Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF658 Psest_0672 Alcohol dehydrogenase, class IV
Query= BRENDA::P0DJA2 (383 letters) >FitnessBrowser__psRCH2:GFF658 Length = 382 Score = 515 bits (1326), Expect = e-151 Identities = 257/380 (67%), Positives = 306/380 (80%) Query: 3 SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62 SSTF+IP VN MG GSL++A+ + GF+ ALIV+D + ++GV ++VA LL A I S Sbjct: 2 SSTFFIPAVNMMGIGSLDEAMVAIANYGFRKALIVTDVGLARAGVAEKVATLLAAADIQS 61 Query: 63 AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122 V+DG PNPTV V +GL L+++ DF+ISLGGGSPHDCAK IAL ATNGG + DYEG Sbjct: 62 VVFDGAQPNPTVGNVEKGLSQLRESACDFIISLGGGSPHDCAKGIALCATNGGHIADYEG 121 Query: 123 IDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVG 182 +D+S KP LPL++INTTAGTASEMTRFCIITDE RHVKMAIVDR+VTP++SVNDP LMV Sbjct: 122 VDRSAKPQLPLVAINTTAGTASEMTRFCIITDESRHVKMAIVDRNVTPLLSVNDPALMVA 181 Query: 183 MPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREA 242 MPKGLTAATGMDALTHA EAY STAATPITDACALKA +I+ NL+TA +G DMPAREA Sbjct: 182 MPKGLTAATGMDALTHAVEAYVSTAATPITDACALKAIELISANLRTAVASGSDMPAREA 241 Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302 MAYAQFLAGMAFNNASLGYVHAMAHQLGG+Y+LPHGVCNAVLLPHV +YNASV RL+D Sbjct: 242 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAVLLPHVESYNASVCPERLRD 301 Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362 + AMG++ L +GAEA + A+R L+ IGIP L ELGAK +D+P LA +A+ DAC Sbjct: 302 IATAMGVETRGLDATQGAEAALAAIRTLSQDIGIPGGLAELGAKADDIPTLAANAMNDAC 361 Query: 363 ALTNPRQGDQKEVEELFLSA 382 LTNPR+ Q+E+E +F SA Sbjct: 362 GLTNPRRATQEEIEAIFHSA 381 Lambda K H 0.316 0.132 0.373 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: 508 Number of extensions: 15 Number of successful extensions: 1 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: 383 Length of database: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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 (21.6 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