Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate SMa0263 SMa0263 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Smeli:SMa0263 Length = 399 Score = 196 bits (499), Expect = 8e-55 Identities = 133/372 (35%), Positives = 194/372 (52%), Gaps = 32/372 (8%) Query: 35 LVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETGEKAVAFARDGKFDLVIG 94 L++TD L + + L + G V V + +P+ P+E+ + A A DLVIG Sbjct: 35 LIVTDTRLAVDADLLALVRRLEEAGLEVMVDSSTLPDVPVESAIVSAAAASGFAPDLVIG 94 Query: 95 VGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISV 154 +GGGS LD+AK +L H G DY G + +P I IPTT+GTGSEVT ++V Sbjct: 95 IGGGSCLDMAKCVTLLLTHGGRPQDYY---GEYAVPGPVMPLIAIPTTAGTGSEVTPVAV 151 Query: 155 LS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDALTHAVEAYVSVNASPT 212 LS + K ++ +L+ V+I DP+LT+S PP +TA G DALTHA+EA+ ++ P Sbjct: 152 LSDAERSLKVGISSPHLIPAVSICDPELTLSCPPGLTAIAGADALTHAIEAFTAIRREPV 211 Query: 213 ---------------SDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLAFFN 257 SD A++AI L+ + L +A +G+D AR + G+ LAGLAF Sbjct: 212 PGIAQQRVFVGKNELSDHFALSAITLLWQGLERACKDGADAGARETVMLGATLAGLAFGV 271 Query: 258 AGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNA--LGGNSSFL 315 AG A HA+ YP+G H AHG A L+PYVM + +A I +A LGG + Sbjct: 272 AGTAAAHAIQYPVGALTHTAHGLGVACLMPYVMTWNAPLIRDELAQIAHAAGLGGPDEVI 331 Query: 316 SEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLLEA 375 + V ER +GIP TL G+ E ++ + + + RL+ +P PL Sbjct: 332 PAL------VSLFER----IGIPATLRDLGLEEDRIDWVAEQSSGIARLIQNNPRPLNPH 381 Query: 376 DIRAIYEAAFAG 387 ++R + AA G Sbjct: 382 EMRNLVAAAHCG 393 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: 394 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 364 Effective length of database: 368 Effective search space: 133952 Effective search space used: 133952 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