Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AO353_24900 AO353_24900 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24900 Length = 386 Score = 191 bits (484), Expect = 4e-53 Identities = 125/390 (32%), Positives = 197/390 (50%), Gaps = 20/390 (5%) Query: 8 FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67 +P H G G + +L + G + L++TD L + + LR G V ++ D Sbjct: 9 YPTSIHFGVGRIAELADTCRSQGIQRPLLVTDSGLARAPITTAALESLRAAGLGVELFCD 68 Query: 68 VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG-- 125 + P P + R GK D V+ GGGS LD+ KL A ++ V D+ ++ Sbjct: 69 LKPNPVEANLAGGLDAWRAGKHDGVVAFGGGSGLDMGKLIAFMSGQTRPVWDFEDIGDYW 128 Query: 126 TRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVS 183 TR E P I +PTT+GTGSEV +V+ E T K ++ H ++ V I DP LTV Sbjct: 129 TRADESSIAPIIAVPTTAGTGSEVGRAAVIIDERTHTKRIIFHPKMMPRVVISDPALTVG 188 Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243 +P +VTA TG+DA H +E+Y + P ++G+AV +RL++ +L +AV SD +AR + Sbjct: 189 MPAKVTAGTGMDAFAHCLESYCAPGFHPMAEGIAVEGMRLVANALVRAVRTPSDLEARAE 248 Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303 M + + G F G+ G+HALA+P+G + HG +NA +PYV+ + R + +R+ Sbjct: 249 MLAAAAM-GATAFQKGLGGMHALAHPVGALYDTHHGMTNATFMPYVLKFNRPAIEERITR 307 Query: 304 IFNAL----GGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359 + L G SFL+ V + D+G+P TL G+ + + + A+ Sbjct: 308 LAAYLRLPTPGFDSFLAFV----------LKLRKDIGVPHTLFELGVDDRQADLIADMAI 357 Query: 360 QQKRLLARSPLPLLEADIRAIYEAAFAGTI 389 +PLPL I+EAA+ G + Sbjct: 358 VDP-CAGGNPLPLTRNGAMEIFEAAYHGRL 386 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: 379 Number of extensions: 25 Number of successful extensions: 6 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: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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