Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_089301950.1 CHB84_RS13525 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_900188115.1:WP_089301950.1 Length = 421 Score = 325 bits (832), Expect = 4e-93 Identities = 168/406 (41%), Positives = 273/406 (67%), Gaps = 8/406 (1%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG+++ ++++ VAE+I++ KK+G VVV SAMGDTTD L++LA+ ++ P Sbjct: 2 ALIVQKYGGSSLESADRIKSVAERIVETKKAGNDVVVVCSAMGDTTDDLLDLAERVNPTP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RE+D+LL+ GE S AL+++A+ +G +A SF+G+Q ++T +G+ARI+D+ + Sbjct: 62 PEREMDMLLTAGERISNALVAMAISAQGAEAWSFSGSQAGVVTTSAHGNARILDVTPGRV 121 Query: 459 SRYLKQDFIPVVAGFQGIT-ETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 + L + ++ +VAGFQG++ +T D+TTLGRGGSD TA+ALA +LGAD CE+Y DVDGVY+ Sbjct: 122 TEALAEGYVALVAGFQGVSQDTKDVTTLGRGGSDTTAVALAAALGADECEIYSDVDGVYS 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI 577 ADPRIV DAR I + +EEM+EL+ G+++L RA E+AR+YGV + +++++ GTL+ Sbjct: 182 ADPRIVSDARKIDTIPYEEMLELAATGSKILHLRAVEYARRYGVPLRVRSSYSSKPGTLV 241 Query: 578 W---EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMK 634 E VE ++ V+ + AK+ + DVPD G AA+I R ++ ++IDM++Q + Sbjct: 242 TGSIEEIPVEQALITGVSHDTSEAKITVTDVPDYEGAAAKIFRAVADAEIDIDMVLQNVS 301 Query: 635 --SGEYNTVAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEIS 690 S + F + +S + L + R +A ++ ++ + KVS+VG + S P ++ Sbjct: 302 RTSSGVTDITFTLSKSNTEEAVKALERVREDAGFDSVLCDENVGKVSLVGAGMRSHPGVT 361 Query: 691 ATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 AT E+LAN G+NI++I+ S RISV+I V+ AV+A+H F L Sbjct: 362 ATFCESLANAGVNIEIINTSEIRISVLIRDADVDAAVQALHGAFGL 407 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: 664 Number of extensions: 27 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: 421 Length adjustment: 36 Effective length of query: 703 Effective length of database: 385 Effective search space: 270655 Effective search space used: 270655 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