Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate RR42_RS06370 RR42_RS06370 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__Cup4G11:RR42_RS06370 Length = 416 Score = 302 bits (774), Expect = 2e-86 Identities = 170/414 (41%), Positives = 261/414 (63%), Gaps = 14/414 (3%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ E+++ VA+++ K ++G + VVV SAM T+ L+ LAK I P Sbjct: 2 ALIVHKYGGTSMGSPERIKNVAKRVAKWHRAGHRVVVVPSAMSGETNRLLGLAKEISAQP 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 PRELD+L +TGE S AL++IAL+ G AIS+TG Q+ + TD + ARI I+ + I Sbjct: 62 SPRELDMLAATGEQASSALLAIALQSEGVDAISYTGWQVPVKTDSSHTKARIESIDDERI 121 Query: 459 SRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTA 518 L + VV GFQGI + G+ITTLGRGGSD +A+A+A ++ A+ C +Y DVDGVYT Sbjct: 122 LADLDAGRVVVVTGFQGIDDNGNITTLGRGGSDTSAVAIAAAIEAEECLIYTDVDGVYTT 181 Query: 519 DPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNA---------H 569 DPR+V+DAR + ++++EEM+E++ G++VLQ R+ EFA KY VK + ++ Sbjct: 182 DPRVVEDARRLDQITFEEMLEMASLGSKVLQIRSVEFAGKYRVKTRVLSSLTDPLMPLEQ 241 Query: 570 KETRGTLIW--EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNID 627 + GTLI E +++E ++ + F AK+ + VPDKPG+A +I+ ++ +++D Sbjct: 242 EMHSGTLITFEENSEMEAAVISGIAFARDEAKITVLGVPDKPGIAYQILGPVADANIDVD 301 Query: 628 MIIQGMKSGEYNTVAFIVPESQLGK---LDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLT 684 MIIQ F VP + + + D +K A + + ++KVS+VGV + Sbjct: 302 MIIQNQSVDGKTDFTFTVPRGEYQRALAILNDSVKAHIGAASVSGDPKVSKVSVVGVGMR 361 Query: 685 STPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDR 738 S I++ +F TL+ EGINI MIS S +ISV+ID KY+E AV+A+H FELD+ Sbjct: 362 SHVGIASKMFRTLSEEGINIQMISTSEIKISVLIDEKYMELAVRALHKVFELDQ 415 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: 703 Number of extensions: 34 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: 416 Length adjustment: 36 Effective length of query: 703 Effective length of database: 380 Effective search space: 267140 Effective search space used: 267140 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 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