Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_012173009.1 AZC_RS23020 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000010525.1:WP_012173009.1 Length = 420 Score = 267 bits (682), Expect = 9e-76 Identities = 153/417 (36%), Positives = 249/417 (59%), Gaps = 19/417 (4%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +VMKFGG +++++E++ VA + + +G + VV+SAM T+ L+ K DP Sbjct: 4 LVMKFGGTSVANIERIRNVARHVKREVDAGYEVAVVVSAMSGKTNELVAWCKESSALYDP 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++++GE + L++I L+ G KA S+ G Q+ I TD+ +GSARI +I+ ++ Sbjct: 64 REYDAVVASGEQVTSGLLAITLQSMGLKARSWQGWQIPISTDEAHGSARIQEIDGTALNT 123 Query: 461 YLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 + V+AGFQG+ TG ITTLGRGGSD +A+A+A ++GA+ C++Y DVDGVYT D Sbjct: 124 GFAAGEVAVIAGFQGMHLPTGRITTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTD 183 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHK--------- 570 PR+V A+ + +++EEM+E++ GA+VLQ R+ E A + V+ ++++ + Sbjct: 184 PRVVPKAKRLDRIAFEEMLEMASLGAKVLQVRSVELAMVHQVRTFVRSSFEDPDAPHMGT 243 Query: 571 -ETRGTLIWE-----GTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGV 624 E+ GTLI + ++E +V + F A+V ++ V DKPGVAA + L+ + Sbjct: 244 VESAGTLICDEEEIVANQMEARVVTGIAFSKDEAQVSIRRVEDKPGVAAAVFVPLADAHI 303 Query: 625 NIDMIIQGMKS-GEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIE--KGLAKVSIVGV 681 N+DMI+Q + + G + F VP + + L K R IE + KVS++G+ Sbjct: 304 NVDMIVQNVSADGRTTDITFTVPTADYERAKDVLNKARDTITFETIEGATDVTKVSVIGI 363 Query: 682 NLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 + S ++A F+ LA +GINI I+ S +IS++ID Y E AV+ +HS + LD+ Sbjct: 364 GMRSHAGVAADAFKALAAKGINIRAITTSEIKISILIDAAYTELAVRTLHSLYGLDK 420 Score = 26.6 bits (57), Expect = 0.003 Identities = 54/294 (18%), Positives = 111/294 (37%), Gaps = 49/294 (16%) Query: 212 DVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVRSGKK---------LKLIG- 261 D Y+V+V+ ++G+ + + E DP +V SG++ L+ +G Sbjct: 31 DAGYEVAVVVSAMSGKTNELVAWCKESSALYDPREYDAVVASGEQVTSGLLAITLQSMGL 90 Query: 262 --------ELDFSTNRYEVRLREVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGR----G 309 ++ ST+ R + N + V G L GR G Sbjct: 91 KARSWQGWQIPISTDEAHGSARIQEIDGTALNTGFAAGEVAVIAGFQGMHLPTGRITTLG 150 Query: 310 AGGYPTASAVIADLFRVAKYKVLGGAEKFSVV-----VMKFGGAAISDVEKLEKVA-EKI 363 GG T++ +A GAE+ + V + ++L+++A E++ Sbjct: 151 RGGSDTSAVAVAAAI---------GAERCDIYTDVDGVYTTDPRVVPKAKRLDRIAFEEM 201 Query: 364 IKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGEI--QSVALMSIA 421 ++ G K + V S + ++ E+PD + + S G + +++ Sbjct: 202 LEMASLGAKVLQVRSVELAMVHQVRTFVRSSFEDPDAPHMGTVESAGTLICDEEEIVANQ 261 Query: 422 LRKRGYKAISFTGNQLKI----ITDKRYGSARII------DINTDIISRYLKQD 465 + R I+F+ ++ ++ + DK +A + IN D+I + + D Sbjct: 262 MEARVVTGIAFSKDEAQVSIRRVEDKPGVAAAVFVPLADAHINVDMIVQNVSAD 315 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: 658 Number of extensions: 28 Number of successful extensions: 5 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: 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