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sequence-518.orf
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sequence-518.orf
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########################################
# Program: patmatmotifs
# Rundate: Wed 25 Nov 2015 13:56:28
# Commandline: patmatmotifs
# -full
# -outfile res/sequence-518.orf
# -sequence res/sequence-518.gb
# Report_format: dbmotif
# Report_file: res/sequence-518.orf
########################################
#=======================================
#
# Sequence: NM_000518 from: 1 to: 626
# HitCount: 11
#
# Full: Yes
# Prune: Yes
# Data_file: /usr/local/Cellar/emboss/6.6.0/share/EMBOSS/data/PROSITE/prosite.lines
#
#=======================================
Length = 12
Start = position 421 of sequence
End = position 432 of sequence
Motif = EGF_1
ATTCACCCCACCAGTGCAGGCT
| |
421 432
Length = 12
Start = position 313 of sequence
End = position 324 of sequence
Motif = EGF_1
TGCCACACTGAGTGAGCTGCAC
| |
313 324
Length = 9
Start = position 369 of sequence
End = position 377 of sequence
Motif = 2FE2S_FER_1
GGCTCCTGGGCAACGTGCT
| |
369 377
Length = 9
Start = position 285 of sequence
End = position 293 of sequence
Motif = 2FE2S_FER_1
CTCACCTGGACAACCTCAA
| |
285 293
Length = 35
Start = position 134 of sequence
End = position 168 of sequence
Motif = ANAPHYLATOXIN_1
GAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGG
| |
134 168
Length = 36
Start = position 133 of sequence
End = position 168 of sequence
Motif = ANAPHYLATOXIN_1
TGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGG
| |
133 168
Length = 46
Start = position 399 of sequence
End = position 444 of sequence
Motif = VWFC_1
TGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAA
| |
399 444
Length = 47
Start = position 398 of sequence
End = position 444 of sequence
Motif = VWFC_1
CTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAA
| |
398 444
Length = 43
Start = position 362 of sequence
End = position 404 of sequence
Motif = VWFC_1
AACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGG
| |
362 404
Length = 51
Start = position 324 of sequence
End = position 374 of sequence
Motif = VWFC_1
GTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGT
| |
324 374
Length = 46
Start = position 43 of sequence
End = position 88 of sequence
Motif = VWFC_1
TCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCC
| |
43 88
#---------------------------------------
#
# Motif: EGF_1
# Count: 2
#
# ******************************************
# * EGF-like domain signatures and profile *
# ******************************************
#
# A sequence of about thirty to forty amino-acid residues long found in the
# sequence of epidermal growth factor (EGF) has been shown [1 to 6] to be
# present, in a more or less conserved form, in a large number of other, mostly
# animal proteins. EGF is a polypeptide of about 50 amino acids with three
# internal disulfide bridges. It first binds with high affinity to specific
# cell-surface receptors and then induces their dimerization, which is essential
# for activating the tyrosine kinase in the receptor cytoplasmic domain,
# initiating a signal transduction that results in DNA synthesis and cell
# proliferation.
#
# A common feature of all EGF-like domains is that they are found in the
# extracellular domain of membrane-bound proteins or in proteins known to be
# secreted (exception: prostaglandin G/H synthase). The EGF-like domain includes
# six cysteine residues which have been shown to be involved in disulfide bonds.
# The structure of several EGF-like domains has been solved. The fold consists
# of two-stranded beta-sheet followed by a loop to a C-terminal short
# two-stranded sheet (see <PDB:1EGF>). Subdomains between the conserved
# cysteines strongly vary in length as shown in the following schematic
# representation of the EGF-like domain:
#
# +-------------------+ +-------------------------+
# | | | |
# x(4)-C-x(0,48)-C-x(3,12)-C-x(1,70)-C-x(1,6)-C-x(2)-G-a-x(0,21)-G-x(2)-C-x
# | | ************************************
# +-------------------+
#
# 'C': conserved cysteine involved in a disulfide bond.
# 'G': often conserved glycine
# 'a': often conserved aromatic amino acid
# '*': position of both patterns.
# 'x': any residue
#
# Some proteins known to contain one or more copies of an EGF-like domain are
# listed below.
#
# - Adipocyte differentiation inhibitor (gene PREF-1) from mouse (6 copies).
# - Agrin, a basal lamina protein that causes the aggregation of acetylcholine
# receptors on cultured muscle fibers (4 copies).
# - Amphiregulin, a growth factor (1 copy).
# - Betacellulin, a growth factor (1 copy).
# - Blastula proteins BP10 and Span from sea urchin which are thought to be
# involved in pattern formation (1 copy).
# - BM86, a glycoprotein antigen of cattle tick (7 copies).
# - Bone morphogenic protein 1 (BMP-1), a protein which induces cartilage and
# bone formation and which expresses metalloendopeptidase activity (1-2
# copies). Homologous proteins are found in sea urchin - suBMP (1 copy) - and
# in Drosophila - the dorsal-ventral patterning protein tolloid (2 copies).
# - Caenorhabditis elegans developmental proteins lin-12 (13 copies) and glp-1
# (10 copies).
# - Caenorhabditis elegans apx-1 protein, a patterning protein (4.5 copies).
# - Calcium-dependent serine proteinase (CASP) which degrades the extracellular
# matrix proteins type I and IV collagen and fibronectin (1 copy).
# - Cartilage matrix protein CMP (1 copy).
# - Cartilage oligomeric matrix protein COMP (4 copies).
# - Cell surface antigen 114/A10 (3 copies).
# - Cell surface glycoprotein complex transmembrane subunit ASGP-2 from rat (2
# copies).
# - Coagulation associated proteins C, Z (2 copies) and S (4 copies).
# - Coagulation factors VII, IX, X and XII (2 copies).
# - Complement C1r components (1 copy).
# - Complement C1s components (1 copy).
# - Complement-activating component of Ra-reactive factor (RARF) (1 copy).
# - Complement components C6, C7, C8 alpha and beta chains, and C9 (1 copy).
# - Crumbs, an epithelial development protein from Drosophila (29 copies).
# - Epidermal growth factor precursor (7-9 copies).
# - Exogastrula-inducing peptides A, C, D and X from sea urchin (1 copy).
# - Fat protein, a Drosophila cadherin-related tumor suppressor (5 copies).
# - Fetal antigen 1, a probable neuroendocrine differentiation protein, which
# is derived from the delta-like protein (DLK) (6 copies).
# - Fibrillin 1 (47 copies) and fibrillin 2 (14 copies).
# - Fibropellins IA (21 copies), IB (13 copies), IC (8 copies), II (4 copies)
# and III (8 copies) from the apical lamina - a component of the
# extracellular matrix - of sea urchin.
# - Fibulin-1 and -2, two extracellular matrix proteins (9-11 copies).
# - Giant-lens protein (protein Argos), which regulates cell determination and
# axon guidance in the Drosophila eye (1 copy).
# - Growth factor-related proteins from various poxviruses (1 copy).
# - Gurken protein, a Drosophila developmental protein (1 copy).
# - Heparin-binding EGF-like growth factor (HB-EGF), transforming growth factor
# alpha (TGF-alpha), growth factors Lin-3 and Spitz (1 copy); the precursors
# are membrane proteins, the mature form is located extracellular.
# - Hepatocyte growth factor (HGF) activator (EC 3.4.21.-) (2 copies).
# - LDL and VLDL receptors, which bind and transport low-density lipoproteins
# and very low-density lipoproteins (3 copies).
# - LDL receptor-related protein (LRP), which may act as a receptor for
# endocytosis of extracellular ligands (22 copies).
# - Leucocyte antigen CD97 (3 copies), cell surface glycoprotein EMR1 (6
# copies) and cell surface glycoprotein F4/80 (7 copies).
# - Limulus clotting factor C, which is involved in hemostasis and host defense
# mechanisms in japanese horseshoe crab (1 copy).
# - Meprin A alpha subunit, a mammalian membrane-bound endopeptidase (1 copy).
# - Milk fat globule-EGF factor 8 (MFG-E8) from mouse (2 copies).
# - Neuregulin GGF-I and GGF-II, two human glial growth factors (1 copy).
# - Neurexins from mammals (3 copies).
# - Neurogenic proteins Notch, Xotch and the human homolog Tan-1 (36 copies),
# Delta (9 copies) and the similar differentiation proteins Lag-2 from
# Caenorhabditis elegans (2 copies), Serrate (14 copies) and Slit (7 copies)
# from Drosophila.
# - Nidogen (also called entactin), a basement membrane protein from chordates
# (2-6 copies).
# - Ookinete surface proteins (24 Kd, 25 Kd, 28 Kd) from Plasmodium (4 copies).
# - Pancreatic secretory granule membrane major glycoprotein GP2 (1 copy).
# - Perforin, which lyses non-specifically a variety of target cells (1 copy).
# - Proteoglycans aggrecan (1 copy), versican (2 copies), perlecan (at least 2
# copies), brevican (1 copy) and chondroitin sulfate proteoglycan (gene PG-M)
# (2 copies).
# - Prostaglandin G/H synthase 1 and 2 (EC 1.14.99.1) (1 copy), which is found
# in the endoplasmatic reticulum.
# - Reelin, an extracellular matrix protein that plays a role in layering of
# neurons in the cerebral cortex and cerebellum of mammals (8 copies).
# - S1-5, a human extracellular protein whose ultimate activity is probably
# modulated by the environment (5 copies).
# - Schwannoma-derived growth factor (SDGF), an autocrine growth factor as well
# as a mitogen for different target cells (1 copy).
# - Selectins. Cell adhesion proteins such as ELAM-1 (E-selectin), GMP-140
# (P-selectin), or the lymph-node homing receptor (L-selectin) (1 copy).
# - Serine/threonine-protein kinase homolog (gene Pro25) from Arabidopsis
# thaliana, which may be involved in assembly or regulation of
# light-harvesting chlorophyll A/B protein (2 copies).
# - Sperm-egg fusion proteins PH-30 alpha and beta from guinea pig (1 copy).
# - Stromal cell derived protein-1 (SCP-1) from mouse (6 copies).
# - TDGF-1, human teratocarcinoma-derived growth factor 1 (1 copy).
# - Tenascin (or neuronectin), an extracellular matrix protein from mammals
# (14.5 copies), chicken (TEN-A) (13.5 copies) and the related proteins human
# tenascin-X (18 copies) and tenascin-like proteins TEN-A and TEN-M from
# Drosophila (8 copies).
# - Thrombomodulin (fetomodulin), which together with thrombin activates
# protein C (6 copies).
# - Thrombospondin 1, 2 (3 copies), 3 and 4 (4 copies), adhesive glycoproteins
# that mediate cell-to-cell and cell-to-matrix interactions.
# - Thyroid peroxidase 1 and 2 (EC 2.7.10.1) from human (1 copy).
# - Transforming growth factor beta-1 binding protein (TGF-B1-BP) (16 or 18
# copies).
# - Tyrosine-protein kinase receptors Tek and Tie (EC 2.7.1.112) (3 copies).
# - Urokinase-type plasminogen activator (EC 3.4.21.73) (UPA) and tissue
# plasminogen activator (EC 3.4.21.68) (TPA) (1 copy).
# - Uromodulin (Tamm-horsfall urinary glycoprotein) (THP) (3 copies).
# - Vitamin K-dependent anticoagulants protein C (2 copies) and protein S (4
# copies) and the similar protein Z, a single-chain plasma glycoprotein of
# unknown function (2 copies).
# - 63 Kd sperm flagellar membrane protein from sea urchin (3 copies).
# - 93 Kd protein (gene nel) from chicken (5 copies).
# - Hypothetical 337.6 Kd protein T20G5.3 from Caenorhabditis elegans (44
# copies).
#
# The region between the 5th and 6th cysteine contains two conserved glycines of
# which at least one is present in most EGF-like domains. We created two
# patterns for this domain, each including one of these C-terminal conserved
# glycine residues. The profile we developed covers the whole domain.
#
# -Consensus pattern: C-x-C-x(2)-{V}-x(2)-G-{C}-x-C
# [The 3 C's are involved in disulfide bonds]
# -Sequences known to belong to this class detected by the pattern: ALL.
# but not those that have very long or very short regions between the last 3
# conserved cysteines of their EGF-like domain(s).
# -Other sequence(s) detected in Swiss-Prot: 87 proteins, of which 27 can be
# considered as possible candidates.
#
# -Consensus pattern: C-x-C-x(2)-[GP]-[FYW]-x(4,8)-C
# [The 3 C's are involved in disulfide bonds]
# -Sequences known to belong to this class detected by the pattern: ALL.
# but not those that have very long or very short regions between the last 3
# conserved cysteines of their EGF-like domain(s).
# -Other sequence(s) detected in Swiss-Prot: 83 proteins, of which 49 can be
# considered as possible candidates.
#
# -Sequences known to belong to this class detected by the profile: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Note: The beta chain of the integrin family of proteins contains 2 cysteine-
# rich repeats which were said to be dissimilar with the EGF pattern [7].
# -Note: Laminin EGF-like repeats (see <PDOC00961>) are longer than the average
# EGF module and contain a further disulfide bond C-terminal of the EGF-like
# region. Perlecan and agrin contain both EGF-like domains and laminin-type
# EGF-like domains.
# -Note: The pattern do not detect all of the repeats of proteins with multiple
# EGF-like repeats.
# -Note: See <PDOC00913> for an entry describing specifically the subset of EGF-
# like domains that bind calcium.
#
# -Last update: April 2006 / Pattern revised.
#
# [ 1] Davis C.G.
# "The many faces of epidermal growth factor repeats."
# New Biol. 2:410-419(1990).
# PubMed=2288911
# [ 2] Blomquist M.C., Hunt L.T., Barker W.C.
# "Vaccinia virus 19-kilodalton protein: relationship to several
# mammalian proteins, including two growth factors."
# Proc. Natl. Acad. Sci. U.S.A. 81:7363-7367(1984).
# PubMed=6334307
# [ 3] Barker W.C., Johnson G.C., Hunt L.T., George D.G.
# Protein Nucl. Acid Enz. 29:54-68(1986).
# [ 4] Doolittle R.F., Feng D.F., Johnson M.S.
# "Computer-based characterization of epidermal growth factor
# precursor."
# Nature 307:558-560(1984).
# PubMed=6607417
# [ 5] Appella E., Weber I.T., Blasi F.
# "Structure and function of epidermal growth factor-like regions in
# proteins."
# FEBS Lett. 231:1-4(1988).
# PubMed=3282918
# [ 6] Campbell I.D., Bork P.
# Curr. Opin. Struct. Biol. 3:385-392(1993).
# [ 7] Tamkun J.W., DeSimone D.W., Fonda D., Patel R.S., Buck C.,
# Horwitz A.F., Hynes R.O.
# "Structure of integrin, a glycoprotein involved in the transmembrane
# linkage between fibronectin and actin."
# Cell 46:271-282(1986).
# PubMed=3487386
#
# ***************
#
# Motif: 2FE2S_FER_1
# Count: 2
#
# ***************************************************************************
# * 2Fe-2S ferredoxin-type iron-sulfur binding domain signature and profile *
# ***************************************************************************
#
# Ferredoxins are small, acidic, electron transfer proteins that are ubiquitous
# in biological redox systems. They have either 4Fe-4S, 3Fe-4S, or 2Fe-2S
# cluster. Among them, ferredoxin with one 2Fe-2S cluster per molecule are
# present in plants, animals, and bacteria, and form a distinct 2Fe-Ferredoxin
# family [1,2]. They are proteins of around one hundred amino acids with four
# conserved cysteine residues to which the 2Fe-2S cluster is ligated. This
# conserved region is also found as a domain in various metabolic enzymes.
#
# Several structures of the 2Fe-2S ferredoxin domain have been determined (see
# for example <PDB:4FXC>) [3]. The domain is classified as a beta-grasp which is
# characterized as having a beta-sheet comprised of four beta-strands and one
# alpha-helix flanking the sheet [4]. The two Fe atoms are coordinated
# tetrahedrally by the two inorganic S atoms and four cysteinyl S atoms.
#
# Some proteins that contains a 2Fe-2S ferredoxin-type domain are listed below:
#
# - Ferredoxin from photosynthetic organisms; namely plants and algae where it
# is located in the chloroplast or cyanelle; and cyanobacteria.
# - Ferredoxin from archaebacteria of the Halobacterium genus.
# - Ferredoxin IV (gene pftA) and V (gene fdxD) from Rhodobacter capsulatus.
# - Ferredoxin in the toluene degradation operon (gene xylT) and naphthalene
# degradation operon (gene nahT) of Pseudomonas putida.
# - Hypothetical Escherichia coli protein yfaE.
#
# - The N-terminal domain of the bifunctional ferredoxin/ferredoxin reductase
# electron transfer component of the benzoate 1,2-dioxygenase complex (gene
# benC) from Acinetobacter calcoaceticus, the toluene 4-monooxygenase complex
# (gene tmoF), the toluate 1,2-dioxygenase system (gene xylZ), and the xylene
# monooxygenase system (gene xylA) from Pseudomonas.
# - The N-terminal domain of phenol hydroxylase protein p5 (gene dmpP) from
# Pseudomonas Putida.
# - The N-terminal domain of methane monooxygenase component C (gene mmoC)
# from Methylococcus capsulatus .
# - The C-terminal domain of the vanillate degradation pathway protein vanB in
# a Pseudomonas species.
# - The N-terminal domain of bacterial fumarate reductase iron-sulfur protein
# (gene frdB).
# - The N-terminal domain of CDP-6-deoxy-3,4-glucoseen reductase (gene ascD)
# from Yersinia pseudotuberculosis.
# - The central domain of eukaryotic succinate dehydrogenase (ubiquinone) iron-
# sulfur protein.
# - The N-terminal domain of eukaryotic xanthine dehydrogenase.
# - The N-terminal domain of eukaryotic aldehyde oxidase.
#
# Three of the four conserved cysteines are clustered together in the same
# region of the protein. Our signature pattern spans that iron-sulfur binding
# region. We also developed a profile that covers the whole domain.
#
# -Consensus pattern: C-{C}-{C}-[GA]-{C}-C-[GAST]-{CPDEKRHFYW}-C
# [The 3 C's are 2Fe-2S ligands]
# -Sequences known to belong to this class detected by the profile: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Sequences known to belong to this class detected by the profile: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Note: Ferredoxins from the adrenodoxin subfamily are slightly divergent and
# are not picked up by our pattern (but they are recognized by the profile). We
# have thus developed a second pattern specific for this subfamily (see
# <PDOC00642>).
#
# -Last update: March 2005 / Text revised; profile added.
#
# [ 1] Meyer J.
# Trends Ecol. Evol. 3:222-226(1988).
# [ 2] Harayama S., Polissi A., Rekik M.
# "Divergent evolution of chloroplast-type ferredoxins."
# FEBS Lett. 285:85-88(1991).
# PubMed=2065785
# [ 3] Fukuyama K., Ueki N., Nakamura H., Tsukihara T., Matsubara H.
# "Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis
# refined at 2.5 A resolution: structural comparisons of plant-type
# ferredoxins and an electrostatic potential analysis."
# J. Biochem. 117:1017-1023(1995).
# PubMed=8586613
# [ 4] Overington J.P.
# Curr. Opin. Struct. Biol. 2:394-401(1992).
#
# ***************
#
# Motif: ANAPHYLATOXIN_1
# Count: 2
#
# **********************************************
# * Anaphylatoxin domain signature and profile *
# **********************************************
#
# Anaphylatoxins [1] are mediators of local inflammatory process that act by
# inducing smooth muscle contraction. There are three different anaphylatoxins:
# C3a, C4a and C5a. They are peptides of about 75 amino-acid residues that are
# derived from the proteolytic degradation of complement C3, C4 and C5 and which
# contains six disulfide-bonded cysteines [2] (see the schematic representation
# below).
#
# +--------------------+
# +-------------|------------+ |
# | | | |
# xxxCCxxxxxxxxxxxxCxxxxxxxxxxxxCxxxxxxCCxxx
# | |
# +--------------------------------+
#
# 'C': conserved cysteine involved in a disulfide bond.
#
# This cysteine-rich region shares similarity with a three times repeated domain
# found in the mammalian extracellular matrix proteins fibulins 1 and 2 [3,4].
# The three disulfide bonds are conserved in the first and last repeats, but the
# first disulfide bond is missing in the second repeat.
#
# Our consensus pattern spans the entire cysteine-rich domain.
#
# -Consensus pattern: [CSH]-C-x(2)-[GAP]-x(7,8)-[GASTDEQR]-C-[GASTDEQL]-x(3,9)-
# [GASTDEQN]-x(2)-[CE]-x(6,7)-C-C
# [The 6 C's are involved in disulfide bonds]
# -Sequences known to belong to this class detected by the pattern: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Sequences known to belong to this class detected by the profile: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Last update: May 2004 / Text revised.
#
# [ 1] Hugli T.E.
# "Biochemistry and biology of anaphylatoxins."
# Complement 3:111-127(1986).
# PubMed=3542363
# [ 2] Huber R., Scholze H., Paques E.P., Deisenhofer J.
# "Crystal structure analysis and molecular model of human C3a
# anaphylatoxin."
# Hoppe-Seyler's Z. Physiol. Chem. 361:1389-1399(1980).
# PubMed=7439885
# [ 3] Argraves W.S., Tran H., Burgess W.H., Dickerson K.
# "Fibulin is an extracellular matrix and plasma glycoprotein with
# repeated domain structure."
# J. Cell Biol. 111:3155-3164(1990).
# PubMed=2269669
# [ 4] Pan T.-C., Sasaki T., Zhang R.-Z., Faessler R., Timpl R., Chu M.L.
# "Structure and expression of fibulin-2, a novel extracellular matrix
# protein with multiple EGF-like repeats and consensus motifs for
# calcium binding."
# J. Cell Biol. 123:1269-1277(1993).
# PubMed=8245130
#
# ***************
#
# Motif: VWFC_1
# Count: 5
#
# *************************************
# * VWFC domain signature and profile *
# *************************************
#
# The VWFC domain is named after the von Willebrand factor (VWF) type C repeat
# which is found twice in this multidomain protein [1,2]. It has a length of
# about 70 amino acids covering 10 well conserved cysteines. Proteins with such
# a domain [1-4] are listed below.
#
# - Human von Willebrand factor (VWF), a multifunctional protein involved in
# maintaining homeostasis. It consists of 4 VWFD domains, 3 VWFA domains, 3
# VWFB domains, 3 VWFC domains, an X domain and a C-terminal cystine knot [2].
# - Silk moth hemocytin, an humoral lectin which is involved in a self-defence
# mechanism. It is composed of 2 FA58C domains (see <PDOC00988>), a C-type
# lectin domain (see <PDOC00537>), 2 VWFC domains, and a CTCK (see
# <PDOC00912>).
# - Several vertebrate heavily glycosylated mucins. Human mucin 2 is secreted
# by the epithelia of different mucus membrane-containing organs. It is a
# highly polymorphic multidomain molecule. Rat intestinal mucin-like peptide
# coats the epithelia of the intestines. Both proteins share a modular
# architecture similar to VWF. Xenopus mucin B.1 contains a Sushi domain, a
# VWFC domain, a X domain and a C-terminal cystine knot. Other mucins that
# contain the VWFC domain are human tracheobronchial mucin (MUC5), bovine
# submaxillary mucin-like protein, human and pig apomucin.
# - Cef-10/cyr61/CTGF/fisp-12/nov protein family. The members of this family
# are structurally related to insulin-like growth factor binding proteins
# (see <PDOC00194>) and could function as growth factor-binding proteins.
# They contain an insulin-like growth factor-binding domain, a VWFC repeat, a
# thrombospondin type 1 repeat (Tsp1) and a C-terminal cystine knot.
# - Vertebrate thrombospondins 1 and 2. These adhesive glycoproteins mediate
# cell-to-cell and cell-to-matrix interactions. They are composed of a common
# thrombospondin N-terminal domain (TspN), a VWFC domain, three Tsp type 1
# repeats (Tsp1), 3 to 4 EGF-like domains and 7 calcium-binding Tsp3 repeats.
# - Vertebrate propeptides of fibrillar collagens alpha 1(I, II & III) and 2(V)
# chains that contain an N-terminal VWFC domain, a collagenous region of
# about 1000 amino acids and a C-terminus common to fibrillar collagens
# (COLFI domain).
# - Vertebrate integral membrane protein DGCR2/IDD, a potential adhesion
# receptor with 1 LDL-receptor class A domain (see <PDOC00929>), a C-type
# lectin and a VWFC domain.
# - Chordin, a Xenopus developmental protein that contains four VWFC domains.
#
# Of these proteins, the best characterized one is the von Willebrand factor for
# which the duplicated VWFC domain is thought to participate in oligomerization,
# but not in the initial dimerization step [4]. The presence of this region in
# other complex-forming proteins leads to the assumption that the VWFC domain
# might be involved in forming larger protein complexes [1,2].
#
# The profile we developed covers the entire VWFC domain.
#
# -Consensus pattern: C-x(2,3)-C-{CG}-C-x(6,14)-C-x(3,4)-C-x(2,10)-C-x(9,16)-
# C-C-x(2,4)-C
# -Sequences known to belong to this class detected by the pattern: ALL.
# -Other sequence(s) detected in Swiss-Prot: 7.
#
# -Sequences known to belong to this class detected by the profile: ALL.
# -Other sequence(s) detected in Swiss-Prot: NONE.
#
# -Expert(s) to contact by email:
# Bork P.; [email protected]
#
# -Last update: December 2004 / Pattern and text revised.
#
# [ 1] Hunt L.T., Barker W.C.
# "von Willebrand factor shares a distinctive cysteine-rich domain with
# thrombospondin and procollagen."
# Biochem. Biophys. Res. Commun. 144:876-882(1987).
# PubMed=3495268
# [ 2] Bork P.
# "The modular architecture of a new family of growth regulators related
# to connective tissue growth factor."
# FEBS Lett. 327:125-130(1993).
# PubMed=7687569
# [ 3] Bork P.
# "Shuffled domains in extracellular proteins."
# FEBS Lett. 286:47-54(1991).
# PubMed=1864378
# [ 4] Voorberg J., Fontijn R., Calafat J., Janssen H., van Mourik J.A.,
# Pannekoek H.
# "Assembly and routing of von Willebrand factor variants: the
# requirements for disulfide-linked dimerization reside within the
# carboxy-terminal 151 amino acids."
# J. Cell Biol. 113:195-205(1991).
# PubMed=2007623
#
# ***************
#
#
#---------------------------------------