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Conserved domains on  [gi|1786632339|gb|KAF0024547|]
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hypothetical protein F2P81_023349 [Scophthalmus maximus]

Protein Classification

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 ...
 1583-1706 4.60e-70

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: 230.54  E-value: 4.60e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQWTGLNDKTIEDDFRWSDGNPLLYE 1662
Cdd:cd03588      1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1786632339 1663 NWYRGQPDSYFLSGEDCVVMVWHDDGRWSDVPCNYHLAYTCKKG 1706
Cdd:cd03588     81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 572-666 5.18e-57

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: 192.24  E-value: 5.18e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMDGQPGLRS 651
Cdd:cd03517      1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                           90
                   ....*....|....*
gi 1786632339  652 YGTMDPDDLFDVYCY 666
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 ...
 673-768 1.52e-53

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: 182.13  E-value: 1.52e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  673 EVIHDSVRKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLYRFSN 752
Cdd:cd03520      1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                           90
                   ....*....|....*.
gi 1786632339  753 QTGFPEPSSLHDVYCF 768
Cdd:cd03520     81 QTGFPDPHSRFDAYCF 96
PWWP_HDGF cd20148
PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility ...
 1-77 3.33e-53

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.


:

Pssm-ID: 438976 [Multi-domain]  Cd Length: 87  Bit Score: 180.99  E-value: 3.33e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNPTVT 77
Cdd:cd20148     11 MKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVK 87
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 453-574 1.20e-27

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 cd05900:

Pssm-ID: 472250  Cd Length: 123  Bit Score: 109.26  E-value: 1.20e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  453 IPHSGPVFASLGRSISIPC-MVSLSTTASTSSSSSPVVPRVKWSVVSGGVETQILVAKGERVKVNEAYRYRAALLNYTSS 531
Cdd:cd05900      1 IPLESPLRVVLGSSLLIPCyFQDPIAKDPGAPTVAPLSPRIKWSFISKEKESVLLVATEGKVRVNTEYLDRVSLPNYPAI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1786632339  532 SDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05900     81 PSDATLEITELRSNDSGTYRCEVMHGIEDNYDTVEVQVKGIVF 123
KOW_RPL26 cd06089
KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at ...
 260-316 2.07e-18

KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage.


:

Pssm-ID: 240513  Cd Length: 65  Bit Score: 80.64  E-value: 2.07e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339  260 GDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATG-DYRGTYIATEAPL 316
Cdd:cd06089      1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQeNPQGGIIEVEAPI 58
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1710-1766 4.04e-08

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: 51.31  E-value: 4.04e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:cd00033      1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTC 56
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 1543-1577 2.68e-06

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: 45.71  E-value: 2.68e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1786632339 1543 DACL-GDPCLNGGTCTDRDGQIKCLCLPSYGGNFCQ 1577
Cdd:cd00054      3 DECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
 
Name Accession Description Interval E-value
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 1583-1706 4.60e-70

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: 230.54  E-value: 4.60e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQWTGLNDKTIEDDFRWSDGNPLLYE 1662
Cdd:cd03588      1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1786632339 1663 NWYRGQPDSYFLSGEDCVVMVWHDDGRWSDVPCNYHLAYTCKKG 1706
Cdd:cd03588     81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 572-666 5.18e-57

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: 192.24  E-value: 5.18e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMDGQPGLRS 651
Cdd:cd03517      1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                           90
                   ....*....|....*
gi 1786632339  652 YGTMDPDDLFDVYCY 666
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 ...
 673-768 1.52e-53

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: 182.13  E-value: 1.52e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  673 EVIHDSVRKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLYRFSN 752
Cdd:cd03520      1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                           90
                   ....*....|....*.
gi 1786632339  753 QTGFPEPSSLHDVYCF 768
Cdd:cd03520     81 QTGFPDPHSRFDAYCF 96
PWWP_HDGF cd20148
PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility ...
 1-77 3.33e-53

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438976 [Multi-domain]  Cd Length: 87  Bit Score: 180.99  E-value: 3.33e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNPTVT 77
Cdd:cd20148     11 MKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVK 87
Xlink pfam00193
Extracellular link domain;
572-666 2.73e-40

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 144.25  E-value: 2.73e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDAlGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMdgqPGLRS 651
Cdd:pfam00193    1 GVFHLESP-GRYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNM---PGVRQ 76

                           90
                   ....*....|....*.
gi 1786632339  652 YGTMDP-DDLFDVYCY 666
Cdd:pfam00193   77 YGFRDPlSERYDAYCY 92
LINK smart00445
Link (Hyaluronan-binding);
570-666 6.44e-40

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 143.25  E-value: 6.44e-40
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   570 KGVVFHYRdALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGdmdGQPGL 649
Cdd:smart00445    1 DGGVFHVE-KNGRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGG---NLPGV 76

                            90
                    ....*....|....*..
gi 1786632339   650 RSYGTMDPDDLFDVYCY 666
Cdd:smart00445   77 RQYGFPDPTSRYDAYCF 93
LINK smart00445
Link (Hyaluronan-binding);
671-769 1.44e-37

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 136.32  E-value: 1.44e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   671 DGEVIHDSV--RKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKtly 748
Cdd:smart00445    1 DGGVFHVEKngRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGNLPGVR--- 77

                            90       100
                    ....*....|....*....|.
gi 1786632339   749 rfsnQTGFPEPSSLHDVYCFR 769
Cdd:smart00445   78 ----QYGFPDPTSRYDAYCFN 94
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 1583-1704 1.03e-36

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: 135.03  E-value: 1.03e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ-----WTGLNDKTIEDDFRWSDGN 1657
Cdd:smart00034    1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAENDFVASLLKNSGssdyyWIGLSDPDSNGSWQWSDGS 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 1786632339  1658 PLL-YENWYRGQPDSyflSGEDCVVMvWHDDGRWSDVPCNYHLAYTCK 1704
Cdd:smart00034   81 GPVsYSNWAPGEPNN---SSGDCVVL-STSGGKWNDVSCTSKLPFVCE 124
Xlink pfam00193
Extracellular link domain;
683-768 1.73e-35

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 130.39  E-value: 1.73e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  683 LSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVktlyrfsNQTGFPEP-SS 761
Cdd:pfam00193   13 LTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNMPGV-------RQYGFRDPlSE 85


                   ....*..
gi 1786632339  762 LHDVYCF 768
Cdd:pfam00193   86 RYDAYCY 92
Lectin_C pfam00059
Lectin C-type domain; This family includes both long and short form C-type
 1601-1705 6.16e-28

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


Pssm-ID: 459655 [Multi-domain]  Cd Length: 105  Bit Score: 109.49  E-value: 6.16e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1601 RLSWEVAEQHCRVLGAHLVSVMTPEEQSYIND---NYKEYQWTGLNDKTIEDDFRWSDGNPLLYENWYRGQPDSYflSGE 1677
Cdd:pfam00059    1 SKTWDEAREACRKLGGHLVSINSAEELDFLSStlkKSNKYFWIGLTDRKNEGTWKWVDGSPVNYTNWAPEPNNNG--ENE 78

                           90       100
                   ....*....|....*....|....*...
gi 1786632339 1678 DCVVMVWhDDGRWSDVPCNYHLAYTCKK 1705
Cdd:pfam00059   79 DCVELSS-SSGKWNDENCNSKNPFVCEK 105
Ig_Aggrecan cd05900
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 453-574 1.20e-27

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: 109.26  E-value: 1.20e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  453 IPHSGPVFASLGRSISIPC-MVSLSTTASTSSSSSPVVPRVKWSVVSGGVETQILVAKGERVKVNEAYRYRAALLNYTSS 531
Cdd:cd05900      1 IPLESPLRVVLGSSLLIPCyFQDPIAKDPGAPTVAPLSPRIKWSFISKEKESVLLVATEGKVRVNTEYLDRVSLPNYPAI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1786632339  532 SDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05900     81 PSDATLEITELRSNDSGTYRCEVMHGIEDNYDTVEVQVKGIVF 123
KOW_RPL26 cd06089
KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at ...
 260-316 2.07e-18

KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage.


Pssm-ID: 240513  Cd Length: 65  Bit Score: 80.64  E-value: 2.07e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339  260 GDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATG-DYRGTYIATEAPL 316
Cdd:cd06089      1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQeNPQGGIIEVEAPI 58
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1-74 3.19e-14

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 69.76  E-value: 3.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339    1 MKGYPHWPARI---DELPEGAVKSP--SNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKR-----KGFAEGLWEI 70
Cdd:pfam00855    8 LKGYPWWPARVvdpEELPENVLKPKkkDGEYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKkkkkkKAFKKALEEA 87


                   ....
gi 1786632339   71 ENNP 74
Cdd:pfam00855   88 EEAL 91
RplX COG0198
Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L24 ...
 259-326 1.16e-13

Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L24 is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439968 [Multi-domain]  Cd Length: 104  Bit Score: 68.55  E-value: 1.16e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDYR-GTYIATEAPLLLRDITLIDP 326
Cdd:COG0198      7 KGDTVIVIAGKDKGKRGKVLKVLPKKNRVIVEGVNIVKKHQKPNQQNPqGGIIEKEAPIHISNVMLVDP 75
rplX_bact TIGR01079
ribosomal protein L24, bacterial/organelle; This model recognizes bacterial and organellar ...
 259-326 6.78e-13

ribosomal protein L24, bacterial/organelle; This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273431 [Multi-domain]  Cd Length: 102  Bit Score: 66.52  E-value: 6.78e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDYR-GTYIATEAPLLLRDITLIDP 326
Cdd:TIGR01079    5 KGDTVKVISGKDKGKRGKVLKVLPKKNKVIVEGVNMVKKHVKPVPANRqGGIIEKEAPIHISNVMLFDP 73
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 1-48 3.48e-11

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 60.05  E-value: 3.48e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1786632339     1 MKGYPHWPARIDELPE-----GAVKSPSNKYQVFFFGTHETAFLGAKDLFSYD 48
Cdd:smart00293   11 MKGFPWWPALVISPKMtpdniMKRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63
rplX PRK12281
50S ribosomal protein L24; Reviewed
 257-316 4.69e-10

50S ribosomal protein L24; Reviewed


Pssm-ID: 183399  Cd Length: 76  Bit Score: 57.36  E-value: 4.69e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1786632339  257 VLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDY-RGTYIATEAPL 316
Cdd:PRK12281     7 VKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNpNGGFIEKEMPI 67
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 259-290 2.40e-08

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 51.23  E-value: 2.40e-08
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILE 290
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1710-1766 4.04e-08

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: 51.31  E-value: 4.04e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:cd00033      1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTC 56
CCP smart00032
Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat ...
 1710-1766 2.57e-07

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: 49.06  E-value: 2.57e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339  1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:smart00032    1 CPPPPDIENGTVTS-SSGTYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 1543-1577 2.68e-06

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: 45.71  E-value: 2.68e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1786632339 1543 DACL-GDPCLNGGTCTDRDGQIKCLCLPSYGGNFCQ 1577
Cdd:cd00054      3 DECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 38
Sushi pfam00084
Sushi repeat (SCR repeat);
1710-1766 3.52e-06

Sushi repeat (SCR repeat);


Pssm-ID: 459664 [Multi-domain]  Cd Length: 56  Bit Score: 45.95  E-value: 3.52e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:pfam00084    1 CPPPPDIPNGKVSA-TKNEYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 1545-1575 3.96e-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: 41.98  E-value: 3.96e-05
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1786632339 1545 CLGDPCLNGGTCTDRDGQIKCLCLPSYGGNF 1575
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31
EGF_CA smart00179
Calcium-binding EGF-like domain;
1543-1577 4.77e-05

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 42.23  E-value: 4.77e-05
                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 1786632339  1543 DACL-GDPCLNGGTCTDRDGQIKCLCLPSY-GGNFCQ 1577
Cdd:smart00179    3 DECAsGNPCQNGGTCVNTVGSYRCECPPGYtDGRNCE 39
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 257-283 1.01e-04

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.77  E-value: 1.01e-04
                            10        20
                    ....*....|....*....|....*..
gi 1786632339   257 VLRGDTVEILAGKDKGKQGKVIQVFRH 283
Cdd:smart00739    2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 1583-1657 1.51e-04

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 45.11  E-value: 1.51e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINdNYKEY--QWTGLNDKTIEDDFRWSDGN 1657
Cdd:PHA02642    88 CPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEELNFLK-RYKDSsdHWIGLNRESSNHPWKWADNS 163
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 456-569 3.65e-04

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 40.95  E-value: 3.65e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   456 SGPVFASLGRSISIPCMVSLSTtastssssspvVPRVKWSVvsggvETQILVAKGERVKVneayryraallnyTSSSDDL 535
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSP-----------PPEVTWYK-----QGGKLLAESGRFSV-------------SRSGSTS 51

                            90       100       110
                    ....*....|....*....|....*....|....
gi 1786632339   536 SLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKV 569
Cdd:smart00410   52 TLTISNVTPEDSGTYTCAATNSSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 1583-1706 4.60e-70

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: 230.54  E-value: 4.60e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQWTGLNDKTIEDDFRWSDGNPLLYE 1662
Cdd:cd03588      1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNNNAQDYQWIGLNDRTIEGDFRWSDGHPLQFE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1786632339 1663 NWYRGQPDSYFLSGEDCVVMVWHDDGRWSDVPCNYHLAYTCKKG 1706
Cdd:cd03588     81 NWRPNQPDNFFATGEDCVVMIWHEEGEWNDVPCNYHLPFTCKKG 124
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 572-666 5.18e-57

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: 192.24  E-value: 5.18e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMDGQPGLRS 651
Cdd:cd03517      1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGCYGDMDGFPGVRN 80

                           90
                   ....*....|....*
gi 1786632339  652 YGTMDPDDLFDVYCY 666
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 ...
 673-768 1.52e-53

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: 182.13  E-value: 1.52e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  673 EVIHDSVRKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLYRFSN 752
Cdd:cd03520      1 EVFYATAPEKFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLYRFPN 80

                           90
                   ....*....|....*.
gi 1786632339  753 QTGFPEPSSLHDVYCF 768
Cdd:cd03520     81 QTGFPDPHSRFDAYCF 96
PWWP_HDGF cd20148
PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility ...
 1-77 3.33e-53

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438976 [Multi-domain]  Cd Length: 87  Bit Score: 180.99  E-value: 3.33e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNPTVT 77
Cdd:cd20148     11 MKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVK 87
PWWP_PSIP cd20151
PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called ...
 1-76 1.70e-44

PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438979 [Multi-domain]  Cd Length: 88  Bit Score: 155.91  E-value: 1.70e-44
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNPTV 76
Cdd:cd20151     11 MKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNEGLWEIDNNPKV 86
PWWP_HDGFL2 cd20149
PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also ...
 1-74 2.11e-44

PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also called HDGF-related protein 2 (HRP-2), or Hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438977 [Multi-domain]  Cd Length: 84  Bit Score: 155.45  E-value: 2.11e-44
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNP 74
Cdd:cd20149     11 MKGYPHWPARIDDIADGAVKPPPNKYPIFFFGTHETAFLGPKDLFPYDKYKDKYGKPNKRKGFNEGLWEIQNNP 84
PWWP_HDGFL3 cd20150
PWWP domain found in Hepatoma-derived growth factor-related protein 3 (HDGFL3); HDGFL3, also ...
 1-77 2.54e-43

PWWP domain found in Hepatoma-derived growth factor-related protein 3 (HDGFL3); HDGFL3, also called HDGF-related protein 3 (HRP-3), is the only hepatoma-derived growth factor (HDGF)-related protein (HRP) family member whose expression is almost restricted to the nervous tissue. It enhances DNA synthesis and may play a role in cell proliferation. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438978 [Multi-domain]  Cd Length: 93  Bit Score: 152.91  E-value: 2.54e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENNPTVT 77
Cdd:cd20150     16 MKGYPHWPARIDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVK 92
PWWP_HRP cd05834
PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The ...
 1-73 1.19e-42

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438959 [Multi-domain]  Cd Length: 82  Bit Score: 150.40  E-value: 1.19e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1786632339    1 MKGYPHWPARIDELPEGAvKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIENN 73
Cdd:cd05834     11 VKGYPPWPARIDEIPEGA-KIPKNKYPVFFYGTHETAFLKPKDLFPYEENKEKYGKPRKRKGFNEGLWEIENN 82
Xlink pfam00193
Extracellular link domain;
572-666 2.73e-40

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 144.25  E-value: 2.73e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDAlGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMdgqPGLRS 651
Cdd:pfam00193    1 GVFHLESP-GRYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNM---PGVRQ 76

                           90
                   ....*....|....*.
gi 1786632339  652 YGTMDP-DDLFDVYCY 666
Cdd:pfam00193   77 YGFRDPlSERYDAYCY 92
LINK smart00445
Link (Hyaluronan-binding);
570-666 6.44e-40

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 143.25  E-value: 6.44e-40
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   570 KGVVFHYRdALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGdmdGQPGL 649
Cdd:smart00445    1 DGGVFHVE-KNGRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGG---NLPGV 76

                            90
                    ....*....|....*..
gi 1786632339   650 RSYGTMDPDDLFDVYCY 666
Cdd:smart00445   77 RQYGFPDPTSRYDAYCF 93
LINK smart00445
Link (Hyaluronan-binding);
671-769 1.44e-37

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 136.32  E-value: 1.44e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   671 DGEVIHDSV--RKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKtly 748
Cdd:smart00445    1 DGGVFHVEKngRYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRCGGNLPGVR--- 77

                            90       100
                    ....*....|....*....|.
gi 1786632339   749 rfsnQTGFPEPSSLHDVYCFR 769
Cdd:smart00445   78 ----QYGFPDPTSRYDAYCFN 94
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 1583-1704 1.03e-36

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: 135.03  E-value: 1.03e-36
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ-----WTGLNDKTIEDDFRWSDGN 1657
Cdd:smart00034    1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAENDFVASLLKNSGssdyyWIGLSDPDSNGSWQWSDGS 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*...
gi 1786632339  1658 PLL-YENWYRGQPDSyflSGEDCVVMvWHDDGRWSDVPCNYHLAYTCK 1704
Cdd:smart00034   81 GPVsYSNWAPGEPNN---SSGDCVVL-STSGGKWNDVSCTSKLPFVCE 124
CLECT cd00037
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 1593-1705 6.25e-36

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: 132.74  E-value: 6.25e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1593 FCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ----WTGLNDKTIEDDFRWSDGNPLL-YENWYRG 1667
Cdd:cd00037      1 SCYKFSTEKLTWEEAQEYCRSLGGHLASIHSEEENDFLASLLKKSSssdvWIGLNDLSSEGTWKWSDGSPLVdYTNWAPG 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1786632339 1668 QPDSYflSGEDCVVMVWHDDGRWSDVPCNYHLAYTCKK 1705
Cdd:cd00037     81 EPNPG--GSEDCVVLSSSSDGKWNDVSCSSKLPFICEK 116
Xlink pfam00193
Extracellular link domain;
683-768 1.73e-35

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 130.39  E-value: 1.73e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  683 LSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVktlyrfsNQTGFPEP-SS 761
Cdd:pfam00193   13 LTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNCGGNMPGV-------RQYGFRDPlSE 85


                   ....*..
gi 1786632339  762 LHDVYCF 768
Cdd:pfam00193   86 RYDAYCY 92
CLECT_DC-SIGN_like cd03590
C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific ...
 1583-1705 1.69e-34

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: 128.96  E-value: 1.69e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYIND--NYKEYQWTGLNDKTIEDDFRWSDGNPLL 1660
Cdd:cd03590      1 CPTNWKSFQSSCYFFSTEKKSWEESRQFCEDMGAHLVIINSQEEQEFISKilSGNRSYWIGLSDEETEGEWKWVDGTPLN 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1786632339 1661 --YENWYRGQPDSYFLSGEDCVVMvWHDDGRWSDVPCNYHLAYTCKK 1705
Cdd:cd03590     81 ssKTFWHPGEPNNWGGGGEDCAEL-VYDSGGWNDVPCNLEYRWICEK 126
CLECT_CEL-1_like cd03589
C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and ...
 1583-1704 4.47e-34

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: 128.24  E-value: 4.47e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLG-----AHLVSVMTPEEQSYINDNYKE-------YQ-WTGLNDKTIED 1649
Cdd:cd03589      1 CPTFWTAFGGYCYRFFGDRLTWEEAELRCRSFSipgliAHLVSIHSQEENDFVYDLFESsrgpdtpYGlWIGLHDRTSEG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339 1650 DFRWSDGNPLLYENWYRGQPDSYFlSGEDCVVMvWH---DDGRWSDVPCNYHLAYTCK 1704
Cdd:cd03589     81 PFEWTDGSPVDFTKWAGGQPDNYG-GNEDCVQM-WRrgdAGQSWNDMPCDAVFPYICK 136
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 572-666 4.87e-34

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: 126.38  E-value: 4.87e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDmdgQPGLRS 651
Cdd:cd01102      1 VVFHLESQNGRYKLTFAEAALACKARGAHLATPGQLEAAWQDGFDVCTAGWLADGSVRYPIVTSRPNCGGR---NPGVRS 77

                           90
                   ....*....|....*
gi 1786632339  652 YGTMDPDDLFDVYCY 666
Cdd:cd01102     78 YGNPAPSGRYDAYCF 92
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 683-768 1.37e-30

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: 116.36  E-value: 1.37e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  683 LSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLyrfsnqtGFPEPSSL 762
Cdd:cd01102     14 LTFAEAALACKARGAHLATPGQLEAAWQDGFDVCTAGWLADGSVRYPIVTSRPNCGGRNPGVRSY-------GNPAPSGR 86


                   ....*.
gi 1786632339  763 HDVYCF 768
Cdd:cd01102     87 YDAYCF 92
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 572-666 7.08e-30

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: 114.45  E-value: 7.08e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  572 VVFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCyGDMDGQPGLRS 651
Cdd:cd03518      1 VVFPYQPRLGRYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPC-GGKRTVPGLRS 79

                           90
                   ....*....|....*.
gi 1786632339  652 YGTMDPD-DLFDVYCY 666
Cdd:cd03518     80 YGERDKMlSRYDAFCF 95
CLECT_REG-1_like cd03594
C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and ...
 1583-1704 2.63e-29

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: 114.39  E-value: 2.63e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVL--GAHLVSVMTPEEQ----SYINDNYKEYQ--WTGLNDKTIEDDFRWS 1654
Cdd:cd03594      1 CPKGWLPYKGNCYGYFRQPLSWSDAELFCQKYgpGAHLASIHSPAEAaaiaSLISSYQKAYQpvWIGLHDPQQSRGWEWS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1786632339 1655 DGNPLLYENWYRGQPdsyFLSGEDCVVMvWHDDG--RWSDVPCNYHLAYTCK 1704
Cdd:cd03594     81 DGSKLDYRSWDRNPP---YARGGYCAEL-SRSTGflKWNDANCEERNPFICK 128
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 683-768 3.31e-28

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: 109.82  E-value: 3.31e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  683 LSFAEAQSYCRAAGAELATTAQLYLAWS-EGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLyrfsnqtGFPEPSS 761
Cdd:cd03519     11 LTFSEAVAACQRDGAQIAKVGQLFAAWKfHGLDRCDAGWLADGSVRYPISRPRPRCGPLEPGVRSF-------GFPDKKH 83


                   ....*...
gi 1786632339  762 -LHDVYCF 768
Cdd:cd03519     84 kLYGVYCY 91
Lectin_C pfam00059
Lectin C-type domain; This family includes both long and short form C-type
 1601-1705 6.16e-28

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


Pssm-ID: 459655 [Multi-domain]  Cd Length: 105  Bit Score: 109.49  E-value: 6.16e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1601 RLSWEVAEQHCRVLGAHLVSVMTPEEQSYIND---NYKEYQWTGLNDKTIEDDFRWSDGNPLLYENWYRGQPDSYflSGE 1677
Cdd:pfam00059    1 SKTWDEAREACRKLGGHLVSINSAEELDFLSStlkKSNKYFWIGLTDRKNEGTWKWVDGSPVNYTNWAPEPNNNG--ENE 78

                           90       100
                   ....*....|....*....|....*...
gi 1786632339 1678 DCVVMVWhDDGRWSDVPCNYHLAYTCKK 1705
Cdd:pfam00059   79 DCVELSS-SSGKWNDENCNSKNPFVCEK 105
Ig_Aggrecan cd05900
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 453-574 1.20e-27

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: 109.26  E-value: 1.20e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  453 IPHSGPVFASLGRSISIPC-MVSLSTTASTSSSSSPVVPRVKWSVVSGGVETQILVAKGERVKVNEAYRYRAALLNYTSS 531
Cdd:cd05900      1 IPLESPLRVVLGSSLLIPCyFQDPIAKDPGAPTVAPLSPRIKWSFISKEKESVLLVATEGKVRVNTEYLDRVSLPNYPAI 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1786632339  532 SDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05900     81 PSDATLEITELRSNDSGTYRCEVMHGIEDNYDTVEVQVKGIVF 123
Ig_Aggrecan_like cd05878
Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core ...
 453-574 1.72e-27

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: 108.86  E-value: 1.72e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  453 IPHSGPVFASLGRSISIPCMVSLSTTASTSSSSsPVVPRVKWSVVSGGV----ETQILVAKGERVKVNEAYRYRAALLNY 528
Cdd:cd05878      1 IPQSSPVRVLLGTSVTLPCYFIDPPHPVTPSTA-PLAPRIKWSKVSVDGkkekEVVLLVATEGRVRVNSAYQGRVSLPNY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1786632339  529 TSSSDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05878     80 PAIPSDATLEVQSLRASDSGLYRCEVMHGIEDSQDTVELVVKGVVF 125
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 680-768 6.69e-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: 100.19  E-value: 6.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  680 RKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQA--GVKTLyrfsnqtGFP 757
Cdd:cd03518     11 RYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPCGGKRTvpGLRSY-------GER 83

                           90
                   ....*....|..
gi 1786632339  758 EPS-SLHDVYCF 768
Cdd:cd03518     84 DKMlSRYDAFCF 95
CLECT_collectin_like cd03591
C-type lectin-like domain (CTLD) of the type found in human collectins including lung ...
 1607-1697 3.16e-22

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: 93.51  E-value: 3.16e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1607 AEQHCRVLGAHLVSVMTPEE----QSYINDnYKEYQWTGLNDKTIEDDFRWSDGNPLLYENWYRGQPDSYFlSGEDCVVM 1682
Cdd:cd03591     16 AQKLCSEAGGTLAMPRNAAEnaaiASYVKK-GNTYAFIGITDLETEGQFVYLDGGPLTYTNWKPGEPNNAG-GGEDCVEM 93

                           90
                   ....*....|....*
gi 1786632339 1683 VwhDDGRWSDVPCNY 1697
Cdd:cd03591     94 Y--TSGKWNDVACNL 106
Ig_CSPGs_LP_like cd05714
Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage ...
 456-574 4.14e-22

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: 93.43  E-value: 4.14e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  456 SGPVFASLGRSISIPCMVSLSTTASTSSSSSPvvpRVKWSVVSGGV----ETQILVAKGERVKVNEAYRYRAALLNYTSS 531
Cdd:cd05714      4 SAKVFSHLGGNVTLPCKFYRDPTAFGSGIHKI---RIKWTKLTSDSgylkEVDVLVAMGNVVYHKKTYGGRVSVPLKPGS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1786632339  532 SDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05714     81 DSDASLVITDLTASDYGLYRCEVIEGIEDDQDVVALDVQGVVF 123
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 585-666 1.15e-21

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: 90.95  E-value: 1.15e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  585 FTFHQAQRACEATGAEIATDYQLLAAYH-DGYEQCDAGWVADQSVRYPIQVPREGCYGDmdgQPGLRSYGTMDPDD-LFD 662
Cdd:cd03519     11 LTFSEAVAACQRDGAQIAKVGQLFAAWKfHGLDRCDAGWLADGSVRYPISRPRPRCGPL---EPGVRSFGFPDKKHkLYG 87


                   ....
gi 1786632339  663 VYCY 666
Cdd:cd03519     88 VYCY 91
Ig_Neurocan cd05902
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 456-574 2.48e-20

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: 88.35  E-value: 2.48e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  456 SGPVFASLGRSISIPCMVSLSTTASTSssssPVVPRVKWSVVSGGVETQ---ILVAKGERVKVNEAYRYRAALLNYTSSS 532
Cdd:cd05902      4 APPVRRPLSSSVLLPCVFTLPPSASSP----PEGPRIKWTKLSTSGGQQqrpVLVARDNVVRVAKAFQGRVSLPGYPKNR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1786632339  533 DDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05902     80 YNASLVLSRLRYSDSGTYRCEVVLGINDEQDTVPLEVTGVVF 121
KOW_RPL26 cd06089
KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at ...
 260-316 2.07e-18

KOW motif of Ribosomal Protein L26; RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage.


Pssm-ID: 240513  Cd Length: 65  Bit Score: 80.64  E-value: 2.07e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339  260 GDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATG-DYRGTYIATEAPL 316
Cdd:cd06089      1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQeNPQGGIIEVEAPI 58
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
 457-574 4.08e-18

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: 81.60  E-value: 4.08e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  457 GPVFASLGRSISIPCMVSLSTTASTSSSSspvvpRVKWSVVS--GGVETQILVAKGERVKVNEAYRYRAALLNytSSSDD 534
Cdd:cd05877      5 AKVFSHRGGNVTLPCRYHYEPELSAPRKI-----RVKWTKLEvdYAKEEDVLVAIGTRHKSYGSYQGRVFLRR--ADDLD 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1786632339  535 LSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05877     78 ASLVITDLRLEDYGRYRCEVIDGLEDESVVVALRLRGVVF 117
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 ...
 573-666 6.70e-18

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: 80.20  E-value: 6.70e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  573 VFHYRDALGRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCygdMDGQPGLRSY 652
Cdd:cd03515      2 VFHLRSRSGKYKLTYTEAKAACEAEGAHLATYSQLSAAQQLGFHLCAAGWLAKGRVGYPIVFPSANC---GFGHVGIVDY 78

                           90
                   ....*....|....*
gi 1786632339  653 GT-MDPDDLFDVYCY 666
Cdd:cd03515     79 GPrLNLSERWDAYCY 93
CLECT_VCBS cd03603
A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein ...
 1595-1697 1.20e-17

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: 80.55  E-value: 1.20e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1595 YRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ--WTGLNDKTIEDDFRWSDGNPLLYENWYRGQPDSY 1672
Cdd:cd03603      3 YKFVDGGMTWEAAQTLAESLGGHLVTINSAEENDWLLSNFGGYGasWIGASDAATEGTWKWSDGEESTYTNWGSGEPHNN 82

                           90       100
                   ....*....|....*....|....*..
gi 1786632339 1673 FLSGEDCVVM--VWHDDGRWSDVPCNY 1697
Cdd:cd03603     83 GGGNEDYAAInhFPGISGKWNDLANSY 109
CLECT_selectins_like cd03592
C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P ...
 1597-1703 2.60e-16

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: 76.65  E-value: 2.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1597 HFS-QRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYK----EYQWTGLNDKTIEDdfRW--SDGNPLLYENWYRGQP 1669
Cdd:cd03592      4 HYStEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFALkynlGYYWIDGNDINNEG--TWvdTDKKELEYKNWAPGEP 81

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1786632339 1670 DSyfLSGEDCVVMVWHDDGRWSDVPCNYHLAYTC 1703
Cdd:cd03592     82 NN--GRNENCLEIYIKDNGKWNDEPCSKKKSAIC 113
Ig_Versican cd05901
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 456-574 4.20e-16

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: 76.54  E-value: 4.20e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  456 SGPVFASLGRSISIPCMVSLSTTASTSSSSSPVVPRVKWSVVSGGV------ETQILVAKGERVKVNEAYRYRAALLNYT 529
Cdd:cd05901      4 SSRVHGSLSGSVVLPCRFSTLPTLPPSYNITSEFLRIKWTKIQVDKngkdhkETTVLVAQNGIIKIGQEYMGRVSVPSHP 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1786632339  530 SSSDDLSLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKVKGVVF 574
Cdd:cd05901     84 EDQGDASLTIVKLRASDAGVYRCEVMHGIEDTQDTVSLDVSGVVF 128
PWWP_GLYR1 cd05836
PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called ...
 1-71 8.35e-16

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438961 [Multi-domain]  Cd Length: 86  Bit Score: 74.18  E-value: 8.35e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1786632339    1 MKGYPHWPARIDELPEGaVKSPSNK---YQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKGFAEGLWEIE 71
Cdd:cd05836     11 MKGFPPWPGKIVNPPPD-LKKPPRKkkmHCVYFFGSENYAWIEDENIKPYEEFKEEMLKSKKSAGFKDAVEAIE 83
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1-74 3.19e-14

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 69.76  E-value: 3.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339    1 MKGYPHWPARI---DELPEGAVKSP--SNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKR-----KGFAEGLWEI 70
Cdd:pfam00855    8 LKGYPWWPARVvdpEELPENVLKPKkkDGEYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKkkkkkKAFKKALEEA 87


                   ....
gi 1786632339   71 ENNP 74
Cdd:pfam00855   88 EEAL 91
RplX COG0198
Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L24 ...
 259-326 1.16e-13

Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]; Ribosomal protein L24 is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 439968 [Multi-domain]  Cd Length: 104  Bit Score: 68.55  E-value: 1.16e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDYR-GTYIATEAPLLLRDITLIDP 326
Cdd:COG0198      7 KGDTVIVIAGKDKGKRGKVLKVLPKKNRVIVEGVNIVKKHQKPNQQNPqGGIIEKEAPIHISNVMLVDP 75
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 1-71 3.01e-13

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 66.75  E-value: 3.01e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339    1 MKGYPHWPARIDELPEGAV----KSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNK--RKGFAEGLWEIE 71
Cdd:cd05162      8 LKGYPWWPARVVDPEELPEevgkKKKKGGVLVQFFGDNDYAWVKSKNIKPFEEGFKKEFKKKKkkSKKFKKAVEEAE 84
rplX_bact TIGR01079
ribosomal protein L24, bacterial/organelle; This model recognizes bacterial and organellar ...
 259-326 6.78e-13

ribosomal protein L24, bacterial/organelle; This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273431 [Multi-domain]  Cd Length: 102  Bit Score: 66.52  E-value: 6.78e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDYR-GTYIATEAPLLLRDITLIDP 326
Cdd:TIGR01079    5 KGDTVKVISGKDKGKRGKVLKVLPKKNKVIVEGVNMVKKHVKPVPANRqGGIIEKEAPIHISNVMLFDP 73
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 ...
 683-768 6.72e-12

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: 63.25  E-value: 6.72e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  683 LSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVKTLyrfsnqtGFPEPSS- 761
Cdd:cd03515     14 LTYTEAKAACEAEGAHLATYSQLSAAQQLGFHLCAAGWLAKGRVGYPIVFPSANCGFGHVGIVDY-------GPRLNLSe 86


                   ....*..
gi 1786632339  762 LHDVYCF 768
Cdd:cd03515     87 RWDAYCY 93
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 1-48 3.48e-11

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 60.05  E-value: 3.48e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1786632339     1 MKGYPHWPARIDELPE-----GAVKSPSNKYQVFFFGTHETAFLGAKDLFSYD 48
Cdd:smart00293   11 MKGFPWWPALVISPKMtpdniMKRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63
CLECT_1 cd03602
C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains ...
 1598-1696 3.50e-10

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: 58.92  E-value: 3.50e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1598 FSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ---WTGLNDKTieDDFRWSDGNPLLYENWYRGQPDsyfl 1674
Cdd:cd03602      6 VNESKTWSEAQQYCRENYTDLATVQNQEDNALLSNLSRVSNsaaWIGLYRDV--DSWRWSDGSESSFRNWNTFQPF---- 79

                           90       100
                   ....*....|....*....|..
gi 1786632339 1675 SGEDCVVMvwHDDGRWSDVPCN 1696
Cdd:cd03602     80 GQGDCATM--YSSGRWYAALCS 99
rplX PRK12281
50S ribosomal protein L24; Reviewed
 257-316 4.69e-10

50S ribosomal protein L24; Reviewed


Pssm-ID: 183399  Cd Length: 76  Bit Score: 57.36  E-value: 4.69e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1786632339  257 VLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYIGATGDY-RGTYIATEAPL 316
Cdd:PRK12281     7 VKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNpNGGFIEKEMPI 67
CLECT_tetranectin_like cd03596
C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived ...
 1589-1703 5.93e-10

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: 58.94  E-value: 5.93e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1589 KFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYIND------NYKEYQWTGLNDKTIEDDFRWSDGNPLLYE 1662
Cdd:cd03596      6 KIHKKCYLVSEETKHYHEASEDCIARGGTLATPRDSDENDALRDyvkasvPGNWEVWLGINDMVAEGKWVDVNGSPISYF 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1786632339 1663 NWYR---GQPDSYFLsgEDCVVMVWHDDGRWSDVPCNYHLAYTC 1703
Cdd:cd03596     86 NWEReitAQPDGGKR--ENCVALSSSAQGKWFDEDCRREKPYVC 127
rpl24 CHL00141
ribosomal protein L24; Validated
 256-316 6.96e-10

ribosomal protein L24; Validated


Pssm-ID: 214374  Cd Length: 83  Bit Score: 57.35  E-value: 6.96e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1786632339  256 SVLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLNTHHRYI-GATGDYRGTYIATEAPL 316
Cdd:CHL00141     8 HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIkPNKENEVGEIKQFEAPI 69
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 1-71 1.08e-09

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438988  Cd Length: 91  Bit Score: 56.80  E-value: 1.08e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1786632339    1 MKGYPHWPARidelpegAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDEcKEKFGKSNKRKGFAEGLWEIE 71
Cdd:cd20160     14 LKGFPFWPAK-------ALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSK-EPPTSVKKKKSGLDEAMEELE 76
CLECT_chondrolectin_like cd03595
C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins ...
 1594-1704 2.06e-09

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: 57.98  E-value: 2.06e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1594 CYR--HF---SQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDNYKEYQ------WTGL--------NDKTIEDDFRWS 1654
Cdd:cd03595     12 CYKiaYFqdsRRRLNFEEARQACREDGGELLSIESENEQKLIERFIQTLRasdgdfWIGLrrssqynvTSSACSSLYYWL 91

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1655 DGNPLLYENWYRGQPDSYFlsgEDCVVMVWHDDG----------RWSDVPCNYHLAYTCK 1704
Cdd:cd03595     92 DGSISTFRNWYVDEPSCGS---EVCVVMYHQPSApagqggpylfQWNDDNCNMKNNFICK 148
Link_domain_CD44_like cd03516
This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates ...
 680-768 9.06e-09

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: 55.93  E-value: 9.06e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  680 RKLLSFAEAQSYCRAAGAELATTAQLYLAWSEGLDRCSPGWLSDGSVRYPIITPRVRCGGPQAGVktlYRFSNQTgfpep 759
Cdd:cd03516     16 RYSLNFTEAKEACRALGLTLASKAQVETALKFGFETCRYGWVEDGFVVIPRIDPNPLCGKNGTGV---YILNSNL----- 87


                   ....*....
gi 1786632339  760 SSLHDVYCF 768
Cdd:cd03516     88 SSRYDAYCY 96
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 259-290 2.40e-08

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 51.23  E-value: 2.40e-08
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1786632339  259 RGDTVEILAGKDKGKQGKVIQVFRHRNWVILE 290
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
CCP cd00033
Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) ...
 1710-1766 4.04e-08

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: 51.31  E-value: 4.04e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:cd00033      1 CPPPPVPENGTVTG-SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTC 56
CLECT_EMBP_like cd03598
C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major ...
 1594-1703 1.42e-07

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: 51.68  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1594 CYRHFSQRLSWEVAEQHCRVL-GAHLVSV---MTPEEQSYINDNYKEYQ-WTG--LNDKTIEDDFRWSDGNPLLYENWYR 1666
Cdd:cd03598      3 CYRFVKSPRTFRDAQVICRRCyRGNLASIhsfAFNYRVQRLVSTLNQAQvWIGgiITGKGRCRRFSWVDGSVWNYAYWAP 82

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1786632339 1667 GQPDSyflSGEDCVVMVwHDDGRWSDVPCNYHLAYTC 1703
Cdd:cd03598     83 GQPGN---RRGHCVELC-TRGGHWRRAHCKLRRPFIC 115
CLECT_NK_receptors_like cd03593
C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); ...
 1583-1659 1.67e-07

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: 51.56  E-value: 1.67e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINDN-YKEYQWTGLNDKTIEDDFRWSDGNPL 1659
Cdd:cd03593      1 CPKDWICYGNKCYYFSMEKKTWNESKEACSSKNSSLLKIDDEEELEFLQSQiGSSSYWIGLSREKSEKPWKWIDGSPL 78
CCP smart00032
Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat ...
 1710-1766 2.57e-07

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: 49.06  E-value: 2.57e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339  1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:smart00032    1 CPPPPDIENGTVTS-SSGTYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56
Ribosomal_L26 pfam16906
Ribosomal proteins L26 eukaryotic, L24P archaeal; Ribosomal_L26 is a family of the 50S and the ...
 234-292 7.09e-07

Ribosomal proteins L26 eukaryotic, L24P archaeal; Ribosomal_L26 is a family of the 50S and the 60S ribosomal proteins from eukaryotes - L26 - and archaea - L25.


Pssm-ID: 465307 [Multi-domain]  Cd Length: 114  Bit Score: 49.43  E-value: 7.09e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1786632339  234 RLNPPGKKRRKVFVEPLaSHE---------WSVLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGL 292
Cdd:pfam16906   11 HFNAPSHIRRKLMSAPL-SKElrekygvrsLPIRKGDEVKVVRGDFKGREGKVVQVYRKKYRIHVEGV 77
CLECT_thrombomodulin_like cd03600
C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, ...
 1594-1704 2.55e-06

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: 48.97  E-value: 2.55e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1594 CYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYIN----------DNYKEYQWTGLN--------DKTIEDDFRW-S 1654
Cdd:cd03600      6 CYTLHPQKLTFLEAQRSCIELGGNLATVRSGEEADVVSlllaagpgrhGRGSLRLWIGLQreprqcsdPSLPLRGFSWvT 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1786632339 1655 DGNPLLYENWYRGQPDSyfLSGEDCVVM----VWHDDGRWSDVPCNYHL-AYTCK 1704
Cdd:cd03600     86 GDQDTDFSNWLQEPAGT--CTSPRCVALsaagSTPDNLKWKDGPCSARAdGYLCK 138
EGF_CA cd00054
Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular ...
 1543-1577 2.68e-06

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: 45.71  E-value: 2.68e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1786632339 1543 DACL-GDPCLNGGTCTDRDGQIKCLCLPSYGGNFCQ 1577
Cdd:cd00054      3 DECAsGNPCQNGGTCVNTVGSYRCSCPPGYTGRNCE 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 ...
 1600-1705 3.43e-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: 47.91  E-value: 3.43e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339 1600 QRLSWEVAEQHCRVLGAHLVSVMTPEeqSYINDNYKEYQ-------WTGLND-KTIEDDFRWSDGNPLL--YENWYRGQP 1669
Cdd:cd03601      8 ETMNYAKAGAFCRSRGMRLASLAMRD--SEMRDAILAFTlvkghgyWVGADNlQDGEYDFLWNDGVSLPtdSDLWAPNEP 85

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1786632339 1670 DSYfLSGEDCVVMvWHDDGRWSDVPCNYHLAYTCKK 1705
Cdd:cd03601     86 SNP-QSRQLCVQL-WSKYNLLDDEYCGRAKRVICEK 119
Sushi pfam00084
Sushi repeat (SCR repeat);
1710-1766 3.52e-06

Sushi repeat (SCR repeat);


Pssm-ID: 459664 [Multi-domain]  Cd Length: 56  Bit Score: 45.95  E-value: 3.52e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1710 CGPPPRVRNASVFGkPRQRYETNAVVRYHCAKGFQQRLNPLVRCRSGGMWERPQIMC 1766
Cdd:pfam00084    1 CPPPPDIPNGKVSA-TKNEYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56
PWWP_HULK cd20147
PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family ...
 1-87 4.91e-06

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438975 [Multi-domain]  Cd Length: 92  Bit Score: 46.71  E-value: 4.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339    1 MKGYPHWPARIDELPEGAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDE-----CKEKFGKSNKRKGFAEGLWEIEnnpt 75
Cdd:cd20147      8 VKGFPAWPAQVSEPEDWGSAPDPKKVFVHFFGTQQIGFCNPGELSEFTEeikqsLLARTLKKKKGSDFSRAVKEIC---- 83

                           90
                   ....*....|..
gi 1786632339   76 vthEDYESSKKD 87
Cdd:cd20147     84 ---ELYEERKGQ 92
Link_domain_CD44_like cd03516
This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates ...
 581-666 1.75e-05

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: 46.30  E-value: 1.75e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339  581 GRYAFTFHQAQRACEATGAEIATDYQLLAAYHDGYEQCDAGWVADQSVRYPIQVPREGCYGDMDGQPGLRSYGTMDpddl 660
Cdd:cd03516     15 GRYSLNFTEAKEACRALGLTLASKAQVETALKFGFETCRYGWVEDGFVVIPRIDPNPLCGKNGTGVYILNSNLSSR---- 90


                   ....*.
gi 1786632339  661 FDVYCY 666
Cdd:cd03516     91 YDAYCY 96
PWWP_NSD_rpt2 cd05838
second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 4-69 1.85e-05

second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play nonredundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). This model corresponds to the second PWWP domain. The family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438963 [Multi-domain]  Cd Length: 96  Bit Score: 44.92  E-value: 1.85e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1786632339    4 YPHWPARI---DELPE--GAVKSPSNKYQVFFFGTHETAFLGAKDLFSYDECKEKFGKSNKRKG---FAEGLWE 69
Cdd:cd05838     13 YRWWPAEIlhpREVPDniQSLPHPPGEFPVRFFGSHDYYWVHRGRVFLFEEGDKGSKEKSKKSLdksFKRALKE 86
PWWP_AtATX1-like cd20142
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 2-71 2.75e-05

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438970 [Multi-domain]  Cd Length: 97  Bit Score: 44.65  E-value: 2.75e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339    2 KGYPHWPAR-IDElpEGAVK------SPSNKYQVF--FFGTHETAFLGAKDLFSYDE-CKEKFGKSNKRKGFAEGLWEIE 71
Cdd:cd20142     11 KGYPMWPALvIDE--EHAERcgleanRPGKKGTVPvqFFGTYEVARLNPKKVVGFSKgLDLKYHSKCKAPVFRQALEEAE 88
EGF pfam00008
EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very ...
 1545-1575 3.96e-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: 41.98  E-value: 3.96e-05
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1786632339 1545 CLGDPCLNGGTCTDRDGQIKCLCLPSYGGNF 1575
Cdd:pfam00008    1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31
EGF_CA smart00179
Calcium-binding EGF-like domain;
1543-1577 4.77e-05

Calcium-binding EGF-like domain;


Pssm-ID: 214542 [Multi-domain]  Cd Length: 39  Bit Score: 42.23  E-value: 4.77e-05
                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 1786632339  1543 DACL-GDPCLNGGTCTDRDGQIKCLCLPSY-GGNFCQ 1577
Cdd:smart00179    3 DECAsGNPCQNGGTCVNTVGSYRCECPPGYtDGRNCE 39
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 257-283 1.01e-04

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.77  E-value: 1.01e-04
                            10        20
                    ....*....|....*....|....*..
gi 1786632339   257 VLRGDTVEILAGKDKGKQGKVIQVFRH 283
Cdd:smart00739    2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 1583-1657 1.51e-04

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 45.11  E-value: 1.51e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1786632339 1583 CEPGWDKFHGFCYRHFSQRLSWEVAEQHCRVLGAHLVSVMTPEEQSYINdNYKEY--QWTGLNDKTIEDDFRWSDGN 1657
Cdd:PHA02642    88 CPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEELNFLK-RYKDSsdHWIGLNRESSNHPWKWADNS 163
PWWP_ScIOC4-like cd05840
PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar ...
 1-61 2.50e-04

PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins; ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438965  Cd Length: 94  Bit Score: 41.90  E-value: 2.50e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1786632339    1 MKGYPHWPARI---DELPE-------GAVKSPSNKYQVFFFGTHETAFLGAKDL--FSYDECKEKFGKSNKRK 61
Cdd:cd05840      8 VKGYPPWPAMVlpeELLPKnvlkakkRKPKSKKTVYPVQFFPDNEYYWVSPSSLkpLTKEEIDKFLSKSKRKN 80
EGF cd00053
Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large ...
 1548-1577 2.89e-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: 39.77  E-value: 2.89e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1786632339 1548 DPCLNGGTCTDRDGQIKCLCLPSYGGNF-CQ 1577
Cdd:cd00053      6 NPCSNGGTCVNTPGSYRCVCPPGYTGDRsCE 36
PWWP_BS69 cd20159
PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger ...
 1-43 3.48e-04

PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438987  Cd Length: 85  Bit Score: 41.04  E-value: 3.48e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1786632339    1 MKGYPHWPARIdelpegaVKSPSNKYQVFFFG-THETAFLGAKD 43
Cdd:cd20159     14 QKGFPYWPAKV-------IQKEDNQYDVRFFGgHHQRAWIPKEN 50
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 456-569 3.65e-04

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 40.95  E-value: 3.65e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786632339   456 SGPVFASLGRSISIPCMVSLSTtastssssspvVPRVKWSVvsggvETQILVAKGERVKVneayryraallnyTSSSDDL 535
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSP-----------PPEVTWYK-----QGGKLLAESGRFSV-------------SRSGSTS 51

                            90       100       110
                    ....*....|....*....|....*....|....
gi 1786632339   536 SLWLEDLRSSDSGHYRCEVQQGLEDASDLVQLKV 569
Cdd:smart00410   52 TLTISNVTPEDSGTYTCAATNSSGSASSGTTLTV 85
rplX_A_E TIGR01080
ribosomal protein uL24, archaeal/eukaryotic form; This model represents the archaeal and ...
 236-293 8.81e-04

ribosomal protein uL24, archaeal/eukaryotic form; This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by related model TIGR01079. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273432  Cd Length: 114  Bit Score: 40.60  E-value: 8.81e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1786632339  236 NPPGKKRRKVFVEPLAS--------HEWSVLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLN 293
Cdd:TIGR01080   13 TAPLHERRKLMSAPLSKelrekygkRALPIRKGDEVRIVRGDFKGHEGKVSKVDRKRYRIYVEGVT 78
PTZ00194 PTZ00194
60S ribosomal protein L26; Provisional
 238-293 9.85e-04

60S ribosomal protein L26; Provisional


Pssm-ID: 185508  Cd Length: 143  Bit Score: 41.27  E-value: 9.85e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1786632339  238 PGKKRRKVFVEPLaSHEWS---------VLRGDTVEILAGKDKGKQGKVIQVFRhRNWVI-LEGLN 293
Cdd:PTZ00194    20 PSHLRRKLMSAPL-SKELRakynvrsmpVRKDDEVMVVRGHHKGREGKVTAVYR-KKWVIhIEKIT 83
hEGF pfam12661
Human growth factor-like EGF; hEGF, or human growth factor-like EGF, domains have six ...
 1550-1569 3.06e-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: 36.54  E-value: 3.06e-03
                           10        20
                   ....*....|....*....|
gi 1786632339 1550 CLNGGTCTDRDGQIKCLCLP 1569
Cdd:pfam12661    1 CQNGGTCVDGVNGYKCQCPP 20
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 248-293 5.22e-03

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 39.10  E-value: 5.22e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1786632339  248 EPLAShewSVLRGDTVEILAGKDKGKQGKVIQVFRHRNWVILEGLN 293
Cdd:TIGR00405   81 KKIIE---SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE 123
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 260-282 9.26e-03

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 35.57  E-value: 9.26e-03
                           10        20
                   ....*....|....*....|...
gi 1786632339  260 GDTVEILAGKDKGKQGKVIQVFR 282
Cdd:cd06084      1 GDTVKVVDGPYKGRQGTVLHIYR 23
 
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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