Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_011305884.1 MBAR_RS04635 aspartate kinase, monofunctional class
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >NCBI__GCF_000195895.1:WP_011305884.1 Length = 472 Score = 308 bits (789), Expect = 5e-88 Identities = 179/465 (38%), Positives = 284/465 (61%), Gaps = 18/465 (3%) Query: 3 VLKFGGTSVGSAENIKTLLRLVGEEKQK-NSPVVVLSAMSGVTNLLTEMAEMAERG---- 57 V+KFGGTSVG + I+ + +L+ +++ N VVV SA+ GVT+ L E A A Sbjct: 4 VMKFGGTSVGDGKKIRHVAQLLKRYREEGNQIVVVTSALGGVTDELLENALFASTKGKVS 63 Query: 58 --EDYDTHLKEIEAKHFAVIRSLL--PAAAQNPVFTRLKIFFNELEDLLQAVANLRELSL 113 +++ T EI KH ++ + P A+ + T L + +ELE L + L EL+ Sbjct: 64 LVKEFKT---EITNKHHKAVKDAIDDPTVAKEVIQT-LDLRIDELEKALVGICYLGELTS 119 Query: 114 QTKDQILSYGERCSTFMISH-IASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLIN 172 ++ D I SYGER + ++S I S I + + G I T S++G A+ + E++ Sbjct: 120 RSIDYICSYGERLAAPIVSGAIRSLGIESTEFTGGEAGIITSSDYGNARPLEKTYELVNK 179 Query: 173 NFYQENKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMT 232 + ++L VTGFI N G +TTLGR GSD+TA++ GAAL A+EI +W +VNG+MT Sbjct: 180 RLGCRLETQILVVTGFIGENEEGIITTLGRSGSDFTASILGAALKADEIWLWKEVNGIMT 239 Query: 233 ADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTY 292 DPR+V +A ++P++SY EAMELSYFGA +++P T+ PA + IP+ +KNTFEP GT Sbjct: 240 TDPRIVPEAKTIPQISYAEAMELSYFGANILHPRTIEPAMREHIPVRVKNTFEPKLPGTL 299 Query: 293 IKSDVKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSS 352 + ++ +K +S I ++++IN++G+ MVG G RLF++L++ +NV++I+Q SS Sbjct: 300 VVAEKFQCKNVVKAVSLIKNVALINISGAEMVGAIGTVARLFAVLAKSGVNVIMISQGSS 359 Query: 353 EHSITFAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSG 412 E +I+F + A+ + +EF + K++ + N+ V+A+VG M TPG++ Sbjct: 360 ESNISFVISEAHVKTALKALHEEFNRGI-VKEI---TSDKNVCVVAVVGAGMAGTPGVAK 415 Query: 413 RLFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAF 457 R+F ALG + IN+ I+QGSS+YNIS ++ ++D AV +HD F Sbjct: 416 RVFGALGNSLINIIMISQGSSQYNISFVVRENDAFAAVKTLHDEF 460 Score = 61.6 bits (148), Expect = 1e-13 Identities = 27/75 (36%), Positives = 48/75 (64%) Query: 304 IKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAVKPT 363 +K I+S ++ ++ + G+GM G G + R+F L IN+++I+Q SS+++I+F V+ Sbjct: 388 VKEITSDKNVCVVAVVGAGMAGTPGVAKRVFGALGNSLINIIMISQGSSQYNISFVVREN 447 Query: 364 DASQAISLIKKEFEL 378 DA A+ + EFEL Sbjct: 448 DAFAAVKTLHDEFEL 462 Lambda K H 0.316 0.133 0.369 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: 795 Number of extensions: 32 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 817 Length of database: 472 Length adjustment: 37 Effective length of query: 780 Effective length of database: 435 Effective search space: 339300 Effective search space used: 339300 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 (21.6 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