Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013706968.1 DESAC_RS10105 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000195295.1:WP_013706968.1 Length = 441 Score = 208 bits (530), Expect = 4e-58 Identities = 149/447 (33%), Positives = 233/447 (52%), Gaps = 17/447 (3%) Query: 17 VRKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEI 76 ++ V+VG+ G GTVG + R+L E + +R+GE I+ KV + + L+ + E Sbjct: 1 MKTVQVGLVGFGTVGSGVVRLLTEHEDRFRRRLGEPLILKKVADIDLARPRLVSLAPELF 60 Query: 77 AFDFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134 +++ + DVV+E IGG A DL+ AL G+ VVT NK L++ +GNE + Sbjct: 61 TDKVQEILADPEIDVVIELIGGVTEAYDLIMAALARGKHVVTANKALLALHGNEIFQAAS 120 Query: 135 KR--KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEMSK-GRHFEEVL 191 + ++ FEASV GGIP+I L+ L + I GI+NGT+NYIL++MS G F++ L Sbjct: 121 RAGVEVGFEASVCGGIPLILTLRQGLAANSIQEIFGILNGTSNYILSKMSMAGASFQQAL 180 Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIV 251 EAQ GYAEADPT D+EG D A+K+++L + G ++ EGITR++P ++ Sbjct: 181 VEAQAQGYAEADPTLDVEGIDAAHKLAILMALAYGTQINFGAIHVEGITRLEPIDIQLAR 240 Query: 252 RSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLKGRG 309 G ++KL+ R E R+ + P D +V G NA+ ++ D G LL G+G Sbjct: 241 EFGYQIKLLAITRDDGQRVEARVHPTMLPLDHIMASVQGAFNAVYITGDAVGPILLYGQG 300 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKS 369 AG PTASAV ADL +A G A + + + F + ++ LE++ R + Sbjct: 301 AGMMPTASAVAADLIDLAYNISHGVAGRVPPLGVNFADQSRRPIKPLEEIVTNYYFRFAA 360 Query: 370 GVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEIQSVALMSIALRKRGYKA 429 +P V+ + G I +A I + + R G + V + A +A Sbjct: 361 VDRPGVLSAISGILARFEISIAAVIQKGREIR--------GSVPVVMITHEAKESHVQQA 412 Query: 430 ISFTGNQLKIITDKRYGSARIIDINTD 456 ++ ++L +IT+K RI D N D Sbjct: 413 LAEI-DRLAVITEKTI-VIRIEDPNLD 437 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: 37 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: 441 Length adjustment: 36 Effective length of query: 703 Effective length of database: 405 Effective search space: 284715 Effective search space used: 284715 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