Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013841940.1 DESRU_RS09750 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000215085.1:WP_013841940.1 Length = 411 Score = 209 bits (533), Expect = 2e-58 Identities = 137/411 (33%), Positives = 219/411 (53%), Gaps = 25/411 (6%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDT-----TDHLIELAKTID 395 +V KFGG ++ E ++VA +I + G PVVV+SA+G TD L+ A Sbjct: 4 LVQKFGGTSLLTQELRDRVATRIAEAVDEGYAPVVVVSAIGRAGEPYATDTLLNFALAAG 63 Query: 396 ENPDPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINT 455 + RELD+L+S GE+ S +M L++ G +A+ TG Q IITD + ARI+ ++ Sbjct: 64 RDLPARELDILMSCGEVISGVVMVNTLQRMGRQAVFLTGAQAGIITDHNHNDARILRVDP 123 Query: 456 DIISRYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGV 515 + K+ I +VAGFQGI+E G+ITTLGRGGSD TA AL +L A+ +++ DV+G+ Sbjct: 124 KNVISQAKEGKIVIVAGFQGISEEGEITTLGRGGSDTTAAALGVALNAECIDIFTDVEGI 183 Query: 516 YTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGT 575 TADPRIV+DAR++ +++ E+ +L+ GA+V+ RA E A + + + +++ + GT Sbjct: 184 MTADPRIVEDARILDNVTYNEICQLAHEGAKVIHPRAVEIAMQKNIPIRVRSTFTNSPGT 243 Query: 576 LIWEGTKVENPI-VRAVTFEDGMA--------KVVLKDVP-DKPGVAARIMRTLSQMGVN 625 L+ +V I + G+A K+ + +V D P A RI + L+ ++ Sbjct: 244 LVASHNQVYGTIDITTDRLASGVAHIAGVTQFKLTVSEVNIDNP--ALRIFKALALADIS 301 Query: 626 IDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNLTS 685 ID I + + F V + K L + I AK+S VG + Sbjct: 302 IDFI-----NVSPELIMFTVKDEVAKKATAVLQNLGIHPQ---IRPNCAKISTVGAGIHG 353 Query: 686 TPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 P + + + E LA E + I S S + I V++ + A++A+H +FEL Sbjct: 354 VPGVMSHIVEALAEEQVEILQSSDSHTTIWVLVQQDQMHKAIQALHRKFEL 404 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: 638 Number of extensions: 29 Number of successful extensions: 3 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: 411 Length adjustment: 36 Effective length of query: 703 Effective length of database: 375 Effective search space: 263625 Effective search space used: 263625 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 Jul 25 2024. The underlying query database was built on Jul 25 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