Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF1358 PS417_06905 alcohol dehydrogenase
Query= BRENDA::P0DJA2 (383 letters) >FitnessBrowser__WCS417:GFF1358 Length = 382 Score = 517 bits (1332), Expect = e-151 Identities = 256/381 (67%), Positives = 307/381 (80%) Query: 3 SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62 SSTF+IP VN MG L++A+ + GF+ ALIV+DA + K+GV +A+ L Q I+S Sbjct: 2 SSTFFIPAVNIMGTDCLDEAMIAIRNYGFRKALIVTDAGLAKAGVASMIAEKLAMQDIDS 61 Query: 63 AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122 +YDG PNP V V +GL +L+++ DFV+SLGGGSPHDCAK IAL ATNGG + DYEG Sbjct: 62 VIYDGAKPNPNVENVEKGLTLLQESACDFVVSLGGGSPHDCAKGIALCATNGGHIGDYEG 121 Query: 123 IDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVG 182 +D+S KP LPL++INTTAGTASEMTRFCIITDE RHVKMAIVDR+VTP++SVNDP LMVG Sbjct: 122 VDQSSKPQLPLVAINTTAGTASEMTRFCIITDETRHVKMAIVDRNVTPLLSVNDPSLMVG 181 Query: 183 MPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREA 242 MPKGLTAATGMDALTHA EAY STAA PITDACA+KA +I+ NL+ A +G D ARE Sbjct: 182 MPKGLTAATGMDALTHAIEAYVSTAANPITDACAIKAIELISANLRLAVRDGSDKAAREN 241 Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302 MAYAQFLAGMAFNNASLG+VHAMAHQLGG+Y+LPHGVCNAVLLPHV ++NASV A RL D Sbjct: 242 MAYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNASVSAKRLSD 301 Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362 VG A+G D+ D+EGA+A I A+R LA + IPA L ELGAK +D+PLLA +ALKDAC Sbjct: 302 VGRALGADVKGFSDEEGAQAAIAAIRSLAHDVEIPAGLRELGAKLQDIPLLATNALKDAC 361 Query: 363 ALTNPRQGDQKEVEELFLSAF 383 LTNPR+ DQ+++EE+F SAF Sbjct: 362 GLTNPRRADQRQIEEIFRSAF 382 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: 517 Number of extensions: 18 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