Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 208394 DVU2885 alcohol dehydrogenase, iron-containing
Query= BRENDA::P0DJA2 (383 letters) >MicrobesOnline__882:208394 Length = 397 Score = 188 bits (477), Expect = 3e-52 Identities = 129/392 (32%), Positives = 201/392 (51%), Gaps = 11/392 (2%) Query: 1 MASSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIV-SDAFMNKSGVVKQVADLLKAQG 59 M TF++P G G LE+ + L G K ++V + M + G + +V LL+ G Sbjct: 1 MLDFTFHVPTRIVFGAGRLEE-LGRLPLPGVKPLVVVGAGGSMRRHGHLDRVLALLRQNG 59 Query: 60 INSAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKD 119 +++ V PNP++ V EG + + N DF++ LGGGSP D AKAIAL A NGG D Sbjct: 60 CEPMLFERVRPNPSLVHVDEGACVARANGCDFIVGLGGGSPIDAAKAIALAAANGGSYWD 119 Query: 120 Y-----EGIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSV 174 Y G + PALP+++I TTAGT +E + ++T + K+ + P++S+ Sbjct: 120 YIQSGTGGRRTPQHPALPVVAIPTTAGTGTEADPWTVVTRDETQEKIGWGNDSTYPVLSI 179 Query: 175 NDPLLMVGMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNG 234 DP L + +P +TA TGMDA HA EAY S + P +D AL+A S++A+ L A G Sbjct: 180 VDPALTITVPPRITAMTGMDAFFHAVEAYLSLSRQPSSDLLALEAVSLLAQFLPQAVRQG 239 Query: 235 KDMPAREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGYY-NLPHGVCNAVLLPHVLAYNA 293 + R +++A AG+ + +S H+M H L Y+ +LPHG +L A Sbjct: 240 DSVEVRSMVSWASTAAGLCESLSSCIAHHSMEHALSAYHPDLPHGAGLVMLSLPFFEVMA 299 Query: 294 SVVAGRLKDVGVAMGLDIANLGDKEGAEATIQAVRDLAASIGI-PANLTELGAKKEDVPL 352 V R D+ MG+ + L + A ++ +R L ++G+ L + G ++P Sbjct: 300 RVQPKRCADLAATMGMPLHGLPPAQQGMAFVEGLRLLIRAVGLDDLRLADHGITAAEIPA 359 Query: 353 LADHALKDACAL--TNPRQGDQKEVEELFLSA 382 LA +A + AL P ++VE +F A Sbjct: 360 LAKNARETMGALFPLTPVDLRPEDVEAIFAKA 391 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: 380 Number of extensions: 15 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: 383 Length of database: 397 Length adjustment: 30 Effective length of query: 353 Effective length of database: 367 Effective search space: 129551 Effective search space used: 129551 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