Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate BPHYT_RS20205 BPHYT_RS20205 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__BFirm:BPHYT_RS20205 Length = 386 Score = 249 bits (636), Expect = 9e-71 Identities = 151/372 (40%), Positives = 219/372 (58%), Gaps = 18/372 (4%) Query: 27 KRLGA---------KHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETG 77 +RLGA + V+TD L + GL++ + L G+ V DV+ +PP Sbjct: 20 RRLGALLRAQFPALSRVCVVTDGFLHRSGLLNPALADLATHGWDATVIDDVIADPPEHIV 79 Query: 78 EKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPKI 137 +A + AR ++V+G+GGGS++D+AKL AVLA + G + LP + Sbjct: 80 LEATSRARTAGAEIVLGLGGGSSMDVAKLIAVLAPQQQQALS--EMYGVNKITVARLPLV 137 Query: 138 LIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDA 196 +PTT+GTGSEVT +S++++ E K V L+AD+AI+D +LT+ +P TAATG+DA Sbjct: 138 QMPTTAGTGSEVTAVSIVTVGEAKKMGVVAPQLIADLAILDAELTLGLPVAATAATGVDA 197 Query: 197 LTHAVEAYVSVNA-SPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLAF 255 + HA+EAY S + +P SD LAV A+ L+SR+L A NG D+ AR M G+ AG AF Sbjct: 198 MVHAIEAYTSAHLKNPVSDLLAVKALDLLSRNLLPACENGDDRAAREAMLLGATFAGQAF 257 Query: 256 FNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNAL--GGNSS 313 N+ VA VHALAYP+GG +H+ HG SNA++LP+V+ + + A++ + G S Sbjct: 258 ANSPVAAVHALAYPIGGIYHVPHGLSNALVLPHVLRFNADAAAPLYAELAEVVVPGVTGS 317 Query: 314 FLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLL 373 S+ +A +E LE+ +A IP L GI +S LE + DA+ Q RLL +P P+ Sbjct: 318 DESKTQA---LIERLEQMIAATAIPARLRDVGIEQSGLERMASDAMLQTRLLVNNPRPVT 374 Query: 374 EADIRAIYEAAF 385 EAD AIY AAF Sbjct: 375 EADALAIYTAAF 386 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: 17 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: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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