Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 350903 BT1375 aspartokinase (NCBI ptt file)
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >FitnessBrowser__Btheta:350903 Length = 439 Score = 213 bits (541), Expect = 2e-59 Identities = 147/463 (31%), Positives = 245/463 (52%), Gaps = 28/463 (6%) Query: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMA--ERGE 58 MKVLKFGGTSVGSA+ +K + +L+ + +QK +VVLSAMSG TN L E+++ + E Sbjct: 1 MKVLKFGGTSVGSAQRMKEVAKLITDGEQK---IVVLSAMSGTTNTLVEISDYLYKKNPE 57 Query: 59 DYDTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQ 118 + + ++E+K+ + L A Q L++ + + + +L +L + Sbjct: 58 GANEIINKLESKYKQHVDELF--ATQEYKQKGLEVIKSHFDYIRSYTKDL--FTLFEEKV 113 Query: 119 ILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQEN 178 +L+ GE ST M++ + S+ + + ++TD N A+ + + + + Sbjct: 114 VLAQGELISTAMVNFYLQECGVKSVLLPALEFMRTDKN---AEPDPVYIKEKLQTQLELY 170 Query: 179 KDKVLFVT-GFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRM 237 D +++T GFI NA G + L RGGSDYTA++ GAA+ A EI+IWTD++GM DPR+ Sbjct: 171 PDMEIYITQGFICRNAYGEIDNLQRGGSDYTASLIGAAVKASEIQIWTDIDGMHNNDPRI 230 Query: 238 VKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDV 297 V K + +L + EA EL+YFGAK+++P + PA IP+ + NT +PD GT I +D Sbjct: 231 VDKTAPVRQLHFEEAAELAYFGAKILHPTCIQPAKYANIPVRLLNTMDPDAPGTLISNDT 290 Query: 298 KASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSIT 357 + IK +++ ++I+ I + S M+ GF ++F + Q ++ +I S S+T Sbjct: 291 EKGK--IKAVAAKNNITAIKIKSSRMLLAHGFLRKVFEIFESYQTSIDMICTSEVGVSVT 348 Query: 358 FAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNA 417 I K E+ D KK V+ ++ ++ +VG+ G + +A Sbjct: 349 -----------IDNTKHLNEILDDLKKYGTVTVDKDMCIICVVGDLEWENVGFEAKALDA 397 Query: 418 LGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTD 460 + I VR I+ G S YNIS +I D A+ ++ D F + Sbjct: 398 M--RDIPVRMISFGGSNYNISFLIRDCDKKTALQSLSDMLFNN 438 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: 735 Number of extensions: 36 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: 817 Length of database: 439 Length adjustment: 37 Effective length of query: 780 Effective length of database: 402 Effective search space: 313560 Effective search space used: 313560 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