Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_026596525.1 H035_RS0111190 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000421465.1:WP_026596525.1 Length = 436 Score = 224 bits (572), Expect = 5e-63 Identities = 151/422 (35%), Positives = 230/422 (54%), Gaps = 13/422 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIAFD 79 V++G+ GLGTVGG +L EI +R G + ++K R P+K + G ++ D Sbjct: 4 VKIGLLGLGTVGGGTVNVLARNTREITRRAGREIQVAKAFTRDPEKPRICGTEGIDLVTD 63 Query: 80 FDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKRK 137 +++ + ++ V E IGGT +A +LV RA+ELG+ VVT NK LI+ +GNE ++ Sbjct: 64 PWEVVEDPEIAIVAELIGGTSLAKELVLRAIELGKHVVTANKALIALHGNEIFSRASEQG 123 Query: 138 LF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEA 194 + FEA+V GGIPII +L++ L ++ + GI+NGT N+ILT M +GR F++VL EA Sbjct: 124 VMVAFEAAVAGGIPIIKVLREGLTGNRIEWVAGIINGTGNFILTGMRDQGRVFDDVLTEA 183 Query: 195 QELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSG 254 Q LGYAEA+P D+EG D A+K+++LA + G + V EGITRI PE ++ G Sbjct: 184 QALGYAEANPAFDVEGIDAAHKLTILAAIAFGIPLQYDKVYTEGITRITPEDIRYAQELG 243 Query: 255 KKLKLIGELDFSTNRYEVR--LREVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGG 312 ++K +G + + E+R L + NV+GV NA+ V D G L G GAG Sbjct: 244 YQIKHLGIARQTPDGIELRVHLCLIPARRLLANVEGVMNAVVVKGDAVGPTLYYGPGAGA 303 Query: 313 YPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISD--VEKLEKVAEKIIKRKKSG 370 PTASAV+ADL V + + V + F A+SD V + ++ R K Sbjct: 304 EPTASAVVADLVDVVRVFTADPGNR--VPHLAFQPDALSDLPVLPISEIETAYYLRLKVA 361 Query: 371 VKPVVVLSAMGDTTDHLIELAKTIDENPDPRELD--LLLSTGEIQSVALMSIALRKRGYK 428 +P V+ DH I + I + P ++D L+ T +++ AL + A + Sbjct: 362 DQPGVLADIARILADHEISIEAVIQKEPQEGQMDLPLIFLTHKVKEKALDAAAAKIEALP 421 Query: 429 AI 430 A+ Sbjct: 422 AV 423 Score = 33.5 bits (75), Expect = 2e-05 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 21/90 (23%) Query: 605 VPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEA 664 V D+PGV A I R L+ ++I+ +IQ E Q G++D+ L+ + Sbjct: 360 VADQPGVLADIARILADHEISIEAVIQ--------------KEPQEGQMDLPLIFLTHKV 405 Query: 665 KEIIIEKGLAKVSIVGVNLTSTPEISATLF 694 KE ++ AK+ + P + A L+ Sbjct: 406 KEKALDAAAAKIE-------ALPAVKAPLY 428 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: 781 Number of extensions: 39 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