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PR00693

Identifier
GMCSFACTOR  [View Relations]  [View Alignment]  
Accession
PR00693
No. of Motifs
6
Creation Date
12-APR-1997  (UPDATE 07-JUN-1999)
Title
Granulocyte-macrophage colony-stimulating factor signature
Database References

PROSITE; PS00702 GM_CSF
BLOCKS; BL00702
PFAM; PF01109 GM_CSF
INTERPRO; IPR000773
PDB; 1CSG
SCOP; 1CSG
CATH; 1CSG
Literature References
1. MORSTYN, G. AND BURGESS, A.W.
Hematopoietic growth-factors - A review.
CANCER RES. 48 5624-5637 (1988).
 
2. WALTER, M.R., COOK, W.J., EALICK, S.E., NAGABHUSHAN, T.L.,
TROTTA, P.P. AND BUGG, C.E.
3-Dimensional structure of recombinant human granulocyte-macrophage
colony-stimulating factor.
J.MOL.BIOL. 224 1075-1085 (1992).

Documentation
Granulocyte-macrophage colony-stimulating factor (GMCSF) is a cytokine
that acts in hematopoiesis to stimulate growth and differentiation of
hematopoietic precursor cells from various lineages (including granulocytes,
macrophages, eosinophils and erythrocytes) [1,2]. GMCSF is a glycoprotein
of ~120 residues that contains 4 conserved cysteines that participate in
disulphide bond formation.
 
The crystal structure of recombinant human GMCSF has been determined to
2.8A resolution [2]. There are two molecules in the asymmetric unit, which
are related by an approximate non-crystallographic 2-fold axis. The overall
structure, which is highly compact and globular with a predominantly
hydrophobic core, is characterised by a 4-alpha-helix bundle. The helices
are arranged in a left-handed anti-parallel fashion, with two overhand
connections. Within the connections is a two-stranded anti-parallel
beta-sheet. The tertiary structure has a topology similar to that of
porcine growth factor and interferon-beta. Most of the proposed critical
regions for receptor binding are located on a continuous surface at one end
of the molecule that includes the C terminus [2].
 
GMCSFACTOR is a 6-element fingerprint that provides a signature for 
granulocyte-macrophage colony-stimulating factors. The fingerprint was
derived from an initial alignment of 6 sequences: the motifs were drawn
from conserved regions spanning the full alignment length - motif 1 spans
the first helix; motif 2 lies in the loop between strand 1 and helix 3;
motif 3 spans helices 3 and 4; motif 4 encompasses helix 5; motif 5 spans
the second strand and the loop preceding it; and motif 6 spans helix 6.
Two iterations on OWL29.2 were required to reach convergence, at which
point a true set comprising 15 sequences was identified.
 
An update on SPTR37_9f identified a true set of 9 sequences.
Summary Information
9 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6999999
5000000
4000000
3000000
2000000
123456
True Positives
CSF2_BOVIN    CSF2_CANFA    CSF2_CEREL    CSF2_FELCA    
CSF2_HUMAN CSF2_MOUSE CSF2_PIG CSF2_RAT
CSF2_SHEEP
Sequence Titles
CSF2_BOVIN  GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - BOS TAURUS (BOVINE). 
CSF2_CANFA GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - CANIS FAMILIARIS (DOG).
CSF2_CEREL GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - CERVUS ELAPHUS (RED DEER).
CSF2_FELCA GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - FELIS SILVESTRIS CATUS (CAT).
CSF2_HUMAN GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) (SARGRAMOSTIM) (MOLGRAMOSTIN) - HOMO SAPIENS (HUMAN).
CSF2_MOUSE GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - MUS MUSCULUS (MOUSE).
CSF2_PIG GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - SUS SCROFA (PIG).
CSF2_RAT GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR (GM-CSF) (COLONY- STIMULATING FACTOR) (CSF) - RATTUS NORVEGICUS (RAT).
CSF2_SHEEP GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR PRECURSOR (GM-CSF) (COLONY-STIMULATING FACTOR) (CSF) - OVIS ARIES (SHEEP).
Scan History
OWL29_2    2  50   NSINGLE    
SPTR37_9f 2 10 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
TRPWQHVDAIKEALSLLN CSF2_SHEEP 27 27 -
TRPWQHVDAIKEALSLLN CSF2_CEREL 27 27 -
TRPWQHVDAIKEALSLLN CSF2_BOVIN 27 27 -
TRPSQHVDAIQEALSLLN CSF2_CANFA 27 27 -
TRPWKHVDAIKEALSLLN CSF2_RAT 10 10 -
TRPWKHVEAIKEALNLLD CSF2_MOUSE 27 27 -

Motif 2 width=14
Element Seqn Id St Int Rpt
EVVSEMFDSQEPTC CSF2_SHEEP 58 13 -
EVVSEMFDSQEPTC CSF2_CEREL 58 13 -
EVVSEKFDSQEPTC CSF2_BOVIN 57 12 -
KVVSEVFDPEGPTC CSF2_CANFA 58 13 -
DIISNEFSIQRPTC CSF2_RAT 41 13 -
EVVSNEFSFKKLTC CSF2_MOUSE 55 10 -

Motif 3 width=18
Element Seqn Id St Int Rpt
CLQTRLELYKQGLRGSLT CSF2_SHEEP 71 -1 -
CLQTRLKLYKQGLRGSLT CSF2_CEREL 71 -1 -
CLQTRLKLYKNGLQGSLT CSF2_BOVIN 70 -1 -
CLETRLQLYKEGLQGSLT CSF2_CANFA 71 -1 -
CVQTRLKLYKQGLRGNLT CSF2_RAT 54 -1 -
CVQTRLKIFEQGLRGNFT CSF2_MOUSE 68 -1 -

Motif 4 width=14
Element Seqn Id St Int Rpt
TSLTGSLTMMASHY CSF2_SHEEP 88 -1 -
TSLSGSLTMMARHY CSF2_CEREL 88 -1 -
TSLMGSLTMMATHY CSF2_BOVIN 87 -1 -
TSLKNPLTMMANHY CSF2_CANFA 88 -1 -
TKLNGALTMIASHY CSF2_RAT 71 -1 -
TKLKGALNMTASYY CSF2_MOUSE 85 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
CPPTQETSCETQIITF CSF2_SHEEP 105 3 -
CPPTQETSCETQTITF CSF2_CEREL 105 3 -
CPPTPETSCGTQFISF CSF2_BOVIN 104 3 -
CPPTPESPCATQNINF CSF2_CANFA 105 3 -
CPPTPETDCEIEVTTF CSF2_RAT 88 3 -
CPPTPETDCETQVTTY CSF2_MOUSE 102 3 -

Motif 6 width=18
Element Seqn Id St Int Rpt
FKSFKENLKDFLFIIPFD CSF2_SHEEP 120 -1 -
FKSFKENLKDFLFIIPFD CSF2_CEREL 120 -1 -
FKNFKEDLKEFLFIIPFD CSF2_BOVIN 119 -1 -
FKSFKENLKDFLFNIPFD CSF2_CANFA 120 -1 -
FEDFIKNLKGFLFDIPFD CSF2_RAT 103 -1 -
YADFIDSLKTFLTDIPFE CSF2_MOUSE 117 -1 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
TRPWQHVDAIKEALSLLN CSF2_SHEEP 27 27 -
TRPWQHVDAIKEALSLLN CSF2_CEREL 27 27 -
TRPWQHVDAIKEALSLLN CSF2_BOVIN 27 27 -
TQPWEHVNAIQEARRLLN CSF2_HUMAN 27 27 -
TRPWQHVDAIKEALSLLN CSF2_PIG 27 27 -
TRPSQHVDAIQEALSLLN CSF2_CANFA 27 27 -
TRPWQHVDAMKEALSLLN CSF2_FELCA 27 27 -
TRPWKHVDAIKEALSLLN CSF2_RAT 10 10 -
TRPWKHVEAIKEALNLLD CSF2_MOUSE 27 27 -

Motif 2 width=14
Element Seqn Id St Int Rpt
EVVSEMFDSQEPTC CSF2_SHEEP 58 13 -
EVVSEMFDSQEPTC CSF2_CEREL 58 13 -
EVVSEKFDSQEPTC CSF2_BOVIN 57 12 -
EVISEMFDLQEPTC CSF2_HUMAN 58 13 -
DVVCEMFDPQEPTC CSF2_PIG 58 13 -
KVVSEVFDPEGPTC CSF2_CANFA 58 13 -
EVVSEMFDPEEPKC CSF2_FELCA 58 13 -
DIISNEFSIQRPTC CSF2_RAT 41 13 -
EVVSNEFSFKKLTC CSF2_MOUSE 55 10 -

Motif 3 width=18
Element Seqn Id St Int Rpt
CLQTRLELYKQGLRGSLT CSF2_SHEEP 71 -1 -
CLQTRLKLYKQGLRGSLT CSF2_CEREL 71 -1 -
CLQTRLKLYKNGLQGSLT CSF2_BOVIN 70 -1 -
CLQTRLELYKQGLRGSLT CSF2_HUMAN 71 -1 -
CVQTRLNLYKQGLRGSLT CSF2_PIG 71 -1 -
CLETRLQLYKEGLQGSLT CSF2_CANFA 71 -1 -
CLQTHLKLYEQGLRGSLI CSF2_FELCA 71 -1 -
CVQTRLKLYKQGLRGNLT CSF2_RAT 54 -1 -
CVQTRLKIFEQGLRGNFT CSF2_MOUSE 68 -1 -

Motif 4 width=14
Element Seqn Id St Int Rpt
TSLTGSLTMMASHY CSF2_SHEEP 88 -1 -
TSLSGSLTMMARHY CSF2_CEREL 88 -1 -
TSLMGSLTMMATHY CSF2_BOVIN 87 -1 -
TKLKGPLTMMASHY CSF2_HUMAN 88 -1 -
TRLKSPLTLLAKHY CSF2_PIG 88 -1 -
TSLKNPLTMMANHY CSF2_CANFA 88 -1 -
ISLKEPLRMMANHY CSF2_FELCA 88 -1 -
TKLNGALTMIASHY CSF2_RAT 71 -1 -
TKLKGALNMTASYY CSF2_MOUSE 85 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
CPPTQETSCETQIITF CSF2_SHEEP 105 3 -
CPPTQETSCETQTITF CSF2_CEREL 105 3 -
CPPTPETSCGTQFISF CSF2_BOVIN 104 3 -
CPPTPETSCATQIITF CSF2_HUMAN 105 3 -
CPLTEETSCETQSITF CSF2_PIG 105 3 -
CPPTPESPCATQNINF CSF2_CANFA 105 3 -
CPLTPETPCETQTITF CSF2_FELCA 105 3 -
CPPTPETDCEIEVTTF CSF2_RAT 88 3 -
CPPTPETDCETQVTTY CSF2_MOUSE 102 3 -

Motif 6 width=18
Element Seqn Id St Int Rpt
FKSFKENLKDFLFIIPFD CSF2_SHEEP 120 -1 -
FKSFKENLKDFLFIIPFD CSF2_CEREL 120 -1 -
FKNFKEDLKEFLFIIPFD CSF2_BOVIN 119 -1 -
FESFKENLKDFLLVIPFD CSF2_HUMAN 120 -1 -
FKSFKDSLNKFLFTIPFD CSF2_PIG 120 -1 -
FKSFKENLKDFLFNIPFD CSF2_CANFA 120 -1 -
FKNFKEKLKDFLFNNPFD CSF2_FELCA 120 -1 -
FEDFIKNLKGFLFDIPFD CSF2_RAT 103 -1 -
YADFIDSLKTFLTDIPFE CSF2_MOUSE 117 -1 -