Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate GFF485 Psest_0490 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__psRCH2:GFF485 Length = 357 Score = 148 bits (374), Expect = 2e-40 Identities = 111/360 (30%), Positives = 174/360 (48%), Gaps = 23/360 (6%) Query: 9 MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68 MKAAV I+++ P+P+I ++ L+++ ICG+D+H G Y V + Sbjct: 4 MKAAVFVEPGRIELQDKPIPEIGPNDALLRITTTTICGTDVHILK----GEYPVAAGLTI 59 Query: 69 GHECAGEIAAVGSSVDQFKVGDRV---AVEPGVTCGRCE--------ACKEGRYNLCPDV 117 GHE G I +GS+V ++ G RV A+ P T C+ C Y Sbjct: 60 GHEPVGVIEKLGSNVKGYQEGQRVIAGAICPSFTSYACQDGLPSQDGGCSCHGYKPMGGW 119 Query: 118 QFLATPPVDGAFVQYIKM--RQDFVFLIPDSLSYEEAALI-EPFSVGIHAAARTKLQPGS 174 +F T +DG +Y+ + Q + +PD L+ E+ + + S G A ++ G Sbjct: 120 RFGNT--IDGTQAEYVLVPDAQANLAPVPDGLTDEQVLMCPDIMSTGFAGAEAANIKIGD 177 Query: 175 TIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIK 234 + I GP+GL A A AK GA TII D RL+ A+KMGA +N R D ++E+ Sbjct: 178 IVVIFAQGPIGLCATAGAKLRGASTIIAVDGVDARLDIARKMGADVTLNFRNVDVVDEVL 237 Query: 235 TITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQN-EIPLNV--PFIADNEI 291 +T+ RG D + E G + +SAL ++ GG L+ +G+ S + IPL + DN+I Sbjct: 238 KLTSGRGADASIEALGLQSTFESALRVLKPGGTLSSLGVYSSDLTIPLGAFHAGLGDNKI 297 Query: 292 DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVMVYP 351 + + +ASG VD LVT +Y+L+ DA + ++ LKV + P Sbjct: 298 VTSLCPGGKERMRRLLNVVASGRVDLGLLVTHKYALDNITDAYDLFANQRDGVLKVAIKP 357 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: 24 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: 357 Length adjustment: 29 Effective length of query: 324 Effective length of database: 328 Effective search space: 106272 Effective search space used: 106272 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