Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 3607669 Dshi_1078 Alcohol dehydrogenase zinc-binding domain protein (RefSeq)
Query= BRENDA::D4GSN2 (353 letters) >FitnessBrowser__Dino:3607669 Length = 345 Score = 273 bits (697), Expect = 6e-78 Identities = 156/352 (44%), Positives = 205/352 (58%), Gaps = 13/352 (3%) Query: 1 MRAAVLREHGEPLDVTEVPDPTCDADGVVVEVEACGICRSDWHSWMGHGEWADDAVPSGQ 60 MRAAVLR + E L + +VP+P C DGVV++V ACG+CRSDWH W+G V GQ Sbjct: 1 MRAAVLRAYNEDLVLEDVPEPVCPEDGVVLKVLACGVCRSDWHGWVGE----HPRVKPGQ 56 Query: 61 ILGHEPAGRVVEAGDRVETIREGDRVALPFNLACGSCGYCQTGHGNVCTGDHPHALGF-E 119 I GHE G V+EAG R + GDRV PF LACGSC CQ G N C GF E Sbjct: 57 IGGHEYCGEVIEAGPRA-AFKPGDRVVAPFILACGSCPSCQAGAQNTCPNQR--LPGFVE 113 Query: 120 PAAQGAFAELVHLPSADYNAIQLPEDVLPTDVAALGCRFMTAYNALDARAGLRAGQWVAV 179 P GAFAE V +P D+N +LP+ + PT A LGCR TA++AL RA ++ +WVAV Sbjct: 114 P---GAFAEYVAVPF-DHNLSRLPDSLSPTVAAGLGCRVTTAWHALTGRAAVQGAEWVAV 169 Query: 180 HGCGGVGLSTIQVANVLGARVVAVDVRESALDAAADLGADAVVDGSAEDPVDAIRGLTDG 239 HG GG+GLS++ +AN LGARV+AVDV + L AA GA+ ++ D I+ +T G Sbjct: 170 HGTGGIGLSSVILANALGARVIAVDVVDEKLTHAAQHGAEVTLNAREGDVAARIKQITGG 229 Query: 240 GAHVSLDALGVAETCRNSVRSVRPRGSHVQVGLTTEAEKGNVSLPTDWMTRHEVSFLGAR 299 GAHV+++ALG+ ET S+ +RP G HVQVGL T + + + + ++ G R Sbjct: 230 GAHVAIEALGIPETVNASLECLRPLGRHVQVGLPT-GHTARMEINMSAIYQGNLAVYGTR 288 Query: 300 GMPPTNADDLLSLLASDAVDPGSLVTKTVSLDEVPERLAAMTDYDTVGVEVM 351 GMP LLSL+ + VD L+ + + L L A GV V+ Sbjct: 289 GMPSWRYPSLLSLIETGRVDMSPLIAREIGLSGTSAELRAFNGPTPPGVAVI 340 Lambda K H 0.317 0.134 0.412 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: 482 Number of extensions: 25 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: 353 Length of database: 345 Length adjustment: 29 Effective length of query: 324 Effective length of database: 316 Effective search space: 102384 Effective search space used: 102384 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: 49 (23.5 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