Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011609992.1 TERY_RS00360 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000014265.1:WP_011609992.1 Length = 604 Score = 285 bits (729), Expect = 5e-81 Identities = 162/420 (38%), Positives = 261/420 (62%), Gaps = 24/420 (5%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 ++V K+GG ++ VE+++ VA++I K S VVV+SAMG TTD L++LA I NP Sbjct: 2 LIVQKYGGTSVGSVERIKAVAQRIAKTA-SDRSVVVVVSAMGKTTDTLVKLANDISPNPC 60 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RE+D+LLSTGE ++AL+S+AL++ G AIS TG Q+ I+T+ ++ ARI+ I T+ I Sbjct: 61 RREMDMLLSTGEQVTIALVSMALQELGVPAISLTGAQVGIVTEAQHSRARILHIQTERIE 120 Query: 460 RYLKQDFIPVVAGFQGITET--GDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 +L+ + VVAGFQGI++T +ITTLGRGGSD +A+ALA +L A CE+Y DV G+ T Sbjct: 121 EHLQLGEVVVVAGFQGISQTRHQEITTLGRGGSDTSAVALAAALQAQRCEIYTDVPGILT 180 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI 577 DPRIV +A+++ E++ +EM+EL+ GA+VL RA E AR YG+ +++ ++ + GT + Sbjct: 181 TDPRIVPEAQLMSEITCDEMLELASLGAKVLHPRAVEIARNYGMPLVVLSSWSDAPGTRV 240 Query: 578 ---------WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDM 628 + ++ P V AV ++ A + + +PD+PGVAA++ ++ +++D+ Sbjct: 241 VSAIPKRPALQDLELTKP-VDAVEYDTNQAGISMLRLPDRPGVAAQLFSGIALQNIDVDL 299 Query: 629 IIQGMKSGEYNTVAF-----------IVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVS 677 IIQ + N +AF V ++ L L + + E + E+ +AKVS Sbjct: 300 IIQSIHESNTNDIAFTVSKDVLKQAAAVADAMLPALGKNAHPSLGEPEVKTEERPIAKVS 359 Query: 678 IVGVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 +VG + PE++A +FE LA G+NI MIS S ++S ++D + + V ++ F++D Sbjct: 360 LVGAGMIGRPEVAAKMFEALAAAGVNIIMISTSEVKVSCVVDAEDCKKTVNSLCQAFDVD 419 Score = 89.0 bits (219), Expect = 7e-22 Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 9/157 (5%) Query: 586 PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTV---- 641 P VR V + A++ ++ VPD PG+AA+I L+Q +++DMIIQ + + V Sbjct: 437 PPVRGVALDIKQARLAVRQVPDHPGMAAKIFGLLAQQNISVDMIIQSQRCHSVDGVLTRD 496 Query: 642 -AFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNLTSTPEISATLFETL 697 AF V + + G+ +L + E+++E +AKVS+VG + S P ++A +FE L Sbjct: 497 IAFTVSQPE-GETAYQILANTAADFGWGEVVLESSIAKVSVVGSGMISHPGVAAQMFEAL 555 Query: 698 ANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 A INI MI+ S +IS +++ + A++AIH F Sbjct: 556 AASQINILMITTSEIKISCVVEEEDGVKALQAIHKAF 592 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: 876 Number of extensions: 41 Number of successful extensions: 10 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: 604 Length adjustment: 38 Effective length of query: 701 Effective length of database: 566 Effective search space: 396766 Effective search space used: 396766 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: 54 (25.4 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