Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010936896.1 DET_RS06220 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000011905.1:WP_010936896.1 Length = 433 Score = 186 bits (472), Expect = 2e-51 Identities = 135/393 (34%), Positives = 199/393 (50%), Gaps = 14/393 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLG--VPKEEIA 77 + VG+ GLG V G + ++L ER + ++G + KV L +P+ + Sbjct: 6 IGVGVIGLGVVAGQVSKVLHEREEFLSAQLGFPLKLKKVKVLPQDMSRPLAKLLPEGVLT 65 Query: 78 FDFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKK 135 D DD D+VVEAIGG A +L+ R L++G+ VVT NK +I+++ E + ++ Sbjct: 66 TDEDDFFNTPGLDIVVEAIGGEYPAFNLLSRGLKMGKCVVTSNKEVIAKHAPELVKLARE 125 Query: 136 RK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVLK 192 L EASVGGGIP+IS Q L + I I+NGTTNYILT M+K G FE LK Sbjct: 126 NNTGLRCEASVGGGIPLISPFQYDLAANHINGIYAIINGTTNYILTRMAKEGLDFETALK 185 Query: 193 EAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVR 252 +AQ LGYAEA+P+NDIEG D YK++++A + + EGI+R+ Sbjct: 186 QAQSLGYAEANPSNDIEGTDAVYKLAIMASINFQCKVKPEDIYREGISRLTSRDFCYADE 245 Query: 253 SGKKLKLIGELDFSTNRYEVRLREV-TPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRGA 310 G +KL+ + E R+ V P+D + VDGV NA+ V DL G L +G+GA Sbjct: 246 LGFNIKLLAITKPGNGQIEARVHPVFLPKDEWLAKVDGVFNAVLVEGDLVGPVLFQGQGA 305 Query: 311 GGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSG 370 G T+SAV+AD+ A+ LG + M++ V+ + + + R Sbjct: 306 GASATSSAVVADVLAAAQDIHLGVGNR-----MRWNMDKPLGVKPMSDILTRYYLRMTVT 360 Query: 371 VKPVVVLSAMGDTTDHLIELAKTIDENPDPREL 403 P V+ DH I ++ I + D L Sbjct: 361 DSPGVLALIARVLGDHNISISSVIQKETDEENL 393 Score = 28.1 bits (61), Expect = 0.001 Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 1/41 (2%) Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFIV 645 V D PGV A I R L ++I +IQ ++ E N A IV Sbjct: 359 VTDSPGVLALIARVLGDHNISISSVIQ-KETDEENLTAEIV 398 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: 739 Number of extensions: 45 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 739 Length of database: 433 Length adjustment: 36 Effective length of query: 703 Effective length of database: 397 Effective search space: 279091 Effective search space used: 279091 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 10 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