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Conserved domains on  [gi|40789268|ref|NP_031815|]
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neurocan core protein precursor [Mus musculus]

Protein Classification

calcium-binding EGF-like domain-containing protein( domain architecture ID 10957711)

calcium-binding epidermal growth factor (EGF)-like domain-containing protein may play a crucial role in numerous protein-protein interactions

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLECT super family cl02432
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 1040-1163 7.30e-67

C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.


The actual alignment was detected with superfamily member cd03588:

Pssm-ID: 470576  Cd Length: 124  Bit Score: 220.91  E-value: 7.30e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSFGHENSWIGLNDRTVERDFQWTDNTGLQYE 1119
Cdd:cd03588    1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 40789268 1120 NWREKQPDNFFAGGEDCVVMVAHESGRWNDVPCNYNLPYVCKKG 1163
Cdd:cd03588   81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 40-161 3.06e-59

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05902:

Pssm-ID: 472250  Cd Length: 121  Bit Score: 198.91  E-value: 3.06e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   40 KSGSGPVRAALAELVALPCFFTLQPRLSSLRDIPRIKWTKVQTaSGQRQDLPILVAKDNVVRVAKGWQGRVSLPAYPRHR 119
Cdd:cd05902    1 RVTAPPVRRPLSSSVLLPCVFTLPPSASSPPEGPRIKWTKLST-SGGQQQRPVLVARDNVVRVAKAFQGRVSLPGYPKNR 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 40789268  120 ANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05902   80 YNASLVLSRLRYSDSGTYRCEVVLGINDEQDTVPLEVTGVVF 121
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 159-253 1.43e-56

Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


:

Pssm-ID: 239594  Cd Length: 95  Bit Score: 190.31  E-value: 1.43e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  159 VVFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRSSLPGVRS 238
Cdd:cd03517    1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                         90
                 ....*....|....*
gi 40789268  239 YGRRDPQELYDVYCF 253
Cdd:cd03517   81 YGVRDPDELYDVYCY 95
Link_domain_CSPGs_modules_2_4 cd03520
Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules ...
 260-355 4.32e-56

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


:

Pssm-ID: 239597  Cd Length: 96  Bit Score: 189.06  E-value: 4.32e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  260 EVFYVGPARRLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTVYRFAN 339
Cdd:cd03520    1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                         90
                 ....*....|....*.
gi 40789268  340 RTGFPAPGARFDAYCF 355
Cdd:cd03520   81 QTGFPDPHSRFDAYCF 96
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 400-851 4.00e-14

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 78.06  E-value: 4.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   400 APDFQEPLMSSGE---GEPPDLTWTQAPEETLGSTPGGPTLASWPSSEKWLFTGAPSSMGVSSPSDMGVDMEATTPLGTQ 476
Cdd:PHA03247 2574 APRPSEPAVTSRArrpDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   477 VAPTPT-MRRGRFKGLNGRHFQQQGPedqlPEVAEPSAQPPTLGATANHMRPSAATEASESdqSHSPWAILTNEVDEPGA 555
Cdd:PHA03247 2654 DDPAPGrVSRPRRARRLGRAAQASSP----PQRPRRRAARPTVGSLTSLADPPPPPPTPEP--APHALVSATPLPPGPAA 2727

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   556 GSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPGAAEAPSvksaiPHLPRLPSEPPAPS----PGPSEALSAVSLQASS 631
Cdd:PHA03247 2728 ARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPA-----PAPPAAPAAGPPRRltrpAVASLSESRESLPSPW 2802

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   632 ADGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPLSPA---SPLPSWVPEEQAVRPvslgAEDLETPFQTTIAAPVEASH 708
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPpppGPPPPSLPLGGSVAP----GGDVRRRPPSRSPAAKPAAP 2878

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   709 RSPDADsieiegtssmRATKHPISGPWASLDSSNVTMNPVPSDagilgtesgvlDLPGSPTSGGQATVEKVLATWLPLPG 788
Cdd:PHA03247 2879 ARPPVR----------RLARPAVSRSTESFALPPDQPERPPQP-----------QAPPPPQPQPQPPPPPQPQPPPPPPP 2937

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40789268   789 QGLDPGSQSTPMEAHGVAVSMEPTVALeGGATEGPMEATREVVPSTADATWESESRSAISSTH 851
Cdd:PHA03247 2938 RPQPPLAPTTDPAGAGEPSGAVPQPWL-GALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGH 2999
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1167-1224 1.02e-11

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.


:

Pssm-ID: 153056 [Multi-domain]  Cd Length: 57  Bit Score: 60.94  E-value: 1.02e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268 1167 CGPPPAVENASLVGvRKIKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMCI 1224
Cdd:cd00033    1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 998-1034 6.37e-10

Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.


:

Pssm-ID: 238011  Cd Length: 38  Bit Score: 55.34  E-value: 6.37e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 40789268  998 DIDDCL-CSPCENGGTCIDEVNGFICLCLPSYGGSLCE 1034
Cdd:cd00054    1 DIDECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 964-994 3.38e-07

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.


:

Pssm-ID: 394967  Cd Length: 31  Bit Score: 47.38  E-value: 3.38e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 40789268    964 CENNPCLHGGTCHTNGTVYGCSCDQGYAGEN 994
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31
 
Name Accession Description Interval E-value
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 1040-1163 7.30e-67

C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins; CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.


Pssm-ID: 153058  Cd Length: 124  Bit Score: 220.91  E-value: 7.30e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSFGHENSWIGLNDRTVERDFQWTDNTGLQYE 1119
Cdd:cd03588    1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 40789268 1120 NWREKQPDNFFAGGEDCVVMVAHESGRWNDVPCNYNLPYVCKKG 1163
Cdd:cd03588   81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Ig_Neurocan cd05902
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 40-161 3.06e-59

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Unlike aggrecan which is widely distributed in connective tissue and extracellular matrices, neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409483  Cd Length: 121  Bit Score: 198.91  E-value: 3.06e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   40 KSGSGPVRAALAELVALPCFFTLQPRLSSLRDIPRIKWTKVQTaSGQRQDLPILVAKDNVVRVAKGWQGRVSLPAYPRHR 119
Cdd:cd05902    1 RVTAPPVRRPLSSSVLLPCVFTLPPSASSPPEGPRIKWTKLST-SGGQQQRPVLVARDNVVRVAKAFQGRVSLPGYPKNR 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 40789268  120 ANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05902   80 YNASLVLSRLRYSDSGTYRCEVVLGINDEQDTVPLEVTGVVF 121
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 159-253 1.43e-56

Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 239594  Cd Length: 95  Bit Score: 190.31  E-value: 1.43e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  159 VVFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRSSLPGVRS 238
Cdd:cd03517    1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                         90
                 ....*....|....*
gi 40789268  239 YGRRDPQELYDVYCF 253
Cdd:cd03517   81 YGVRDPDELYDVYCY 95
Link_domain_CSPGs_modules_2_4 cd03520
Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules ...
 260-355 4.32e-56

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 239597  Cd Length: 96  Bit Score: 189.06  E-value: 4.32e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  260 EVFYVGPARRLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTVYRFAN 339
Cdd:cd03520    1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                         90
                 ....*....|....*.
gi 40789268  340 RTGFPAPGARFDAYCF 355
Cdd:cd03520   81 QTGFPDPHSRFDAYCF 96
LINK smart00445
Link (Hyaluronan-binding);
158-254 9.66e-44

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 153.65  E-value: 9.66e-44
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     158 GVVFHYRAaRDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDrssLPGVR 237
Cdd:smart00445    2 GGVFHVEK-NGRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGN---LPGVR 77

                            90
                    ....*....|....*..
gi 40789268     238 SYGRRDPQELYDVYCFA 254
Cdd:smart00445   78 QYGFPDPTSRYDAYCFN 94
LINK smart00445
Link (Hyaluronan-binding);
259-356 6.79e-43

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 151.34  E-value: 6.79e-43
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     259 GEVFYVGPARR--LTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRtvyr 336
Cdd:smart00445    2 GGVFHVEKNGRykLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGNLPGVR---- 77

                            90       100
                    ....*....|....*....|
gi 40789268     337 fanRTGFPAPGARFDAYCFR 356
Cdd:smart00445   78 ---QYGFPDPTSRYDAYCFN 94
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 1040-1161 4.02e-41

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.


Pssm-ID: 214480 [Multi-domain]  Cd Length: 124  Bit Score: 147.36  E-value: 4.02e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF-----GHENSWIGLNDRTVERDFQWTDNT 1114
Cdd:smart00034    1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAENDFVASLlknsgSSDYYWIGLSDPDSNGSWQWSDGS 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 40789268    1115 GL-QYENWREKQPDNffaGGEDCVVMVAHeSGRWNDVPCNYNLPYVCK 1161
Cdd:smart00034   81 GPvSYSNWAPGEPNN---SSGDCVVLSTS-GGKWNDVSCTSKLPFVCE 124
Xlink pfam00193
Extracellular link domain;
159-253 2.91e-39

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 140.79  E-value: 2.91e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    159 VVFHYRAaRDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRsslPGVRS 238
Cdd:pfam00193    1 GVFHLES-PGRYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNM---PGVRQ 76

                           90
                   ....*....|....*.
gi 40789268    239 YGRRDPQ-ELYDVYCF 253
Cdd:pfam00193   77 YGFRDPLsERYDAYCY 92
Xlink pfam00193
Extracellular link domain;
260-355 8.55e-39

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 139.25  E-value: 8.55e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    260 EVFYVGPARR--LTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTvyrf 337
Cdd:pfam00193    1 GVFHLESPGRykLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNMPGVRQ---- 76

                           90
                   ....*....|....*....
gi 40789268    338 anrTGFPAP-GARFDAYCF 355
Cdd:pfam00193   77 ---YGFRDPlSERYDAYCY 92
Lectin_C pfam00059
Lectin C-type domain; This family includes both long and short form C-type
 1061-1162 1.39e-29

Lectin C-type domain; This family includes both long and short form C-type


Pssm-ID: 459655 [Multi-domain]  Cd Length: 105  Bit Score: 113.73  E-value: 1.39e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   1061 WEDAERDCRRRAGHLTSVHSPEEHKFINSF---GHENSWIGLNDRTVERDFQWTDNTGLQYENWREKQPDNffAGGEDCV 1137
Cdd:pfam00059    4 WDEAREACRKLGGHLVSINSAEELDFLSSTlkkSNKYFWIGLTDRKNEGTWKWVDGSPVNYTNWAPEPNNN--GENEDCV 81

                           90       100
                   ....*....|....*....|....*
gi 40789268   1138 VMvAHESGRWNDVPCNYNLPYVCKK 1162
Cdd:pfam00059   82 EL-SSSSGKWNDENCNSKNPFVCEK 105
PHA03247 PHA03247
large tegument protein UL36; Provisional
 400-851 4.00e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 78.06  E-value: 4.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   400 APDFQEPLMSSGE---GEPPDLTWTQAPEETLGSTPGGPTLASWPSSEKWLFTGAPSSMGVSSPSDMGVDMEATTPLGTQ 476
Cdd:PHA03247 2574 APRPSEPAVTSRArrpDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   477 VAPTPT-MRRGRFKGLNGRHFQQQGPedqlPEVAEPSAQPPTLGATANHMRPSAATEASESdqSHSPWAILTNEVDEPGA 555
Cdd:PHA03247 2654 DDPAPGrVSRPRRARRLGRAAQASSP----PQRPRRRAARPTVGSLTSLADPPPPPPTPEP--APHALVSATPLPPGPAA 2727

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   556 GSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPGAAEAPSvksaiPHLPRLPSEPPAPS----PGPSEALSAVSLQASS 631
Cdd:PHA03247 2728 ARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPA-----PAPPAAPAAGPPRRltrpAVASLSESRESLPSPW 2802

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   632 ADGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPLSPA---SPLPSWVPEEQAVRPvslgAEDLETPFQTTIAAPVEASH 708
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPpppGPPPPSLPLGGSVAP----GGDVRRRPPSRSPAAKPAAP 2878

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   709 RSPDADsieiegtssmRATKHPISGPWASLDSSNVTMNPVPSDagilgtesgvlDLPGSPTSGGQATVEKVLATWLPLPG 788
Cdd:PHA03247 2879 ARPPVR----------RLARPAVSRSTESFALPPDQPERPPQP-----------QAPPPPQPQPQPPPPPQPQPPPPPPP 2937

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40789268   789 QGLDPGSQSTPMEAHGVAVSMEPTVALeGGATEGPMEATREVVPSTADATWESESRSAISSTH 851
Cdd:PHA03247 2938 RPQPPLAPTTDPAGAGEPSGAVPQPWL-GALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGH 2999
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1167-1224 1.02e-11

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.


Pssm-ID: 153056 [Multi-domain]  Cd Length: 57  Bit Score: 60.94  E-value: 1.02e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268 1167 CGPPPAVENASLVGvRKIKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMCI 1224
Cdd:cd00033    1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57
CCP smart00032
Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat ...
 1167-1223 4.45e-10

Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.


Pssm-ID: 214478 [Multi-domain]  Cd Length: 56  Bit Score: 56.38  E-value: 4.45e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 40789268    1167 CGPPPAVENASLVGVRKiKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMC 1223
Cdd:smart00032    1 CPPPPDIENGTVTSSSG-TYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 998-1034 6.37e-10

Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.


Pssm-ID: 238011  Cd Length: 38  Bit Score: 55.34  E-value: 6.37e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 40789268  998 DIDDCL-CSPCENGGTCIDEVNGFICLCLPSYGGSLCE 1034
Cdd:cd00054    1 DIDECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 42-157 7.92e-10

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 57.47  E-value: 7.92e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     42 GSGPVRAALAELVALPCFFTLqprlSSLRDIPRIKWTKVQTasGQRQDLPILVAKDNVVRVAKgwQGRVSLPAYPRhRAN 121
Cdd:pfam07686    2 TPREVTVALGGSVTLPCTYSS----SMSEASTSVYWYRQPP--GKGPTFLIAYYSNGSEEGVK--KGRFSGRGDPS-NGD 72

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 40789268    122 ATLLLGPLRASDSGLYRCQVV-KGIEDEQDLVTLEVT 157
Cdd:pfam07686   73 GSLTIQNLTLSDSGTYTCAVIpSGEGVFGKGTRLTVL 109
Sushi pfam00084
Sushi repeat (SCR repeat);
1167-1223 9.08e-10

Sushi repeat (SCR repeat);


Pssm-ID: 459664 [Multi-domain]  Cd Length: 56  Bit Score: 55.58  E-value: 9.08e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 40789268   1167 CGPPPAVENASLVGVRKiKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMC 1223
Cdd:pfam00084    1 CPPPPDIPNGKVSATKN-EYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56
EGF_CA smart00179
Calcium-binding EGF-like domain;
998-1034 5.89e-09

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 52.63  E-value: 5.89e-09
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 40789268     998 DIDDCL-CSPCENGGTCIDEVNGFICLCLPSY-GGSLCE 1034
Cdd:smart00179    1 DIDECAsGNPCQNGGTCVNTVGSYRCECPPGYtDGRNCE 39
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 964-994 3.38e-07

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.


Pssm-ID: 394967  Cd Length: 31  Bit Score: 47.38  E-value: 3.38e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 40789268    964 CENNPCLHGGTCHTNGTVYGCSCDQGYAGEN 994
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 962-996 6.46e-07

Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.


Pssm-ID: 238011  Cd Length: 38  Bit Score: 46.86  E-value: 6.46e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 40789268  962 DPCE-NNPCLHGGTCH-TNGTvYGCSCDQGYAGENCE 996
Cdd:cd00054    3 DECAsGNPCQNGGTCVnTVGS-YRCSCPPGYTGRNCE 38
EGF_CA smart00179
Calcium-binding EGF-like domain;
962-996 4.20e-05

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 41.85  E-value: 4.20e-05
                            10        20        30
                    ....*....|....*....|....*....|....*...
gi 40789268     962 DPCE-NNPCLHGGTCH-TNGTvYGCSCDQGY-AGENCE 996
Cdd:smart00179    3 DECAsGNPCQNGGTCVnTVGS-YRCECPPGYtDGRNCE 39
hEGF pfam12661
Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six ...
 1007-1026 4.53e-05

Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteriztic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC. These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin. Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.


Pssm-ID: 463660  Cd Length: 22  Bit Score: 41.55  E-value: 4.53e-05
                           10        20
                   ....*....|....*....|
gi 40789268   1007 CENGGTCIDEVNGFICLCLP 1026
Cdd:pfam12661    1 CQNGGTCVDGVNGYKCQCPP 20
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 456-812 5.49e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 47.84  E-value: 5.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    456 GVSSPSDMGVDMEATTPlgtqVAPTPTMRRGRF-KGLNGRHFQQQGPEDQLPEVAEPSAQPPTLGATANHMRPSAATEAS 534
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSP----SIPSPQDNESDSdSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPS 205

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    535 ESDQSHSPWAILTNEVDEPGAGSLGSRSLPEslMWSPSLISPSVPSTDSTPSAKPGAAEAPSVKSAIPHLPRlpsePPAP 614
Cdd:pfam03154  206 VPPQGSPATSQPPNQTQSTAAPHTLIQQTPT--LHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQM----PPMP 279

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    615 SP---GPSEALSAVSLQassadGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPLSPASPLPSWVPEEQAVRPVSLGAED 691
Cdd:pfam03154  280 HSlqtGPSHMQHPVPPQ-----PFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPH 354

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    692 LETPFQTTIAA-PVEASHRSPDADSI--------------EIEGTSSMrATKHPISG--PWASLDSSNVTMNPVPSDAGI 754
Cdd:pfam03154  355 IKPPPTTPIPQlPNPQSHKHPPHLSGpspfqmnsnlppppALKPLSSL-STHHPPSAhpPPLQLMPQSQQLPPPPAQPPV 433

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    755 LgTESGVLDLPGS--PTSGGQATVekvlATWLPLPGQGLDPGSQSTPMEAHGVAVSMEPT 812
Cdd:pfam03154  434 L-TQSQSLPPPAAshPPTSGLHQV----PSQSPFPQHPFVPGGPPPITPPSGPPTSTSSA 488
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 1040-1114 9.03e-05

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 45.11  E-value: 9.03e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40789268  1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF-GHENSWIGLNDRTVERDFQWTDNT 1114
Cdd:PHA02642   88 CPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEELNFLKRYkDSSDHWIGLNRESSNHPWKWADNS 163
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 1032-1161 1.18e-04

polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half.


Pssm-ID: 188093 [Multi-domain]  Cd Length: 2740  Bit Score: 46.61  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   1032 LCEKDTEgcdrgWHKFQGHCYRYFAHRRAWEDAERDCRRRAG-HLTSVHSPEEHKFINS----FGHENSWIGLND-RTVE 1105
Cdd:TIGR00864  317 HCPKDGE-----IFEENGHCFQIVPEEAAWLDAQEQCLARAGaALAIVDNDALQNFLARkvthSLDRGVWIGFSDvNGAE 391

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268   1106 RD-FQWTDNTGLQY-ENWREKQPDnfFAGGEDCVVMvaHESGRWNDVPCNYNLPYVCK 1161
Cdd:TIGR00864  392 KGpAHQGEAFEAEEcEEGLAGEPH--PARAEHCVRL--DPRGQCNSDLCNAPHAYVCE 445
 
Name Accession Description Interval E-value
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 1040-1163 7.30e-67

C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins; CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.


Pssm-ID: 153058  Cd Length: 124  Bit Score: 220.91  E-value: 7.30e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSFGHENSWIGLNDRTVERDFQWTDNTGLQYE 1119
Cdd:cd03588    1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 40789268 1120 NWREKQPDNFFAGGEDCVVMVAHESGRWNDVPCNYNLPYVCKKG 1163
Cdd:cd03588   81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Ig_Neurocan cd05902
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 40-161 3.06e-59

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Unlike aggrecan which is widely distributed in connective tissue and extracellular matrices, neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409483  Cd Length: 121  Bit Score: 198.91  E-value: 3.06e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   40 KSGSGPVRAALAELVALPCFFTLQPRLSSLRDIPRIKWTKVQTaSGQRQDLPILVAKDNVVRVAKGWQGRVSLPAYPRHR 119
Cdd:cd05902    1 RVTAPPVRRPLSSSVLLPCVFTLPPSASSPPEGPRIKWTKLST-SGGQQQRPVLVARDNVVRVAKAFQGRVSLPGYPKNR 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 40789268  120 ANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05902   80 YNASLVLSRLRYSDSGTYRCEVVLGINDEQDTVPLEVTGVVF 121
Ig_Aggrecan_like cd05878
Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core ...
 40-161 8.04e-58

Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core protein (CSPG); The members here are composed of the immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core proteins (CSPGs). Included in this group are the Ig domains of other CSPGs: versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409462  Cd Length: 125  Bit Score: 195.14  E-value: 8.04e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   40 KSGSGPVRAALAELVALPCFFTLQPRL---SSLRDIPRIKWTKVQTASGQRQDLPILVAKDNVVRVAKGWQGRVSLPAYP 116
Cdd:cd05878    1 IPQSSPVRVLLGTSVTLPCYFIDPPHPvtpSTAPLAPRIKWSKVSVDGKKEKEVVLLVATEGRVRVNSAYQGRVSLPNYP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 40789268  117 RHRANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05878   81 AIPSDATLEVQSLRASDSGLYRCEVMHGIEDSQDTVELVVKGVVF 125
Ig_CSPGs_LP_like cd05714
Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage ...
 40-161 2.14e-57

Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. There is considerable evidence that HA-binding CSPGs are involved in developmental processes in the central nervous system. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409379  Cd Length: 123  Bit Score: 193.97  E-value: 2.14e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   40 KSGSGPVRAALAELVALPCFFTLQPRL-SSLRDIPRIKWTKVQTASGQRQDLPILVAKDNVVRVAKGWQGRVSLPAYPRH 118
Cdd:cd05714    1 EAESAKVFSHLGGNVTLPCKFYRDPTAfGSGIHKIRIKWTKLTSDSGYLKEVDVLVAMGNVVYHKKTYGGRVSVPLKPGS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 40789268  119 RANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05714   81 DSDASLVITDLTASDYGLYRCEVIEGIEDDQDVVALDVQGVVF 123
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 159-253 1.43e-56

Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 239594  Cd Length: 95  Bit Score: 190.31  E-value: 1.43e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  159 VVFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRSSLPGVRS 238
Cdd:cd03517    1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                         90
                 ....*....|....*
gi 40789268  239 YGRRDPQELYDVYCF 253
Cdd:cd03517   81 YGVRDPDELYDVYCY 95
Link_domain_CSPGs_modules_2_4 cd03520
Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules ...
 260-355 4.32e-56

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 239597  Cd Length: 96  Bit Score: 189.06  E-value: 4.32e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  260 EVFYVGPARRLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTVYRFAN 339
Cdd:cd03520    1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                         90
                 ....*....|....*.
gi 40789268  340 RTGFPAPGARFDAYCF 355
Cdd:cd03520   81 QTGFPDPHSRFDAYCF 96
LINK smart00445
Link (Hyaluronan-binding);
158-254 9.66e-44

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 153.65  E-value: 9.66e-44
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     158 GVVFHYRAaRDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDrssLPGVR 237
Cdd:smart00445    2 GGVFHVEK-NGRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGN---LPGVR 77

                            90
                    ....*....|....*..
gi 40789268     238 SYGRRDPQELYDVYCFA 254
Cdd:smart00445   78 QYGFPDPTSRYDAYCFN 94
LINK smart00445
Link (Hyaluronan-binding);
259-356 6.79e-43

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 151.34  E-value: 6.79e-43
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     259 GEVFYVGPARR--LTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRtvyr 336
Cdd:smart00445    2 GGVFHVEKNGRykLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGNLPGVR---- 77

                            90       100
                    ....*....|....*....|
gi 40789268     337 fanRTGFPAPGARFDAYCFR 356
Cdd:smart00445   78 ---QYGFPDPTSRYDAYCFN 94
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 159-253 1.38e-42

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


Pssm-ID: 238534  Cd Length: 92  Bit Score: 150.26  E-value: 1.38e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  159 VVFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRsslPGVRS 238
Cdd:cd01102    1 VVFHLESQNGRYKLTFAEAALACKARGAHLATPGQLEAAWQDGFDVCTAGWLADGSVRYPIVTSRPNCGGRN---PGVRS 77

                         90
                 ....*....|....*
gi 40789268  239 YGRRDPQELYDVYCF 253
Cdd:cd01102   78 YGNPAPSGRYDAYCF 92
CLECT_DC-SIGN_like cd03590
C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific ...
 1040-1162 4.56e-42

C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR); CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.


Pssm-ID: 153060 [Multi-domain]  Cd Length: 126  Bit Score: 150.15  E-value: 4.56e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYrYFAH-RRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF--GHENSWIGLNDRTVERDFQWTDNTGL 1116
Cdd:cd03590    1 CPTNWKSFQSSCY-FFSTeKKSWEESRQFCEDMGAHLVIINSQEEQEFISKIlsGNRSYWIGLSDEETEGEWKWVDGTPL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 40789268 1117 Q--YENWREKQPDNFFAGGEDCVVMVaHESGRWNDVPCNYNLPYVCKK 1162
Cdd:cd03590   80 NssKTFWHPGEPNNWGGGGEDCAELV-YDSGGWNDVPCNLEYRWICEK 126
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 1040-1161 4.02e-41

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.


Pssm-ID: 214480 [Multi-domain]  Cd Length: 124  Bit Score: 147.36  E-value: 4.02e-41
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF-----GHENSWIGLNDRTVERDFQWTDNT 1114
Cdd:smart00034    1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAENDFVASLlknsgSSDYYWIGLSDPDSNGSWQWSDGS 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 40789268    1115 GL-QYENWREKQPDNffaGGEDCVVMVAHeSGRWNDVPCNYNLPYVCK 1161
Cdd:smart00034   81 GPvSYSNWAPGEPNN---SSGDCVVLSTS-GGKWNDVSCTSKLPFVCE 124
CLECT cd00037
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 1050-1162 1.30e-39

C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.


Pssm-ID: 153057 [Multi-domain]  Cd Length: 116  Bit Score: 142.76  E-value: 1.30e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1050 HCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF----GHENSWIGLNDRTVERDFQWTDNTG-LQYENWREK 1124
Cdd:cd00037    1 SCYKFSTEKLTWEEAQEYCRSLGGHLASIHSEEENDFLASLlkksSSSDVWIGLNDLSSEGTWKWSDGSPlVDYTNWAPG 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 40789268 1125 QPDNffAGGEDCVVMVAHESGRWNDVPCNYNLPYVCKK 1162
Cdd:cd00037   81 EPNP--GGSEDCVVLSSSSDGKWNDVSCSSKLPFICEK 116
Xlink pfam00193
Extracellular link domain;
159-253 2.91e-39

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 140.79  E-value: 2.91e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    159 VVFHYRAaRDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRsslPGVRS 238
Cdd:pfam00193    1 GVFHLES-PGRYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNM---PGVRQ 76

                           90
                   ....*....|....*.
gi 40789268    239 YGRRDPQ-ELYDVYCF 253
Cdd:pfam00193   77 YGFRDPLsERYDAYCY 92
CLECT_CEL-1_like cd03589
C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and ...
 1040-1161 4.71e-39

C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina; CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CEL-1 CTLD binds three calcium ions and has a high specificity for N-acteylgalactosamine (GalNAc). CEL-1 exhibits strong cytotoxicity which is inhibited by GalNAc. This protein may play a role as a toxin defending against predation. Echinoidin is found in the coelomic fluid of the sea urchin and is specific for GalBeta1-3GalNAc. Echinoidin has a cell adhesive activity towards human cancer cells which is not mediated through the CTLD. Both CEL-1 and Echinoidin are multimeric proteins comprised of multiple dimers linked by disulfide bonds.


Pssm-ID: 153059  Cd Length: 137  Bit Score: 141.73  E-value: 4.71e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCR-----RRAGHLTSVHSPEEHKFINSF------GHENS--WIGLNDRTVER 1106
Cdd:cd03589    1 CPTFWTAFGGYCYRFFGDRLTWEEAELRCRsfsipGLIAHLVSIHSQEENDFVYDLfessrgPDTPYglWIGLHDRTSEG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 40789268 1107 DFQWTDNTGLQYENWREKQPDNFFaGGEDCVVMVAHES--GRWNDVPCNYNLPYVCK 1161
Cdd:cd03589   81 PFEWTDGSPVDFTKWAGGQPDNYG-GNEDCVQMWRRGDagQSWNDMPCDAVFPYICK 136
Xlink pfam00193
Extracellular link domain;
260-355 8.55e-39

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 139.25  E-value: 8.55e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    260 EVFYVGPARR--LTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTvyrf 337
Cdd:pfam00193    1 GVFHLESPGRykLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNMPGVRQ---- 76

                           90
                   ....*....|....*....
gi 40789268    338 anrTGFPAP-GARFDAYCF 355
Cdd:pfam00193   77 ---YGFRDPlSERYDAYCY 92
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 159-253 6.73e-32

Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239595  Cd Length: 95  Bit Score: 119.84  E-value: 6.73e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  159 VVFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCyGDRSSLPGVRS 238
Cdd:cd03518    1 VVFPYQPRLGRYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPC-GGKRTVPGLRS 79

                         90
                 ....*....|....*.
gi 40789268  239 YGRRDPQE-LYDVYCF 253
Cdd:cd03518   80 YGERDKMLsRYDAFCF 95
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 260-355 1.09e-31

Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239596  Cd Length: 91  Bit Score: 119.06  E-value: 1.09e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  260 EVFYVGPARRLTLAGARAQCQRQGAALASVGQLHLAWH-EGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTVyrfa 338
Cdd:cd03519    1 GVFYLLHPGKLTFSEAVAACQRDGAQIAKVGQLFAAWKfHGLDRCDAGWLADGSVRYPISRPRPRCGPLEPGVRSF---- 76

                         90
                 ....*....|....*...
gi 40789268  339 nrtGFPAPGAR-FDAYCF 355
Cdd:cd03519   77 ---GFPDKKHKlYGVYCY 91
CLECT_REG-1_like cd03594
C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and ...
 1040-1161 1.09e-31

C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2); CLECT_REG-1_like: C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. REG-1 is a proliferating factor which participates in various kinds of tissue regeneration including pancreatic beta-cell regeneration, regeneration of intestinal mucosa, regeneration of motor neurons, and perhaps in tissue regeneration of damaged heart. REG-1 may play a role on the pathophysiology of Alzheimer's disease and in the development of gastric cancers. Its expression is correlated with reduced survival from early-stage colorectal cancer. REG-1 also binds and aggregates several bacterial strains from the intestinal flora and it has been suggested that it is involved in the control of the intestinal bacterial ecosystem. Rat lithostathine has calcium carbonate crystal inhibitor activity in vitro. REG-IV is unregulated in pancreatic, gastric, hepatocellular, and prostrate adenocarcinomas. REG-IV activates the EGF receptor/Akt/AP-1 signaling pathway in colorectal carcinoma. Ansocalcin, SCA-1 and -2 are found at high concentration in the calcified egg shell layer of goose and ostrich, respectively and tend to form aggregates. Ansocalcin nucleates calcite crystal aggregates in vitro.


Pssm-ID: 153064 [Multi-domain]  Cd Length: 129  Bit Score: 120.55  E-value: 1.09e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRR--AGHLTSVHSPEEHKFINSF------GHENSWIGLNDRTVERDFQWT 1111
Cdd:cd03594    1 CPKGWLPYKGNCYGYFRQPLSWSDAELFCQKYgpGAHLASIHSPAEAAAIASLissyqkAYQPVWIGLHDPQQSRGWEWS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 40789268 1112 DNTGLQYENWREKQPdnfFAGGEDCVVMVAhESG--RWNDVPCNYNLPYVCK 1161
Cdd:cd03594   81 DGSKLDYRSWDRNPP---YARGGYCAELSR-STGflKWNDANCEERNPFICK 128
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 260-355 2.10e-31

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


Pssm-ID: 238534  Cd Length: 92  Bit Score: 118.29  E-value: 2.10e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  260 EVFYVGPAR---RLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVRTVyr 336
Cdd:cd01102    1 VVFHLESQNgryKLTFAEAALACKARGAHLATPGQLEAAWQDGFDVCTAGWLADGSVRYPIVTSRPNCGGRNPGVRSY-- 78

                         90
                 ....*....|....*....
gi 40789268  337 fanrtGFPAPGARFDAYCF 355
Cdd:cd01102   79 -----GNPAPSGRYDAYCF 92
Ig_Versican cd05901
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 43-161 7.78e-30

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Like aggrecan, versican has a wide distribution in connective tissue and extracellular matrices. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409482  Cd Length: 128  Bit Score: 115.44  E-value: 7.78e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   43 SGPVRAALAELVALPCFF----TLQPRLSSLRDIPRIKWTKVQTASGQR--QDLPILVAKDNVVRVAKGWQGRVSLPAYP 116
Cdd:cd05901    4 SSRVHGSLSGSVVLPCRFstlpTLPPSYNITSEFLRIKWTKIQVDKNGKdhKETTVLVAQNGIIKIGQEYMGRVSVPSHP 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 40789268  117 RHRANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05901   84 EDQGDASLTIVKLRASDAGVYRCEVMHGIEDTQDTVSLDVSGVVF 128
Lectin_C pfam00059
Lectin C-type domain; This family includes both long and short form C-type
 1061-1162 1.39e-29

Lectin C-type domain; This family includes both long and short form C-type


Pssm-ID: 459655 [Multi-domain]  Cd Length: 105  Bit Score: 113.73  E-value: 1.39e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   1061 WEDAERDCRRRAGHLTSVHSPEEHKFINSF---GHENSWIGLNDRTVERDFQWTDNTGLQYENWREKQPDNffAGGEDCV 1137
Cdd:pfam00059    4 WDEAREACRKLGGHLVSINSAEELDFLSSTlkkSNKYFWIGLTDRKNEGTWKWVDGSPVNYTNWAPEPNNN--GENEDCV 81

                           90       100
                   ....*....|....*....|....*
gi 40789268   1138 VMvAHESGRWNDVPCNYNLPYVCKK 1162
Cdd:pfam00059   82 EL-SSSSGKWNDENCNSKNPFVCEK 105
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 269-355 6.67e-25

Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239595  Cd Length: 95  Bit Score: 99.81  E-value: 6.67e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  269 RLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGP--APGVRTVyrfanrtGFPAP 346
Cdd:cd03518   13 NLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPCGGKrtVPGLRSY-------GERDK 85

                         90
                 ....*....|
gi 40789268  347 G-ARFDAYCF 355
Cdd:cd03518   86 MlSRYDAFCF 95
CLECT_collectin_like cd03591
C-type lectin-like domain (CTLD) of the type found in human collectins including lung ...
 1062-1160 1.74e-24

C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1); CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CTLDs of these collectins bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, or apoptotic cells) and mediate functions associated with killing and phagocytosis. MBPs recognize high mannose oligosaccharides in a calcium dependent manner, bind to a broad range of pathogens, and trigger cell killing by activating the complement pathway. MBP also acts directly as an opsonin. SP-A and SP-D in addition to functioning as host defense components, are components of pulmonary surfactant which play a role in surfactant homeostasis. Pulmonary surfactant is a phospholipid-protein complex which reduces the surface tension within the lungs. SP-A binds the major surfactant lipid: dipalmitoylphosphatidylcholine (DPPC). SP-D binds two minor components of surfactant that contain sugar moieties: glucosylceramide and phosphatidylinositol (PI). MBP and SP-A, -D monomers are homotrimers with an N-terminal collagen region and three CTLDs. Multiple homotrimeric units associate to form supramolecular complexes. MBL deficiency results in an increased susceptibility to a large number of different infections and to inflammatory disease, such as rheumatoid arthritis.


Pssm-ID: 153061 [Multi-domain]  Cd Length: 114  Bit Score: 99.29  E-value: 1.74e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1062 EDAERDCRRRAGHLTSVHSPEEHKFINSF---GHENSWIGLNDRTVERDFQWTDNTGLQYENWREKQPDNfFAGGEDCVV 1138
Cdd:cd03591   14 DDAQKLCSEAGGTLAMPRNAAENAAIASYvkkGNTYAFIGITDLETEGQFVYLDGGPLTYTNWKPGEPNN-AGGGEDCVE 92

                         90       100
                 ....*....|....*....|..
gi 40789268 1139 MVAheSGRWNDVPCNYNLPYVC 1160
Cdd:cd03591   93 MYT--SGKWNDVACNLTRLFVC 112
Ig_Aggrecan cd05900
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 45-161 1.70e-22

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggrecan has a wide distribution in connective tissue and extracellular matrices. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409481  Cd Length: 123  Bit Score: 94.24  E-value: 1.70e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   45 PVRAALAELVALPCFF-------TLQPRLSSLRdiPRIKWTKVQtasgQRQDLPILVAKDNVVRVAKGWQGRVSLPAYPR 117
Cdd:cd05900    6 PLRVVLGSSLLIPCYFqdpiakdPGAPTVAPLS--PRIKWSFIS----KEKESVLLVATEGKVRVNTEYLDRVSLPNYPA 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 40789268  118 HRANATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05900   80 IPSDATLEITELRSNDSGTYRCEVMHGIEDNYDTVEVQVKGIVF 123
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
 44-161 3.44e-21

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 90.08  E-value: 3.44e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   44 GPVRAALAELVALPCFFTLQPRLSSLRDIpRIKWTKVQTASGQRQDlpILVAKDNVVRVAKGWQGRVSLpayprHRA--- 120
Cdd:cd05877    5 AKVFSHRGGNVTLPCRYHYEPELSAPRKI-RVKWTKLEVDYAKEED--VLVAIGTRHKSYGSYQGRVFL-----RRAddl 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 40789268  121 NATLLLGPLRASDSGLYRCQVVKGIEDEQDLVTLEVTGVVF 161
Cdd:cd05877   77 DASLVITDLRLEDYGRYRCEVIDGLEDESVVVALRLRGVVF 117
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 172-253 3.19e-20

Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239596  Cd Length: 91  Bit Score: 86.32  E-value: 3.19e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  172 LTFAEAQEACRLSSATIAAPRHLQAAFE-DGFDNCDAGWLSDRTVRYPITQSRPGCYGDRsslPGVRSYGRRDPQE-LYD 249
Cdd:cd03519   11 LTFSEAVAACQRDGAQIAKVGQLFAAWKfHGLDRCDAGWLADGSVRYPISRPRPRCGPLE---PGVRSFGFPDKKHkLYG 87


                 ....
gi 40789268  250 VYCF 253
Cdd:cd03519   88 VYCY 91
CLECT_VCBS cd03603
A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein ...
 1050-1159 6.83e-19

A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; CLECT_VCBS: A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Bacterial CTLDs within this group are functionally uncharacterized. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer.


Pssm-ID: 153073 [Multi-domain]  Cd Length: 118  Bit Score: 83.63  E-value: 6.83e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1050 HCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFI--NSFGHENSWIGLNDRTVERDFQWTDNTGLQYENWREKQPD 1127
Cdd:cd03603    1 HFYKFVDGGMTWEAAQTLAESLGGHLVTINSAEENDWLlsNFGGYGASWIGASDAATEGTWKWSDGEESTYTNWGSGEPH 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 40789268 1128 NFFAGGEDCVVM--VAHESGRWNDVPCNYNLPYV 1159
Cdd:cd03603   81 NNGGGNEDYAAInhFPGISGKWNDLANSYNTLGY 114
CLECT_selectins_like cd03592
C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P ...
 1052-1160 7.96e-19

C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels); CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. P- E- and L-sels are cell adhesion receptors that mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. L- sel is expressed constitutively on most leukocytes. P-sel is stored in the Weibel-Palade bodies of endothelial cells and in the alpha granules of platlets. E- sels are present on endothelial cells. Following platelet and/or endothelial cell activation P- sel is rapidly translocated to the cell surface and E-sel expression is induced. The initial step in leukocyte migration involves interactions of selectins with fucosylated, sialylated, and sulfated carbohydrate moieties on target ligands displayed on glycoprotein scaffolds on endothelial cells and leucocytes. A major ligand of P- E- and L-sels is PSGL-1 (P-sel glycoprotein ligand). Interactions of E- and P- sels with tumor cells may promote extravasation of cancer cells. Regulation of L-sel and P-sel function includes proteolytic shedding of the most extracellular portion (containing the CTLD) from the cell surface. Increased levels of the soluble form of P-sel in the plasma have been found in a number of diseases including coronary disease and diabetes. E- and P- sel also play roles in the development of synovial inflammation in inflammatory arthritis. Platelet P-sel, but not endothelial P-sel, plays a role in the inflammatory response and neointimal formation after arterial injury. Selectins may also function as signal-transducing receptors.


Pssm-ID: 153062  Cd Length: 115  Bit Score: 83.19  E-value: 7.96e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1052 YRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSFG--HENS--WIGLNDRTVERDFQWTDNTGLQYENWREKQPD 1127
Cdd:cd03592    3 YHYSTEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFAlkYNLGyyWIDGNDINNEGTWVDTDKKELEYKNWAPGEPN 82

                         90       100       110
                 ....*....|....*....|....*....|...
gi 40789268 1128 NffAGGEDCVVMVAHESGRWNDVPCNYNLPYVC 1160
Cdd:cd03592   83 N--GRNENCLEIYIKDNGKWNDEPCSKKKSAIC 113
Link_domain_TSG_6_like cd03515
This is the extracellular link domain of the type found in human TSG-6. The link domain is a ...
 160-253 3.36e-17

This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accumulate in vascular tissues during aging and diabetes, these receptors may be implicated in the pathologies of these states. Both stabilins are present in the early endocytic pathway in hepatic sinusoidal epithelium associating with clathrin/AP-2. Stabilin-1 is expressed in macrophages. Stabilin-2 is absent from the latter. In macrophages: stabilin-1 is involved in trafficking between early/sorting endosomes and the trans-Golgi network. Stabilin-1 has also been implicated in angiogenesis and possibly leucocyte trafficking. Both stabilins bind gram-positive and gram-negative bacteria. TSG-6 and stabilins contain a single link module which supports high affinity binding to HA.


Pssm-ID: 239592  Cd Length: 93  Bit Score: 77.89  E-value: 3.36e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  160 VFHYRAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCYGDRSslpGVRSY 239
Cdd:cd03515    2 VFHLRSRSGKYKLTYTEAKAACEAEGAHLATYSQLSAAQQLGFHLCAAGWLAKGRVGYPIVFPSANCGFGHV---GIVDY 78

                         90
                 ....*....|....*
gi 40789268  240 G-RRDPQELYDVYCF 253
Cdd:cd03515   79 GpRLNLSERWDAYCY 93
CLECT_NK_receptors_like cd03593
C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); ...
 1040-1162 2.80e-15

C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.


Pssm-ID: 153063  Cd Length: 116  Bit Score: 73.14  E-value: 2.80e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF-GHENSWIGLNDRTVERDFQWTDNTglQY 1118
Cdd:cd03593    1 CPKDWICYGNKCYYFSMEKKTWNESKEACSSKNSSLLKIDDEEELEFLQSQiGSSSYWIGLSREKSEKPWKWIDGS--PL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 40789268 1119 ENWREkqpDNFFAGGEDCVVMvahESGRWNDVPCNYNLPYVCKK 1162
Cdd:cd03593   79 NNLFN---IRGSTKSGNCAYL---SSTGIYSEDCSTKKRWICEK 116
PHA03247 PHA03247
large tegument protein UL36; Provisional
 400-851 4.00e-14

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 78.06  E-value: 4.00e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   400 APDFQEPLMSSGE---GEPPDLTWTQAPEETLGSTPGGPTLASWPSSEKWLFTGAPSSMGVSSPSDMGVDMEATTPLGTQ 476
Cdd:PHA03247 2574 APRPSEPAVTSRArrpDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   477 VAPTPT-MRRGRFKGLNGRHFQQQGPedqlPEVAEPSAQPPTLGATANHMRPSAATEASESdqSHSPWAILTNEVDEPGA 555
Cdd:PHA03247 2654 DDPAPGrVSRPRRARRLGRAAQASSP----PQRPRRRAARPTVGSLTSLADPPPPPPTPEP--APHALVSATPLPPGPAA 2727

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   556 GSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPGAAEAPSvksaiPHLPRLPSEPPAPS----PGPSEALSAVSLQASS 631
Cdd:PHA03247 2728 ARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPA-----PAPPAAPAAGPPRRltrpAVASLSESRESLPSPW 2802

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   632 ADGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPLSPA---SPLPSWVPEEQAVRPvslgAEDLETPFQTTIAAPVEASH 708
Cdd:PHA03247 2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPpppGPPPPSLPLGGSVAP----GGDVRRRPPSRSPAAKPAAP 2878

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   709 RSPDADsieiegtssmRATKHPISGPWASLDSSNVTMNPVPSDagilgtesgvlDLPGSPTSGGQATVEKVLATWLPLPG 788
Cdd:PHA03247 2879 ARPPVR----------RLARPAVSRSTESFALPPDQPERPPQP-----------QAPPPPQPQPQPPPPPQPQPPPPPPP 2937

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40789268   789 QGLDPGSQSTPMEAHGVAVSMEPTVALeGGATEGPMEATREVVPSTADATWESESRSAISSTH 851
Cdd:PHA03247 2938 RPQPPLAPTTDPAGAGEPSGAVPQPWL-GALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGH 2999
CLECT_EMBP_like cd03598
C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major ...
 1049-1160 3.31e-13

C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major basic protein (EMBP) and prepro major basic protein homolog (MBPH); CLECT_EMBP_like: C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major basic protein (EMBP) and prepro major basic protein homolog (MBPH). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Eosinophils and basophils carry out various functions in allergic, parasitic, and inflammatory diseases. EMBP is stored in eosinophil crystalloid granules and is released upon degranulation. EMBP is also expressed in basophils. The proform of EMBP is expressed in placental X cells and breast tissue and increases significantly during human pregnancy. EMBP has cytotoxic properties and damages bacteria and mammalian cells, in vitro, as well as, helminth parasites. EMBP deposition has been observed in the inflamed tissue of allergy patients in a variety of diseases including asthma, atopic dermatitis, and rhinitis. In addition to its cytotoxic functions, EMBP activates cells and stimulates cytokine production. EMBP has been shown to bind the proteoglycan heparin. The binding site is similar to the carbohydrate binding site of other classical CTLD, such as mannose-binding protein (MBP1), however, heparin binding to EMBP is calcium ion independent. MBPH has reduced potency in cytotoxic and cytostimulatory assays compared with EMBP.


Pssm-ID: 153068  Cd Length: 117  Bit Score: 67.48  E-value: 3.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1049 GHCYRYFAHRRAWEDAERDCRR-RAGHLTSVHSPEEH----KFINSFGHENSWIG--LNDRTVERDFQWTDNTGLQYENW 1121
Cdd:cd03598    1 GRCYRFVKSPRTFRDAQVICRRcYRGNLASIHSFAFNyrvqRLVSTLNQAQVWIGgiITGKGRCRRFSWVDGSVWNYAYW 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 40789268 1122 REKQPDNffaGGEDCVVMVAHEsGRWNDVPCNYNLPYVC 1160
Cdd:cd03598   81 APGQPGN---RRGHCVELCTRG-GHWRRAHCKLRRPFIC 115
CLECT_chondrolectin_like cd03595
C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins ...
 1040-1161 1.30e-12

C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins chondrolectin (CHODL) and layilin; CLECT_chondrolectin_like: C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins chondrolectin (CHODL) and layilin. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. CHODL is predominantly expressed in muscle cells and is associated with T-cell maturation. Various alternatively spliced isoforms have been of CHODL have been identified. The transmembrane form of CHODL is localized in the ER-Golgi apparatus. Layilin is widely expressed in different cell types. The extracellular CTLD of layilin binds hyaluronan (HA), a major constituent of the extracellular matrix (ECM). The cytoplasmic tail of layilin binds various members of the band 4.1/ERM superfamily (talin, radixin, and merlin). The ERM proteins are cytoskeleton-membrane linker molecules which link actin to receptors in the plasma membrane. Layilin co-localizes in with talin in membrane ruffles and may mediate signals from the ECM to the cell cytoskeleton.


Pssm-ID: 153065  Cd Length: 149  Bit Score: 66.84  E-value: 1.30e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGwhkFQGHCYR--YF--AHRRA-WEDAERDCRRRAGHLTSVHSPEEHKFINSFGHE------NSWIGL---NDRTVE 1105
Cdd:cd03595    4 CRRG---TEKPCYKiaYFqdSRRRLnFEEARQACREDGGELLSIESENEQKLIERFIQTlrasdgDFWIGLrrsSQYNVT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 40789268 1106 RD-----FQWTDNTGLQYENWREKQPDnffAGGEDCVVMVAHESG----------RWNDVPCNYNLPYVCK 1161
Cdd:cd03595   81 SSacsslYYWLDGSISTFRNWYVDEPS---CGSEVCVVMYHQPSApagqggpylfQWNDDNCNMKNNFICK 148
CLECT_tetranectin_like cd03596
C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived ...
 1040-1160 1.72e-12

C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF); CLECT_tetranectin_like: C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. TN binds to plasminogen and stimulates activation of plasminogen, playing a key role in the regulation of proteolytic processes. The TN CTLD binds two calcium ions. Its calcium free form binds to various kringle-like protein ligands. Two residues involved in the coordination of calcium are critical for the binding of TN to the fourth kringle (K4) domain of plasminogen (Plg K4). TN binds the kringle 1-4 form of angiostatin (AST K1-4). AST K1-4 is a fragment of Plg, commonly found in cancer tissues. TN inhibits the binding of Plg and AST K1-4 to the extracellular matrix (EMC) of endothelial cells and counteracts the antiproliferative effects of AST K1-4 on these cells. TN also binds the tenth kringle domain of apolipoprotein (a). In addition, TN binds fibrin and complex polysaccharides in a Ca2+ dependent manner. The binding site for complex sulfated polysaccharides is N-terminal to the CTLD. TN is homotrimeric; N-terminal to the CTLD is an alpha helical domain responsible for trimerization of monomeric units. TN may modulate angiogenesis through interactions with angiostatin and coagulation through interaction with fibrin. TN may play a role in myogenesis and in bone development. Mice having a deletion in the TN gene exhibit a kyphotic spine abnormality. TN is a useful prognostic marker of certain cancer types. CLECSF1 is expressed in cartilage tissue, which is primarily intracellular matrix (ECM), and is a candidate for organizing ECM. SCGF is strongly expressed in bone marrow and is a cytokine for primitive hematopoietic progenitor cells.


Pssm-ID: 153066  Cd Length: 129  Bit Score: 65.49  E-value: 1.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1040 CDRGwHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFI-----NSFGHENS-WIGLNDRTVERdfQWTDN 1113
Cdd:cd03596    1 CLKG-TKIHKKCYLVSEETKHYHEASEDCIARGGTLATPRDSDENDALrdyvkASVPGNWEvWLGINDMVAEG--KWVDV 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 40789268 1114 TGLQ--YENWR---EKQPDnffaGG--EDCVVMVAHESGRWNDVPCNYNLPYVC 1160
Cdd:cd03596   78 NGSPisYFNWEreiTAQPD----GGkrENCVALSSSAQGKWFDEDCRREKPYVC 127
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1167-1224 1.02e-11

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.


Pssm-ID: 153056 [Multi-domain]  Cd Length: 57  Bit Score: 60.94  E-value: 1.02e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268 1167 CGPPPAVENASLVGvRKIKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMCI 1224
Cdd:cd00033    1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57
CLECT_1 cd03602
C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains ...
 1061-1160 1.47e-11

C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; CLECT_1: C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer.


Pssm-ID: 153072  Cd Length: 108  Bit Score: 62.39  E-value: 1.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1061 WEDAERDCRRRAGHLTSVHSPEEHKFINSFGHENS---WIGLNDRTVErdFQWTDNTGLQYENWREKQPDnffaGGEDCV 1137
Cdd:cd03602   12 WSEAQQYCRENYTDLATVQNQEDNALLSNLSRVSNsaaWIGLYRDVDS--WRWSDGSESSFRNWNTFQPF----GQGDCA 85

                         90       100
                 ....*....|....*....|...
gi 40789268 1138 VMvaHESGRWNDVPCNYNLPYVC 1160
Cdd:cd03602   86 TM--YSSGRWYAALCSALKPFIC 106
Link_domain_TSG_6_like cd03515
This is the extracellular link domain of the type found in human TSG-6. The link domain is a ...
 269-355 5.44e-11

This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accumulate in vascular tissues during aging and diabetes, these receptors may be implicated in the pathologies of these states. Both stabilins are present in the early endocytic pathway in hepatic sinusoidal epithelium associating with clathrin/AP-2. Stabilin-1 is expressed in macrophages. Stabilin-2 is absent from the latter. In macrophages: stabilin-1 is involved in trafficking between early/sorting endosomes and the trans-Golgi network. Stabilin-1 has also been implicated in angiogenesis and possibly leucocyte trafficking. Both stabilins bind gram-positive and gram-negative bacteria. TSG-6 and stabilins contain a single link module which supports high affinity binding to HA.


Pssm-ID: 239592  Cd Length: 93  Bit Score: 60.17  E-value: 5.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  269 RLTLAGARAQCQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGGPAPGVrTVYRF-ANRTgfpapg 347
Cdd:cd03515   13 KLTYTEAKAACEAEGAHLATYSQLSAAQQLGFHLCAAGWLAKGRVGYPIVFPSANCGFGHVGI-VDYGPrLNLS------ 85


                 ....*...
gi 40789268  348 ARFDAYCF 355
Cdd:cd03515   86 ERWDAYCY 93
CCP smart00032
Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat ...
 1167-1223 4.45e-10

Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.


Pssm-ID: 214478 [Multi-domain]  Cd Length: 56  Bit Score: 56.38  E-value: 4.45e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 40789268    1167 CGPPPAVENASLVGVRKiKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMC 1223
Cdd:smart00032    1 CPPPPDIENGTVTSSSG-TYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 998-1034 6.37e-10

Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.


Pssm-ID: 238011  Cd Length: 38  Bit Score: 55.34  E-value: 6.37e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 40789268  998 DIDDCL-CSPCENGGTCIDEVNGFICLCLPSYGGSLCE 1034
Cdd:cd00054    1 DIDECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 42-157 7.92e-10

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 57.47  E-value: 7.92e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268     42 GSGPVRAALAELVALPCFFTLqprlSSLRDIPRIKWTKVQTasGQRQDLPILVAKDNVVRVAKgwQGRVSLPAYPRhRAN 121
Cdd:pfam07686    2 TPREVTVALGGSVTLPCTYSS----SMSEASTSVYWYRQPP--GKGPTFLIAYYSNGSEEGVK--KGRFSGRGDPS-NGD 72

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 40789268    122 ATLLLGPLRASDSGLYRCQVV-KGIEDEQDLVTLEVT 157
Cdd:pfam07686   73 GSLTIQNLTLSDSGTYTCAVIpSGEGVFGKGTRLTVL 109
Sushi pfam00084
Sushi repeat (SCR repeat);
1167-1223 9.08e-10

Sushi repeat (SCR repeat);


Pssm-ID: 459664 [Multi-domain]  Cd Length: 56  Bit Score: 55.58  E-value: 9.08e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 40789268   1167 CGPPPAVENASLVGVRKiKYNVHATVRYQCDEGFSQHRVATIRCRNNGKWDRPQIMC 1223
Cdd:pfam00084    1 CPPPPDIPNGKVSATKN-EYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56
CLECT_thrombomodulin_like cd03600
C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, ...
 1048-1161 2.04e-09

C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR; CLECT_thrombomodulin_like: C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In these thrombomodulin-like proteins the residues involved in coordinating Ca2+ in the classical MBP-A CTLD are not conserved. TM exerts anti-fibrinolytic and anti-inflammatory activity. TM also regulates blood coagulation in the anticoagulant protein C pathway. In this pathway, the procoagulant properties of thrombin (T) are lost when it binds TM. TM also plays a key role in tumor biology. It is expressed on endothelial cells and on several type of tumor cell including squamous cell carcinoma. Loss of TM expression correlates with advanced stage and poor prognosis. Loss of function of TM function may be associated with arterial or venous thrombosis and with late fetal loss. Soluble molecules of TM retaining the CTLD are detected in human plasma and urine where higher levels indicate injury and/or enhanced turnover of the endothelium. C1qR is expressed on endothelial cells and stem cells. It is also expressed on monocots and neutrophils, where it is subject to ectodomain shedding. Soluble forms of C1qR retaining the CTLD is detected in human plasma. C1qR modulates the phagocytosis of apoptotic cells in vivo. C1qR-deficient mice are defective in clearance of apoptotic cells in vivo. The cytoplasmic tail of C1qR, C-terminal to the CTLD of CD93, contains a PDZ binding domain which interacts with the PDZ domain-containing adaptor protein, GIPC. The juxtamembrane region of this tail interacts with the ezrin/radixin/moesin family. Endosialin functions in the growth and progression of abdominal tumors and is expressed in the stroma of several tumors.


Pssm-ID: 153070  Cd Length: 141  Bit Score: 57.06  E-value: 2.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1048 QGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF----------GHENSWIGLNDRTVE--------RDFQ 1109
Cdd:cd03600    3 SDACYTLHPQKLTFLEAQRSCIELGGNLATVRSGEEADVVSLLlaagpgrhgrGSLRLWIGLQREPRQcsdpslplRGFS 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268 1110 W-TDNTGLQYENWREKQPDNffAGGEDCVVMVAHESG----RWNDVPCNYNLP-YVCK 1161
Cdd:cd03600   83 WvTGDQDTDFSNWLQEPAGT--CTSPRCVALSAAGSTpdnlKWKDGPCSARADgYLCK 138
EGF_CA smart00179
Calcium-binding EGF-like domain;
998-1034 5.89e-09

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 52.63  E-value: 5.89e-09
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 40789268     998 DIDDCL-CSPCENGGTCIDEVNGFICLCLPSY-GGSLCE 1034
Cdd:smart00179    1 DIDECAsGNPCQNGGTCVNTVGSYRCECPPGYtDGRNCE 39
Link_domain_CD44_like cd03516
This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates ...
 160-253 2.25e-07

This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marker for the detection and characterization of lymphatic vessels in tumors.


Pssm-ID: 239593  Cd Length: 144  Bit Score: 51.31  E-value: 2.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  160 VFHYrAARDRYALTFAEAQEACRLSSATIAAPRHLQAAFEDGFDNCDAGWLSDRTVRYPITQSRPGCygdRSSLPGVrsY 239
Cdd:cd03516    8 VFLV-EKNGRYSLNFTEAKEACRALGLTLASKAQVETALKFGFETCRYGWVEDGFVVIPRIDPNPLC---GKNGTGV--Y 81

                         90
                 ....*....|....*
gi 40789268  240 GRRDP-QELYDVYCF 253
Cdd:cd03516   82 ILNSNlSSRYDAYCY 96
PHA03247 PHA03247
large tegument protein UL36; Provisional
 379-765 2.30e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 2.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   379 VSAEGPPGRELKPSLGEQEVIAPDFQEPLMSSGEGEPPDLTWTQAPEETLGSTPGGPTLASWPSSEKWLFTGAPSSMGVS 458
Cdd:PHA03247 2667 ARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPA 2746

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   459 SPSDMGVDMEATTPLGTQVAPTPTMRRGRFKGLNGRHFQQQGPEDQLPEVAEPSAQPPTlGATANHMRPSAATEASESDQ 538
Cdd:PHA03247 2747 GPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPA-DPPAAVLAPAAALPPAASPA 2825

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   539 SHSPwailTNEVDEPGAGSLGSRSLPESLMW-------------SPSLISPSVPSTDSTPSAKPGAAEAPSVKSAIPHLP 605
Cdd:PHA03247 2826 GPLP----PPTSAQPTAPPPPPGPPPPSLPLggsvapggdvrrrPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALP 2901

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   606 RLPSEPPAPSPGPSEALSAVSLQAsSADGSPDFPIVAMLRAPklwLLPRSTLVPNMTPVPLSPASPLPSWVPEEQAV--R 683
Cdd:PHA03247 2902 PDQPERPPQPQAPPPPQPQPQPPP-PPQPQPPPPPPPRPQPP---LAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVprF 2977

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   684 PVSLGAEDLETPFQTT-----IAAPVEASHRSPDADSIEIE-GTSSMRATKHPISGPWASLDSSNVTMNPVPSDAGILGT 757
Cdd:PHA03247 2978 RVPQPAPSREAPASSTppltgHSLSRVSSWASSLALHEETDpPPVSLKQTLWPPDDTEDSDADSLFDSDSERSDLEALDP 3057


                  ....*...
gi 40789268   758 ESGVLDLP 765
Cdd:PHA03247 3058 LPPEPHDP 3065
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 964-994 3.38e-07

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.


Pssm-ID: 394967  Cd Length: 31  Bit Score: 47.38  E-value: 3.38e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 40789268    964 CENNPCLHGGTCHTNGTVYGCSCDQGYAGEN 994
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 962-996 6.46e-07

Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.


Pssm-ID: 238011  Cd Length: 38  Bit Score: 46.86  E-value: 6.46e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 40789268  962 DPCE-NNPCLHGGTCH-TNGTvYGCSCDQGYAGENCE 996
Cdd:cd00054    3 DECAsGNPCQNGGTCVnTVGS-YRCSCPPGYTGRNCE 38
CLECT_TC14_like cd03601
C-type lectin-like domain (CTLD) of the type found in lectins TC14, TC14-2, TC14-3, and TC14-4 ...
 1054-1162 6.25e-06

C-type lectin-like domain (CTLD) of the type found in lectins TC14, TC14-2, TC14-3, and TC14-4 from the budding tunicate Polyandrocarpa misakiensis and PfG6 from the Acorn worm; CLECT_TC14_like: C-type lectin-like domain (CTLD) of the type found in lectins TC14, TC14-2, TC14-3, and TC14-4 from the budding tunicate Polyandrocarpa misakiensis and PfG6 from the Acorn worm. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. TC14 is homodimeric. The CTLD of TC14 binds D-galactose and D-fucose. TC14 is expressed constitutively by multipotent epithelial and mesenchymal cells and plays in role during budding, in inducing the aggregation of undifferentiated mesenchymal cells to give rise to epithelial forming tissue. TC14-2 and TC14-3 shows calcium-dependent galactose binding activity. TC14-3 is a cytostatic factor which blocks cell growth and dedifferentiation of the atrial epithelium during asexual reproduction. It may also act as a differentiation inducing factor. Galactose inhibits the cytostatic activity of TC14-3. The gene for Acorn worm PfG6 is gill-specific; PfG6 may be a secreted protein.


Pssm-ID: 153071  Cd Length: 119  Bit Score: 46.76  E-value: 6.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268 1054 YFAHRRA-WEDAERDCRRRAGHLTSVHSP--EEHKFINSF----GHeNSWIGLND-RTVERDFQWTDNTGL--QYENWRE 1123
Cdd:cd03601    4 LCSDETMnYAKAGAFCRSRGMRLASLAMRdsEMRDAILAFtlvkGH-GYWVGADNlQDGEYDFLWNDGVSLptDSDLWAP 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 40789268 1124 KQPDNfFAGGEDCVVMvAHESGRWNDVPCNYNLPYVCKK 1162
Cdd:cd03601   83 NEPSN-PQSRQLCVQL-WSKYNLLDDEYCGRAKRVICEK 119
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 46-142 7.90e-06

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 46.29  E-value: 7.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   46 VRAALAELVALPCFFTLqprlSSLRDIPRIKWTKVQTasGQRQDLPILVAKDNVVrVAKGWQGRVSLPAYPRHRANATLL 125
Cdd:cd05718    9 VTGFLGGSVTLPCSLTS----PGTTKITQVTWMKIGA--GSSQNVAVFHPQYGPS-VPNPYAERVEFLAARLGLRNATLR 81

                         90
                 ....*....|....*..
gi 40789268  126 LGPLRASDSGLYRCQVV 142
Cdd:cd05718   82 IRNLRVEDEGNYICEFA 98
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
511-713 1.91e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 49.10  E-value: 1.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   511 PSAQPPTLGATANHMRPSAATEASESDQSHSPWAILTNEVDEPGAGSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPG 590
Cdd:PRK12323  376 TAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPA 455

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   591 AAEAPSVKSAIPHlprlPSEPPAPSPGPSEALSAVSLQASSADGSPdfpivamlrapklwllPRSTLVPNMTPVPLSPAS 670
Cdd:PRK12323  456 AAPAAAARPAAAG----PRPVAAAAAAAPARAAPAAAPAPADDDPP----------------PWEELPPEFASPAPAQPD 515

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 40789268   671 PLPSWVPEEQAVRPvslGAEDLETPFQTTIAAPVEASHRSPDA 713
Cdd:PRK12323  516 AAPAGWVAESIPDP---ATADPDDAFETLAPAPAAAPAPRAAA 555
EGF cd00053
Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large ...
 1005-1034 3.36e-05

Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium.


Pssm-ID: 238010  Cd Length: 36  Bit Score: 42.08  E-value: 3.36e-05
                         10        20        30
                 ....*....|....*....|....*....|.
gi 40789268 1005 SPCENGGTCIDEVNGFICLCLPSYGGSL-CE 1034
Cdd:cd00053    6 NPCSNGGTCVNTPGSYRCVCPPGYTGDRsCE 36
EGF_CA smart00179
Calcium-binding EGF-like domain;
962-996 4.20e-05

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 41.85  E-value: 4.20e-05
                            10        20        30
                    ....*....|....*....|....*....|....*...
gi 40789268     962 DPCE-NNPCLHGGTCH-TNGTvYGCSCDQGY-AGENCE 996
Cdd:smart00179    3 DECAsGNPCQNGGTCVnTVGS-YRCECPPGYtDGRNCE 39
hEGF pfam12661
Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six ...
 1007-1026 4.53e-05

Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteriztic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC. These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin. Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.


Pssm-ID: 463660  Cd Length: 22  Bit Score: 41.55  E-value: 4.53e-05
                           10        20
                   ....*....|....*....|
gi 40789268   1007 CENGGTCIDEVNGFICLCLP 1026
Cdd:pfam12661    1 CQNGGTCVDGVNGYKCQCPP 20
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
498-696 4.67e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 47.95  E-value: 4.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   498 QQGPEDQLPEVAEPSAQPPTLGATANHMRPSAATEASESDQSHSPWAILTNEVDEPGAGSLGSRSLPESLMwspslisPS 577
Cdd:PRK12323  384 QPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAP-------AA 456

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   578 VPStdstPSAKPGAAEAPSVKSAIPHLPRLPSEPPAPSPG-----PSEALSAVSLQASSADGSPDFPIVAMLRAPKLWLL 652
Cdd:PRK12323  457 APA----AAARPAAAGPRPVAAAAAAAPARAAPAAAPAPAdddppPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATA 532

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 40789268   653 PRSTLVPNMTPVPLSPASPLPSWVPEEQ-AVRPVSLGAEDLETPF 696
Cdd:PRK12323  533 DPDDAFETLAPAPAAAPAPRAAAATEPVvAPRPPRASASGLPDMF 577
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 1002-1031 4.82e-05

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.


Pssm-ID: 394967  Cd Length: 31  Bit Score: 41.60  E-value: 4.82e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 40789268   1002 CLCSPCENGGTCIDEVNGFICLCLPSYGGS 1031
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGK 30
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 456-812 5.49e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 47.84  E-value: 5.49e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    456 GVSSPSDMGVDMEATTPlgtqVAPTPTMRRGRF-KGLNGRHFQQQGPEDQLPEVAEPSAQPPTLGATANHMRPSAATEAS 534
Cdd:pfam03154  130 GSSDPKDIDQDNRSTSP----SIPSPQDNESDSdSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPS 205

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    535 ESDQSHSPWAILTNEVDEPGAGSLGSRSLPEslMWSPSLISPSVPSTDSTPSAKPGAAEAPSVKSAIPHLPRlpsePPAP 614
Cdd:pfam03154  206 VPPQGSPATSQPPNQTQSTAAPHTLIQQTPT--LHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQM----PPMP 279

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    615 SP---GPSEALSAVSLQassadGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPLSPASPLPSWVPEEQAVRPVSLGAED 691
Cdd:pfam03154  280 HSlqtGPSHMQHPVPPQ-----PFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPH 354

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    692 LETPFQTTIAA-PVEASHRSPDADSI--------------EIEGTSSMrATKHPISG--PWASLDSSNVTMNPVPSDAGI 754
Cdd:pfam03154  355 IKPPPTTPIPQlPNPQSHKHPPHLSGpspfqmnsnlppppALKPLSSL-STHHPPSAhpPPLQLMPQSQQLPPPPAQPPV 433

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    755 LgTESGVLDLPGS--PTSGGQATVekvlATWLPLPGQGLDPGSQSTPMEAHGVAVSMEPT 812
Cdd:pfam03154  434 L-TQSQSLPPPAAshPPTSGLHQV----PSQSPFPQHPFVPGGPPPITPPSGPPTSTSSA 488
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 1040-1114 9.03e-05

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 45.11  E-value: 9.03e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40789268  1040 CDRGWHKFQGHCYRYFAHRRAWEDAERDCRRRAGHLTSVHSPEEHKFINSF-GHENSWIGLNDRTVERDFQWTDNT 1114
Cdd:PHA02642   88 CPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEELNFLKRYkDSSDHWIGLNRESSNHPWKWADNS 163
EGF cd00053
Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large ...
 963-996 1.14e-04

Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium.


Pssm-ID: 238010  Cd Length: 36  Bit Score: 40.54  E-value: 1.14e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 40789268  963 PCE-NNPCLHGGTCHTNGTVYGCSCDQGYAGE-NCE 996
Cdd:cd00053    1 ECAaSNPCSNGGTCVNTPGSYRCVCPPGYTGDrSCE 36
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 1032-1161 1.18e-04

polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half.


Pssm-ID: 188093 [Multi-domain]  Cd Length: 2740  Bit Score: 46.61  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   1032 LCEKDTEgcdrgWHKFQGHCYRYFAHRRAWEDAERDCRRRAG-HLTSVHSPEEHKFINS----FGHENSWIGLND-RTVE 1105
Cdd:TIGR00864  317 HCPKDGE-----IFEENGHCFQIVPEEAAWLDAQEQCLARAGaALAIVDNDALQNFLARkvthSLDRGVWIGFSDvNGAE 391

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 40789268   1106 RD-FQWTDNTGLQY-ENWREKQPDnfFAGGEDCVVMvaHESGRWNDVPCNYNLPYVCK 1161
Cdd:TIGR00864  392 KGpAHQGEAFEAEEcEEGLAGEPH--PARAEHCVRL--DPRGQCNSDLCNAPHAYVCE 445
Link_domain_KIAA0527_like cd03521
Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, ...
 270-354 2.53e-04

Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.


Pssm-ID: 239598  Cd Length: 95  Bit Score: 41.45  E-value: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  270 LTLAGARAQCQRQGAALASVGQL-HLAWHEGLDQCDPGWLADGSVRYPIQTPrrRCGGPAPGVRTVYRFANRtgfPAPGA 348
Cdd:cd03521   14 LGLRAARQSCASLGARLASAAELrRAVVECFFSACARGWLADGTVGTTVCNP--VVAEALKAVDVKVEIETN---PIPFA 88


                 ....*.
gi 40789268  349 RFDAYC 354
Cdd:cd03521   89 HYNALC 94
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 574-924 3.82e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   574 ISPSVPSTDSTPSAKPGAAEAPSVKSAIPHLPRLPSEPPAPSPGPSEALSAVSLQASSADGSPDFPIVAMLRAPKLWLLP 653
Cdd:PRK07764  385 LGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSA 464

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   654 RSTLVPNMTPVPLSPASPLPSWVPEEQAVRPVslgaedletpfqttiAAPVEASHRSPDADSIEiEGTSSMRATKHPISG 733
Cdd:PRK07764  465 QPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAA---------------PAAPAAPAGADDAATLR-ERWPEILAAVPKRSR 528

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   734 PWASLDSSNVTMNPVPSDAGILGTESGVL----DLPGSPTS---------GGQATVEKVLATwlplPGQGLDPGSQSTPM 800
Cdd:PRK07764  529 KTWAILLPEATVLGVRGDTLVLGFSTGGLarrfASPGNAEVlvtalaeelGGDWQVEAVVGP----APGAAGGEGPPAPA 604

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   801 EAHGVAVSMEPTvalEGGATEGPMEATREVVPSTADATWESESRSAISSTHiavtMARAQGMPTLTSTSSEGHPEPKGQm 880
Cdd:PRK07764  605 SSGPPEEAARPA---APAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEH----HPKHVAVPDASDGGDGWPAKAGGA- 676

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 40789268   881 vAQESLEPLNTLPSHPWSSLVVPMDEVASVSSGEPTGLWDIPST 924
Cdd:PRK07764  677 -APAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAA 719
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 520-922 6.16e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 6.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   520 ATANHMRPSAATEASESDQSHSPWAILTNEVDEPGAGSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPGAAEAPSVKS 599
Cdd:PHA03307   53 VTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAP 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   600 AIPHLPRLPSEPPAPSPGPSEA--LSAVSLQASSADGSPDFPIVAMLRAPKLWLL-PRSTLVPNMTPVPLSPASPLPSWV 676
Cdd:PHA03307  133 DLSEMLRPVGSPGPPPAASPPAagASPAAVASDAASSRQAALPLSSPEETARAPSsPPAEPPPSTPPAAASPRPPRRSSP 212

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   677 PEEQAVRPVSLGAEDLETPfqttiaAPVEASHRSPDADSIEIEGTSSMRATKHPISGPWASLDSSNVTMNPVPSDAGILG 756
Cdd:PHA03307  213 ISASASSPAPAPGRSAADD------AGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPAS 286

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   757 TESGVLD-----LPGSPTSGGQATVEKVLATWLPLPGQGLD-PGSQSTPMEAHGVAVSMEPTVALEGGATEGPMEATREV 830
Cdd:PHA03307  287 SSSSPRErspspSPSSPGSGPAPSSPRASSSSSSSRESSSSsTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPR 366

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   831 VPSTADATWESESRSAISSTHIAVTMARAQGMPTLTSTSSEGHPEPKGQMVAQESL-------EPLNTLPSHPW-SSLVV 902
Cdd:PHA03307  367 KRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAAsgafyarYPLLTPSGEPWpGSPPP 446

                         410       420
                  ....*....|....*....|.
gi 40789268   903 PMDEVASVSSGEP-TGLWDIP 922
Cdd:PHA03307  447 PPGRVRYGGLGDSrPGLWDAP 467
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 360-632 6.42e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 6.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   360 HTAQHGDSEIPSSGDEGEIVSAEGPPGRELKPSLGEQEVIAPDFQEPLMSSGEGEPPDLTWTQAPEETLGSTPGGPTLAS 439
Cdd:PHA03307   99 SPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSS 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   440 WPSSEKWLFTGAPSSMGVSSPSDMGVDMEATTPLGTQVAPTPTMRRGR-------FKGLNGRHFQQQGPEDQlPEVAEPS 512
Cdd:PHA03307  179 PEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRsaaddagASSSDSSSSESSGCGWG-PENECPL 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   513 AQPPTLGATANHMRPSAATEASESDQSHSPWAILTNEVDEPGAGSLGSRSLPESLMWSPSLISPSVPSTDSTPSAKPGAA 592
Cdd:PHA03307  258 PRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSR 337

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 40789268   593 EAPSVKSAIPHLPRLPSEPPAPSPGPSEALSAVSLQASSA 632
Cdd:PHA03307  338 GAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSS 377
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
580-839 6.87e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.10  E-value: 6.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   580 STDSTPSAKPGAAEAPSVKSAIPHLPRlPSEPPAPsPGPSEALSAVSLQASSADGSPDfPIVAMLRAPKLWLLPRSTLVP 659
Cdd:PRK12323  372 AGPATAAAAPVAQPAPAAAAPAAAAPA-PAAPPAA-PAAAPAAAAAARAVAAAPARRS-PAPEALAAARQASARGPGGAP 448

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   660 NMTPVPlsPASPLPSWVPEEQAVRPVSLGAEDLETPfqttiAAPVEASHRSPDADSieiegtssmratkhpisgPWASLD 739
Cdd:PRK12323  449 APAPAP--AAAPAAAARPAAAGPRPVAAAAAAAPAR-----AAPAAAPAPADDDPP------------------PWEELP 503

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   740 SSNVTMNPVPSDAGILGTEsgvldlpgsptsggqatvekvlATWLPLPGQGLDPGSQSTPMEAHGVAVSMEPTVALEGGA 819
Cdd:PRK12323  504 PEFASPAPAQPDAAPAGWV----------------------AESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVV 561

                         250       260
                  ....*....|....*....|
gi 40789268   820 TEGPMEATREVVPSTADATW 839
Cdd:PRK12323  562 APRPPRASASGLPDMFDGDW 581
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 516-697 8.76e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 8.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    516 PTLGATANHMRPSAATEASESDQSHSPWAiLTNEVDEPGAGSLG------SRSLPESLMWSPSLI-------SPSVPSTD 582
Cdd:pfam03154   74 PSPLKSAKRQREKGASDTEEPERATAKKS-KTQEISRPNSPSEGegessdGRSVNDEGSSDPKDIdqdnrstSPSIPSPQ 152

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268    583 STPSAKPGAAEAPSVKSAIPHLPRLPSEPPAPSPGPSEALSA-----------VSLQASSADGSPdfPIVAMLRAPKLWL 651
Cdd:pfam03154  153 DNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAatagptpsapsVPPQGSPATSQP--PNQTQSTAAPHTL 230

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 40789268    652 LPRS-TLVPNMTPVPLSPASPLPSWVPEEQaVRPVSLGAEDLETPFQ 697
Cdd:pfam03154  231 IQQTpTLHPQRLPSPHPPLQPMTQPPPPSQ-VSPQPLPQPSLHGQMP 276
Link_domain_CD44_like cd03516
This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates ...
 261-384 1.67e-03

This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marker for the detection and characterization of lymphatic vessels in tumors.


Pssm-ID: 239593  Cd Length: 144  Bit Score: 40.14  E-value: 1.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268  261 VFYVGPARRLTLAGARAQ--CQRQGAALASVGQLHLAWHEGLDQCDPGWLADGSVRYPIQTPRRRCGgpAPGVRTVYRFA 338
Cdd:cd03516    8 VFLVEKNGRYSLNFTEAKeaCRALGLTLASKAQVETALKFGFETCRYGWVEDGFVVIPRIDPNPLCG--KNGTGVYILNS 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 40789268  339 NRTGfpapgaRFDAYCFRAhhhtaqhgdSEIPSSGDEGEIVSAEGP 384
Cdd:cd03516   86 NLSS------RYDAYCYNS---------SDTWINSCLPEILTTDDP 116
PHA03379 PHA03379
EBNA-3A; Provisional
 405-635 2.83e-03

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 41.97  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   405 EPLMSSGEGEPPDLTwtQAPEETLGSTPGGPTLASWPSSEKWLFTGAPSSMGVSSPSDMGVDMEATTPLgTQVAPTPTMR 484
Cdd:PHA03379  600 QPYQASVEVQPPQLT--QVSPQQPMEYPLEPEQQMFPGSPFSQVADVMRAGGVPAMQPQYFDLPLQQPI-SQGAPLAPLR 676

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   485 rgrfKGLNGRhfqQQGPEDQLPEVAEPSAQPPTLGATANHMRPSAATE-----------ASESDQSHSPWAILTNEVDEP 553
Cdd:PHA03379  677 ----ASMGPV---PPVPATQPQYFDIPLTEPINQGASAAHFLPQQPMEgplvperwmfqGATLSQSVRPGVAQSQYFDLP 749

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   554 GAGSLGSRSLPESLMWSPSLISPSVPSTDSTPSA--KPGAAEAPSVKSAIPHLPRLPSEPPAP-SPGPSE-ALSAVSL-- 627
Cdd:PHA03379  750 LTQPINHGAPAAHFLHQPPMEGPWVPEQWMFQGAppSQGTDVVQHQLDALGYVLHVLNHPGVPvSPAVNQyHVSQAAFgl 829

                         250
                  ....*....|.
gi 40789268   628 ---QASSADGS 635
Cdd:PHA03379  830 pidEDESGEGS 840
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 501-713 3.68e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.51  E-value: 3.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   501 PEDQLPEVAEPSAQPPTLGATANHMRPSAATEASESDQSHSPWAiLTNEVDEPGAGSLGSRSLPESLMWSPSLISPSVPS 580
Cdd:PRK07764  601 PAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPA-PGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPA 679

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   581 TDSTPSAkPGAAEAPSVKSAIPHLPRLPSEPPApsPGPSEALSAVSLQASSADGSPDFPIVAMLRAPKLWLLPRSTLVPN 660
Cdd:PRK07764  680 APPPAPA-PAAPAAPAGAAPAQPAPAPAATPPA--GQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPA 756

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 40789268   661 MTPVPLSPASPlPSWVPEEQAVRPvslgaEDLETPFQTTIAAPVEASHRSPDA 713
Cdd:PRK07764  757 QPPPPPAPAPA-AAPAAAPPPSPP-----SEEEEMAEDDAPSMDDEDRRDAEE 803
hEGF pfam12661
Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six ...
 969-990 4.28e-03

Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteriztic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC. These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin. Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.


Pssm-ID: 463660  Cd Length: 22  Bit Score: 35.77  E-value: 4.28e-03
                           10        20
                   ....*....|....*....|..
gi 40789268    969 CLHGGTCHTNGTVYGCSCDQGY 990
Cdd:pfam12661    1 CQNGGTCVDGVNGYKCQCPPGY 22
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 501-624 5.59e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 41.00  E-value: 5.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   501 PEDQLPEVAEPSAQPPTLGATANHMRPSAATEASESDQSHSPwailtnevDEPGAGSLGSRSLPESLMWSPSLISPSVPS 580
Cdd:PRK07994  361 PAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPP--------PASAPQQAPAVPLPETTSQLLAARQQLQRA 432

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 40789268   581 TDSTPSAKPGAAEAPSVKSAIPHLPRLPSEPPAPSPGPSEALSA 624
Cdd:PRK07994  433 QGATKAKKSEPAAASRARPVNSALERLASVRPAPSALEKAPAKK 476
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
423-713 5.87e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.99  E-value: 5.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   423 APEETLGSTPGGPTLASWPSSekwlfTGAPSSMGVSSPSDMGVDMEATTPLGTQVAPTPTMRRGRFKGLNGRHFQQQGPE 502
Cdd:PRK07003  359 EPAVTGGGAPGGGVPARVAGA-----VPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPP 433

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   503 DQLPEVAEPSAQPPTLGATANhmrPSAATEASESDQSHSPWAiltnevdEPGAGSLGSRSLPESLMWSPSliSPSVPSTD 582
Cdd:PRK07003  434 ATADRGDDAADGDAPVPAKAN---ARASADSRCDERDAQPPA-------DSGSASAPASDAPPDAAFEPA--PRAAAPSA 501

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   583 STPSAkPGAAEAPSVKSAiPHLPRLPSEPPAPSPGPSEALSAVSLQASSADGSPDfpivaMLRAPKLWLLPRSTLVPNMT 662
Cdd:PRK07003  502 ATPAA-VPDARAPAAASR-EDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALD-----VLRNAGMRVSSDRGARAAAA 574

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 40789268   663 PVPLSPASPLPSWVPEEQAVRPVSLGAEDLETPFQTTIAAPVEASHRSPDA 713
Cdd:PRK07003  575 AKPAAAPAAAPKPAAPRVAVQVPTPRARAATGDAPPNGAARAEQAAESRGA 625
PHA03377 PHA03377
EBNA-3C; Provisional
 366-677 5.96e-03

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 41.19  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   366 DSEIPSSGDEGEIVSAEGPPG---RELKPSLGEQEVIAPD-----FQEPLMSSGEGEPPDLTW-TQAPEETLG-----ST 431
Cdd:PHA03377  589 DMAPPSTGPRQQAKCKDGPPAsgpHEKQPPSSAPRDMAPSvvrmfLRERLLEQSTGPKPKSFWeMRAGRDGSGiqqepSS 668

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   432 PGGPTLASWPSSEKWLftgaPSSMGVSSpsdmgvdMEATTPLGTQVAPTPTMRRGRfKGLNGRHFQQQGPEDQLPEVAEP 511
Cdd:PHA03377  669 RRQPATQSTPPRPSWL----PSVFVLPS-------VDAGRAQPSEESHLSSMSPTQ-PISHEEQPRYEDPDDPLDLSLHP 736

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   512 --SAQPPTLGATANHMRPSAATEASESDQSHSPWAILTNEVDEPGAGSLGSRSLP-ESLMWSPSLISPSVPSTDSTPSAK 588
Cdd:PHA03377  737 dqAPPPSHQAPYSGHEEPQAQQAPYPGYWEPRPPQAPYLGYQEPQAQGVQVSSYPgYAGPWGLRAQHPRYRHSWAYWSQY 816

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   589 PGAAEapsvkSAIPHLPRLPSEPP--APSPGPSEALSAVSLQASSADGSPDFPIVAMLRAPKLWLLPRSTLVPNMTPVPL 666
Cdd:PHA03377  817 PGHGH-----PQGPWAPRPPHLPPqwDGSAGHGQDQVSQFPHLQSETGPPRLQLSQVPQLPYSQTLVSSSAPSWSSPQPR 891

                         330
                  ....*....|.
gi 40789268   667 SPASPLPSWVP 677
Cdd:PHA03377  892 APIRPIPTRFP 902
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
553-739 7.31e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.60  E-value: 7.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   553 PGAGSLGSRSLPESL---MWSPSLISPSVPSTDSTPSAKPGAAEAPSVKSAIPHLPRLPSEPPAPSPGPSEALSAVSLQA 629
Cdd:PRK07003  362 VTGGGAPGGGVPARVagaVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDD 441

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   630 SSADGSP-----DFPIVAMLRAPKLWLLPRSTLVPNMTPVPlsPASPLPSWVPEEQAVRPVSLGAEDLETPFQTTIA--- 701
Cdd:PRK07003  442 AADGDAPvpakaNARASADSRCDERDAQPPADSGSASAPAS--DAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAAsre 519

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 40789268   702 -APVEASHRSPDADSIE-IEGTSSMRATkhpisGPWASLD 739
Cdd:PRK07003  520 dAPAAAAPPAPEARPPTpAAAAPAARAG-----GAAAALD 554
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 378-602 9.60e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 9.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   378 IVSAEGPPGRELKPSLGEQEVIAPDFQEPLMSSGEGEPPDLTWTQAPEE-TLGSTPGGPTLASWPSSEKWLFTGAPSSmg 456
Cdd:PRK07764  587 VVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAApAEASAAPAPGVAAPEHHPKHVAVPDASD-- 664

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40789268   457 vsSPSDMGVDMEATTPLGTQVAPTPTMRRGRFkglnGRHFQQQGPEDQLPEVAEPSAQPPTLGatanhmrPSAATEASES 536
Cdd:PRK07764  665 --GGDGWPAKAGGAAPAAPPPAPAPAAPAAPA----GAAPAQPAPAPAATPPAGQADDPAAQP-------PQAAQGASAP 731

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40789268   537 DQSHSPWAILTNEVDEPGAGSLGSRSLPeslmwsPSLISPSVPSTDSTPSAKPGAAEAPSVKSAIP 602
Cdd:PRK07764  732 SPAADDPVPLPPEPDDPPDPAGAPAQPP------PPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAP 791
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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