Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate BPHYT_RS21770 BPHYT_RS21770 aldehyde dehydrogenase
Query= BRENDA::A0A0H3W5U9 (873 letters) >FitnessBrowser__BFirm:BPHYT_RS21770 Length = 481 Score = 236 bits (603), Expect = 2e-66 Identities = 149/434 (34%), Positives = 226/434 (52%), Gaps = 9/434 (2%) Query: 23 RLREAQSVYATYTQEQVDKIFFEAAMAANK--MRIPLAKMAVEETGMGVVEDKVIKNHYA 80 + R AQ + Q+ +D AA A + LA+ AV +TG+G +DK KN+ Sbjct: 29 KARAAQRAFEQAGQQALDTAADAAAWAIMEPERNRQLAERAVHDTGLGNADDKFRKNYRK 88 Query: 81 SEYIYNAYKNTKTCGVIEEDPAFGIKKIAEPLGVIAAVIPTTNPTSTAIFKTLIALKTRN 140 + + KT GVI ED A G+ +IA +GV+AA+ P+TNP +T K + ALK N Sbjct: 89 TLGLLRDLHEQKTTGVIAEDKASGLVEIARAVGVVAAITPSTNPAATPANKIINALKCGN 148 Query: 141 AIIISPHPRAKNSTIEAAKIVLEAAVKAGAPEGIIGWIDVP-SLELTNLVMREADVILAT 199 A+I++P P+ +S + + KAG ++ + P S T +MR+ D+++AT Sbjct: 149 AVIVAPSPKGYSSCALLIEFIHAQFAKAGIDPDLVQMLPAPISKAATAALMRQCDLVVAT 208 Query: 200 GGPGLVKAAYSSGKPAIGVGAGNTPAIIDDSADIVLAVNSIIHSKTFDNGMICASEQSVI 259 G V+ AY+SG PA GVGAGN +I+ SAD+ A I+ SKTFDN C+SE S++ Sbjct: 209 GSQANVRMAYASGTPAFGVGAGNVASIVTASADLHDAARKILRSKTFDNATSCSSENSIV 268 Query: 260 VLDGVYKEVKKEFEKRGCYFLNEDETEKVRKTIIINGALNAKIVGQKAHTIANLAGFE-- 317 + + VY+ + E G L+ + K++ + +NG L+ + + A IA +AG E Sbjct: 269 IEEAVYQPMLAELTSCGGVLLDAAQKAKLQTAMWVNGKLSEQCTAKSAEVIARVAGLEEV 328 Query: 318 VPETTKILIGEVTSVDISEEFAHEKLCPVLAMYRAKDFDDALDKAERLVADGGFGHTSSL 377 L+ E + F+ EKL PVL +YRA FD A + + A G GH+ L Sbjct: 329 AARHPAFLMVEESGAGSDYPFSGEKLAPVLTVYRAAGFDAAAEVVRSIYAYMGAGHSVGL 388 Query: 378 YIDTVTQKEKLQKFSERMKTCRILVNTPSSQGGIGDLYNFKLAPSLTLGCGSWGGNSVSD 437 + Q +L + R++VN G+ N L SL++GCG+WG N+ S Sbjct: 389 HSSDAAQAVQL---GVTLPVARVIVNQAHCLATGGNFDN-GLPFSLSMGCGTWGRNNFSG 444 Query: 438 NVGVKHLLNIKTVA 451 N+G +H LN VA Sbjct: 445 NLGFRHYLNTTRVA 458 Lambda K H 0.318 0.134 0.382 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: 885 Number of extensions: 42 Number of successful extensions: 4 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: 873 Length of database: 481 Length adjustment: 38 Effective length of query: 835 Effective length of database: 443 Effective search space: 369905 Effective search space used: 369905 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: 54 (25.4 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