Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PfGW456L13_3512 Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3512 Length = 387 Score = 198 bits (504), Expect = 2e-55 Identities = 123/372 (33%), Positives = 199/372 (53%), Gaps = 6/372 (1%) Query: 15 GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74 G G+ + K GA+ +LV++DP ++ G V V + L+ G +Y+DV P P + Sbjct: 19 GAGSRHSVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQALGIEYCLYSDVSPNPRV 78 Query: 75 ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134 E R+ D+++ VGGGS +D K ++ H S+ D+ G T+ Sbjct: 79 EEVMLGAEMYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRSILDF---EGVDTIRVPSP 135 Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192 P ILIPTT+GT ++V+ ++S E K + ++ DV+++DP+ T+S+ P ++A T Sbjct: 136 PLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDPETTLSMDPFLSACT 195 Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252 GIDAL HA+EA+VS P +D A+ A+RLI+ +L + +AN +D R + GS AG Sbjct: 196 GIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPTDIALREKIMLGSMQAG 255 Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312 LAF NA + VHA+++ LGG + HG NAVL+ +V+ + S +R I G + Sbjct: 256 LAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAETFGIDC 315 Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372 L+ + R VE L +G +TLG G+ S + L++ A+ +L +P Sbjct: 316 RGLNHRQICGRLVEHLIALKHAIGFHETLGLHGVRTSDIPFLSQHAMHDPCILT-NPRES 374 Query: 373 LEADIRAIYEAA 384 + D+ +Y A Sbjct: 375 SQRDVEVVYGEA 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: 396 Number of extensions: 17 Number of successful extensions: 3 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: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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