Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_004308554.1 C665_RS10585 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::Q8H0L8 (359 letters) >NCBI__GCF_000310185.1:WP_004308554.1 Length = 353 Score = 313 bits (801), Expect = 6e-90 Identities = 162/331 (48%), Positives = 217/331 (65%), Gaps = 6/331 (1%) Query: 25 LSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGHEVVGVVIEVGSK 84 L +RR G VQ ++ +CG+CHSDLHQ+++EW T YP VPGHE+VG V VG+ Sbjct: 15 LEAMEITRRAPGAHDVQIEIAFCGVCHSDLHQVRSEWPGTLYPCVPGHEIVGRVSAVGAH 74 Query: 85 VEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPRQIPTYNGYSLDGT-LTFGGYSDMMV 143 V+ FK G+ VGVGC+V SC+ CE+C LENYC + TYN D T GGYS +V Sbjct: 75 VKGFKTGELVGVGCIVDSCQHCEDCDAGLENYCDGMVGTYNSPIADAPGHTLGGYSQRIV 134 Query: 144 SDEHFV--VRWPENLSMDAAPLLCAGITTYSPLKYFGLDKPGMHIGVVGLGGLGHMAVKF 201 E +V +R PE APLLCAGITT+SPL+++ + PG +G+VG+GGLGHM VK Sbjct: 135 VHERYVLRIRHPEAQLAAVAPLLCAGITTWSPLRHWKVG-PGQKVGIVGIGGLGHMGVKL 193 Query: 202 AKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDGIIDTVSAVHPIL 261 A A G V ++S +K+ A+ LGAD ++SRD MKA +LD I++TV+A H + Sbjct: 194 AHALGAHVVAFTSSESKRAAAL-ALGADEVVVSRDEGAMKARRKSLDFILNTVAAPHDLD 252 Query: 262 PLLMLMKSHGKLVMVGAPEKPVELP-VFPLLMGRKLVAGSCIGGMKETQEMLDFAAKHNI 320 L L+K G + +VGAP P P VF L+M R+ +AGS IGG+ ETQEMLDF A+H I Sbjct: 253 ACLALLKRDGTMSLVGAPASPHPSPQVFHLIMKRRKLAGSMIGGIPETQEMLDFCAEHGI 312 Query: 321 TPDIEVVPMDYVNTALERLLKSDVKYRFVLD 351 DIE++ + ++ A ER+L+ DVKYRFV+D Sbjct: 313 VADIEMIRAEQIDAAYERMLRGDVKYRFVID 343 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: 342 Number of extensions: 17 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: 353 Length adjustment: 29 Effective length of query: 330 Effective length of database: 324 Effective search space: 106920 Effective search space used: 106920 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