Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF5024 PS417_25740 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__WCS417:GFF5024 Length = 382 Score = 319 bits (817), Expect = 1e-91 Identities = 176/373 (47%), Positives = 247/373 (66%), Gaps = 7/373 (1%) Query: 15 GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74 G GA++QL E+ RL + L++TD LVK G V L + Y + + V+P+P + Sbjct: 15 GAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVALALVHLGERSYEI--FDRVLPDPEI 72 Query: 75 ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134 E + R+G D +IG+GGGSA+D+AK A A + G++AD L G + +KG Sbjct: 73 AIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALAD---LFGVDQVPRKGP 129 Query: 135 PKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192 P I IPTT+GTGSEVTN+++LS + K + DYLL DVA++ PQ+T++ P VTAA+ Sbjct: 130 PLIAIPTTAGTGSEVTNVAILSDKAAQLKKGIVSDYLLPDVALISPQMTLTCPRSVTAAS 189 Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252 G+DAL HA+E+Y+S+NASP +D LA+ AI+LI+ +L KA AN ++ QAR DMA S +AG Sbjct: 190 GVDALVHAIESYLSLNASPITDALAIGAIKLIAHALPKAYANPANLQARDDMATASLMAG 249 Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312 +AF NAGV VHALAYPLGG+F+IAHG SNA+LLPYVM + + +C +RM DI A+G N Sbjct: 250 MAFGNAGVGAVHALAYPLGGRFNIAHGVSNALLLPYVMHWNKLACVERMQDIAQAMGVNV 309 Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372 + LS +A+ + VE + R A V IP L FG+PE A+ ++ +A +RL+ +P L Sbjct: 310 TGLSVNDAADQAVEAMTRLCAAVEIPAGLHSFGVPEDAIPAMAVEAAGIERLMRNNPRKL 369 Query: 373 LEADIRAIYEAAF 385 ADI IY AA+ Sbjct: 370 SAADIEKIYRAAY 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: 427 Number of extensions: 21 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: 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 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