Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF1391 Psest_1428 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__psRCH2:GFF1391 Length = 362 Score = 142 bits (359), Expect = 1e-38 Identities = 118/361 (32%), Positives = 173/361 (47%), Gaps = 48/361 (13%) Query: 29 WLGSKVWRYPEVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTG 88 W G K ++R+E+VP P +P + I+V CGICGSD+H G + P Sbjct: 12 WHGRK-----DIRLEQVPLPGAPQPGWVQIRVHWCGICGSDLHEYLA---GPVFIPVDAP 63 Query: 89 FPVT-------LGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGF 141 P+T LGHEF G +V G + + G+ V A+ CG CR C G Sbjct: 64 HPLTGIKGQCILGHEFCGEIVAIGEGV------EGYAPGDKVAADACQHCGQCRFCKTGQ 117 Query: 142 PNHCENLNELGFNVDGAFAEYVKVDAKYAWSLRE---LEGVYEGDRLFLAGSLVEPTSVA 198 N CE L G +GAFAE+V V A+ + L E LE AG+L+EP +V Sbjct: 118 YNLCEQLAFTGLMNNGAFAEFVNVPAELLYRLPEGFPLE----------AGALIEPLAVG 167 Query: 199 YNAVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGAD 258 +AV + G G+ VV++G G IGL + K AGA +VI E S R+ A E+GA+ Sbjct: 168 MHAV--KKAGSLLGETVVVVGAGTIGLCTIMCAKAAGAGQVIALEMSAARKAKALEVGAN 225 Query: 259 HVIDPTKENFVEAVLDYTNGLGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARA 318 VIDP++ + + + T G GA + E G I+ + R G V I Sbjct: 226 WVIDPSECDAIAEIKALTGGYGAGVSFECIGHKATAKLAIDVI--RKAGRCVMVGIFEE- 282 Query: 319 DAKIPLTGEVFQV--RRAQIVGSQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEIP 375 P F++ Q++GS ++G F VI+L+ G +D+T +I+ + ++ I Sbjct: 283 ----PSEFNFFEIVATEKQVIGSLAYAGE--FADVIALIDDGRIDVTPLITGRIGLDNIL 336 Query: 376 E 376 E Sbjct: 337 E 337 Lambda K H 0.319 0.138 0.418 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: 397 Number of extensions: 18 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: 395 Length of database: 362 Length adjustment: 30 Effective length of query: 365 Effective length of database: 332 Effective search space: 121180 Effective search space used: 121180 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: 50 (23.9 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