Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_004309492.1 C665_RS11135 L-threonine 3-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_000310185.1:WP_004309492.1 Length = 345 Score = 184 bits (466), Expect = 4e-51 Identities = 113/322 (35%), Positives = 174/322 (54%), Gaps = 8/322 (2%) Query: 20 IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAV 79 + + ++ P++ ++VLIK+ ICG+D+H + + P +GHE G IA + Sbjct: 13 LTLTSVEKPEVGPNDVLIKIKKTAICGTDIHIWKWDEWAQKTIPVPMHVGHEYVGVIAEM 72 Query: 80 GSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDF 139 G V FK+GDRV+ E +TCG C C+ GR +LC + + GAF +Y+ + Sbjct: 73 GQEVRGFKIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNRA-GAFAEYLAIPAVN 131 Query: 140 VFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGT 199 F IPD +S + AA+ +PF H A L G + I G GP+G+MAVA A+ GA Sbjct: 132 AFKIPDDISDDLAAIFDPFGNATHTALSFNLV-GEDVLITGAGPIGIMAVAIARHVGARH 190 Query: 200 IIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKT-ITNDRGVDVAWETAGNPAALQSA 258 +++TD+ RLE A+KMGAT +N+ ++ L ++KT + G DV E +G P+A S Sbjct: 191 VVITDVNDHRLELARKMGATRAVNVSREN-LADVKTELHMVEGFDVGLEMSGVPSAFTSM 249 Query: 259 LASVRRGGKLAIVGLPSQN-EIPLNVPFIADNEI-DIYGIFRYANTYPKGIEFLASGIVD 316 L + GGK+A++G+P N I N EI IYG + T+ K + L SG+ D Sbjct: 250 LEHMNHGGKIALLGIPPSNTAIDWNQVIFKGLEIKGIYGREMF-ETWYKMVAMLQSGL-D 307 Query: 317 TKHLVTDQYSLEQTQDAMERAL 338 ++T Y +E+ + E L Sbjct: 308 LSPIITHHYPVEEFKTGFETML 329 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: 304 Number of extensions: 13 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: 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 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