Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_062060608.1 N456_RS18225 aspartate kinase
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >NCBI__GCF_001401755.1:WP_062060608.1 Length = 445 Score = 212 bits (540), Expect = 3e-59 Identities = 150/470 (31%), Positives = 249/470 (52%), Gaps = 36/470 (7%) Query: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60 M+VLKFGGTSVGS EN+ + ++ ++ + +VV SAMSGVT+ L + E R D Sbjct: 1 MRVLKFGGTSVGSVENLNRVREILTSDQ--DDKIVVCSAMSGVTDQLVRLVENI-RFNDT 57 Query: 61 DT---HLKEIEAKHFAVIRSLLP-AAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTK 116 D +L ++E+KH VI +L+ +N + + I E+ ++ + +E S Sbjct: 58 DAITRNLHKLESKHTDVIDTLIEDQEIRNTLKDGVSIMITEMFEI-----SSQEYSEIIN 112 Query: 117 DQILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTD--SNFGQAKVETELTEMLINNF 174 +I++YGE T++ S + ++ ++ + + D N KV +L +L Sbjct: 113 SKIITYGETLLTYIFSGFLNSVGITNVLLDAKEFMHVDVIENPNLDKVGNKLKAIL---- 168 Query: 175 YQENKDKVLFVT-GFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTA 233 + + L++T GF+ N G+++ L RGGSDYTA + GAAL A E++IWTD++G+ Sbjct: 169 -KSKEQSSLYITQGFVCKNEKGQISHLKRGGSDYTATIIGAALYASEVQIWTDIDGLHNN 227 Query: 234 DPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYI 293 DPR V + L+Y EA EL+YFGAK+++P T+ P K IP+++KNTF+P+ +GT I Sbjct: 228 DPRYVDDTHPISHLTYNEAAELAYFGAKILHPQTVSPVVGKDIPVLLKNTFDPEASGTVI 287 Query: 294 KSDVKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSE 353 + K +K IS+ D I+ I + + M+ G+ R+F + ++ +IT S Sbjct: 288 SN--KTYKKGLKAISAKDGITAIKIKSNRMLMAHGYLRRIFEVFDNHNTSIDMITTSEIA 345 Query: 354 HSITFAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGR 413 S+T D + I KE E + VE + +++ IVGE++ S + Sbjct: 346 ISLTI-----DNINNLDKIIKEIEAYAEI------TVEQDHSIICIVGESVINDKN-SYK 393 Query: 414 LFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKR 463 LF L N I VR ++ G S NIS+++ D + +++ F K+ Sbjct: 394 LFEIL--NYIPVRMVSYGGSNNNISLLVDTKDKIPTLRFLNEKLFQTQKK 441 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: 759 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 817 Length of database: 445 Length adjustment: 37 Effective length of query: 780 Effective length of database: 408 Effective search space: 318240 Effective search space used: 318240 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