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PR01100

Identifier
SHIKIMTKNASE  [View Relations]  [View Alignment]  
Accession
PR01100
No. of Motifs
5
Creation Date
21-DEC-1998  (UPDATE 10-JUN-1999)
Title
Shikimate kinase family signature
Database References

PROSITE; PS01128 SHIKIMATE_KINASE
BLOCKS; BL01128
PFAM; PF01202 SKI
INTERPRO; IPR000623
Literature References
1. GRIFFIN, H.C. AND GASSON, M.J.
The gene (aroK) encoding shikimate kinase-I from Eschericha coli.
DNA SEQ. 5 195-197 (1995).
 
2. MATSUO, Y. AND NISHIKAWA, K.
Protein structural similarities predicted by a sequence structure
compatibility method.
PROTEIN SCI. 3 2055-2063 (1994).
 
3. KRELL, T., COGGINS, J.R. AND LAPTHORN, A.J.
The three-dimensional structure of shikimate kinase.
J.MOL.BIOL. 278 983-997 (1998).

Documentation
Shikimate kinase (EC 2.7.1.71) catalyses the fifth step in the biosynthesis
of aromatic amino acids from chorismate (the so-called shikimate pathway) 
[1]:
 
	     ATP + shikimate = ADP + shikimate-3-phosphate	     
 
The protein is found in bacteria, plants and fungi (where it is part of
a multifunctional enzyme that catalyses five consecutive steps in this 
pathway).
 
In 1994, the 3D structure of shikimate kinase was predicted to be very close
to that of adenylate kinase, suggesting a functional similarity as well as
an evolutionary relationship [2]. This prediction has since been confirmed
experimentally [3]. The protein is reported to possess an alpha/beta fold,
consisting of a central sheet of five parallel beta-strands flanked by
alpha-helices [3]. Such a topology is very similar to that of adenylate
kinase [3].
 
SHIKIMTKNASE is a 5-element fingerprint that provides a signature for the
shikimate kinase family. The fingerprint was derived from an initial
alignment of 12 sequences: the motifs were drawn from the central portion of
the alignment - motifs 3 and 4 span the region encoded by PROSITE pattern 
SHIKIMATE_KINASE (PS001128), which includes a run of 3 conserved glycines.
Two iterations on OWL30.2 were required to reach convergence, at which point
a true set comprising 13 sequences was identified. Several partial matches
were also found, all of which are related sequences or fragments that fail
to match one or more motifs.
 
An update on SPTR37_9f identified a true set of 13 sequences, and 2
partial matches.
Summary Information
  13 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
51313131313
400000
300000
211000
12345
True Positives
ARO1_EMENI    ARO1_PNECA    ARO1_YEAST    AROK_ECOLI    
AROK_HAEIN AROK_HELPY AROK_LACLA AROK_MYCTU
AROK_SYNY3 AROL_ECOLI AROL_ERWCH AROL_LYCES
O67925
True Positive Partials
Codes involving 2 elements
AROK_BACSU
Sequence Titles
ARO1_EMENI  PENTAFUNCTIONAL AROM POLYPEPTIDE [INCLUDES: 3-DEHYDROQUINATE SYNTHASE (EC 4.6.1.3); 3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10) (3-DEHYDROQUINASE); SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25); SHIKIMATE KINASE (EC 2.7.1.71); EPSP SYNTHASE (EC 2.5.1.19)] - EMERICELLA NIDULANS (ASPERGILLUS NIDULANS). 
ARO1_PNECA PENTAFUNCTIONAL AROM POLYPEPTIDE [INCLUDES: 3-DEHYDROQUINATE SYNTHASE (EC 4.6.1.3); 3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10) (3-DEHYDROQUINASE); SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25); SHIKIMATE KINASE (EC 2.7.1.71); EPSP SYNTHASE (EC 2.5.1.19)] - PNEUMOCYSTIS CARINII.
ARO1_YEAST PENTAFUNCTIONAL AROM POLYPEPTIDE [INCLUDES: 3-DEHYDROQUINATE SYNTHASE (EC 4.6.1.3); 3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10) (3-DEHYDROQUINASE); SHIKIMATE 5-DEHYDROGENASE (EC 1.1.1.25); SHIKIMATE KINASE (EC 2.7.1.71); EPSP SYNTHASE (EC 2.5.1.19)] - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
AROK_ECOLI SHIKIMATE KINASE I (EC 2.7.1.71) (SKI) - ESCHERICHIA COLI.
AROK_HAEIN SHIKIMATE KINASE (EC 2.7.1.71) (SK) - HAEMOPHILUS INFLUENZAE.
AROK_HELPY SHIKIMATE KINASE (EC 2.7.1.71) (SK) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
AROK_LACLA SHIKIMATE KINASE (EC 2.7.1.71) (SK) - LACTOCOCCUS LACTIS (SUBSP. LACTIS) (STREPTOCOCCUS LACTIS).
AROK_MYCTU SHIKIMATE KINASE (EC 2.7.1.71) (SK) - MYCOBACTERIUM TUBERCULOSIS.
AROK_SYNY3 SHIKIMATE KINASE (EC 2.7.1.71) (SK) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
AROL_ECOLI SHIKIMATE KINASE II (EC 2.7.1.71) (SKII) - ESCHERICHIA COLI.
AROL_ERWCH SHIKIMATE KINASE (EC 2.7.1.71) (SK) - ERWINIA CHRYSANTHEMI.
AROL_LYCES SHIKIMATE KINASE PRECURSOR (EC 2.7.1.71) - LYCOPERSICON ESCULENTUM (TOMATO).
O67925 SHIKIMATE KINASE - AQUIFEX AEOLICUS.

AROK_BACSU SHIKIMATE KINASE (EC 2.7.1.71) (SK) - BACILLUS SUBTILIS.
Scan History
OWL30_2    2  375  NSINGLE    
SPTR37_9f 2 110 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
LFLIGMMGSGKSTVGP AROK_SYNY3 15 15 -
IFLVGPMGAGKSTIGR AROK_ECOLI 6 6 -
IFLVGPMGAGKSTIGR AROK_HAEIN 7 7 -
VYLVGMMGCGKTTVGR AROL_LYCES 107 107 -
IFMVGARGCGKTTVGR AROL_ERWCH 5 5 -
LFLIGPRGCGKTTVGM AROL_ECOLI 5 5 -
IILIGFMGAGKSTVAK AROK_LACLA 3 3 -
IYIIGMRGAGKSTAGN ARO1_EMENI 867 867 -
LVLIGFMGSGKSSLAQ AROK_HELPY 4 4 -
AVLVGLPGSGKSTIGR AROK_MYCTU 5 5 -
IFLIGMRGAGKTTLGQ ARO1_PNECA 871 871 -
VVIIGMRAAGKTTISK ARO1_YEAST 891 891 -

Motif 2 width=14
Element Seqn Id St Int Rpt
RFFDADVLIERVAG AROK_SYNY3 39 8 -
EFYDSDQEIEKRTG AROK_ECOLI 30 8 -
DFIDSDAVIEERTG AROK_HAEIN 31 8 -
SFFDCDRLIEQAVG AROL_LYCES 131 8 -
EFVDTDIFMQHTSG AROL_ERWCH 29 8 -
RFVDTDQWLQSQLN AROL_ECOLI 29 8 -
EFTDLDKLIEEEIE AROK_LACLA 23 4 -
PFVDLDTELETVEG ARO1_EMENI 891 8 -
EVLDTDMIISERVG AROK_HELPY 28 8 -
GLLDTDVAIEQRTG AROK_MYCTU 29 8 -
EFIDLDSIIEEDIK ARO1_PNECA 895 8 -
KLVDLDELFEQQHN ARO1_YEAST 915 8 -

Motif 3 width=9
Element Seqn Id St Int Rpt
FRDLETEVL AROK_SYNY3 67 14 -
FRDREEKVI AROK_ECOLI 58 14 -
FRKREERII AROK_HAEIN 59 14 -
FRDNETEVL AROL_LYCES 160 15 -
FRRRESEAL AROL_ERWCH 57 14 -
FRARETAAL AROL_ECOLI 57 14 -
FRKIENEVF AROK_LACLA 51 14 -
FRNAELEIL ARO1_EMENI 919 14 -
FRMFEKNLI AROK_HELPY 56 14 -
FRRIEEDVV AROK_MYCTU 57 14 -
FRRKELHFL ARO1_PNECA 923 14 -
FREEETRIF ARO1_YEAST 944 15 -

Motif 4 width=10
Element Seqn Id St Int Rpt
VIATGGGVVL AROK_SYNY3 85 9 -
VLATGGGSVK AROK_ECOLI 76 9 -
VLSTGGGAVL AROK_HAEIN 77 9 -
VVSTGGGAVV AROL_LYCES 178 9 -
VVATGGGMVL AROL_ERWCH 74 8 -
VIATGGGIIL AROL_ECOLI 74 8 -
IIATGGGIIE AROK_LACLA 68 8 -
VFACGGGVVE ARO1_EMENI 939 11 -
VISTGGGIVM AROK_HELPY 75 10 -
VLSLGGGAVT AROK_MYCTU 75 9 -
IISCGGGIIE ARO1_PNECA 943 11 -
VFSTGGGIVE ARO1_YEAST 965 12 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GLVIWLDGSLELLLARLQ AROK_SYNY3 105 10 -
GVVVYLETTIEKQLARTQ AROK_ECOLI 97 11 -
GIVIYLETTVEKQFQRTQ AROK_HAEIN 98 11 -
GISVWLDVPLEALAKRIT AROL_LYCES 198 10 -
GTVVYLFAPAEELALRLQ AROL_ERWCH 95 11 -
GIVVYLCAPVSVLVNRLQ AROL_ECOLI 95 11 -
SRVVFLTADFDTLWKRIS AROK_LACLA 89 11 -
GNVLLLMRDIKKIMDFLS ARO1_EMENI 964 15 -
GTTFYLKMDFETLIKRLN AROK_HELPY 92 7 -
HTVVYLEISAAEGVRRTG AROK_MYCTU 95 10 -
GIVIHIHRNIQDIIKYLN ARO1_PNECA 968 15 -
GYVLHLHRDIEETIVFLQ ARO1_YEAST 990 15 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
LFLIGMMGSGKSTVGP AROK_SYNY3 15 15 -
IFLVGPMGAGKSTIGR AROK_ECOLI 6 6 -
IFLVGPMGAGKSTIGR AROK_HAEIN 7 7 -
VYLVGMMGCGKTTVGR AROL_LYCES 107 107 -
IFMVGARGCGKTTVGR AROL_ERWCH 5 5 -
LFLIGPRGCGKTTVGM AROL_ECOLI 5 5 -
IILIGFMGAGKSTVAK AROK_LACLA 3 3 -
IYLIGFMCSGKSTVGS O67925 3 3 -
IYIIGMRGAGKSTAGN ARO1_EMENI 867 867 -
LVLIGFMGSGKSSLAQ AROK_HELPY 4 4 -
AVLVGLPGSGKSTIGR AROK_MYCTU 5 5 -
IFLIGMRGAGKTTLGQ ARO1_PNECA 871 871 -
VVIIGMRAAGKTTISK ARO1_YEAST 891 891 -

Motif 2 width=14
Element Seqn Id St Int Rpt
RFFDADVLIERVAG AROK_SYNY3 39 8 -
EFYDSDQEIEKRTG AROK_ECOLI 30 8 -
DFIDSDAVIEERTG AROK_HAEIN 31 8 -
SFFDCDRLIEQAVG AROL_LYCES 131 8 -
EFVDTDIFMQHTSG AROL_ERWCH 29 8 -
RFVDTDQWLQSQLN AROL_ECOLI 29 8 -
EFTDLDKLIEEEIE AROK_LACLA 23 4 -
PFYDVDEEVQKREG O67925 27 8 -
PFVDLDTELETVEG ARO1_EMENI 891 8 -
EVLDTDMIISERVG AROK_HELPY 28 8 -
GLLDTDVAIEQRTG AROK_MYCTU 29 8 -
EFIDLDSIIEEDIK ARO1_PNECA 895 8 -
KLVDLDELFEQQHN ARO1_YEAST 915 8 -

Motif 3 width=9
Element Seqn Id St Int Rpt
FRDLETEVL AROK_SYNY3 67 14 -
FRDREEKVI AROK_ECOLI 58 14 -
FRKREERII AROK_HAEIN 59 14 -
FRDNETEVL AROL_LYCES 160 15 -
FRRRESEAL AROL_ERWCH 57 14 -
FRARETAAL AROL_ECOLI 57 14 -
FRKIENEVF AROK_LACLA 51 14 -
FRKLEFEVL O67925 55 14 -
FRNAELEIL ARO1_EMENI 919 14 -
FRMFEKNLI AROK_HELPY 56 14 -
FRRIEEDVV AROK_MYCTU 57 14 -
FRRKELHFL ARO1_PNECA 923 14 -
FREEETRIF ARO1_YEAST 944 15 -

Motif 4 width=10
Element Seqn Id St Int Rpt
VIATGGGVVL AROK_SYNY3 85 9 -
VLATGGGSVK AROK_ECOLI 76 9 -
VLSTGGGAVL AROK_HAEIN 77 9 -
VVSTGGGAVV AROL_LYCES 178 9 -
VVATGGGMVL AROL_ERWCH 74 8 -
VIATGGGIIL AROL_ECOLI 74 8 -
IIATGGGIIE AROK_LACLA 68 8 -
VISTGGGLGA O67925 73 9 -
VFACGGGVVE ARO1_EMENI 939 11 -
VISTGGGIVM AROK_HELPY 75 10 -
VLSLGGGAVT AROK_MYCTU 75 9 -
IISCGGGIIE ARO1_PNECA 943 11 -
VFSTGGGIVE ARO1_YEAST 965 12 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GLVIWLDGSLELLLARLQ AROK_SYNY3 105 10 -
GVVVYLETTIEKQLARTQ AROK_ECOLI 97 11 -
GIVIYLETTVEKQFQRTQ AROK_HAEIN 98 11 -
GISVWLDVPLEALAKRIT AROL_LYCES 198 10 -
GTVVYLFAPAEELALRLQ AROL_ERWCH 95 11 -
GIVVYLCAPVSVLVNRLQ AROL_ECOLI 95 11 -
SRVVFLTADFDTLWKRIS AROK_LACLA 89 11 -
GTTVFIDIPFEVFLERCK O67925 94 11 -
GNVLLLMRDIKKIMDFLS ARO1_EMENI 964 15 -
GTTFYLKMDFETLIKRLN AROK_HELPY 92 7 -
HTVVYLEISAAEGVRRTG AROK_MYCTU 95 10 -
GIVIHIHRNIQDIIKYLN ARO1_PNECA 968 15 -
GYVLHLHRDIEETIVFLQ ARO1_YEAST 990 15 -