Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate Pf1N1B4_2542 Alcohol dehydrogenase (EC 1.1.1.1)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2542 Length = 382 Score = 320 bits (819), Expect = 6e-92 Identities = 174/373 (46%), Positives = 246/373 (65%), 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 GAGAIEQLAAELTRLDIDNPLIVTDAALVKSGTVELALAQLGERSYEI--FDRVLPDPEI 72 Query: 75 ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134 E + R+G D +IG+GGGSA+D+AK A A + G++ D L G + +KG Sbjct: 73 AIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALED---LFGIDQVPRKGP 129 Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192 P I IPTT+GTGSEVTN+++LS + K + DYLL DVA++ PQ+T++ P VTAA+ Sbjct: 130 PLIAIPTTAGTGSEVTNVAILSDKIAQLKKGIVSDYLLPDVALISPQMTLTCPRSVTAAS 189 Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252 G+DAL HA+E+Y+S+NASP +D LA+ AI+LI+++L KA AN S QAR DMA S +AG Sbjct: 190 GVDALVHAIESYLSLNASPITDALAIGAIKLITKALPKAYANPSHLQAREDMATASLMAG 249 Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312 +AF NAGV VHALAYPLGG+F+IAHG SNA+LLPYVM + + +C +RM DI A+G + Sbjct: 250 MAFGNAGVGAVHALAYPLGGRFNIAHGVSNALLLPYVMTWNKMACVERMQDIAEAMGVKT 309 Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372 + LS EA+ + VE + A V IP L FG+PE A+ ++ +A +RL+ +P L Sbjct: 310 AHLSANEAADKAVEAMTELCAAVEIPLGLRSFGVPEDAIPAMAVEAAGIERLMRNNPRKL 369 Query: 373 LEADIRAIYEAAF 385 DI IY AA+ Sbjct: 370 STVDIEKIYRAAY 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: 400 Number of extensions: 23 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