Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate NP_346919.1 CA_C0278 aspartate kinase
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_000008765.1:NP_346919.1 Length = 437 Score = 185 bits (470), Expect = 4e-51 Identities = 145/469 (30%), Positives = 225/469 (47%), Gaps = 46/469 (9%) Query: 1 MKII--KFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQ------LLQCAN 52 MKI+ KFGGSS+A+ +KV II+ + ++ ++ SA G T + LL N Sbjct: 1 MKIVVTKFGGSSLADSNQFKKVKGIIDSDANRKY--IIPSAPGKRTNKDYKITDLLYLCN 58 Query: 53 IAQQSEESYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKEC 112 ++ + + + + +R+ EIV +L + L VK Sbjct: 59 AHVKNGIPFDDVFKLISQRYTEIVSELNIDMDIAYYLEKVKKNIE--------------- 103 Query: 113 SNRTMDYVLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDR--FGHAKVNFKTTNK 170 + + DY S GE L+ ILA L A+ ++DA +++ D F K K K Sbjct: 104 NGASSDYAASRGEYLNGVILAKYLNAE-----FIDAAEVIFFDKSGCFDEKKSYEKIKEK 158 Query: 171 LIQDHFKSHDDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGV 230 ++ + VI GF GS+ G+ T R GSD T SI +A + A+ E WTDVSG Sbjct: 159 VLSCNKA------VIPGFYGSSFNGDVKTFSRGGSDVTGSIISAGVNADLYENWTDVSGF 212 Query: 231 MTADPRLVYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAG 290 + ADPR+V TI ++SY E ELS+ GA V+ + P IPI IKNT KP + G Sbjct: 213 LMADPRIVENPKTISKISYKELRELSYMGATVLHEEAIFPVKDSGIPINIKNTNKPSDPG 272 Query: 291 TRISKDSGEG---KIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILIS 347 T I D+ + I GI+ N +++ ++ L VG ++ L G++ + Sbjct: 273 TLILSDTHKEINLGTITGIAGKKNFTVIAIEKALLNSEVGFCRKILSILEMYGVSFEHMP 332 Query: 348 QASSEHSICVAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNP 407 S+ + D K I EE + + D I+I P+MA++A VG M Sbjct: 333 SGVDSVSLVIEDCKLDGKCDK--IIEEIKKQCNP---DSIEIHPNMALVATVGTGMAKTK 387 Query: 408 GASGRMFQALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAF 456 G + ++F AL + NVN+ I QGSSE+N+ + D +KA+ +++ AF Sbjct: 388 GIANKIFTALSKENVNIRMIDQGSSEINVIVGVETVDFEKAVKSIYNAF 436 Lambda K H 0.317 0.134 0.375 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: 756 Number of extensions: 38 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: 815 Length of database: 437 Length adjustment: 37 Effective length of query: 778 Effective length of database: 400 Effective search space: 311200 Effective search space used: 311200 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