Align Sorbitol dehydrogenase; SDH; (R,R)-butanediol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.4; EC 1.1.1.14; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate PfGW456L13_3657 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q00796 (357 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3657 Length = 339 Score = 172 bits (436), Expect = 1e-47 Identities = 108/335 (32%), Positives = 173/335 (51%), Gaps = 30/335 (8%) Query: 14 VHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLGHEAS 73 +HGP DLR++ P+P PG +VL+ + + G+CGSD+ ++E G I PM LGHE S Sbjct: 10 LHGPRDLRVDEVPLPSPGETDVLVEVAACGVCGSDLGFYESGGIRRD--GAPMPLGHEFS 67 Query: 74 GTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCATPPDDGNLCRFY 133 G + +VG++V H +PG RV + P A N +G D+G L Sbjct: 68 GVIREVGTAVVHYRPGMRVVVNPMA---NGAMIGVGS--------------DEGALANLV 110 Query: 134 K----HNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIGMVTL 189 + ++ ++LP N+ E AL+EPL+V +HA R VT G VLV GAG IG+ + Sbjct: 111 RVRNVNSGPILHQLPANLPLEVAALVEPLAVALHAVNRSRVTAGESVLVLGAGAIGLGIV 170 Query: 190 LVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESP-QEIAR---KVEGQLGCK-- 243 KA G +Q+ V DLSA RL A +GA+L L +++ E+AR V LG + Sbjct: 171 ACLKARGISQIAVADLSAGRLEIAAGLGANLTLDPTRDDLWSELARAHGSVPTFLGTQAP 230 Query: 244 -PEVTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYCN 302 +V EC+G + I R + + + + ++E+++ G Y Sbjct: 231 ATQVIFECSGVSGVLHEAIARARDAARITVASVYKQPQAFDFSILQVKELELIGTLCYPT 290 Query: 303 TWPVAISMLASKSVNVKPLVTHRFPLEKALEAFET 337 + A+ +LAS + + + +++HRF L+ +A++T Sbjct: 291 EFAQALELLASGAFDPESMISHRFSLDDVAQAYKT 325 Lambda K H 0.319 0.137 0.415 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: 286 Number of extensions: 12 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: 357 Length of database: 339 Length adjustment: 29 Effective length of query: 328 Effective length of database: 310 Effective search space: 101680 Effective search space used: 101680 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 (21.7 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