Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012475797.1 CPHAMN1_RS12085 lysine-sensitive aspartokinase 3
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >NCBI__GCF_000020545.1:WP_012475797.1 Length = 471 Score = 284 bits (726), Expect = 9e-81 Identities = 167/472 (35%), Positives = 286/472 (60%), Gaps = 23/472 (4%) Query: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMA--ERGE 58 M V+KFGGTS+G+A +K +++VG EK+KN P+VVLSA SG+TN L ++AE A R + Sbjct: 1 MAVMKFGGTSIGTASAMKRAMQIVGREKEKNIPLVVLSACSGITNRLIQIAEAAGDSRLD 60 Query: 59 DYDTHLKEIEAKHFAVIRSLL-PAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKD 117 + E+ H ++ L+ A+ + + ++ + EL+ L+Q V + EL+ ++ D Sbjct: 61 EAMRLSGEVREHHLELVEELINDASLRQSLKEKVDAYIGELDMLIQGVDIVGELTARSFD 120 Query: 118 QILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQE 177 S+GE ST + S + D+++ + +++ TD NF A+ +L E + N + Sbjct: 121 TFCSFGELLSTTVFSDAMREAGYDTVWKDIREVMITDDNFSAARPFEDLCEKNVQNSLRP 180 Query: 178 --NKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADP 235 + ++ GFI S G+ TT+GRGGSDYTAA+ GA L ++EI+IWTDV+G+MT DP Sbjct: 181 LLEQGSIVVTQGFIGSTRDGKTTTMGRGGSDYTAALLGAWLPSDEIQIWTDVDGVMTCDP 240 Query: 236 RMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKS 295 R+V A S+ +++TEA ELSY GAKV++P T+ PA + IP+ + N+ P+ GT I + Sbjct: 241 RIVPDARSIRVMTFTEAAELSYLGAKVLHPDTIAPAVKQNIPVYVLNSLCPESKGTVITN 300 Query: 296 DVK-----ASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQS 350 + + + +K I+ IIN + M+G+ GF +F + +R ++V ++ S Sbjct: 301 NPETLEGMSYGGLVKSIAVKKGQCIINFRSNRMLGRHGFMADIFGVFARAGVSVEMV--S 358 Query: 351 SSEHSITFAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGM 410 +SE S++ V S++ SL +L D +K+ E+E ++A +++VG+N++ GM Sbjct: 359 TSEVSVSLTV-----SESASL----EQLLDDLRKMGEVEIEPDVATISVVGDNLRTAKGM 409 Query: 411 SGRLFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLK 462 +GR+F+A+ +N+R I+QG+SE N+ ++ +D+ +AV +H FF+D++ Sbjct: 410 AGRIFSAM--KDVNIRMISQGASEINVGFVVEGEDVFRAVQHLHHEFFSDIE 459 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: 834 Number of extensions: 42 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: 471 Length adjustment: 37 Effective length of query: 780 Effective length of database: 434 Effective search space: 338520 Effective search space used: 338520 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 10 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