Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PfGW456L13_2712 Alcohol dehydrogenase (EC 1.1.1.1)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2712 Length = 386 Score = 189 bits (480), Expect = 1e-52 Identities = 125/390 (32%), Positives = 198/390 (50%), Gaps = 20/390 (5%) Query: 8 FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67 +P G G + +L + G + L++TD L + + LR G V ++ D Sbjct: 9 YPTSVRFGVGRIAELAEVCRSQGIQRPLLVTDSGLARAPITTAALDALRAAGLGVALFCD 68 Query: 68 VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG-- 125 + P P + R G+ D VI GGGS LD+ KL A ++ V D+ ++ Sbjct: 69 LKPNPVEANLAGGLDAWRAGQHDGVIAFGGGSGLDMGKLIAFMSGQTRPVWDFEDIGDYW 128 Query: 126 TRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVS 183 TR + + P I +PTT+GTGSEV +V+ E T K ++ H ++ V I DP LTV Sbjct: 129 TRADDSRIAPVIAVPTTAGTGSEVGRAAVIIDERTHTKRIIFHPKMMPRVVISDPALTVG 188 Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243 +P ++TA TG+DAL+H +EAY + P +DG+AV +RL++ SL KAV SD +AR Sbjct: 189 MPAKITAGTGMDALSHCLEAYCAPGFHPLADGIAVEGMRLVANSLVKAVHTPSDLEARAQ 248 Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303 M + + G F G+ G+HAL++P+G + HG +NA +PYV+ + R + +R+ Sbjct: 249 MLAAAAM-GATAFQKGLGGMHALSHPVGALYDTHHGMTNATFMPYVLHFNRSAIEERITR 307 Query: 304 IFNAL----GGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359 + L G SFL+ V + D+G+P TL G+ + + + A+ Sbjct: 308 LAAYLRLPSPGFDSFLAFV----------LKLRKDIGVPHTLVELGVDDRQADLIADMAI 357 Query: 360 QQKRLLARSPLPLLEADIRAIYEAAFAGTI 389 +PLPL + I++AA G + Sbjct: 358 VDPS-AGGNPLPLTRDGVAKIFDAALHGRL 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: 389 Number of extensions: 27 Number of successful extensions: 5 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