Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 203967 SOA0164 iron-containing alcohol dehydrogenase (NCBI ptt file)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__MR1:203967 Length = 383 Score = 220 bits (561), Expect = 5e-62 Identities = 135/378 (35%), Positives = 212/378 (56%), Gaps = 5/378 (1%) Query: 9 PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68 PP+S +G A+ L E++ L++TD LV I LVD++T L + ++ V Sbjct: 8 PPMSLMGQHAIKLLGTELQARNFNKALIVTDKALVDIKLVDKLTDELSAHDIAFAIFDGV 67 Query: 69 VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128 P P + + +A K D VI GGGS+ D AK A++A + G + DY G Sbjct: 68 KPNPTEKNIVQGLALLEAQKCDFVISFGGGSSHDCAKGIALVAANGGHIRDYSK--GVHL 125 Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLSLET--TKDVVTHDYLLADVAIVDPQLTVSVPP 186 K LP + + TT+GT +E+T ++++ E TK + L +A+ D +L V++P Sbjct: 126 SAKPQLPLVTVNTTAGTAAEMTIFAIVTNEEDETKYPIVDKNLTPIIAVNDSELMVAMPK 185 Query: 187 RVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246 +TAATG+DALTHAVEAYVS A+P +D A+ AI LI+++L+ AV NG D++AR M Sbjct: 186 FLTAATGMDALTHAVEAYVSTAATPITDASAIKAIELIAQNLKAAVDNGEDREAREAMQY 245 Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306 G YLAG+AF NA + VH++A+ LGG + + HG NA+LLP V + +R A++ Sbjct: 246 GEYLAGMAFSNASLGYVHSMAHQLGGVYDLVHGLCNAILLPVVSRFNSAEKVERFAEVAK 305 Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLA 366 A+G ++ ++ ++A+ + +E+ A VG + L G+ E LE + +A+ L Sbjct: 306 AMGVDTVGMTLIDAAESGILAIEKLSASVGTDQKLSDLGVKEDKLEFMAINALNDACSLT 365 Query: 367 RSPLPLLEADIRAIYEAA 384 +P DI I++ A Sbjct: 366 -NPRKATTEDIINIFKKA 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: 310 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: 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