Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 1937064 b3589 predicted Fe-containing alcohol dehydrogenase (NCBI)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Keio:1937064 Length = 383 Score = 208 bits (530), Expect = 2e-58 Identities = 126/386 (32%), Positives = 201/386 (52%), Gaps = 6/386 (1%) Query: 1 MSVARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGY 60 M+ + P ++ +G +L + + G L++TD ML K+G+ V L + Sbjct: 1 MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60 Query: 61 SVHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADY 120 +Y P P E + ++ D VI +GGGS D AK A++A + G + DY Sbjct: 61 FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120 Query: 121 LNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDP 178 G K LP I I TT+GT SE+T +++ E K + ++ +++ D Sbjct: 121 ---EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDS 177 Query: 179 QLTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDK 238 L + +P +TAATG+DALTHA+EAYVS+ A+P +D A+ A+ +I+ +L AV +GS+ Sbjct: 178 SLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNA 237 Query: 239 QARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCT 298 +AR MA +LAG+AF NA + VHA+A+ LGG +++ HG NAVLLP+V + + Sbjct: 238 KAREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAA 297 Query: 299 KRMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDA 358 R+ D A+G N + ++ E + C+ + V IP L + E L +A Sbjct: 298 ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNA 357 Query: 359 VQQKRLLARSPLPLLEADIRAIYEAA 384 ++ +P+ +I AIY AA Sbjct: 358 LKDACGFT-NPIQATHEEIVAIYRAA 382 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: 17 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: 383 Length adjustment: 30 Effective length of query: 365 Effective length of database: 353 Effective search space: 128845 Effective search space used: 128845 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