Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >NCBI__GCF_900167125.1:WP_078716111.1 Length = 382 Score = 244 bits (622), Expect = 4e-69 Identities = 142/354 (40%), Positives = 210/354 (59%), Gaps = 6/354 (1%) Query: 9 PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68 PP G GA+ Q+ E RLG++ ++V + G ++ VT+ L + G ++ +V Sbjct: 9 PPRIIFGNGAVAQVGRETARLGSRALIVTGKSSSTRTGSLEAVTASLNEAGVHPVLFAEV 68 Query: 69 VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128 +P ++T E A AR+ + D+++G+GGGS LD AK +L H G + DY + + Sbjct: 69 ESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDYTS----QP 124 Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPP 186 + G+P I IPTT+GT SE+T +V++ + K + L+ VA++DPQLTV++P Sbjct: 125 ADGPGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLTVTMPQ 184 Query: 187 RVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246 VTAATG+DALTHA+EAY+S A+P SD A+ AIRLI +L KAV + + AR M Sbjct: 185 HVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAREAMLR 244 Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306 G AGLAF NA VA VH+++ PLG F IAHG++NA+LLP VM + R + R I Sbjct: 245 GQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADRYRHIAE 304 Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQ 360 ALG N LS +A+ V +E + G+ + L +G+ E + L KDA++ Sbjct: 305 ALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAME 358 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: 359 Number of extensions: 12 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: 382 Length adjustment: 30 Effective length of query: 365 Effective length of database: 352 Effective search space: 128480 Effective search space used: 128480 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 Apr 09 2024. 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