFRVTVFDEVVADPPEAVLLRCVEHARAARVDL 96 Query: 92 VIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPKILIPTTSGTGSEVTN 151 VIG+GGGS++D+AKLAAVL V +A+ + G ++ +P + +PTT+GTGSEVTN Sbjct: 97 VIGLGGGSSMDIAKLAAVLVVSGQPLAE---MYGIGNVKGARVPLVQMPTTAGTGSEVTN 153 Query: 152 ISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDALTHAVEAYVSVNA- 209 IS++S+ ETTK + L AD I+D +LTV +P + TAATGIDA+ HA+EAY S + Sbjct: 154 ISIVSVGETTKMGIVAPQLYADRVILDAELTVGLPRQHTAATGIDAMVHAIEAYTSKHKK 213 Query: 210 SPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLAFFNAGVAGVHALAYP 269 + SD LA A+RL+S +L A NG+D+ AR M G+ LAG AF NA VA VHALAYP Sbjct: 214 NAISDALAREALRLLSANLLPACENGNDRGAREAMLLGATLAGQAFANAPVAAVHALAYP 273 Query: 270 LGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNSSFLSEVEASYRCVEELE 329 LGG FHI HG SNA++L V+ + + + A++ ALG + + + + +E Sbjct: 274 LGGHFHIPHGLSNALMLGPVLRFNAAAAAAQYAELAGALGIGQADGDDEARTAAFIGFME 333 Query: 330 RFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLLEADIRAIYEAAF 385 + G P+ L G+ +L L DA+QQ+RLL +P+ + +AD +YE A+ Sbjct: 334 DLMDRSGAPRRLRDAGVTRESLAMLAADAMQQQRLLQNNPVEVQQADALRLYEQAY 389 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: 352 Number of extensions: 14 Number of successful extensions: 5 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: 389 Length adjustment: 31 Effective length of query: 364 Effective length of database: 358 Effective search space: 130312 Effective search space used: 130312 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 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