Align alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate N515DRAFT_0381 N515DRAFT_0381 uncharacterized zinc-type alcohol dehydrogenase-like protein
Query= BRENDA::Q8H0L8 (359 letters) >FitnessBrowser__Dyella79:N515DRAFT_0381 Length = 353 Score = 322 bits (826), Expect = 7e-93 Identities = 170/345 (49%), Positives = 229/345 (66%), Gaps = 8/345 (2%) Query: 15 GWATRHTSGVLSPFNFSRRVTGEKHVQFKVMYCGICHSDLHQLKNEWGNTKYPMVPGHEV 74 G+A + + L+P F RR V ++YCG+CHSD+HQ +NEW N+ YPMVPGHE+ Sbjct: 7 GYAAQSATTPLAPHRFERRDPRPDDVVIDILYCGVCHSDIHQARNEWHNSIYPMVPGHEI 66 Query: 75 VGVVIEVGSKVEKFKVGDKVGVGCMVGSCRKCENCTVDLENYCPRQIP-TYNGYS-LDGT 132 +G V VG++V KFKVGD VGVGCMV SC+ C C LE YC TYNG DG Sbjct: 67 IGRVSAVGAQVSKFKVGDMVGVGCMVDSCQHCGACHAGLEQYCVEGATWTYNGMDRRDGL 126 Query: 133 LTFGGYSDMMVSDEHFVVRWPENLS-MDAAPLLCAGITTYSPLKYFGLDKPGMHIGVVGL 191 TFGGYS+ +VS + FVV + L AAPLLCAGITT+SPL+++ + + G + +VGL Sbjct: 127 PTFGGYSERIVSSDKFVVSISDKLDPKAAAPLLCAGITTWSPLRHWKIGQ-GSRVAIVGL 185 Query: 192 GGLGHMAVKFAKAFGTKVTVISTSANKKQEAIERLGADSFLISRDPEQMKAAMNTLDGII 251 GGLGHM +KFAKA G VT+ + + +K+ EA RLGAD ++S DP QMKA D I+ Sbjct: 186 GGLGHMGLKFAKAMGADVTLFTRTPDKEAEA-RRLGADHVVLSTDPAQMKAVSRAFDFIL 244 Query: 252 DTVSAVHPILPLLMLMKSHGKLVMVGAPEKPVE--LPVFPLLMGRKLVAGSCIGGMKETQ 309 DTV + H + P L + G L +VG E P+E + +++GR+ +AGS IGG+ ETQ Sbjct: 245 DTVPSPHDLNPYLETLDIDGTLCLVGLLE-PIEPAVAAHNVVLGRRSIAGSGIGGIAETQ 303 Query: 310 EMLDFAAKHNITPDIEVVPMDYVNTALERLLKSDVKYRFVLDIGN 354 EMLD+ A+H I DIE++ + +N A ER+LKSDV+YRFV+D+ + Sbjct: 304 EMLDYCAEHGIVSDIEMIDIQDINKAYERMLKSDVRYRFVIDLAS 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: 358 Number of extensions: 21 Number of successful extensions: 7 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 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