Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_010960842.1 MCA_RS07740 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q8H0L8 (359 letters) >NCBI__GCF_000008325.1:WP_010960842.1 Length = 355 Score = 340 bits (871), Expect = 4e-98 Identities = 178/348 (51%), Positives = 233/348 (66%), Gaps = 6/348 (1%) Query: 13 AFGWATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGH 72 A +A L+PF RR + ++ ++YCG+CHSDLHQ +NEW T YP VPGH Sbjct: 4 AKAYAAFSADSALAPFVLQRRDPLPQDIRIGILYCGVCHSDLHQARNEWNATTYPCVPGH 63 Query: 73 EVVGVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPR-QIPTYNGYSLDG 131 E+VG V+EVG V KFK GD V VGCMV SCR C NC LE +C + TYN G Sbjct: 64 EIVGKVLEVGRSVTKFKPGDTVAVGCMVDSCRTCPNCVDALEQHCEHGPVFTYNSPDPHG 123 Query: 132 T-LTFGGYSDMMVSDEHFVVRWPENLSMDAA-PLLCAGITTYSPLKYFGLDKPGMHIGVV 189 +TFGGY++ +V DE FV+R P+ L + AA PLLCAGITTYSPL+++ + G +GVV Sbjct: 124 GGMTFGGYAESIVVDEAFVLRIPDGLDLAAAAPLLCAGITTYSPLRHWKVGA-GQRVGVV 182 Query: 190 GLGGLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDG 249 GLGGLGHMA+KFA FG + + +T+ +K ++A RLGAD ++SRDPE M D Sbjct: 183 GLGGLGHMALKFAHTFGAETVLFTTTPDKAEDA-RRLGADEVVVSRDPEAMARQAGRFDF 241 Query: 250 IIDTVSAVHPILPLLMLMKSHGKLVMVGAPEKPVELPVFPLLMGRKLVAGSCIGGMKETQ 309 I+DTVSA H I L L++ G L +VG P + V++ F L+ GR+ +AGS IGG++ETQ Sbjct: 242 ILDTVSAPHDIDAYLNLLRRDGTLTLVGVPPQGVQVMPFSLIGGRRRLAGSLIGGIRETQ 301 Query: 310 EMLDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDIGNTLN 357 EMLDF +H I DIE++P+ +N A ER+LKSDVKYRFV+D+ TLN Sbjct: 302 EMLDFCGEHGIVCDIELIPIQGINDAFERMLKSDVKYRFVIDMA-TLN 348 Lambda K H 0.320 0.137 0.417 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: 370 Number of extensions: 12 Number of successful extensions: 5 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: 359 Length of database: 355 Length adjustment: 29 Effective length of query: 330 Effective length of database: 326 Effective search space: 107580 Effective search space used: 107580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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