Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011320349.1 AVA_RS18465 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000204075.1:WP_011320349.1 Length = 604 Score = 313 bits (802), Expect = 2e-89 Identities = 172/419 (41%), Positives = 268/419 (63%), Gaps = 20/419 (4%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V KFGG+++ VE+++ VA+++ K K+G VVV+SAMG TTD L++LA I NP Sbjct: 2 ALIVQKFGGSSVGSVERIQAVAQRVYKTVKAGNSLVVVVSAMGKTTDGLVKLANEISRNP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 + RE+D+LLSTGE ++AL+S+AL++ G AIS TG Q+ I+T+ + ARI+ I T+ + Sbjct: 62 NRREMDMLLSTGEQVTIALLSMALQELGQPAISMTGAQVGIVTEAEHTRARILHIETERV 121 Query: 459 SRYLKQDFIPVVAGFQGITETG--DITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVY 516 ++++ + VVAGFQGI+ G +ITTLGRGGSD +A+ALA +L AD CE+Y DV G+ Sbjct: 122 EGHIQEGKVVVVAGFQGISSNGSLEITTLGRGGSDTSAVALAAALQADFCEIYTDVPGIL 181 Query: 517 TADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTL 576 T DPRIV +A+++ E++ EM+EL+ GA+VL RA E AR YG+ +++K++ + GT Sbjct: 182 TTDPRIVPEAQLMGEITCNEMLELASLGAKVLHPRAVEIARNYGMPLVVKSSWTDDPGTW 241 Query: 577 IW----EGTKVEN----PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDM 628 + +G + N V V + AKV L VPDKPGVAA++ +S+ V++D+ Sbjct: 242 VTTPKPQGRSLINLELARPVDDVELDTDQAKVALLRVPDKPGVAAKLFGEISRQKVDVDL 301 Query: 629 IIQGMKSGEYNTVAFIVPESQLGKLDI----------DLLKTRSEAKEIIIEKGLAKVSI 678 IIQ + G N +AF V L + + +S+ E+++E+ +AKVSI Sbjct: 302 IIQSIHEGNSNDIAFTVTTPILKRAEAVAAAIAPSLRSPSHPKSDEAEVMVEQNIAKVSI 361 Query: 679 VGVNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 G + P ++A +F TLA G+NI MIS S ++S +ID + + A+ A+ FE++ Sbjct: 362 AGAGMIGRPGVAAKMFTTLAEAGVNIQMISTSEVKVSCVIDAQDGDRAIIALRKAFEIE 420 Score = 92.4 bits (228), Expect = 6e-23 Identities = 53/159 (33%), Positives = 88/159 (55%), Gaps = 7/159 (4%) Query: 585 NPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTV--- 641 +P VR V + A++ ++ VPD+PG+AA++ L+Q +++DMIIQ + + V Sbjct: 436 SPPVRGVALDLNQARLAIRQVPDRPGMAAQLFGILAQNNISVDMIIQSQRCRIVDGVPRR 495 Query: 642 --AFIVPESQLGKLDIDLLKTRSEAK--EIIIEKGLAKVSIVGVNLTSTPEISATLFETL 697 AF VP L + E +++++ +AKVSIVG + P ++A +FE L Sbjct: 496 DIAFTVPRMDGETAQKLLCQVAPELGWGDVVLDSAIAKVSIVGAGMVGQPGVAAKMFEAL 555 Query: 698 ANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 A INI MI+ S +IS ++ + A++ IH+ FEL Sbjct: 556 AKHQINIQMIATSEIKISCVVSQEQGVQALQVIHTAFEL 594 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: 915 Number of extensions: 50 Number of successful extensions: 9 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 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