Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_041278220.1 DP_RS02240 aspartate kinase
Query= SwissProt::A4VFY3 (476 letters) >NCBI__GCF_000025945.1:WP_041278220.1 Length = 463 Score = 372 bits (956), Expect = e-107 Identities = 209/464 (45%), Positives = 288/464 (62%), Gaps = 12/464 (2%) Query: 4 VEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVYQR 63 +EKIGGT+MSRF EVLDN+ E ++ RI+VVSAYSG+TN LLEHKKT +PG+YQ Sbjct: 6 IEKIGGTTMSRFGEVLDNVIFYDSED--IFNRIYVVSAYSGVTNALLEHKKTHQPGIYQT 63 Query: 64 FADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQKLC 123 F + A A+E ++ + N +L AN FI RI DA E +HS+ + Sbjct: 64 FVQNE---ACDMAMERLKTTLCEINRGFADIGLDLEVANNFICKRIQDAVEVLHSMANVL 120 Query: 124 AYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFEEM 183 + G+ SE L+ RE+LAS+GE HSAFNS L+ RG A DL+GWQ + ++ Sbjct: 121 SSGYVNRSEMLLAARELLASIGEMHSAFNSANILQNRGYKASYVDLSGWQDSRDMTIDQR 180 Query: 184 ISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEFHL 243 I F FD S + +ATGY EG+M FDRGYSE+TF++IA A EAIIHKE+HL Sbjct: 181 ILETFTKFDPSDTICIATGYAKGREGIMREFDRGYSEVTFSKIAVLLKASEAIIHKEYHL 240 Query: 244 SSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEPEH 303 S DP ++G DKV I TNYDVADQL+++GMEAIHP+A+K + AG+ +RIKN+F+P H Sbjct: 241 CSGDPLIIGEDKVHPICNTNYDVADQLADVGMEAIHPKASKQIEIAGISIRIKNSFDPSH 300 Query: 304 GGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVVNKD 363 GTL +++Y + E+I G V +EV D M+G++G+DM+I ++L ++ +NK Sbjct: 301 SGTLFTKEYICPQSKTEVITGSDKVTCLEVHDTRMVGEVGFDMKIMEVLSAHQVSYINKA 360 Query: 364 SDANSI--TYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKTV 421 ++AN+I Y + + + R R E VT + AIV AIGS++ GILAK Sbjct: 361 TNANTIGVIVYDNDCTEELLRDLRAEFEL-----VTDMHTAIVCAIGSNIAKPGILAKAT 415 Query: 422 AALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIE 465 ALA + I+I A+ Q+ RQ MQ ++N E + A LH AL E Sbjct: 416 NALATSHINILAVSQTSRQTNMQFIINREHFKEAQRVLHAALCE 459 Lambda K H 0.318 0.133 0.372 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: 561 Number of extensions: 19 Number of successful extensions: 5 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: 476 Length of database: 463 Length adjustment: 33 Effective length of query: 443 Effective length of database: 430 Effective search space: 190490 Effective search space used: 190490 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 (21.7 bits) S2: 51 (24.3 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