Align alcohol dehydrogenase (EC 1.1.1.1); aryl-alcohol dehydrogenase (EC 1.1.1.90); aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) (characterized)
to candidate WP_019388773.1 P735_RS0114520 NAD(P)-dependent alcohol dehydrogenase
Query= BRENDA::W6CX26 (339 letters) >NCBI__GCF_000283015.1:WP_019388773.1 Length = 334 Score = 366 bits (940), Expect = e-106 Identities = 164/333 (49%), Positives = 233/333 (69%), Gaps = 2/333 (0%) Query: 4 IKSYAAKEAGSELELYEYDAGELRPEDVEVQVDYCGICHSDLSMIDNEWGFSQYPLVAGH 63 + YAA E ++L + Y+ GE+ E+V+++V YCGICHSDLSMI+N+WG +QYP+V GH Sbjct: 3 VNGYAALEQKAKLVPFSYELGEIGSEEVDIKVSYCGICHSDLSMINNDWGMTQYPMVPGH 62 Query: 64 EVIGRVAALGSAAQEKGVKVGQRVGVGWTARSCGHCDACISGNQINCLEGAVATILNRGG 123 E+IG V A G+A K + VG +VG+GW + SC CD C+ G C + + GG Sbjct: 63 EIIGEVIAKGNAV--KNISVGDKVGLGWMSASCMSCDQCMDGEHHLCAKSEATIVGRNGG 120 Query: 124 FAEKLRADWQWVIPLPESIDIESAGPLLCGGITVFKPLLMHHITATSRVGVIGIGGLGHI 183 FA+K+R W W IPLP+ ID+ AGPLLCGGITVF P+++ + T RVGVIGIGGLGH+ Sbjct: 121 FADKVRGHWSWAIPLPKGIDMSKAGPLLCGGITVFNPIILAGVKPTDRVGVIGIGGLGHM 180 Query: 184 AIKLLHAMGCEVTAFSSNPSKEQEVLAMGADKVVNSRDPDALNALAGQFDLIINTVNVDL 243 A+K L GCEV AFSSNP+K++ +L MGA +V++S P+ L +++G+ + I+NT NV L Sbjct: 181 AVKFLKHWGCEVIAFSSNPAKKKSILKMGASQVIDSTSPEELESISGKLNFILNTTNVSL 240 Query: 244 DWQPYFEALAYGGHFHTVGAVMKPLPVPAFTLIAGDRSISGSATGTPYELRKLMKFAGRS 303 DW Y LA G FHTVGAV++P+ + AF+LI G++S+ GS G+P + ++ F R Sbjct: 241 DWNSYLATLAPKGKFHTVGAVLEPMEISAFSLIMGEKSVGGSPIGSPALTKTMLDFCVRH 300 Query: 304 KVSPTTELFPMSQINEAIQHVRDGKARYRVVLQ 336 + P E FPM+++NEA++H+ GKAR+R+VL+ Sbjct: 301 NIYPDVEEFPMAKVNEALEHLEKGKARFRIVLK 333 Lambda K H 0.320 0.137 0.415 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: 312 Number of extensions: 12 Number of successful extensions: 2 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: 339 Length of database: 334 Length adjustment: 28 Effective length of query: 311 Effective length of database: 306 Effective search space: 95166 Effective search space used: 95166 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