Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010959942.1 MCA_RS02965 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000008325.1:WP_010959942.1 Length = 436 Score = 211 bits (536), Expect = 8e-59 Identities = 144/386 (37%), Positives = 207/386 (53%), Gaps = 11/386 (2%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 V++GI GLGTVGG +L+ +EI +R G + + + R + + + D Sbjct: 4 VKIGILGLGTVGGGTVNVLRRNADEITRRAGREIQVCRASTRDLTRSRICDTTGIALTDD 63 Query: 80 FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 +++ + D+ VVE IGG A DLV +AL G+ VVT NK LI+ +GNE ++R Sbjct: 64 PYEIVSDPDIQIVVETIGGETPARDLVMKALANGKHVVTANKMLIALHGNEIFAAARERG 123 Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 L FEA+V GGIPII +++ L KV + GI+NGT+N+ILTEM KGR F +VL+EA Sbjct: 124 LMVAFEAAVAGGIPIIKTIREGLAGNKVEWLAGIINGTSNFILTEMWEKGRDFADVLQEA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEADPT DIEG D A+K+++LA + G V EGIT I +K G Sbjct: 184 QRLGYAEADPTFDIEGVDAAHKLTILASIAFGIPLQFGKVYIEGITGITAADVKYAEALG 243 Query: 255 KKLKLIGELDFSTNRYEVRLRE--VTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++KL+G + E+R+ + NV+GV NA+ + D G L G GAG Sbjct: 244 YRIKLLGIARRTPKGIELRVHPTLIPARRLIANVNGVMNAVLIKGDAVGPTLHYGAGAGA 303 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVE--KLEKVAEKIIKRKKSG 370 PTASAV+AD+ V + L + V + F AAIS++ +E + R + Sbjct: 304 EPTASAVVADIVDVV--RTLTSDPENRVPHLAFQPAAISEIPILPIEAIETAYYLRLSAE 361 Query: 371 VKPVVVLSAMGDTTDHLIELAKTIDE 396 KP V+ H I + + + Sbjct: 362 DKPGVLADVTRILAAHHISIEAVLQK 387 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: 756 Number of extensions: 43 Number of successful extensions: 6 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: 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 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