Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_041098312.1 SUTH_RS07530 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000828635.1:WP_041098312.1 Length = 436 Score = 213 bits (542), Expect = 2e-59 Identities = 139/402 (34%), Positives = 216/402 (53%), Gaps = 9/402 (2%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ + VG+ G+GTVGG + +L EI +R G I+KV +++ + + + E+ Sbjct: 1 MKPINVGLLGIGTVGGGTFNVLARNEAEITRRAGRPIRITKVADKNLELARQVTAGRAEV 60 Query: 77 AFDFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEF--SEY 132 D ++ + D+V+E IGG +A +LV +A+ G+ VVT NK L++ +GNE + + Sbjct: 61 TDDAFSVVSDPEIDIVIELIGGYGIARELVLKAIANGKHVVTANKALLAVHGNEIFAAAH 120 Query: 133 IKKRKLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191 K + FEA+V GGIPII L++ L ++ I GI+NGTTN+IL+EM KG F+ VL Sbjct: 121 EKGVMVGFEAAVAGGIPIIKALREGLSANRIQWIAGIINGTTNFILSEMRDKGLSFDTVL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 KEAQ LGYAEADPT DIEG D A+K+++L+ + G + EGI+++D + +K Sbjct: 181 KEAQRLGYAEADPTFDIEGIDAAHKITILSALAFGIRMQFDKAHVEGISKLDADDIKYAE 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309 + G ++KL+G E+R+ + + NV+G NA+ V D G L G+G Sbjct: 241 QLGYRIKLLGITRRRPEGVELRVHPTLIPAKRLIANVEGAMNAVLVQGDAVGATLYYGKG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AG PTASAVIADL V + + + + G + + L +V R + Sbjct: 301 AGAEPTASAVIADLVDVTRMHTADPEHRVPHLAFQPGAVEDTPILPLSEVETSYYLRLRV 360 Query: 370 GVKPVVVLSAMGDTTDHLIELAKTIDENPDPRE--LDLLLST 409 KP V+ D I + I P E D+++ T Sbjct: 361 EDKPGVLADITRILADQQISIDAMIQREPAEGESQTDIIMLT 402 Score = 30.0 bits (66), Expect = 3e-04 Identities = 19/64 (29%), Positives = 31/64 (48%) Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEA 664 V DKPGV A I R L+ ++ID +IQ + + I+ + ++D R EA Sbjct: 360 VEDKPGVLADITRILADQQISIDAMIQREPAEGESQTDIIMLTHITREKNVDAAIARIEA 419 Query: 665 KEII 668 ++ Sbjct: 420 LPVV 423 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: 741 Number of extensions: 35 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: 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