Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate CA265_RS12755 CA265_RS12755 hydroxyacid dehydrogenase
Query= BRENDA::Q8H0L8 (359 letters) >FitnessBrowser__Pedo557:CA265_RS12755 Length = 347 Score = 357 bits (917), Expect = e-103 Identities = 184/341 (53%), Positives = 243/341 (71%), Gaps = 5/341 (1%) Query: 15 GWATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGHEV 74 G+A ++ L+P+NF RR G VQF++++CG+CHSDLHQ+KN+W +PMVPGHE+ Sbjct: 6 GYAAQNAETDLAPWNFERREVGPHDVQFEILFCGVCHSDLHQIKNDWFPGIFPMVPGHEI 65 Query: 75 VGVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYC-PRQIPTYNGYSLDG-T 132 VG V++VG V+KFKVGD G GCMV SC+ CENC +LE YC TYNG DG T Sbjct: 66 VGRVVKVGDHVKKFKVGDLAGTGCMVDSCQVCENCKQNLEQYCLEGNTQTYNGLERDGKT 125 Query: 133 LTFGGYSDMMVSDEHFVVRWPENLSMDA-APLLCAGITTYSPLKYFGLDKPGMHIGVVGL 191 T+GGYSD +V E FV+ + L++ A APLLCAGITTYSPLK++ + K G + V+GL Sbjct: 126 PTYGGYSDSIVVREEFVLHVSDKLNLAAVAPLLCAGITTYSPLKHWKVGK-GHKLAVLGL 184 Query: 192 GGLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDGII 251 GGLGHMAVKF AFG +VTV+STS KK+E ++LGA F+++ DP Q+KAA T D I+ Sbjct: 185 GGLGHMAVKFGVAFGAEVTVLSTSP-KKEEDAKKLGAHHFVVTTDPAQVKAARGTFDFIL 243 Query: 252 DTVSAVHPILPLLMLMKSHGKLVMVGAPEKPVELPVFPLLMGRKLVAGSCIGGMKETQEM 311 DTVSA H L L++++G + VG P KP E+ F LL GRK +AGS IGG+ ETQEM Sbjct: 244 DTVSAEHDFNMYLSLLRTNGIHICVGVPPKPAEIAAFSLLGGRKSLAGSGIGGIAETQEM 303 Query: 312 LDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDI 352 LDF A++NI DIE++ + ++ A ER+ K DV+YRFV+D+ Sbjct: 304 LDFCAENNIVSDIEMIDIKDIHHAYERMEKGDVRYRFVIDM 344 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: 348 Number of extensions: 15 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: 347 Length adjustment: 29 Effective length of query: 330 Effective length of database: 318 Effective search space: 104940 Effective search space used: 104940 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