Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_068462230.1 APY04_RS10130 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_001541235.1:WP_068462230.1 Length = 420 Score = 270 bits (689), Expect = 1e-76 Identities = 158/419 (37%), Positives = 251/419 (59%), Gaps = 18/419 (4%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +VVVMKFGG ++++VE++ VA + + +G K VV+SAM T+ L+ + Sbjct: 2 AVVVMKFGGTSVANVERIRNVARHVKREVDAGNKVCVVVSAMSGVTNQLVAYVREASLLH 61 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 D RE D +++TGE + L++I L+ G +A S+ G Q+ I +GSARI I+ I Sbjct: 62 DAREYDAVVATGEQVTAGLLAIVLQSMGLQARSWQGWQVPITASAAHGSARITGIDGSEI 121 Query: 459 SRYLKQDFIPVVAGFQGI-TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYT 517 R + D + VV GFQGI E + TLGRGGSD +A+A+A +L AD+C++Y DVDGVYT Sbjct: 122 LRRFESDEVAVVTGFQGIEPERQRVATLGRGGSDTSAVAMAVALKADVCDIYTDVDGVYT 181 Query: 518 ADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNA--------- 568 DPRIV A+ + ++S+EEM+E++ G++VLQ R+ E A + ++V + ++ Sbjct: 182 TDPRIVAKAKRLPKISYEEMLEMASLGSKVLQTRSVELAMNHRMRVRVLSSFVAPEAMAP 241 Query: 569 ----HKETRGTLIW-EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMG 623 E GT++ E VE+ +V + + AKV L V DKPG+AARI L+ Sbjct: 242 VRLGQLEDIGTVVCDEDEIVESQVVSGIAYVKDEAKVTLIKVEDKPGIAARIFGPLADAN 301 Query: 624 VNIDMIIQGM-KSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKG--LAKVSIVG 680 +N+DMI+Q + G++ + F V ++L + L +SE E I+ +AK+S++G Sbjct: 302 INVDMIVQSVTPDGKHTDMTFTVQATELPRTLETLKAAKSEIGEFEIQSSADVAKISVIG 361 Query: 681 VNLTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELDRE 739 + + S ++A +F+ L+++GINI I+ S +ISV+ID Y E AV+ +HS + LD + Sbjct: 362 IGMRSHAGVAALMFKALSDKGINILAITTSEIKISVLIDAAYAELAVRTLHSIYGLDAD 420 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: 617 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 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