Tetratricopeptide (TPR) repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 203 EAKTKRSASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYR 282
Cdd:COG0457    2 ELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNN 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 688583691 283 RGSALMGLKRYSEAEKAMEQVLKLDGDCEEAVNDLLYCkvqqLTELGyDEEQSIQLLEK 341
Cdd:COG0457   82 LGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLA----LLELG-RYDEAIEAYER 135

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

                          10        20
                  ....*....|....*....|...
gi 688583691  469 ECYFWRTTG-CHFGDRCRYKHIP 490
Cdd:pfam00642   5 LCRFFLRTGyCKYGDRCKFAHGQ 27

Tetratricopeptide (TPR) repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 203 EAKTKRSASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYR 282
Cdd:COG0457    2 ELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNN 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 688583691 283 RGSALMGLKRYSEAEKAMEQVLKLDGDCEEAVNDLLYCkvqqLTELGyDEEQSIQLLEK 341
Cdd:COG0457   82 LGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLA----LLELG-RYDEAIEAYER 135

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHE-----RFCAFVNFKNANMASRAMEKLNGHFIENTRLVVR 435
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70); [Transport and binding proteins, Amino acids, peptides and amines]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691  136 SGPPLASGNKSNRQQGARSGEEDpgwdvnsafvANAVSHIRPKAKSKGKSKENKENESrpAEVIGFSEA-KTKRSASLVE 214
Cdd:TIGR00990  65 SKPKISKKERRKRKQAEKETEGK----------TEEKKSTAPKNAPVEPADELPEIDE--SSVANLSEEeRKKYAAKLKE 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691  215 KGIRFVQEGQYTQAVSLFTEAIKCDPkDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLKRYS 294
Cdd:TIGR00990 133 KGNKAYRNKDFNKAIKLYSKAIECKP-DPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGLGKYA 211

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 688583691  295 EAekameqVLKLDGDCeeaVNDllyckvqqltelGYDEEQSIQLLEKYNTVQAVVAAK 352
Cdd:TIGR00990 212 DA------LLDLTASC---IID------------GFRNEQSAQAVERLLKKFAESKAK 248

SGT1, suppressor of G2 allele of SKP1; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 219 FVQEgQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLKRYSEAEK 298
Cdd:PLN03088  13 FVDD-DFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKA 91

                 ...
gi 688583691 299 AME 301
Cdd:PLN03088  92 ALE 94

Tetratricopeptide repeat; This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 688583691  277 PKGYYRRGSALMGLKRYSEAEKAMEQVLKLD 307
Cdd:pfam07719   1 AEALYNLGLAYYKLGDYEEALEAYEKALELD 31

Tetratricopeptide (TPR) repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 203 EAKTKRSASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYR 282
Cdd:COG0457    2 ELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNN 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 688583691 283 RGSALMGLKRYSEAEKAMEQVLKLDGDCEEAVNDLLYCkvqqLTELGyDEEQSIQLLEK 341
Cdd:COG0457   82 LGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLA----LLELG-RYDEAIEAYER 135

Tetratricopeptide (TPR) repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 211 SLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGL 290
Cdd:COG0457   44 ALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLALLEL 123

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 688583691 291 KRYSEAEKAMEQVLKLDGDCEEAVNDLLYCkvqqLTELGyDEEQSIQLLEKY 342
Cdd:COG0457  124 GRYDEAIEAYERALELDPDDADALYNLGIA----LEKLG-RYEEALELLEKL 170

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHE-----RFCAFVNFKNANMASRAMEKLNGHFIENTRLVVR 435
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 688583691 367 NSLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERF------CAFVNFKNANMASRAMEKLNGHFIENTRLVVR 435
Cdd:COG0724    2 MKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDREtgrsrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVN 76

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 688583691 364 GPCNSLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKLNGHFIENTRLVVRY-PDR 439
Cdd:cd12262    1 GASRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYgKDR 77

Tetratricopeptide (TPR) repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 210 ASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMG 289
Cdd:COG0457   77 EALNNLGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEK 156

                         90       100
                 ....*....|....*....|
gi 688583691 290 LKRYSEAEKAMEQVLKLDGD 309
Cdd:COG0457  157 LGRYEEALELLEKLEAAALA 176

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 688583691  369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHE-----RFCAFVNFKNANMASRAMEKLNGHFIENTRL 432
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetgrsKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 206 TKRSASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGS 285
Cdd:COG4783    1 AACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGL 80

                         90       100
                 ....*....|....*....|....*...
gi 688583691 286 ALMGLKRYSEAEKAMEQVLKLDGDCEEA 313
Cdd:COG4783   81 ALLKAGDYDEALALLEKALKLDPEHPEA 108

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 221 QEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALAdAEKSIQMAPDWPKGYYRRGSALMGLKRYSEAEKAM 300
Cdd:COG3063    4 KLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDPNNAEALLNLAELLLELGDYDEALAYL 82

                 ....*....
gi 688583691 301 EQVLKLDGD 309
Cdd:COG3063   83 ERALELDPS 91

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 688583691 368 SLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKLNGH 425
Cdd:cd12227    4 TLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNH 61

SGT1, suppressor of G2 allele of SKP1; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 219 FVQEgQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLKRYSEAEK 298
Cdd:PLN03088  13 FVDD-DFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKA 91

                 ...
gi 688583691 299 AME 301
Cdd:PLN03088  92 ALE 94

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 203 EAKTKRSASLVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYR 282
Cdd:COG2956  104 ELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLL 183

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 283 RGSALMGLKRYSEAEKAMEQVLKLDGDCEEAVNDLLYCkvqqLTELGyDEEQSIQLLEKY 342
Cdd:COG2956  184 LAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAEL----YEKLG-DPEEALELLRKA 238

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 227 QAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLKRYSEAEKAMEQVLKL 306
Cdd:COG4235    1 EAIARLRQALAANPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALAL 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 688583691 307 DGDCEEAvndlLYCKVQQLTELGyDEEQSIQLLEK 341
Cdd:COG4235   81 DPDNPEA----LYLLGLAAFQQG-DYAEAIAAWQK 110

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691  283 RGSALMGLKRYSEAEKAMEQV--LKLDGDCEeavNDLLY-CKVQQLTElgyDEEQSIQLLEKYNtVQAVVAAKASNqdca 359
Cdd:TIGR01628 219 RGFAFVNFEKHEDAAKAVEEMngKKIGLAKE---GKKLYvGRAQKRAE---REAELRRKFEELQ-QERKMKAQGVN---- 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691  360 llqpgpcnsLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHE-----RFCAFVNFKNANMASRAMEKLNGHFIENTRLVV 434
Cdd:TIGR01628 288 ---------LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDekgvsRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

                  ....*....
gi 688583691  435 RYPDRRIQR 443
Cdd:TIGR01628 359 ALAQRKEQR 367

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRV------LHERFCaFVNFKNANMASRAMEKLNGHFIENTRLVVRYPD 438
Cdd:cd12297    3 LWVTNFPPSYDERSIRDLFGDYGVILSVRLpslrynTSRRFC-YIDFTSPESARAAVELLNGLLEEGYTLVVKISD 77

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 688583691 368 SLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKLNGHFIE 428
Cdd:cd12354    2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAIVSVNGTIIN 62

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 688583691 251 YCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLKRYSEAEKAMEQVLKLDGDCEEAVNDL--LYCKVQQLTE 327
Cdd:COG5010   62 NLYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLaaLLLSLGQDDE 140

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 688583691 212 LVEKGIRFVQEGQYTQAVSLFTEAIKCDPKDYRFFGNRSYCYCCLEQYALALADAEKSIQMAPDWPKGYYRRGSALMGLK 291
Cdd:COG2956  147 YCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLG 226

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 688583691 292 RYSEAEKAMEQVLKLDGDceeavNDLLYCKVQQLTELGyDEEQSIQLLEKY 342
Cdd:COG2956  227 DPEEALELLRKALELDPS-----DDLLLALADLLERKE-GLEAALALLERQ 271

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 688583691 364 GPCNSLWVGNV--TTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKLNGH 425
Cdd:cd12522    1 GASRNVYIGNIddVRVLTEERLRHDFSQYGEIEQVNFLREKNCAFVNFTNIANAIKAIDKIKSK 64

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which 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). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

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gi 688583691 371 VGNVTTELTEKHLRDLFKIYGEIDSIRVL------HERFcAFVNFKNANMASRAMEKLNGHFIENTRLVV 434
Cdd:cd12565    5 VKNLPKYVTEKRLKEHFSKKGEITDVKVMrtkdgkSRRF-GFIGFKSEEEAQKAVKYFNKTFIDTSKISV 73

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

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gi 688583691 364 GPCNSLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKL 422
Cdd:cd12523    1 GASRNVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

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gi 688583691  368 SLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFC------AFVNFKNANMASRAMEKLN 423
Cdd:TIGR01628   2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTrrslgyGYVNFQNPADAERALETMN 63

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.

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gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVL-----HERFCAFVNFKNANMASRAMEKLNGHFIENTRLVV 434
Cdd:cd12380    4 VYVKNFGEDVDDDELKELFEKYGKITSAKVMkddsgKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents 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 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. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

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gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFC------AFVNFKNANMASRAMEKLNGHFIENTRLVVRY 436
Cdd:cd12375    2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKITgqslgyGFVNYRDPNDARKAINTLNGLDLENKRLKVSY 75

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.

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gi 688583691 369 LWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHE------RFCAFVNFKNANMASRAMEKLNGHFI 427
Cdd:cd12361    2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQILRDkqtgqsKGCAFVTFSTREEALRAIEALHNKKT 66

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.

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gi 688583691 368 SLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERFCAFVNFKNANMASRAMEKLN 423
Cdd:cd12462    4 TLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLS 59

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.

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gi 688583691 365 PCNSLWVGNVTTELTEKHLRDLFKIYGEIDSIRVLHERF--CAFVNFKNANMASRAMEKLNG 424
Cdd:cd12245    1 PCNTLFVANLGPNVSEQELRQLFSRQPGFRRLRMHNKGGgpVCFVEFEDVPFATQALNHLQG 62