Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate CA265_RS09655 CA265_RS09655 aspartate kinase
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >FitnessBrowser__Pedo557:CA265_RS09655 Length = 437 Score = 228 bits (580), Expect = 7e-64 Identities = 162/466 (34%), Positives = 254/466 (54%), Gaps = 38/466 (8%) Query: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60 MK+LKFGGTSVGS E + LL ++ +++ +VVLSA+SG TN L E+A G+ Sbjct: 1 MKILKFGGTSVGSPERMTKLLDIINPNEEQ---IVVLSAVSGTTNSLVEIANYFLAGDKK 57 Query: 61 DTH--LKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELED----LLQAVANLRELSLQ 114 ++ + K+ + LLPAA + NE+ D L +AN S++ Sbjct: 58 KGSECVENLYQKYKTFVVELLPAA-------EFQEQGNEVIDYHFGFLAGLANDIFTSIE 110 Query: 115 TKDQILSYGERCSTFMISHIASKNIG-DSIYVNGSDLIKTDSNFGQAKVETELTEMLINN 173 K +L+ GE ST + HI K+IG S+ + D +KTD + + + T + Sbjct: 111 EK-VVLAQGELLSTTLY-HIYLKSIGVPSVLLPALDFMKTDED---NEPDIPFTTKHLTP 165 Query: 174 FYQENKDKVLFVT-GFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMT 232 +++KD LF+T G+I N+ G V L RGGSDYTA++ GAA+ AEE++IWTD++GM Sbjct: 166 LLEQHKDNKLFITQGYICRNSFGEVDNLRRGGSDYTASLLGAAILAEEVQIWTDIDGMHN 225 Query: 233 ADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTY 292 DPR+VK + +LS+ EA EL+YFGAK+++P ++ PA KIP+ + NT EP AGT Sbjct: 226 NDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQKYKIPVRLLNTMEPSAAGTL 285 Query: 293 IKSDVKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSS 352 I D + IK I++ D I+ I + S M+ GF R+F + R + + +IT S Sbjct: 286 ITHDSERGK--IKSIAAKDGITAIRIQSSRMLLAYGFLRRVFEVFERYKTPIDMITTSEV 343 Query: 353 EHSITFAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSG 412 S+T D + + I +E E EV+ N +++ +VG+ G + Sbjct: 344 AVSLTI-----DETAHLPQIIEELE------SFGTVEVDTNHSIVCVVGDFGSEKHGFAS 392 Query: 413 RLFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFF 458 R+ G I +R I+ G S YN+S++I + ++A+ ++H+ F Sbjct: 393 RVLE--GLKHIPIRMISYGGSNYNVSLLILSEYKTEALRSLHNRLF 436 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: 731 Number of extensions: 42 Number of successful extensions: 6 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: 817 Length of database: 437 Length adjustment: 37 Effective length of query: 780 Effective length of database: 400 Effective search space: 312000 Effective search space used: 312000 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 09 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