Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_011973392.1 MAEO_RS03365 aspartate kinase
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >NCBI__GCF_000017185.1:WP_011973392.1 Length = 468 Score = 315 bits (806), Expect = 5e-90 Identities = 184/468 (39%), Positives = 294/468 (62%), Gaps = 22/468 (4%) Query: 3 VLKFGGTSVGSAENIKTLLRLVGEEKQKNSP--VVVLSAMSGVTNLLTEMAEMAERGEDY 60 V+KFGGTSVG + I+ + +++ ++ K + VVV SAMS +TN L M++ A D Sbjct: 4 VMKFGGTSVGDGQRIRNVAKIIVDKSNKENTDIVVVTSAMSQITNALVNMSKQALNVRDI 63 Query: 61 ---DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFN----ELEDLLQAVANLRELSL 113 + ++E++ KH I A + + T ++ N EL +L V+ L EL+ Sbjct: 64 AKINNFVEELKEKHAIAIDE---AVKNDDIRTEVRHVINSSIDELGKVLVGVSYLGELTP 120 Query: 114 QTKDQILSYGERCSTFMISHIASKNIG-DSIYVNGSDL-IKTDSNFGQAKVETELTEMLI 171 ++KD ILS+GER S ++S A +++G +S+++ G + + TD N+G A+ + + Sbjct: 121 KSKDYILSFGERLSAPILSG-AVRDLGKNSLFLLGGEAGLITDENYGCARPIKIKIKEKV 179 Query: 172 NNFYQENKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMM 231 N +EN + +TGF+A G +TT GRGGSDY+AA+ GA L+A+ +EIWTDV+G++ Sbjct: 180 NPLLEENI--IPIITGFVAGTENGDITTFGRGGSDYSAALVGAGLDADTVEIWTDVSGIL 237 Query: 232 TADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGT 291 T+DPR+VK +P++SY EAMEL+YFGAKV++P T+ P K IP+ IKNTFEP+ GT Sbjct: 238 TSDPRIVKNVKRIPKMSYIEAMELAYFGAKVLHPRTVEPLMEKNIPLRIKNTFEPENEGT 297 Query: 292 YIKSDVKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSS 351 +I + + S+ +K +S+I + +IN+ G+GMVG +G + R+FS L R NV+LITQ S Sbjct: 298 FITNCKELSNSVMKAVSAIRDVFLINIFGAGMVGVSGTAARIFSALGRADANVLLITQGS 357 Query: 352 SEHSITFAV--KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPG 409 SE +++ + DA+ + ++KEF+ K + + E N+AV++ VG MK + G Sbjct: 358 SETNVSVVIYGDEVDANNCMKELRKEFKNSNLVKDISIDE---NVAVISAVGVGMKGSKG 414 Query: 410 MSGRLFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAF 457 ++G+LF A+ +G N++ IAQGSSE NIS +I +++L + +H F Sbjct: 415 IAGKLFGAVAESGANIKMIAQGSSEVNISFVIGEEELENCLRILHGRF 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: 968 Number of extensions: 51 Number of successful extensions: 7 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: 468 Length adjustment: 37 Effective length of query: 780 Effective length of database: 431 Effective search space: 336180 Effective search space used: 336180 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 Jul 25 2024. The underlying query database was built on Jul 25 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