Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (characterized)
to candidate N515DRAFT_4364 N515DRAFT_4364 homoserine dehydrogenase
Query= SwissProt::P31116 (359 letters) >FitnessBrowser__Dyella79:N515DRAFT_4364 Length = 362 Score = 198 bits (504), Expect = 2e-55 Identities = 133/352 (37%), Positives = 199/352 (56%), Gaps = 18/352 (5%) Query: 8 VAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAAST 67 + + G GVVG A L +LL + + LV A + R S + +D +A Sbjct: 24 IVLFGTGVVGGALL-KLLNTPAAASLRLVGAANSRRQQTSAEQL-----AD-RALREKLK 76 Query: 68 TKTLPLDD--LIAHLKTSPKPV-ILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDL 124 + P DD L+ L TS V +++D T++A +A + ++ G + T NK +L Sbjct: 77 SHGDPRDDATLLRALDTSGAAVKVIIDATANANLAARHADWLARGYHVVTANKALAGGEL 136 Query: 125 ATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEF 184 W+AL + G ATVGAGLP++S LR + GD + +EG+FSG+LSY+FN++ Sbjct: 137 PGWRALQAAVAQGGRYGDAATVGAGLPVLSTLRRLRACGDALLTLEGVFSGSLSYLFNQY 196 Query: 185 STSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQ 244 SQ FS +++ A+KLGYTEPDPR DL+G DVARK+ I+ R +G + V+ Sbjct: 197 DGSQ----PFSGLLREARKLGYTEPDPRSDLSGEDVARKLLIIARNAGFAL-GTDEVEVE 251 Query: 245 SLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEK 304 SL+P+ L SV D FL +L + D+ L + EA VLRF+ +++ K+ VG+ + Sbjct: 252 SLVPEALRSV-DTDSFLARLEELDEPLARRHAEAKARGGVLRFLARLNQRGKA-RVGLVE 309 Query: 305 YDYSHPFASLKGSDNVISIKTKRY-TNPVVIQGAGAGAAVTAAGVLGDVIKI 355 +HP A L G+DN ++ T RY + P+VIQG GAG VTA +LGDV+ + Sbjct: 310 VPATHPAARLYGTDNQFALTTTRYHSQPLVIQGPGAGPEVTAQALLGDVLAL 361 Lambda K H 0.314 0.132 0.361 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: 205 Number of extensions: 9 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: 359 Length of database: 362 Length adjustment: 29 Effective length of query: 330 Effective length of database: 333 Effective search space: 109890 Effective search space used: 109890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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