Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_089216565.1 CHB69_RS13635 Zn-dependent alcohol dehydrogenase
Query= BRENDA::P00326 (375 letters) >NCBI__GCF_900188185.1:WP_089216565.1 Length = 363 Score = 261 bits (667), Expect = 2e-74 Identities = 149/367 (40%), Positives = 207/367 (56%), Gaps = 10/367 (2%) Query: 11 KAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVAAGICRSDEHVVSGNLVTPLPVILGHEA 70 KAAVL E KP +EEV V P HEVRI+ A G+C SD H + G PLP I GHEA Sbjct: 3 KAAVLIEPGKPLIVEEVVVDKPGPHEVRIRTAACGLCHSDLHFIDGAYPHPLPAIPGHEA 62 Query: 71 AGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRICKNPESNYCLKNDLGNPRGTLQDGTRR 130 AGIVE+VG V TVKPGD V+ + CG C C + C+ D G TR Sbjct: 63 AGIVEAVGSEVRTVKPGDAVVTCLSAFCGHCEFCVTGRMSLCMGGDTRRAPGEPPRITRP 122 Query: 131 FTCSGKPIHHFVGVSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKV 190 G ++ + +S FS+ +V E+A ID PL++ +IGC +TG G+ K+ Sbjct: 123 ---DGSVVNQMLNLSAFSEVMLVHEHACVAIDPDMPLDRAAVIGCAVTTGAGTIFNACKL 179 Query: 191 TPGSTCAVFGLGGVGLSVVMGCKAAGAARIIAVDINKDKFAKAKELGATECIN--PQDYK 248 TPG T AV G GGVGL+ + K AGA RIIA D +K A A++LGAT+ ++ D Sbjct: 180 TPGETVAVVGCGGVGLATINAAKIAGAGRIIAADPVPEKRALAEKLGATDTVDALADDAA 239 Query: 249 KPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPDSQNLSINPML 308 K I EMT GGVD + E +GR + ++ GT+ I+G+ P ++ + + M Sbjct: 240 KQI----VEMTRGGVDHAIEAVGRPASASLAVASLRRG-GTATILGMMPLAEKVGLGAMD 294 Query: 309 LLTGRTWKGAIFGGFKSKESVPKLVADFMAKKFSLDALITNILPFEKINEGFDLLRSGKS 368 LL+G+ +GAI GG + +P+LV ++ LD+++ +P EKINEGFD ++ G S Sbjct: 295 LLSGKKLQGAIMGGNRFPVDIPRLVDFYLRGLLDLDSIVAETIPLEKINEGFDKMKKGDS 354 Query: 369 IRTVLTF 375 R+V+ F Sbjct: 355 ARSVIVF 361 Lambda K H 0.320 0.137 0.412 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: 376 Number of extensions: 20 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: 375 Length of database: 363 Length adjustment: 30 Effective length of query: 345 Effective length of database: 333 Effective search space: 114885 Effective search space used: 114885 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