Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011814438.1 HHAL_RS08325 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000015585.1:WP_011814438.1 Length = 416 Score = 322 bits (824), Expect = 3e-92 Identities = 171/402 (42%), Positives = 267/402 (66%), Gaps = 5/402 (1%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPD 399 +VV KFGG ++ E+++ VAE++ +++G VVV+SAM T+ L+ELA++I NP Sbjct: 3 LVVKKFGGTSVGTTERIQAVAEQVKASREAGDDVVVVVSAMSGETNRLVELAESIHPNPP 62 Query: 400 PRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIIS 459 RE+D+LLSTGE ++AL+++AL + A +TG Q++I+TD + ARI+DI+ + + Sbjct: 63 AREVDVLLSTGEQVTIALLTMALEQIDCPARCYTGAQVRILTDSSFSRARILDIDAEPLQ 122 Query: 460 RYLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTAD 519 L++ + VVAGFQG+ E G +TTLGRGGSD TA+ALA +L A C++Y DVDGVYT D Sbjct: 123 EDLQRGRVVVVAGFQGVDEEGALTTLGRGGSDTTAVALAAALEASECQIYTDVDGVYTTD 182 Query: 520 PRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGTLI-W 578 PR+V +AR + ++ +EM+ELS G++VLQ RA EFA KY V + + ++ +E GTLI + Sbjct: 183 PRVVPEARRLDRITVDEMLELSSLGSKVLQIRAVEFAGKYRVPLRVLSSFEEGPGTLITY 242 Query: 579 EGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEY 638 E +E P++ + F AK+ + VPD PG+AA+I+ +++ + +DMIIQ + Sbjct: 243 EEEGMEEPLISGIAFNRDEAKISVIGVPDTPGIAAKILGAVAEANIEVDMIIQNISQQGL 302 Query: 639 NTVAFIVPESQLGKLDIDLLKTRSE---AKEIIIEKGLAKVSIVGVNLTSTPEISATLFE 695 F V + + +DL++ +E A+E+ + + K+S+VGV + S ++ T+F Sbjct: 303 TDFTFTVHKRDY-QATLDLVRDNAEQLGAREVYGDDKIVKLSLVGVGMRSHAGVANTMFR 361 Query: 696 TLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 L+NEGINI MIS S +ISV+++ KY+E V+A+H FELD Sbjct: 362 ALSNEGINIQMISTSEIKISVVVEEKYLELGVRALHKAFELD 403 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: 727 Number of extensions: 41 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 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