RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699 1075 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1146
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  909 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 979
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105699  980 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1030
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498

N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1-4.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  821 TTQQLQTTSPKVIQPLVQQPILPV-VKQSVKERLGPVPSATTEPAEAQSATSELPQVLS-TSTGLTKTVY---NPAALKA 895
Cdd:cd22540    285 VLQQVQVLQPKQEQQVVQIPQQALrVVQAASATLPTVPQKPLQNIQIQNSEPTPTQVYIkTPSGEVQTVLlqeAPAATAT 364

                           90       100
                   ....*....|....*....|.
gi 1907105699  896 AQKTLSVSTPAVDNNEAQKKK 916
Cdd:cd22540    365 PSSSTSTVQQQVTANNGTGTS 385

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699 1075 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1146
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  909 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 979
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105699  980 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1030
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498

RNA recognition motif;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699  1091 DREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA--AIHGARFKGQDLKL 1144
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrDKETGKskgfAFVEFESEEDAEKAleALNGKELDGRPLKV 73

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105699  752 VPPELNNiSKLNEHFSRFGTLVNLQVAY--NGDPEG-ALIQFATYEEAKKAISST-EAVLNNRFIK 813
Cdd:pfam00076    6 LPPDTTE-EDLKDLFSKFGPIKSIRLVRdeTGRSKGfAFVEFEDEEDAEKAIEALnGKELGGRELK 70

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  910 NEAQKKKQEALKLQQDVRKRKQEILEKHIETQKMLISKLEKNKTMKSEDKAEI-------MKTLEILTKNITKLKDEVKS 982
Cdd:pfam02463  166 RLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKleleeeyLLYLDYLKLNEERIDLLQEL 245

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699  983 TSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVTELRRKYTELQLEAAKRGILSSGR 1044
Cdd:pfam02463  246 LRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 307

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  891 AALKAAQKTLSVSTPAVDNNEAQKKKQEA-LKLQQDVRKRKQE------------ILEKHIETQKMLISKLEknktmksE 957
Cdd:COG1579     38 DELAALEARLEAAKTELEDLEKEIKRLELeIEEVEARIKKYEEqlgnvrnnkeyeALQKEIESLKRRISDLE-------D 110

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  958 DKAEIMKTLEILTKNITKLKDEVKstspgrclpksiktktQMQKEL--LDTELDlykkmqagEEVTELRRKYTELQLEAA 1035
Cdd:COG1579    111 EILELMERIEELEEELAELEAELA----------------ELEAELeeKKAELD--------EELAELEAELEELEAERE 166

                   .
gi 1907105699 1036 K 1036
Cdd:COG1579    167 E 167

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  821 TTQQLQTTSPKVIQPLVQQPILPV-VKQSVKERLGPVPSATTEPAEAQSATSELPQVLS-TSTGLTKTVY---NPAALKA 895
Cdd:cd22540    285 VLQQVQVLQPKQEQQVVQIPQQALrVVQAASATLPTVPQKPLQNIQIQNSEPTPTQVYIkTPSGEVQTVLlqeAPAATAT 364

                           90       100
                   ....*....|....*....|.
gi 1907105699  896 AQKTLSVSTPAVDNNEAQKKK 916
Cdd:cd22540    365 PSSSTSTVQQQVTANNGTGTS 385

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105699  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 819
Cdd:cd12517      1 NTKLEVRKIPQELNNITQLNEHFSKFGTIVNIQVAFGGDPEAALIQYTTNEEARRAISSTEAVLNNRFIRVLWHRE 76

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907105699  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNgdPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWH 817
Cdd:cd12257      1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYN--PESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72

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).

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105699 1091 DREDLLPHFAQYGEIEDCQIDDASL-----HAIITFKTRAEAEAA--AIHGARFKGQDLKL 1144
Cdd:cd00590     11 TEEDLRELFSKFGEVVSVRIVRDRDgkskgFAFVEFESPEDAEKAleALNGTELGGRPLKV 71

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  909 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 979
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105699  980 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1030
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907105699 1093 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGAR---FKGQDLKLAWNK 1148
Cdd:cd12224     16 KDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAAERTFNkliIKGRRLKVKWGR 74

RNA recognition motif;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699  1091 DREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA--AIHGARFKGQDLKL 1144
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrDKETGKskgfAFVEFESEEDAEKAleALNGKELDGRPLKV 73

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105699 1091 DREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA-----AIHGARFkgqdLKLAW 1146
Cdd:cd12257     15 NITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAyrspeAVFNNRF----IKVFW 71

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (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. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105699 1087 FTEsdrEDLLPHFAQYGEIEDCQI-DDASLH-----AIITFKTRAEAEAA--AIHG 1134
Cdd:cd12361     11 ASE---EDVRPLFEQFGNIEEVQIlRDKQTGqskgcAFVTFSTREEALRAieALHN 63

Nup53/35/40-type RNA recognition motif;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1907105699 1079 PRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA 1130
Cdd:pfam14605    1 STWIVVSGYPAELAYLVRRHFADFGEIVKHYFPPETNSMYLKYASRKDAEQA 52

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  910 NEAQKKKQEALKLQQDVRKRKQEILEKHIETQKMLISKLEKNKTMKSEDKAEI-------MKTLEILTKNITKLKDEVKS 982
Cdd:pfam02463  166 RLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKleleeeyLLYLDYLKLNEERIDLLQEL 245

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105699  983 TSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVTELRRKYTELQLEAAKRGILSSGR 1044
Cdd:pfam02463  246 LRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 307

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  891 AALKAAQKTLSVSTPAVDNNEAQKKKQEA-LKLQQDVRKRKQE------------ILEKHIETQKMLISKLEknktmksE 957
Cdd:COG1579     38 DELAALEARLEAAKTELEDLEKEIKRLELeIEEVEARIKKYEEqlgnvrnnkeyeALQKEIESLKRRISDLE-------D 110

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105699  958 DKAEIMKTLEILTKNITKLKDEVKstspgrclpksiktktQMQKEL--LDTELDlykkmqagEEVTELRRKYTELQLEAA 1035
Cdd:COG1579    111 EILELMERIEELEEELAELEAELA----------------ELEAELeeKKAELD--------EELAELEAELEELEAERE 166

                   .
gi 1907105699 1036 K 1036
Cdd:COG1579    167 E 167

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105699 1091 DREDLLPHFAQYGEIEDCQI--DDASL----HAIITFKTRAEAEAA--AIHGARFKGQDLK 1143
Cdd:COG0724     14 TEEDLRELFSEYGEVTSVKLitDRETGrsrgFGFVEMPDDEEAQAAieALNGAELMGRTLK 74

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105699 1091 DREDLLPHFAQYGEIEDCQI---DDASLH--AIITFKTRAEAEA---AAIHGARFKGQDLKLAWNK 1148
Cdd:cd12226     12 TEDDLERRFSRFGTVSDVEIirkKDAPDRgfAYIDLRTSEAALQkclSTLNGVKWKGSRLKIQLAK 77

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105699  760 SKLNEHFSRFGTLVNLQVAYNGDPEG---ALIQFATYEEAKKAISSTEAV-LNNRFIKVYW 816
Cdd:cd12414     14 DDLKKLFSKFGKVLEVTIPKKPDGKLrgfAFVQFTNVADAAKAIKGMNGKkIKGRPVAVDW 74

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).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907105699 1088 TESDREDLLPHFAQYGEIEDCQI-----DD----ASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAWNKPI 1150
Cdd:cd12223     11 PSVTEEVLLREFGRFGPLASVKImwprtEEerrrNRNCGFVAFMSRADAERAmrELNGKDVMGYELKLGWGKAV 84

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105699 1093 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAW 1146
Cdd:cd12354     15 ALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAivSVNGTIINGQAVKCSW 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                           10        20
                   ....*....|....*....|..
gi 1907105699  496 RCRDYDEKGFCMRGDMCPFDHG 517
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26