Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 207887 DVU2396 alcohol dehydrogenase
Query= BRENDA::P0DJA2 (383 letters) >MicrobesOnline__882:207887 Length = 380 Score = 245 bits (626), Expect = 1e-69 Identities = 138/370 (37%), Positives = 218/370 (58%), Gaps = 5/370 (1%) Query: 1 MASSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGI 60 M + F IP + G GSL G L+VSD + SG V++V D+L+A G+ Sbjct: 1 MRITKFAIPEII-FGNGSLNHLAPCARRLGAARVLLVSDKGLEASGWVERVVDILEADGL 59 Query: 61 NSAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDY 120 ++ NP V G ++ ++ +D VI+LGGGSP D AK I + NGG + DY Sbjct: 60 EWVYFNDCNSNPRDHQVHHGARVYQEERADVVIALGGGSPMDTAKGIGTIVGNGGRINDY 119 Query: 121 EGIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLM 180 EG ++ +P P++ + TTAG+ S++++FCIITD R +KM+I+ R + P VS+ DP ++ Sbjct: 120 EGANRIMRPLPPMIFLPTTAGSGSDISQFCIITDVERRLKMSIISRSLVPNVSIIDPQVL 179 Query: 181 VGMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAR 240 + M + L A+ +DA HA E+Y S A+P TD AL+A +I NL A + +D A Sbjct: 180 MTMSEELVIASAIDAFAHAVESYLSRLASPFTDHQALRAMELIMDNLMPAVER-RDPAAL 238 Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRL 300 E ++ A AGM+F+NA LG H++AH LGG +++ HG+ + VLLPHV+ +N V +L Sbjct: 239 ERLSIASTEAGMSFSNAGLGIGHSLAHSLGGMFDVMHGLVHPVLLPHVMRFNLPVSVEKL 298 Query: 301 KDVG-VAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALK 359 +G + +G +A+ + A A I+ + + +++G+P L +L + + +A AL Sbjct: 299 AAIGRIVVGPRVASA--ECIARAGIERLHEFFSALGVPVRLGQLLPDRGVLETIARTALN 356 Query: 360 DACALTNPRQ 369 DAC +TNPR+ Sbjct: 357 DACTVTNPRE 366 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: 334 Number of extensions: 14 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: 380 Length adjustment: 30 Effective length of query: 353 Effective length of database: 350 Effective search space: 123550 Effective search space used: 123550 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