Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate PP_0552 PP_0552 2,3-butanediol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Putida:PP_0552 Length = 362 Score = 197 bits (502), Expect = 3e-55 Identities = 121/361 (33%), Positives = 187/361 (51%), Gaps = 15/361 (4%) Query: 1 MTHTVPQNMKAAVMHNTREIKIETLPVP-DINHDEVLIKVMAVGICGSDLHYYTNGRIGN 59 ++HT +M+AAV H +I++E +P+P D V IKV GICGSDLH Y G + Sbjct: 4 LSHT---HMRAAVWHGRHDIRVEQVPLPADPAPGWVQIKVDWCGICGSDLHEYVAGPVFI 60 Query: 60 YV--------VEKPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRY 111 V ++ ILGHE G IA +G V+ + VGD VA + CG C C G Y Sbjct: 61 PVEAPHPLTGIQGQCILGHEFCGHIAKLGEGVEGYAVGDPVAADACQHCGTCYYCTHGLY 120 Query: 112 NLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQ 171 N+C + F +GAF + + + + ++ +P E ALIEP +VG+HA + Sbjct: 121 NICERLAFTGLMN-NGAFAELVNVPANLLYRLPQGFPAEAGALIEPLAVGMHAVKKAGSL 179 Query: 172 PGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALE 231 G T+ ++G G +GL + AKA GA +I ++ R AK+ GA +++ + DAL Sbjct: 180 LGQTVVVVGAGTIGLCTIMCAKAAGAAQVIALEMSSARKAKAKEAGANVVLDPSQCDALA 239 Query: 232 EIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEI 291 EI+ +T G DV++E GN + A+ ++R+ GK +VG+ + N + E Sbjct: 240 EIRALTAGLGADVSFECIGNKHTAKLAIDTIRKAGKCVLVGI-FEEPSEFNFFELVSTEK 298 Query: 292 DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQD-AMERALQFKNECLKVMVY 350 + G Y + I F+A G +D + LVT + LEQ + E + K E +K++V Sbjct: 299 QVLGALAYNGEFADVIAFIADGRLDIRPLVTGRIGLEQIVELGFEELVNNKEENVKIIVS 358 Query: 351 P 351 P Sbjct: 359 P 359 Lambda K H 0.320 0.137 0.401 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: 323 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: 353 Length of database: 362 Length adjustment: 29 Effective length of query: 324 Effective length of database: 333 Effective search space: 107892 Effective search space used: 107892 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