Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012991396.1 THAL_RS01760 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000025605.1:WP_012991396.1 Length = 414 Score = 335 bits (860), Expect = 2e-96 Identities = 179/398 (44%), Positives = 263/398 (66%), Gaps = 4/398 (1%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 ++V+KFGG ++ +E+++ A K+I + + G K VVV SAM TD LI LAK ID P Sbjct: 4 LLVVKFGGTSVGSIERIKNAARKVIDKVQQGYKVVVVSSAMAGETDRLINLAKEIDPLPP 63 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RELD+L+STGE Q++AL ++ L GY A+S G Q+ IITD + AR+ I + Sbjct: 64 ERELDMLVSTGEQQAIALFAMVLNSMGYPAVSLCGWQVPIITDSVHTKARVRKIGVQRLK 123 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 LK+ +IPVVAGFQG+TE +ITTLGRGGSDLTA+ALAY+LGAD CE+Y DV+GV+TAD Sbjct: 124 NILKEGYIPVVAGFQGVTEDWEITTLGRGGSDLTAVALAYALGAD-CEIYTDVEGVFTAD 182 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGT-LIW 578 PRIV AR I +S+EEM+E++ GA+V+QAR+ EFA KY V++ ++++ + GT ++ Sbjct: 183 PRIVPSARKIARISYEEMLEMASLGAKVMQARSVEFAMKYNVRIHVRSSFSDQEGTWIVP 242 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 E +E VRA+T E +++ + VPD+PG+A RI + L + +DMI+Q + Y Sbjct: 243 EEEVMEKVAVRAITLETKESRITVVRVPDRPGIAYRIFKALGDAHIVVDMIVQNVSHQGY 302 Query: 639 NTVAFIVPESQLGKLDIDLLKTRSE--AKEIIIEKGLAKVSIVGVNLTSTPEISATLFET 696 ++F V ++ + + + K E A+E++ + +AKVS+VG+ + S+ +A +FE Sbjct: 303 TDLSFTVNKADAPRAEEIVRKVAQEIGAQEVVRDDNVAKVSVVGIGMKSSYGTAAKMFEV 362 Query: 697 LANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRF 734 L INI IS S +IS +ID KY E AV+ +HS F Sbjct: 363 LYKNNINIMAISTSEIKISCLIDQKYGELAVRELHSAF 400 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: 743 Number of extensions: 33 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: 414 Length adjustment: 36 Effective length of query: 703 Effective length of database: 378 Effective search space: 265734 Effective search space used: 265734 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