Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate HSERO_RS05485 HSERO_RS05485 phosphoesterase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__HerbieS:HSERO_RS05485 Length = 345 Score = 213 bits (543), Expect = 5e-60 Identities = 119/330 (36%), Positives = 185/330 (56%), Gaps = 9/330 (2%) Query: 13 VMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHEC 72 V+H +++I+ L + ++ +KV A GICGSDLHYY +G G +++P +LGHE Sbjct: 6 VIHAPHDLRIQALDTGALQPQQLKVKVKAGGICGSDLHYYHHGGFGVVRIKEPMVLGHEV 65 Query: 73 AGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQF----LATPPVDGA 128 +G+IA VG++V G R+A+ P CG C+ C+EG+ N C D++F + TP V GA Sbjct: 66 SGQIAEVGTAVTDIAPGTRIAISPSRPCGACKYCQEGKQNHCLDMRFYGSAMRTPHVQGA 125 Query: 129 FVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMA 188 F Q I + + ++ D +S EAA+ EP SV +HA R G + + G GP+G + Sbjct: 126 FRQEIIIERSQAHVVADHVSDGEAAMAEPLSVALHAVRRAGPLVGKRVLVTGCGPIGALV 185 Query: 189 VAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGV-DVAWE 247 V AA+ GA ++VTD+ + L+AA ++GA IN+ E A +K D+G DV +E Sbjct: 186 VVAARRAGALEVVVTDVASMPLQAALQVGADSAINMAETPA--ALKAYAADKGTFDVLFE 243 Query: 248 TAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYANTYPKGI 307 +GN AL AL ++R + VGL + P N+ + E++ G FR+ + + Sbjct: 244 ASGNERALVGALEALRPQAIIVQVGLGGDIQFPANL--LVGKELEWRGAFRFHEEFAMAV 301 Query: 308 EFLASGIVDTKHLVTDQYSLEQTQDAMERA 337 E + +VD K L+T Y + Q +A E A Sbjct: 302 ELMNRKLVDVKPLITATYPIAQAVEAFEIA 331 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: 263 Number of extensions: 13 Number of successful extensions: 4 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: 345 Length adjustment: 29 Effective length of query: 324 Effective length of database: 316 Effective search space: 102384 Effective search space used: 102384 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