Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 8500664 DvMF_1412 homoserine dehydrogenase (RefSeq)
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Miya:8500664 Length = 436 Score = 189 bits (479), Expect = 3e-52 Identities = 138/414 (33%), Positives = 209/414 (50%), Gaps = 22/414 (5%) Query: 16 GVRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEE 75 G +++ +G+AG GTVG + R+L E I +R G + +I ++ R K VP + Sbjct: 9 GGKRLVIGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPRAWPVP-QG 67 Query: 76 IAFDFDDLILNSD----VVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSE 131 D +L D V+VE +GG +++RALE G+ VVT NK L++E G + Sbjct: 68 ATLTADPAVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAEDGYDLYR 127 Query: 132 YIKKRK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFE 188 +++ L EASV GGIPI+ L++ L ++ + GI+NGT NYIL+EM S G F Sbjct: 128 LAEQKNVGLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMTSNGLDFA 187 Query: 189 EVLKEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGR---FPGINSVQFEGITRIDPE 245 L +AQELGYAEADPT DIEG+D A+K+ +L + G + + GI R+D E Sbjct: 188 TALAQAQELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAGIDRMDIE 247 Query: 246 YLKEIVRSGKKLKLIGELDFSTNRYEVRLREVTPEDPFF--NVDGVDNAIEVSTDLAGDF 303 + +E+ G ++KL+ ++ + E + + F V G NAI + + G Sbjct: 248 FAREL---GFRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNAVGPV 304 Query: 304 LLKGRGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKI 363 L G GAG PTASAV+ADL VA+ G A + + A D+ Sbjct: 305 FLHGLGAGSLPTASAVLADLMTVAR----GAAPHNTGFQRQVPPRA--DILPPADAESSY 358 Query: 364 IKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVAL 417 R P V+ G DH I +A+ I + P+ + L+ T ++ A+ Sbjct: 359 YVRAMVPDNPGVLRDLAGAMADHSISIAQAIQKGQHPQGVPLVFMTHAAKASAI 412 Lambda K H 0.318 0.137 0.377 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: 712 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 436 Length adjustment: 36 Effective length of query: 703 Effective length of database: 400 Effective search space: 281200 Effective search space used: 281200 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: 41 (21.7 bits) S2: 53 (25.0 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