Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate Echvi_0924 Echvi_0924 Alcohol dehydrogenase, class IV
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Cola:Echvi_0924 Length = 381 Score = 203 bits (517), Expect = 6e-57 Identities = 131/374 (35%), Positives = 192/374 (51%), Gaps = 10/374 (2%) Query: 15 GWGALDQLVPEVKRLGAKHI-LVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPP 73 G G + V + K I +++ P+L +D ++ G V V EP Sbjct: 15 GVGGFSRFVEDTVAASHKRIWILVAQPLL---DTLDGGLQEMKSAGLEVEVAVYDAGEPT 71 Query: 74 LETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKG 133 E + +D D ++G+GGGS LDLAKL A + G ++D++ G LE + Sbjct: 72 FSHYEDFLKQVKDFGADTIVGIGGGSVLDLAKLLAAMQDSTGQLSDFV---GINLLESRN 128 Query: 134 LPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVSVPPRVTAA 191 + IPTT+GTGSEV+ ++L E T K + +L+ D +DP LTV +PP++TA Sbjct: 129 THMVCIPTTAGTGSEVSPNAILLDEATLEKKGIISPFLVPDATYIDPALTVGLPPKITAE 188 Query: 192 TGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLA 251 TGIDAL+H +EAY + + P D A+ I LI ++L +A D AR +A GS Sbjct: 189 TGIDALSHCIEAYTNKFSHPLVDDYALRGIALIGQNLHRAFEVPEDMDARTAVALGSMYG 248 Query: 252 GLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGN 311 GL A VHAL+YPLGG++H+ HG +NAVLLP VM Y S ++ I A+G Sbjct: 249 GLCLGPVNTAAVHALSYPLGGKYHVPHGLANAVLLPEVMAYNLSSNIQKHEQIALAMGAE 308 Query: 312 SSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLP 371 E AS V++++ V IP+ L G+ + + LT A++ RLL +P Sbjct: 309 QGNSPEETAS-NGVQKVKELVKRCDIPQDLTTLGVQQEDVPELTALAMKVTRLLKNNPRE 367 Query: 372 LLEADIRAIYEAAF 385 + AD IY F Sbjct: 368 VTFADAEEIYGRLF 381 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: 358 Number of extensions: 15 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: 381 Length adjustment: 30 Effective length of query: 365 Effective length of database: 351 Effective search space: 128115 Effective search space used: 128115 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