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Conserved domains on  [gi|24583400|ref|NP_723580|]
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CCR4-NOT transcription complex subunit 4, isoform C [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MOT2 super family cl28713
Transcriptional repressor [Transcription];
5-232 2.88e-83

Transcriptional repressor [Transcription];


The actual alignment was detected with superfamily member COG5175:

Pssm-ID: 227502 [Multi-domain]  Cd Length: 480  Bit Score: 278.49  E-value: 2.88e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    5 SSNDDAVECPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRKEYPENPADFKPLSQEEM---IAFKSQK 81
Cdd:COG5175    9 NSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSPEELkmeLARKEER 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400   82 RQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRLAD---ADILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASA 158
Cdd:COG5175   89 KMREKERKEAEGQNRKHLSNIRVVQKNLVYVIGIPPKVADeevAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGV 168
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24583400  159 YVTYVNNSDALRAIQSVNNIMIDGRLIKTSLGTTKYCSHFMKNQQCPKGDCMYLHELGDPEASFTKEEMHQGKH 232
Cdd:COG5175  169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQH 242
cwf18 super family cl07070
cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been ...
301-375 5.82e-03

cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.


The actual alignment was detected with superfamily member pfam08315:

Pssm-ID: 462423  Cd Length: 135  Bit Score: 38.36  E-value: 5.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    301 EAAATATsssgKSKREKLRNEKRHEKNKAKNKNGSNTNANASNKE-----NYVPETRS--------STSTETFAEATADA 367
Cdd:pfam08315    3 EEAALAR----KERLAALRSLKRKQPSEDDDEENSSEPEEEEELPvlkfrNYDPETRGlklgfvapPTPGETVEEQAAEL 78

                   ....*...
gi 24583400    368 PASTKAEP 375
Cdd:pfam08315   79 LEETKAED 86
 
Name Accession Description Interval E-value
MOT2 COG5175
Transcriptional repressor [Transcription];
5-232 2.88e-83

Transcriptional repressor [Transcription];


Pssm-ID: 227502 [Multi-domain]  Cd Length: 480  Bit Score: 278.49  E-value: 2.88e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    5 SSNDDAVECPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRKEYPENPADFKPLSQEEM---IAFKSQK 81
Cdd:COG5175    9 NSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSPEELkmeLARKEER 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400   82 RQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRLAD---ADILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASA 158
Cdd:COG5175   89 KMREKERKEAEGQNRKHLSNIRVVQKNLVYVIGIPPKVADeevAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGV 168
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24583400  159 YVTYVNNSDALRAIQSVNNIMIDGRLIKTSLGTTKYCSHFMKNQQCPKGDCMYLHELGDPEASFTKEEMHQGKH 232
Cdd:COG5175  169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQH 242
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
103-200 3.41e-60

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 200.45  E-value: 3.41e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  103 RVVQKNLVFVVGLPPRLADADILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDG 182
Cdd:cd12438    1 RVVQKNLVYVVGLPPRLADEEVLKRPEYFGQYGKIKKIVINRSTSYAGSQGPSASAYVTYSRKEDALRAIQAVDGFVLDG 80
                         90
                 ....*....|....*...
gi 24583400  183 RLIKTSLGTTKYCSHFMK 200
Cdd:cd12438   81 RTLKASFGTTKYCSSFLR 98
zf-RING_4 pfam14570
RING/Ubox like zinc-binding domain;
13-59 8.24e-27

RING/Ubox like zinc-binding domain;


Pssm-ID: 405286 [Multi-domain]  Cd Length: 47  Bit Score: 103.46  E-value: 8.24e-27
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 24583400     13 CPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRKEY 59
Cdd:pfam14570    1 CPLCDEKLDETDKDFYPCECGYQICRFCYHDILENEGGRCPGCREPY 47
RRM smart00360
RNA recognition motif;
110-186 3.00e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.52  E-value: 3.00e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400     110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINPSTTYAGVQGpsaSAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:smart00360    2 LFVGNLPPDTTEEEL---RELFSKFGKVESVRLVRDKETGKSKG---FAFVEFESEEDAEKALEALNGKELDGRPLK 72
PLN02638 PLN02638
cellulose synthase A (UDP-forming), catalytic subunit
13-94 2.52e-04

cellulose synthase A (UDP-forming), catalytic subunit


Pssm-ID: 215343 [Multi-domain]  Cd Length: 1079  Bit Score: 45.30  E-value: 2.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    13 CPLCMEPL--EVDDLTFFPC-TCGYQICRFCWHRIRTDENKLCPACRKEY------PENPADFKPLSQEEMIAFKSQKRQ 83
Cdd:PLN02638   20 CQICGDNVgkTVDGEPFVACdVCAFPVCRPCYEYERKDGNQSCPQCKTKYkrhkgsPAILGDEEEDGDADDGASDFNYPS 99
                          90
                  ....*....|.
gi 24583400    84 RDQQRKQKITE 94
Cdd:PLN02638  100 SNQDQKQKIAE 110
cwf18 pfam08315
cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been ...
301-375 5.82e-03

cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.


Pssm-ID: 462423  Cd Length: 135  Bit Score: 38.36  E-value: 5.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    301 EAAATATsssgKSKREKLRNEKRHEKNKAKNKNGSNTNANASNKE-----NYVPETRS--------STSTETFAEATADA 367
Cdd:pfam08315    3 EEAALAR----KERLAALRSLKRKQPSEDDDEENSSEPEEEEELPvlkfrNYDPETRGlklgfvapPTPGETVEEQAAEL 78

                   ....*...
gi 24583400    368 PASTKAEP 375
Cdd:pfam08315   79 LEETKAED 86
 
Name Accession Description Interval E-value
MOT2 COG5175
Transcriptional repressor [Transcription];
5-232 2.88e-83

Transcriptional repressor [Transcription];


Pssm-ID: 227502 [Multi-domain]  Cd Length: 480  Bit Score: 278.49  E-value: 2.88e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    5 SSNDDAVECPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRKEYPENPADFKPLSQEEM---IAFKSQK 81
Cdd:COG5175    9 NSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSPEELkmeLARKEER 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400   82 RQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRLAD---ADILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASA 158
Cdd:COG5175   89 KMREKERKEAEGQNRKHLSNIRVVQKNLVYVIGIPPKVADeevAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGV 168
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24583400  159 YVTYVNNSDALRAIQSVNNIMIDGRLIKTSLGTTKYCSHFMKNQQCPKGDCMYLHELGDPEASFTKEEMHQGKH 232
Cdd:COG5175  169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQH 242
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
103-200 3.41e-60

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 200.45  E-value: 3.41e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  103 RVVQKNLVFVVGLPPRLADADILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDG 182
Cdd:cd12438    1 RVVQKNLVYVVGLPPRLADEEVLKRPEYFGQYGKIKKIVINRSTSYAGSQGPSASAYVTYSRKEDALRAIQAVDGFVLDG 80
                         90
                 ....*....|....*...
gi 24583400  183 RLIKTSLGTTKYCSHFMK 200
Cdd:cd12438   81 RTLKASFGTTKYCSSFLR 98
mRING-HC-C4C4_CNOT4 cd16618
Modified RING finger, HC subclass (C4C4-type), found in CCR4-NOT transcription complex subunit ...
11-57 4.29e-31

Modified RING finger, HC subclass (C4C4-type), found in CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; NOT4, also known as CCR4-associated factor 4, E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4, is a component of the multifunctional CCR4-NOT complex, a global regulator of RNA polymerase II transcription. It associates with polysomes and contributes to the negative regulation of protein synthesis. NOT4 functions as an E3 ubiquitin-protein ligase that interacts with a specific E2, Ubc4/5 in yeast, and the ortholog UbcH5B in humans, and ubiquitylates a wide range of substrates, including ribosome-associated factors. Thus, it plays a role in cotranslational quality control (QC) through ribosome-associated ubiquitination and degradation of aberrant peptides. NOT4 contains a C4C4-type RING finger motif, whose overall folding is similar to that of the C3HC4-type RING-HC finger, a central RNA recognition motif (RRM), and a C-terminal domain predicted to be unstructured.


Pssm-ID: 438280 [Multi-domain]  Cd Length: 47  Bit Score: 115.80  E-value: 4.29e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   11 VECPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRK 57
Cdd:cd16618    1 PECPLCMEELDITDLNFFPCPCGYQICLFCWHRIREDENGRCPACRK 47
zf-RING_4 pfam14570
RING/Ubox like zinc-binding domain;
13-59 8.24e-27

RING/Ubox like zinc-binding domain;


Pssm-ID: 405286 [Multi-domain]  Cd Length: 47  Bit Score: 103.46  E-value: 8.24e-27
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 24583400     13 CPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKLCPACRKEY 59
Cdd:pfam14570    1 CPLCDEKLDETDKDFYPCECGYQICRFCYHDILENEGGRCPGCREPY 47
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
110-186 2.69e-10

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 57.29  E-value: 2.69e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINPSTTyagvQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd00590    1 LFVGNLPPDTTEEDL---RELFSKFGEVVSVRIVRDRD----GKSKGFAFVEFESPEDAEKALEALNGTELGGRPLK 70
RRM smart00360
RNA recognition motif;
110-186 3.00e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.52  E-value: 3.00e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400     110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINPSTTYAGVQGpsaSAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:smart00360    2 LFVGNLPPDTTEEEL---RELFSKFGKVESVRLVRDKETGKSKG---FAFVEFESEEDAEKALEALNGKELDGRPLK 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
110-186 4.23e-09

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 53.78  E-value: 4.23e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24583400    110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINPSTTyagvqGPSA-SAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:pfam00076    1 LFVGNLPPDTTEEDL---KDLFSKFGPIKSIRLVRDET-----GRSKgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
108-188 7.43e-09

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 53.06  E-value: 7.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  108 NLVFVVGLPPRLADADILkkhEYFGKYGKIHKVVINPSTTYAgvqgpSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKT 187
Cdd:cd21603    1 NAIFVKNLPLDTNNDEIL---DFFSKVGPIKSVFTSPKYKYN-----SLWAFVTYKKGSDTEKAIKLLNGTLFKGRTIEV 72

                 .
gi 24583400  188 S 188
Cdd:cd21603   73 T 73
RRM_1 smart00361
RNA recognition motif;
129-186 8.05e-09

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 53.18  E-value: 8.05e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 24583400     129 EYFGKYGKIHKVVINPSTTYAGVQGpsaSAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:smart00361   14 EYFGEVGKINKIYIDDVGYENHKRG---NVYITFERSEDAARAIVDLNGRYFDGRLVK 68
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
12-55 1.12e-07

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 49.02  E-value: 1.12e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 24583400   12 ECPLCMEPLevDDLTFFPCtcGYQICRFCWHRIRTDENKLCPAC 55
Cdd:cd16449    2 ECPICLERL--KDPVLLPC--GHVFCRECIRRLLESGSIKCPIC 41
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
107-188 3.92e-07

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 48.43  E-value: 3.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  107 KNLVFVVGLPPRLADADIlkkHEYFGKYGKIHKVVI--NPSTTYA-GVqgpsasAYVTYVNNSDALRAIQSVNNIMIDGR 183
Cdd:cd12393    1 KSTVYVSNLPFSLTNNDL---HQIFSKYGKVVKVTIlkDKETRKSkGV------AFVLFLDRESAHNAVRAMNNKELFGR 71

                 ....*
gi 24583400  184 LIKTS 188
Cdd:cd12393   72 TLKCS 76
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
111-185 6.56e-07

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 47.63  E-value: 6.56e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400  111 FVVGLPPRLaDADILKKHeyFGKYGKI--HKVVINPSTTYAGVQGpsasaYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12417    3 WISGLSDTT-KAADLKKI--FSKYGKVvsAKVVTSARTPGSRCYG-----YVTMASVEEADLCIKSLNKTELHGRVI 71
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
110-187 5.39e-06

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 45.07  E-value: 5.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIH--KVVINPSTTyagvqGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKT 187
Cdd:cd12353    2 IFVGDLSPEIETEDL---KEAFAPFGEISdaRVVKDTQTG-----KSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNIRT 73
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
106-189 2.27e-05

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 43.47  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  106 QKNLVFVVGLPPRLADADIlkkHEYFGKYGKIHKVVInpSTTYAGVqgPSASAYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12392    1 EKNKLFVKGLPFSCTKEEL---EELFKQHGTVKDVRL--VTYRNGK--PKGLAYVEYENEADASQAVLKTDGTEIKDHTI 73

                 ....
gi 24583400  186 KTSL 189
Cdd:cd12392   74 SVAI 77
RRM_SKAR cd12681
RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; ...
110-189 2.73e-05

RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410082 [Multi-domain]  Cd Length: 69  Bit Score: 43.03  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADILkkhEYFGKYGKIHKvvinpsttyAGVQGPsASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12681    3 LTVSNLHPSVTEDDIV---ELFSVIGALKR---------ARLVRP-GVAEVVYVRREDAITAIKKYNNRELDGQPMKCKL 69
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
12-58 2.85e-05

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 42.39  E-value: 2.85e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   12 ECPLCMEPLEVDDLTFfpcTCGYQICRFCWHRIRTDENKLCPACRKE 58
Cdd:cd16564    2 ECPVCYEDFDDAPRIL---SCGHSFCEDCLVKQLVSMTISCPICRRV 45
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
103-188 2.89e-05

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409679 [Multi-domain]  Cd Length: 89  Bit Score: 43.73  E-value: 2.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  103 RVVQ-KNLVFvvglPPRLAD----ADILKK-HEYFGKYGKIHKVVInPSTTYAGVQGPSA-SAYVTYVNNSDALRAIQSV 175
Cdd:cd12232    2 RVLClLNMVT----PEELEDdeeyEEILEDvKEECSKYGKVLSVVI-PRPEAEGVDVPGVgKVFVEFEDVEDAQKAQKAL 76
                         90
                 ....*....|...
gi 24583400  176 NNIMIDGRLIKTS 188
Cdd:cd12232   77 AGRKFDGRTVVAS 89
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
12-55 3.21e-05

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 42.04  E-value: 3.21e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 24583400     12 ECPLCMEPLEvDDLTFFPCtcGYQICRFCWHRIRTDENKlCPAC 55
Cdd:pfam13923    1 MCPICMDMLK-DPSTTTPC--GHVFCQDCILRALEASNE-CPLC 40
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
110-189 3.66e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 42.96  E-value: 3.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADILkkhEYFGKYGKIHK--VVINP-STTYAGVqgpsasAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd12413    2 LFVRNLPYDTTDEQLE---ELFSDVGPVKRcfVVKDKgKDKCRGF------GYVTFALAEDAQRALEEVKGKKFGGRKIK 72

                 ...
gi 24583400  187 TSL 189
Cdd:cd12413   73 VEL 75
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
110-190 6.19e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 41.92  E-value: 6.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADiLKKHeyFGKYGKIHKVVINPSttyagvqgpSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12346    4 VFVGGLDPNVTEED-LRVL--FGPFGEIVYVKIPPG---------KGCGFVQFVNRASAEAAIQKLQGTPIGGSRIRLSW 71

                 .
gi 24583400  190 G 190
Cdd:cd12346   72 G 72
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
110-190 6.45e-05

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 41.88  E-value: 6.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADILKKheyFGKYGKIHKVVINPSTTYAgvqgpsasaYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12354    3 VYVGNITKGLTEALLQQT---FSPFGQILEVRVFPDKGYA---------FIRFDSHEAATHAIVSVNGTIINGQAVKCSW 70

                 .
gi 24583400  190 G 190
Cdd:cd12354   71 G 71
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
108-183 6.84e-05

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 42.13  E-value: 6.84e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  108 NLVFVVGLPPRLADADILKkheYFGKYGKIHKVVINPSTTYAGVQGpSASAYVTYVNNSDALRAIQSVNNIMIDGR 183
Cdd:cd21619    2 NTIYVGNIDMTINEDALEK---IFSRYGQVESVRRPPIHTDKADRT-TGFGFIKYTDAESAERAMQQADGILLGRR 73
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
13-63 7.59e-05

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 41.28  E-value: 7.59e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24583400   13 CPLCMEplevddltFF--PC--TCGYQICRFC----WHRIRtdENKLCPACRKEYPENP 63
Cdd:cd16611    7 CPLCLD--------FFrdPVmlSCGHNFCQSCitgfWELQA--EDTTCPECRELCQYRN 55
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
110-187 9.16e-05

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 42.01  E-value: 9.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADI-LKKHEYFGKYGKIHKVVI---NPSTTYAGVQgpsasayvtYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12453    5 LFVASLSSARSDEELcAAVTNHFSKWGELLNVKVlkdWSNRPYAFVQ---------YTNTEDAKNALVNGHNTLLDGRHL 75

                 ..
gi 24583400  186 KT 187
Cdd:cd12453   76 RV 77
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
112-191 1.08e-04

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 41.61  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  112 VVGLPPRLADADIlkkHEYFGKYGKIHKVVI--NPsttyagvQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12407    5 VSNIPFRFRDPDL---RQMFGQFGTILDVEIifNE-------RGSKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNN 74

                 ..
gi 24583400  190 GT 191
Cdd:cd12407   75 AT 76
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
124-185 1.20e-04

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 41.38  E-value: 1.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  124 ILKKH--EYFGKYGKIHKV--VINPsttyaGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12365   10 VTKDHlkEIFSVYGTVKNVdlPIDR-----EPNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
112-187 1.32e-04

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 41.45  E-value: 1.32e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400  112 VVGLPPRLADADIlkkHEYFGKYGKIHKVVInpstTYAGVQGPSAS-AYVTYVNNSDALRAIQSVNNIMIDGRLIKT 187
Cdd:cd12363    6 VFGLSLYTTERDL---REVFSRYGPIEKVQV----VYDQQTGRSRGfGFVYFESVEDAKEAKERLNGQEIDGRRIRV 75
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
110-186 1.76e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 41.24  E-value: 1.76e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400  110 VFVVGLPprlADADILKKHEYFGKYGKIHKVVINPSTTYAGVQGpsaSAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd12382    4 LFIGGLN---TETNEKALEAVFGKYGRIVEVLLMKDRETNKSRG---FAFVTFESPADAKDAARDMNGKELDGKAIK 74
RING-HC_SIAHs cd16571
RING finger, HC subclass, found in Drosophila melanogaster protein Seven-in-Absentia (sina) ...
12-56 2.22e-04

RING finger, HC subclass, found in Drosophila melanogaster protein Seven-in-Absentia (sina) and its homologs; This subfamily includes the Drosophila melanogaster protein Seven-in-Absentia (sina), its mammalian orthologs, SIAH1 and SIAH2, plant SINA-related proteins, and similar proteins. Sina plays an important role in the phyllopod-dependent degradation of the transcriptional repressor tramtrack to allow the formation of the R7 photoreceptor in the developing eye of Drosophila melanogaster. Both SIAH1 and SIAH2 are E3 ubiquitin-protein ligases, mediating the ubiquitinylation and subsequent proteasomal degradation of biologically important target proteins that regulate general functions, such as cell cycle control, apoptosis, and DNA repair. They are inducible by the tumor suppressor and transcription factor p53. SIAH2 can also be regulated by sex hormones and cytokine signaling. Moreover, they share high sequence similarity, but possess contrary roles in cancer, with SIAH1 more often acting as a tumor suppressor while SIAH2 functions as a proto-oncogene. Plant SINAT1-5 are putative E3 ubiquitin ligases involved in the regulation of stress responses. All subfamily members possess two characteristic domains, an N-terminal C3HC4-type RING-HC finger and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD).


Pssm-ID: 438233 [Multi-domain]  Cd Length: 39  Bit Score: 39.55  E-value: 2.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 24583400   12 ECPLCMEPLEVDdltFFPCTCGYQICRFCWHRIrtdeNKLCPACR 56
Cdd:cd16571    2 ECPVCFEPLLPP---IYQCSNGHLLCSSCRSKL----TNKCPTCR 39
zf-RING_2 pfam13639
Ring finger domain;
12-56 2.31e-04

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 39.70  E-value: 2.31e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 24583400     12 ECPLCMEPLEVDDLTFfPCTCGYQICRFC---WHRIrtdeNKLCPACR 56
Cdd:pfam13639    2 ECPICLEEFEEGDKVV-VLPCGHHFHRECldkWLRS----SNTCPLCR 44
mRING-HC-C4C4_CesA cd16617
Modified RING finger, HC subclass (C4C4-type), found in Arabidopsis thaliana cellulose ...
13-56 2.51e-04

Modified RING finger, HC subclass (C4C4-type), found in Arabidopsis thaliana cellulose synthase A (CesA) catalytic subunits 1-10, and similar proteins from plants; This subfamily includes plant catalytic subunits of cellulose synthase terminal complexes ("rosettes") required for beta-1,4-glucan microfibril crystallization, a major mechanism of cell wall formation. CesA1, also known as protein RADIALLY SWOLLEN 1 (RSW1), is required during embryogenesis for cell elongation, orientation of cell expansion and complex cell wall formations, such as interdigitated pattern of epidermal pavement cells, stomatal guard cells, and trichomes. It plays a role in lateral roots formation, but seems unnecessary for the development of tip-growing cells such as root hairs. CesA2, also known as Ath-A, is involved in the primary cell wall formation. It forms a homodimer. CesA3, also known as constitutive expression of VSP1 protein 1, isoxaben-resistant protein 1, Ath-B, protein ECTOPIC LIGNIN 1, or protein RADIALLY SWOLLEN 5 (RSW5), is involved in primary cell wall formation, especially in roots. CesA4, also known as protein IRREGULAR XYLEM 5 (IRX5), is involved in the secondary cell wall formation, and required for xylem cell wall thickening. CesA5 may be partially redundant with CesA6. CesA6, also known as AraxCelA, isoxaben-resistant protein 2, protein PROCUSTE 1, or protein QUILL, is involved in primary cell wall formation. Like CesA1, CesA6 is critical for cell expansion. CESA6-dependent cell elongation seems to be independent of gibberellic acid, auxin, and ethylene. CesA6 interacts with and moves along cortical microtubules for the process of cellulose deposition. CesA7, also known as protein FRAGILE FIBER 5, or protein IRREGULAR XYLEM 3 (IRX3), and CesA8, also known as protein IRREGULAR XYLEM 1 (IRX1) or protein LEAF WILTING 2, are both involved in secondary cell wall formation and also required for xylem cell wall thickening. The biological function of CesA9 and CesA10 remain unclear. CesA1, CesA3, and CesA6 form a functional complex essential for primary cell wall cellulose synthesis, while CesA4, CesA7, and CesA8 form a functional complex located in secondary cell wall deposition sites. All family members contain an N-terminal C4C4-type RING-HC finger and a C-terminal glycosyltransferase family A (GT-A) domain.


Pssm-ID: 438279 [Multi-domain]  Cd Length: 51  Bit Score: 39.74  E-value: 2.51e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   13 CPLCMEPLEVDDL--TFFPCT-CGYQICRFCWHRIRTDENKLCPACR 56
Cdd:cd16617    3 CQICGDEIGLTVNgeLFVACNeCGFPVCRPCYEYERKEGNQCCPQCK 49
PLN02638 PLN02638
cellulose synthase A (UDP-forming), catalytic subunit
13-94 2.52e-04

cellulose synthase A (UDP-forming), catalytic subunit


Pssm-ID: 215343 [Multi-domain]  Cd Length: 1079  Bit Score: 45.30  E-value: 2.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    13 CPLCMEPL--EVDDLTFFPC-TCGYQICRFCWHRIRTDENKLCPACRKEY------PENPADFKPLSQEEMIAFKSQKRQ 83
Cdd:PLN02638   20 CQICGDNVgkTVDGEPFVACdVCAFPVCRPCYEYERKDGNQSCPQCKTKYkrhkgsPAILGDEEEDGDADDGASDFNYPS 99
                          90
                  ....*....|.
gi 24583400    84 RDQQRKQKITE 94
Cdd:PLN02638  100 SNQDQKQKIAE 110
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
107-186 3.08e-04

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 40.47  E-value: 3.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  107 KNLvFVVGLPPRLADADIlkkHEYFGKYGKIH--KVVINPSTtyagvqGPSAS-AYVTYVNNSDALRAIQSVNNIMIDGR 183
Cdd:COG0724    2 MKI-YVGNLPYSVTEEDL---RELFSEYGEVTsvKLITDRET------GRSRGfGFVEMPDDEEAQAAIEALNGAELMGR 71

                 ...
gi 24583400  184 LIK 186
Cdd:COG0724   72 TLK 74
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
110-189 3.53e-04

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 39.90  E-value: 3.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINpsttYaGVQGPS-ASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTS 188
Cdd:cd12680    3 LLVSNLDFGVSDADI---KELFAEFGTLKKAAVH----Y-DRSGRSlGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQ 74

                 .
gi 24583400  189 L 189
Cdd:cd12680   75 L 75
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
110-189 5.29e-04

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 39.55  E-value: 5.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQsVNNIMIDGRLIKTSL 189
Cdd:cd12298    3 IRVRNLDFELDEEAL---RGIFEKFGEIESINIPKKQKNRKGRHNNGFAFVTFEDADSAESALQ-LNGTLLDNRKISVSL 78
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
13-55 6.57e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 38.26  E-value: 6.57e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 24583400      13 CPLCMEPLEvDDLTFFPCtcGYQICRFCWHRIRTDENKLCPAC 55
Cdd:smart00184    1 CPICLEEYL-KDPVILPC--GHTFCRSCIRKWLESGNNTCPIC 40
RING-HC_TRIM32_C-VII cd16587
RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...
11-57 7.35e-04

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.


Pssm-ID: 438249 [Multi-domain]  Cd Length: 51  Bit Score: 38.54  E-value: 7.35e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24583400   11 VECPLCMEPLEVDDLTFFPCTCGYQICRFCWHRIRTDENKL---CPACRK 57
Cdd:cd16587    1 LECPICLESFDEGQLRPKLLHCGHTICEQCLEKLLASLSINgvrCPFCRK 50
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
110-185 7.39e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 39.25  E-value: 7.39e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  110 VFVVGLPPRLADADILKKHEYFGKYGKIHkVVINPSTtyagvQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12316    2 LFVRNLPFTATEDELRELFEAFGKISEVH-IPLDKQT-----KRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLL 71
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
108-183 7.91e-04

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 39.13  E-value: 7.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  108 NLVFVVGLPPRLADADIlkkHEYFGKYGKIHKVVInpSTTYAGVqgPSASAYVTYVNNSDALRAIQSVNNIMIDGR 183
Cdd:cd12412    3 NRIFVGGIDWDTTEEEL---REFFSKFGKVKDVKI--IKDRAGV--SKGYGFVTFETQEDAEKIQKWGANLVFKGK 71
BRcat_RBR_RNF216 cd20339
BRcat domain found in RING finger protein 216 (RNF216); RNF216, also called Triad ...
8-46 8.22e-04

BRcat domain found in RING finger protein 216 (RNF216); RNF216, also called Triad domain-containing protein 3 (Triad3A), ubiquitin-conjugating enzyme 7-interacting protein 1, or zinc finger protein inhibiting NF-kappa-B (ZIN), is an RBR-type E3 ubiquitin-protein ligase that interacts with several components of the Toll-like receptor (TLR) signaling pathway and promotes their proteolytic degradation. It negatively regulates the RIG-I RNA sensing pathway through Lys48-linked, ubiquitin-mediated degradation of the tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) adapter following RNA virus infection. It also controls ubiquitination and proteasomal degradation of receptor-interacting protein 1 (RIP1), a serine/threonine protein kinase that is critically involved in TNF receptor-1-induced NF-kappa B activation, following disruption of Hsp90 binding. Moreover, RNF216 is involved in inflammatory diseases by strongly inhibiting autophagy in macrophages. It interacts with and ubiquitinates BECN1, a key regulator in autophagy, thereby contributing to BECN1 degradation. It regulates synaptic strength by ubiquitination of Arc, resulting in its rapid proteasomal degradation. It is also a key negative regulator of sustained 2DL4/KIR2DL4 (killer cell Ig-like receptor with two Ig-like domains and a long cytoplasmic domain 4)-mediated NF-kappaB signaling from internalized 2DL4, which functions by promoting ubiquitylation and degradation of endocytosed receptor from early endosomes. Furthermore, RNF216 interacts with human immunodeficiency virus type 1 (HIV-1) virion infectivity factor (Vif) protein, which is essential for the productive infection of primary human CD4 T lymphocytes and macrophages. Mutations in RNF216 may result in Gordon Holmes syndrome, a condition defined by hypogonadotropic hypogonadism and cerebellar ataxia, as well as in autosomal recessive Huntington-like disorder. RNF216 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF216 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439000  Cd Length: 54  Bit Score: 38.48  E-value: 8.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400    8 DDAVECPLCMEP--LEVDDLTFFPC---TCGYQICRFC---WHRIRT 46
Cdd:cd20339    2 EGLERCPFCNYAaiLDPTEVKVFRCpnpECRKESCRKCkkeWHIPLT 48
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
110-186 8.92e-04

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 39.10  E-value: 8.92e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKVVIN--PSTTYAGVqgpsasAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd12418    3 VRVSNLHPDVTEEDL---RELFGRVGPVKSVKINydRSGRSTGT------AYVVFERPEDAEKAIKQFDGVLLDGQPMK 72
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
103-185 9.31e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 39.07  E-value: 9.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  103 RVVQKNLVFVvglpprlADADILKKHeyFGKYGKIHKVVI--NPSTTYAGVqgpsasAYVTYVNNSDALRAIQSVNNIMI 180
Cdd:cd12414    1 RLIVRNLPFK-------CTEDDLKKL--FSKFGKVLEVTIpkKPDGKLRGF------AFVQFTNVADAAKAIKGMNGKKI 65

                 ....*
gi 24583400  181 DGRLI 185
Cdd:cd12414   66 KGRPV 70
RING-HC_SH3RF2 cd16749
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and ...
11-56 9.47e-04

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and similar proteins; SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438407 [Multi-domain]  Cd Length: 46  Bit Score: 37.99  E-value: 9.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   11 VECPLCMEPLEVddlTFFPCTCGYQICRFCWHRIRTDENKL-CPACR 56
Cdd:cd16749    1 LECPVCFEKLDV---TAKVLPCQHTFCKPCLQRIFKARKELrCPECR 44
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
110-189 1.12e-03

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 38.84  E-value: 1.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPrlaDADILKKHEYFGKYGKIHKVVINPSTTYAGVQGpsaSAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12377    2 IFVYNLAP---DADESLLWQLFGPFGAVQNVKIIRDFTTNKCKG---YGFVTMTNYDEAAVAIASLNGYRLGGRVLQVSF 75
RRM_MCM3A_like cd12443
RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar ...
114-151 1.28e-03

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409877 [Multi-domain]  Cd Length: 75  Bit Score: 38.45  E-value: 1.28e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 24583400  114 GLPPRLADADILKKHeyFGKYGKIHKVVINPSTTYAGV 151
Cdd:cd12443    7 NIPEELNDKEILRRH--FSKFGKVARVFCNPRKNLAIV 42
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
110-185 1.32e-03

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 38.30  E-value: 1.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKIHKV-VINPSTTyagvqGPSAS-AYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd21608    2 LYVGNLSWDTTEDDL---RDLFSEFGEVESAkVITDRET-----GRSRGfGFVTFSTAEAAEAAIDALNGKELDGRSI 71
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
110-185 1.37e-03

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 38.43  E-value: 1.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  110 VFVVGLPPRLADADILKkheYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLI 185
Cdd:cd12355    2 LWIGNLDPRLTEYHLLK---LLSKYGKIKKFDFLFHKTGPLKGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKL 74
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
13-64 1.49e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 38.06  E-value: 1.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24583400   13 CPLCMEPLevDDltffPCT--CGYQICRFC----WHRIRTDENkLCPACRKEYPENPA 64
Cdd:cd16597    8 CSICLELF--KD----PVTlpCGHNFCGVCiektWDSQHGSEY-SCPQCRATFPRRPE 58
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
12-56 1.66e-03

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 37.25  E-value: 1.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   12 ECPLCMEplevddLTFFPCT--CGYQICRFCWHRIrTDENKLCPACR 56
Cdd:cd16514    3 ECSLCLR------LLYEPVTtpCGHTFCRACLERC-LDHSPKCPLCR 42
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
110-190 1.87e-03

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 38.43  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADILKkheYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12223    4 LYVGNLPPSVTEEVLLR---EFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLGW 80

                 .
gi 24583400  190 G 190
Cdd:cd12223   81 G 81
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
13-63 2.05e-03

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).


Pssm-ID: 438160 [Multi-domain]  Cd Length: 52  Bit Score: 37.10  E-value: 2.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24583400   13 CPLCMEpLEVDDLTFfpcTCGYQICRFC----WHRIRTDEnklCPACRKEYPENP 63
Cdd:cd16497    4 CHCCYD-LLVNPTTL---NCGHSFCRHClalwWKSSKKTE---CPECRQKWEGFP 51
RING-HC_SH3RF1 cd16748
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and ...
9-56 2.14e-03

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. It also plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and c-Jun N-terminal kinase (JNK) mediated apoptosis, linking Rac1 to downstream components. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. Moreover, SH3RF1 assembles an inhibitory complex with the actomyosin regulatory protein Shroom3, which links to the actin-myosin network to regulate neuronal process outgrowth. It also forms a complex with apoptosis-linked gene-2 (ALG-2) and ALG-2-interacting protein (ALIX/AIP1) in a calcium-dependent manner to play a role in the regulation of the JNK pathway. Furthermore, direct interaction of SH3RF1 and another molecular scaffold JNK-interacting protein (JIP) is required for apoptotic activation of JNKs. Interaction of SH3RF1 and E3 ubiquitin-protein isopeptide ligases, Siah proteins, further promotes JNK activation and apoptosis. In addition, SH3RF1 binds to and degrades TAK1, a crucial activator of both the JNK and the Relish signaling pathways. SH3RF1 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438406 [Multi-domain]  Cd Length: 48  Bit Score: 36.91  E-value: 2.14e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24583400    9 DAVECPLCMEPLevdDLTFFPCTCGYQICRFCWHRIRTDENKL-CPACR 56
Cdd:cd16748    1 DLLECPVCLERL---DATAKVLPCQHTFCRRCLLGIVGSRSELrCPECR 46
RING-HC_RBR_RNF19 cd16629
RING finger, HC subclass, found in the family of RING finger proteins RNF19A, RNF19B and ...
11-55 2.20e-03

RING finger, HC subclass, found in the family of RING finger proteins RNF19A, RNF19B and similar proteins; The family includes RING finger protein RNF19A and RNF19B, both of which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF19A, also known as double ring-finger protein (Dorfin) or p38, localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies, multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. RNF19B, also known as IBR domain-containing protein 3 or natural killer lytic-associated molecule (NKLAM), plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. Both RNF19A and RNF19B contain an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438291 [Multi-domain]  Cd Length: 56  Bit Score: 37.43  E-value: 2.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24583400   11 VECPLCMEPLEVddlTFFP--CTCGYQICRFCWH---RIRTDE---NKLCPAC 55
Cdd:cd16629    1 LECPLCLDDLSP---EFFPilLSCEHRSCRDCLRqylTIEISEsrvNISCPEC 50
PLN02915 PLN02915
cellulose synthase A [UDP-forming], catalytic subunit
9-59 2.27e-03

cellulose synthase A [UDP-forming], catalytic subunit


Pssm-ID: 215494 [Multi-domain]  Cd Length: 1044  Bit Score: 42.23  E-value: 2.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 24583400     9 DAVECPLCMEPLEVDD--LTFFPCT-CGYQICRFCWHRIRTDENKLCPACRKEY 59
Cdd:PLN02915   14 DAKTCRVCGDEVGVKEdgQPFVACHvCGFPVCKPCYEYERSEGNQCCPQCNTRY 67
RING-HC_RGLG_plant cd16729
RING finger, HC subclass, found in RING domain ligase RGLG1, RGLG2 and similar proteins from ...
9-58 2.37e-03

RING finger, HC subclass, found in RING domain ligase RGLG1, RGLG2 and similar proteins from plant; RGLG1 is a ubiquitously expressed E3 ubiquitin-protein ligase that interacts with UBC13 and, together with UBC13, catalyzes the formation of K63-linked polyubiquitin chains, which is involved in DNA damage repair. RGLG1 mediates the formation of canonical, K48-linked polyubiquitin chains that target proteins for degradation. It also regulates apical dominance by acting on the auxin transport proteins abundance. RGLG1 has overlapping functions with its closest sequelog, RGLG2. They both function as RING E3 ligases that interact with ethylene response factor 53 (ERF53) in the nucleus and negatively regulate the plant drought stress response. Members of this subfamily contain a Von Willebrand factor type A (vWA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438389  Cd Length: 48  Bit Score: 37.07  E-value: 2.37e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24583400    9 DAVECPLCMepLEVDDLTFfpcTCGYQICRFCWHRIRTdenklCPACRKE 58
Cdd:cd16729    1 DDQLCPICL--SNPKDMAF---GCGHQTCCECGQSLTH-----CPICRQP 40
RING-HC_SH3RFs cd16570
RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, ...
11-56 2.58e-03

RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, SH3RF3, and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH) that is required for pro-apoptotic JNK activation. SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2) and may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438232 [Multi-domain]  Cd Length: 44  Bit Score: 36.64  E-value: 2.58e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24583400   11 VECPLCMEPLEVDDlTFFPCTcgYQICRFCWHRIRTDENKL-CPACR 56
Cdd:cd16570    1 LECPVCLERLDVSA-KVLPCQ--HTFCKRCLQIIVASRGELrCPECR 44
RING-CH-C4HC3_ZSWM2 cd16494
RING-CH finger, H2 subclass (C4HC3-type), found in zinc finger SWIM domain-containing protein ...
13-59 2.63e-03

RING-CH finger, H2 subclass (C4HC3-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins; ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3, and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It also acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination and two RING fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the first RING finger, which is a C4HC3-type RING-CH finger, also known as vRING or RINGv, rather than the canonical C3H2C3-type RING-H2 finger.


Pssm-ID: 438157 [Multi-domain]  Cd Length: 57  Bit Score: 36.93  E-value: 2.63e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24583400   13 CPLCMEPL--EVDDLTFFPCTCGYQICRFC---W--HRIRTDENKLCPACRKEY 59
Cdd:cd16494    4 CPICYEEMleKGEPLTYCRFGCGNNVHIHCmkvWaeHQRQSDEPVTCPLCRSDW 57
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
9-56 2.72e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 36.96  E-value: 2.72e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24583400    9 DAVECPLCMEPLEVDDLTffpcTCGYQICRFC---WhrIRTDENKLCPACR 56
Cdd:cd16568    3 ETQECIICHEYLYEPMVT----TCGHTYCYTClntW--FKSNRSLSCPDCR 47
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
9-58 3.84e-03

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.


Pssm-ID: 438216 [Multi-domain]  Cd Length: 59  Bit Score: 36.52  E-value: 3.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24583400    9 DAVECPLCMeplevdDLTFFP---CTCGYQICRFCWHRIRTDE--NKLCPACRKE 58
Cdd:cd16554    1 ESLTCPVCL------DLYYDPymcYPCGHIFCEPCLRQLAKSSpkNTPCPLCRTT 49
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
110-188 3.86e-03

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 37.21  E-value: 3.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  110 VFVVGLPPRLADADIlkkHEYFGKYGKI--HKVVINPSTtyagvqGPSAS-AYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd12362    1 LFVYHLPNEFTDQDL---YQLFAPFGNVvsAKVFVDKNT------GRSKGfGFVSYDNPLSAQAAIKAMNGFQVGGKRLK 71

                 ..
gi 24583400  187 TS 188
Cdd:cd12362   72 VQ 73
RING-HC_SH3RF3 cd16750
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 3 (SH3RF3) and ...
9-56 3.96e-03

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 3 (SH3RF3) and similar proteins; SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in a screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1. Both contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438408 [Multi-domain]  Cd Length: 46  Bit Score: 36.25  E-value: 3.96e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24583400    9 DAVECPLCMEPLevdDLTFFPCTCGYQICRFCWHRIRTDENKL-CPACR 56
Cdd:cd16750    1 DLLECSVCLERL---DTTSKVLPCQHTFCRRCLESIVSSRKELrCPECR 46
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
110-187 4.26e-03

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 37.21  E-value: 4.26e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24583400  110 VFVVGLPPRLADADILkkhEYFGKYGKIHKVVINPSttyAGVQGPSaSAYVTYVNNSDALRAIQSVNniMIDGRLIKT 187
Cdd:cd12348    2 LWVGNLPENVREEKII---EHFKRFGRVESVKILPK---RGSEGGV-AAFVDFVDIKSAQKAHSAVN--KMGGRDLRT 70
RING-HC_ORTHRUS_rpt1 cd23138
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
9-60 5.57e-03

first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one.


Pssm-ID: 438500 [Multi-domain]  Cd Length: 48  Bit Score: 35.88  E-value: 5.57e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24583400    9 DAVECPLCMEPLEvddltfFPCT--CGYQICRFCWHRIRTDENKLCPACRKEYP 60
Cdd:cd23138    1 DELNCSFCMQLPE------RPVTtpCGHNFCLKCFQKWMGQGKKTCGTCRSPIP 48
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
107-186 5.57e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 36.39  E-value: 5.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  107 KNLVFVVGLPPRLADADILKKHeyFGKYGKIHKVVINPSttyagvqgpSASAYVTYVNNSDALRAIQS----VNNimidg 182
Cdd:cd12257    1 KTTLEVRNIPPELNNITKLREH--FSKFGTIVNIQVNYN---------PESALVQFSTSEEANKAYRSpeavFNN----- 64

                 ....
gi 24583400  183 RLIK 186
Cdd:cd12257   65 RFIK 68
RRM_NCBP2 cd12240
RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
128-189 5.59e-03

RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.


Pssm-ID: 409686 [Multi-domain]  Cd Length: 78  Bit Score: 36.78  E-value: 5.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24583400  128 HEYFGKYGKIHKVVI--NPSTtyagvQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIKTSL 189
Cdd:cd12240   16 YELFSKCGDIKRIIMglDKFK-----KTPCGFCFVEYYSREDAENAVKYLNGTKLDDRIIRVDW 74
cwf18 pfam08315
cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been ...
301-375 5.82e-03

cwf18 pre-mRNA splicing factor; The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.


Pssm-ID: 462423  Cd Length: 135  Bit Score: 38.36  E-value: 5.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400    301 EAAATATsssgKSKREKLRNEKRHEKNKAKNKNGSNTNANASNKE-----NYVPETRS--------STSTETFAEATADA 367
Cdd:pfam08315    3 EEAALAR----KERLAALRSLKRKQPSEDDDEENSSEPEEEEELPvlkfrNYDPETRGlklgfvapPTPGETVEEQAAEL 78

                   ....*...
gi 24583400    368 PASTKAEP 375
Cdd:pfam08315   79 LEETKAED 86
RING-HC_ZNF598 cd16615
RING finger, HC subclass, found in zinc finger protein 598 (ZNF598) and similar proteins; ...
12-61 5.95e-03

RING finger, HC subclass, found in zinc finger protein 598 (ZNF598) and similar proteins; ZNF598 associates with eukaryotic initiation factor 4E (eIF4E) homologous protein from mammals (m4EHP) by binding to Grb10-interacting GYF protein 2 (GIGYF2). The m4EHP-GIGYF2 complex functions as a translational repressor and is essential for normal embryonic development of mammalian. ZNF598 harbors a C3HC4-type RING-HC finger at its N-terminus.


Pssm-ID: 438277 [Multi-domain]  Cd Length: 51  Bit Score: 35.67  E-value: 5.95e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24583400   12 ECPLCMEPLEVDDLTffpcTCGYQICRFCWHRIRT-DENKLCPACRKEYPE 61
Cdd:cd16615    2 TCVICCEEIEYFAVG----PCNHPVCYKCSLRMRVlYKDKYCPICRTELDK 48
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
13-55 6.14e-03

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 35.41  E-value: 6.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 24583400     13 CPLCMEPLEVDDLTFfpcTCGYQICRFCWHRIRTDENKLCPAC 55
Cdd:pfam00097    1 CPICLEEPKDPVTLL---PCGHLFCSKCIRSWLESGNVTCPLC 40
RRM_XMAS2 cd12457
RNA recognition motif (RRM) found in X-linked male sterile 2 (Xmas-2) and similar proteins; ...
116-171 6.19e-03

RNA recognition motif (RRM) found in X-linked male sterile 2 (Xmas-2) and similar proteins; This subfamily corresponds to the RRM in Xmas-2, the Drosophila homolog of yeast Sac3p protein, together with E(y)2, the Drosophila homologue of yeast Sus1p protein, forming an endogenous complex that is required in the regulation of mRNA transport and also involved in the efficient transcription regulation of the heat-shock protein 70 (hsp70) loci. All family members are found in insects and contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a PCI domain.


Pssm-ID: 409890 [Multi-domain]  Cd Length: 71  Bit Score: 36.55  E-value: 6.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24583400  116 PPRLADADILKkhEYFGKYGKIHKVVINPSTTyagvqgpsaSAYVTYVNNSDALRA 171
Cdd:cd12457    9 PEELLDKTAAK--EYFRKFGKIKKITLRPKRR---------TCTVEYTNKEEAERA 53
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
13-63 6.34e-03

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 36.13  E-value: 6.34e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24583400   13 CPLCMEplevddltFF--PCT--CGYQICRFC----WHRirTDENKLCPACRKEYPENP 63
Cdd:cd16594    8 CPICLD--------YFtdPVTldCGHSFCRACiarcWEE--PETSASCPQCRETCPQRN 56
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
9-58 6.98e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 35.81  E-value: 6.98e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 24583400      9 DAVECPLCMEplEVDDLTFFPCTCGYqICRFCWHRIRTdENKLCPACRKE 58
Cdd:pfam13920    1 EDLLCVICLD--RPRNVVLLPCGHLC-LCEECAERLLR-KKKKCPICRQP 46
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
121-180 7.43e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 36.78  E-value: 7.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  121 DADILkkHEYFGKYGKIHKVVINPSTTyaGVQgpsasAYVTYVNNSDALRAIQSVNNIMI 180
Cdd:cd12422   14 TVDVL--HQVFSPYGAVEKIVIFEKGT--GVQ-----ALVQFDSVESAEAAKKALNGRNI 64
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
110-186 8.48e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 36.07  E-value: 8.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24583400  110 VFVVGLPPRLADADILKKheyFGKYGKIHKVVInpsttyagVQGPSASAYVTYVNNSDALRAIQSVNNIMIDGRLIK 186
Cdd:cd12373    2 VYVGNLGPRVTKRELEDA---FEKYGPLRNVWV--------ARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVR 67
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
123-182 8.70e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 36.44  E-value: 8.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24583400  123 DILKKHeyFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVNNSDALRAIQSVNNIMIDG 182
Cdd:cd12318   15 EALKKH--FEKCGPIRSVTIAKKKDPKGPLLSMGYGFVEFKSPEAAQKALKQLQGTVLDG 72
PLN02436 PLN02436
cellulose synthase A
13-59 9.37e-03

cellulose synthase A


Pssm-ID: 215239 [Multi-domain]  Cd Length: 1094  Bit Score: 40.24  E-value: 9.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 24583400    13 CPLCMEPLE--VDDLTFFPCT-CGYQICRFCWHRIRTDENKLCPACRKEY 59
Cdd:PLN02436   39 CQICGDEIEltVDGEPFVACNeCAFPVCRPCYEYERREGNQACPQCKTRY 88
 
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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