Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate Ga0059261_2135 Ga0059261_2135 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q8H0L8 (359 letters) >FitnessBrowser__Korea:Ga0059261_2135 Length = 355 Score = 297 bits (761), Expect = 3e-85 Identities = 161/351 (45%), Positives = 216/351 (61%), Gaps = 8/351 (2%) Query: 10 PIKAFGWATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMV 69 P A +A + + L+PF+F RR V +++CG+CHSDLHQ ++EW T +P V Sbjct: 2 PSPAKAYAAQSATTPLAPFSFERRDVQPDDVAIDILFCGVCHSDLHQARSEWEGTLFPCV 61 Query: 70 PGHEVVGVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPRQ--IPTYNGY 127 PGHE+VG V +GS V F VGD VGVGCMV SC C +C E YC + TYNG Sbjct: 62 PGHEIVGRVTAIGSDVTTFAVGDLVGVGCMVDSCGTCPSCHEGEEQYCEGTGFVGTYNGP 121 Query: 128 SLD-GTLTFGGYSDMMVSDEHFVVR--WPENLSMDAAPLLCAGITTYSPLKYFGLDKPGM 184 G TFGGYSD +V + FV+R E APLLCAGITTYSPLK++G PG Sbjct: 122 DAHLGGHTFGGYSDTIVVKQGFVLRIGHDEQDLAAVAPLLCAGITTYSPLKHWGAG-PGK 180 Query: 185 HIGVVGLGGLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAM 244 +GVVG+GGLGHM VK A A G V +TS K+ +A+ LGA ++SR+ ++M A Sbjct: 181 KVGVVGIGGLGHMGVKIAAAMGAHVVAFTTSEGKRADAL-ALGAHEVVVSRNADEMAAHA 239 Query: 245 NTLDGIIDTVSAVHPILPLLMLMKSHGKLVMVGAPEKPVELP-VFPLLMGRKLVAGSCIG 303 + D I++TV+A H + L+K G + +VG PE P V L+ R+ +AGS IG Sbjct: 240 GSFDFILNTVAASHDLDAFTNLLKRDGTMTLVGVPEHAHPSPSVLNLVFRRRSIAGSLIG 299 Query: 304 GMKETQEMLDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDIGN 354 G+ ETQEMLDF H IT DIE + + ++ + +R++K DVKYRFV+D+ + Sbjct: 300 GIAETQEMLDFCRDHGITADIETIAIQDIDASFDRMVKGDVKYRFVIDMAS 350 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: 310 Number of extensions: 19 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 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