Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 18052 b4024 aspartate kinase III (NCBI)
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >FitnessBrowser__Keio:18052 Length = 449 Score = 213 bits (542), Expect = 2e-59 Identities = 148/463 (31%), Positives = 246/463 (53%), Gaps = 27/463 (5%) Query: 3 VLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDYDT 62 V KFGGTSV + + +V + N +VVLSA +G+TNLL +AE E GE ++ Sbjct: 6 VSKFGGTSVADFDAMNRSADIVLSDA--NVRLVVLSASAGITNLLVALAEGLEPGERFEK 63 Query: 63 HLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELS-LQTK----D 117 L I FA++ L + P R E+E LL+ + L E + L T D Sbjct: 64 -LDAIRNIQFAILERL-----RYPNVIR-----EEIERLLENITVLAEAAALATSPALTD 112 Query: 118 QILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVE-TELTEMLINNFYQ 176 +++S+GE ST + I + + + + +++T+ FG+A+ + L E+ Sbjct: 113 ELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLP 172 Query: 177 ENKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPR 236 + ++ GFI S GR TTLGRGGSDYTAA+ AL+A ++IWTDV G+ T DPR Sbjct: 173 RLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPR 232 Query: 237 MVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSD 296 +V A + E+++ EA E++ FGAKV++P T++PA IP+ + ++ +P GT + + Sbjct: 233 VVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNK 292 Query: 297 VKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSI 356 + L + ++ + +++ L M+ GF +F +L+R I+V LIT +SE S+ Sbjct: 293 TENPPL-FRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLIT--TSEVSV 349 Query: 357 TFAVKPT-DASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLF 415 + T S +L+ + +EL A L EVE LA++A++G ++ + G+ +F Sbjct: 350 ALTLDTTGSTSTGDTLLTQSLLMELSA--LCRVEVEEGLALVALIGNDLSKACGVGKEVF 407 Query: 416 NALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFF 458 L N+R I G+S +N+ ++ +D + V +H F Sbjct: 408 GVL--EPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLF 448 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: 684 Number of extensions: 31 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: 449 Length adjustment: 37 Effective length of query: 780 Effective length of database: 412 Effective search space: 321360 Effective search space used: 321360 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