Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 353293 BT3767 lactaldehyde reductase (NCBI ptt file)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Btheta:353293 Length = 384 Score = 213 bits (542), Expect = 8e-60 Identities = 129/384 (33%), Positives = 203/384 (52%), Gaps = 5/384 (1%) Query: 5 RIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHV 64 RI+ S+ G G + E R G K +TD L+K G+ ++ + Sbjct: 3 RIILNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYEL 62 Query: 65 YTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLT 124 Y+DV P + + VA + D ++ +GGGS++D AK ++ V++ AD +L Sbjct: 63 YSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIV-VNNPDFADVKSLE 121 Query: 125 GTRTLEKKGLPKILIPTTSGTGSEVT-NISVLSLETTKDVVTHDYL-LADVAIVDPQLTV 182 G + K +P +PTT+GT +EVT N ++ + K +V D + VAIVDP+L Sbjct: 122 GVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMY 181 Query: 183 SVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARI 242 S+P +TAATG+DALTHA+E+Y++ A SD + AI +I+++L+ AV NG D AR Sbjct: 182 SMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVARE 241 Query: 243 DMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQS-CTKRM 301 M+ Y+AG+ F N G+ VH++A+PLG + HG +NA+LLPYVM Y +S + Sbjct: 242 AMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKY 301 Query: 302 ADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQ 361 I A+G N+ ++E E +E ++ +GIP+ L + E + +L A Sbjct: 302 IHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFND 361 Query: 362 KRLLARSPLPLLEADIRAIYEAAF 385 +P P A+I +Y AF Sbjct: 362 V-CTGGNPRPTSVAEIEVLYRKAF 384 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: 348 Number of extensions: 24 Number of successful extensions: 4 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: 384 Length adjustment: 30 Effective length of query: 365 Effective length of database: 354 Effective search space: 129210 Effective search space used: 129210 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