Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate 350063 BT0535 iron-containing alcohol dehydrogenase (NCBI ptt file)
Query= BRENDA::U6CL97 (387 letters) >FitnessBrowser__Btheta:350063 Length = 381 Score = 374 bits (959), Expect = e-108 Identities = 194/386 (50%), Positives = 258/386 (66%), Gaps = 6/386 (1%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 M NF P K++ G G IA L KEIP+D RI+IT+GGGSVK NGV DQV AL+ Sbjct: 1 MENFIFQNPVKLIMGHGMIARLSKEIPSDKRIMITFGGGSVKKNGVYDQVKEALKDHFTI 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDPWHIL 120 EF GIEPNP ETL KA+ + + +K+D+LLAVGGGSV+DGTK I+A Y D W ++ Sbjct: 61 EFWGIEPNPAIETLRKAIALGKEQKVDYLLAVGGGSVIDGTKLISAGLLYDG--DAWDLV 118 Query: 121 QTGGAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPVVT 180 G + + V L+ VLTLPATGSE NNGAVI+R T +K F S PLF++LDP VT Sbjct: 119 -LAGRPVTKTVPLSTVLTLPATGSEMNNGAVISRHETKEKYPFYSNF--PLFSILDPEVT 175 Query: 181 YTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENYKV 240 +TLP Q+A G+ D FVH +EQY+T + ++V DR+AEG+L TLVE P+ +Y++ Sbjct: 176 FTLPPHQVACGLADTFVHVMEQYMTVAGQSRVMDRWAEGILQTLVEIAPKIRENQHDYQL 235 Query: 241 RANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKSQK 300 A+ M SATMALNG I GV QDW+THM+GHE+TALHGL H TL I+LPA L + K Sbjct: 236 MADFMLSATMALNGFIAMGVSQDWATHMIGHEITALHGLTHGHTLVIILPATLRVLREAK 295 Query: 301 RDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDYQLDGSSIPTLVAKL 360 DKL+QY ERVW + G++++RID AI T +FF +G+ TRL + + ++ + + Sbjct: 296 GDKLVQYGERVWGITSGTKEERIDEAIDRTEEFFRSLGLTTRLHEENIGEETVLEIERRF 355 Query: 361 SEHGLTALGEHRDITLEESQKIYEAA 386 +E G GE+ ++T ++KI EAA Sbjct: 356 NERG-AKYGENENVTGAVARKILEAA 380 Lambda K H 0.317 0.134 0.383 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: 423 Number of extensions: 21 Number of successful extensions: 3 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: 387 Length of database: 381 Length adjustment: 30 Effective length of query: 357 Effective length of database: 351 Effective search space: 125307 Effective search space used: 125307 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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