Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013133979.1 ARNIT_RS00825 homoserine dehydrogenase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000092245.1:WP_013133979.1 Length = 420 Score = 179 bits (455), Expect = 2e-49 Identities = 129/396 (32%), Positives = 204/396 (51%), Gaps = 15/396 (3%) Query: 20 VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIIS-KVINRSPQKYELLGVPKEEIAF 78 +++ I G+GTVG S+ ILK+ + I R G + + + V+N +K ++ E+ Sbjct: 2 LKIAIIGVGTVGASVANILKDNKDIITSRAGVEIVPTIGVVNDLSKKRDV----SIELTD 57 Query: 79 DFDDLILNS--DVVVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKKR 136 D D + + D++VE +GG + ++++RAL G+ VVT NK L++ + + + Sbjct: 58 DLDKALNDDSIDIIVELMGGVERPYEIIKRALSKGKPVVTANKALLAYHRYDLEKLAGDI 117 Query: 137 KLFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLKEAQ 195 +EA+V GGIPII+ L+D L + IRGI+NGT NY+LT M + G +E +LKEAQ Sbjct: 118 PFEYEAAVAGGIPIINALRDGLSANNIESIRGILNGTCNYMLTRMINDGIDYESILKEAQ 177 Query: 196 ELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSGK 255 ELGYAEADPT D+ G+D A+K+ +LA + + EGI ID + Sbjct: 178 ELGYAEADPTFDVGGFDAAHKLLILASIAYDVDAKPEDILIEGIQNIDTPDIDFANEFNY 237 Query: 256 KLKLIGELDFSTNRYEVRLREV--TPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRGAGGY 313 +KL+ + E+R+ V + VDGV N I V D G+ + G GAGG Sbjct: 238 SIKLLAIAKRVGKQIELRVHPVFIPKTEMIAKVDGVMNGISVIGDKVGETMYYGPGAGGN 297 Query: 314 PTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKP 373 TASAVIA++ +A+ + ++ +F A + +++ K R + K Sbjct: 298 ATASAVIANIVDIAR-----RGKGAPMLGFEFDYKANLTIMPKDEIETKYYLRLRIEDKV 352 Query: 374 VVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLST 409 V+ +H I + K I + + LLLST Sbjct: 353 GVLAKVTKILGEHEISIEKMIQKPYNTTCAHLLLST 388 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: 793 Number of extensions: 37 Number of successful extensions: 4 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: 420 Length adjustment: 36 Effective length of query: 703 Effective length of database: 384 Effective search space: 269952 Effective search space used: 269952 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