Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate 3610773 Dshi_4159 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Dino:3610773 Length = 350 Score = 144 bits (363), Expect = 4e-39 Identities = 115/372 (30%), Positives = 176/372 (47%), Gaps = 42/372 (11%) Query: 29 WLGSKVWRYPEVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYP---- 84 W G+K ++RVE+V EP E+ IKV GICGSD+H G I P Sbjct: 6 WHGAK-----DIRVEDVDEPT-PGAGEVKIKVAWTGICGSDLHEFLA---GPIFVPVGED 56 Query: 85 ---GLTGFPVTLGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGF 141 P+T+GHE+ G + E G + +G+ V E + CG C C +G Sbjct: 57 HPLSHDKAPITMGHEYCGEITELGDGVTD------LSVGDRVAIEPIFACGTCAACRDGR 110 Query: 142 PNHCENLNELGFNVD-GAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYN 200 N CE L +G + G FA Y V A+ + E + +G +LVEP +VA + Sbjct: 111 YNLCEKLGFVGLSGGHGGFAAYSVVPARMLHRMPEGLSMEQG-------ALVEPAAVALH 163 Query: 201 AVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHV 260 AV R + GD + G GPIGL V L+ AGASK+++ EPSE RR A ELGA Sbjct: 164 AV--RVSAFKAGDRAAVFGAGPIGLLVVESLRIAGASKIVVVEPSETRRAKAMELGATTA 221 Query: 261 IDPTKENFVEAVLDYTNGLGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARADA 320 +DP E+ V AV G G ++ E TGVP ++ I+ A +V+ + Sbjct: 222 VDPGAEDAVAAVQAACPG-GVEVAFEVTGVPAVLAQAID-----ATRYEGETLVVSIWET 275 Query: 321 KIPLTGEVFQVRRAQIVGSQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEI-PEYI 378 + ++ I G+ + +P V+ LM G +++++ + +++I + Sbjct: 276 EASFQPNTVVLKERNIKGTIAY--RNVYPAVMDLMQQGYFQAERLVTRRIGLDDIVRDGF 333 Query: 379 KRLQTDKSLVKV 390 + L +KS +K+ Sbjct: 334 EALVAEKSQIKI 345 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: 367 Number of extensions: 20 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: 350 Length adjustment: 30 Effective length of query: 365 Effective length of database: 320 Effective search space: 116800 Effective search space used: 116800 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