Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate PP_2492 PP_2492 alcohol dehydrogenase, NAD(P)-dependent
Query= BRENDA::U6CL97 (387 letters) >FitnessBrowser__Putida:PP_2492 Length = 385 Score = 488 bits (1255), Expect = e-142 Identities = 240/386 (62%), Positives = 294/386 (76%), Gaps = 2/386 (0%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 MLNF H PT+I+FG IA L + IP +ARIL+ YGG S + +G L +V AL R V+ Sbjct: 1 MLNFDFHNPTRIIFGNQTIARLDELIPTEARILLLYGGQSARASGTLHEVREALGFREVQ 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDPWHIL 120 EF GIEPNP+YETL++AV+ VR ++DFLLAVGGGSV+DGTKF++AA Y D W IL Sbjct: 61 EFGGIEPNPSYETLIRAVDTVRIHRLDFLLAVGGGSVIDGTKFVSAAVGYDG--DAWDIL 118 Query: 121 QTGGAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPVVT 180 +T GA I + + VLTLPATGSE NNG V+TR++T DKL FRSPH P F++LDP T Sbjct: 119 ETRGASIRQALPFGTVLTLPATGSEMNNGGVVTRRATQDKLPFRSPHVFPQFSILDPTKT 178 Query: 181 YTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENYKV 240 TLP RQ+ANGVVDAFVH +EQYLTY +DA+VQDRFAEGLL TL+E GP L E +Y Sbjct: 179 QTLPTRQLANGVVDAFVHVMEQYLTYPIDARVQDRFAEGLLQTLIEIGPLMLEESADYST 238 Query: 241 RANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKSQK 300 RAN+MW+AT+ALNGLIGAGVPQDWSTHM+GHELTA HG+DHA+TLAIVLPA L R+ K Sbjct: 239 RANLMWTATLALNGLIGAGVPQDWSTHMIGHELTAQHGIDHARTLAIVLPANLEVRREAK 298 Query: 301 RDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDYQLDGSSIPTLVAKL 360 R KLLQYAERVW++ G E+QRID AI TR FE +G+PTRLS YQL I L+ +L Sbjct: 299 RAKLLQYAERVWHISQGDEEQRIDAAIQQTRTLFESLGLPTRLSAYQLGADVIDALINQL 358 Query: 361 SEHGLTALGEHRDITLEESQKIYEAA 386 + H LTALGEH D++L+ S+++ EA+ Sbjct: 359 AAHRLTALGEHADVSLDVSRRVLEAS 384 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: 469 Number of extensions: 16 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: 387 Length of database: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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