Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011156172.1 TX73_RS03125 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000195775.1:WP_011156172.1 Length = 417 Score = 266 bits (679), Expect = 2e-75 Identities = 155/413 (37%), Positives = 247/413 (59%), Gaps = 15/413 (3%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++++E+++ VA + + +G + VV+SAM T+ L+ D Sbjct: 4 LVMKFGGTSVANIERIQNVARHVKREVDAGHEVAVVVSAMSGKTNELVAWCTEASPLHDA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDIN-TDIIS 459 RE D ++++GE + L++IAL+ G +A S+ G Q+ I+T + SARI+ I+ ++II Sbjct: 64 REYDAVVASGEQVTSGLLAIALQSLGIQARSWQGWQIPILTSDAHASARIVGIDGSEIIK 123 Query: 460 RYLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 R+ ++ + V+AGFQGI ETG ITTLGRGGSD +A+A+A +L AD C++Y DVDGVYT Sbjct: 124 RFSERKEVAVIAGFQGIHAETGRITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTT 183 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNA---------H 569 DPR+V AR + ++S+EEM+EL+ GA+VLQ R+ E + + + ++++ H Sbjct: 184 DPRVVPKARRLDKVSFEEMLELASLGAKVLQVRSVELGMVHNMPIFVRSSFDKPEDIDPH 243 Query: 570 KETRGTLI-WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDM 628 GTLI E +EN +V + F A++ ++ + DKPGVAA I L+ +N+DM Sbjct: 244 GTPPGTLISSEENSMENHVVTGIAFSKDEAQISVRRIEDKPGVAASIFGPLADANINVDM 303 Query: 629 IIQGM-KSGEYNTVAFIVPESQL--GKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTS 685 I+Q + + G+ + F VP S K I + + E +AKVS++G + S Sbjct: 304 IVQNVSEDGKTTDLTFTVPASDFARAKQTITSAQDKIGYARFDSETDVAKVSVIGSGMRS 363 Query: 686 TPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 ++A F LA INI I+ S + SV+ID Y E AV+ +H+ + LD+ Sbjct: 364 HAGVAAQAFAALAARNINIRAITTSEIKFSVLIDAAYTELAVRTLHTLYGLDQ 416 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: 638 Number of extensions: 30 Number of successful extensions: 5 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: 417 Length adjustment: 36 Effective length of query: 703 Effective length of database: 381 Effective search space: 267843 Effective search space used: 267843 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