RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C); This subgroup corresponds to the RRM of TNRC6C, one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425 1508 TSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFAGEE 1587
Cdd:cd12713    1 SSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFASEE 80

                 ....*...
gi 33413425 1588 EVNRFLAQ 1595
Cdd:cd12713   81 EVNRFLAQ 88

UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins; TNRC6C is one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 33413425  941 SRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEK 978
Cdd:cd14283    1 SRLLKQLTDMGFKREPAEEALKSNNMNLEQAVSALLSK 38

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   250 GLSPGNPATGNSNSGFSQGNGDTVNSALSAKQNGSSSAVQKEGSG-GNAWDSGPPAGPGILA---WGRGSGN---NGVGN 322
Cdd:NF033849  294 SESTGQSSSVGTSESQSHGTTEGTSTTDSSSHSQSSSYNVSSGTGvSSSHSDGTSQSTSISHsesSSESTGTsvgHSTSS 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   323 IHSGAWGHpSRSTSNGVNGEWG---KPPNQHSNS-DINGKGSTGW---ESPSVTSQNPTVQPGGEHMNSWAKAASSGTTA 395
Cdd:NF033849  374 SVSSSESS-SRSSSSGVSGGFSggiAGGGVTSEGlGASQGGSEGWgsgDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSS 452

                         170       180
                  ....*....|....*....|....*.
gi 33413425   396 SEGSSDGSGN-HNEGSTGREGTGEGR 420
Cdd:NF033849  453 GQADSVSQGTsWSEGTGTSQGQSVGT 478

RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C); This subgroup corresponds to the RRM of TNRC6C, one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425 1508 TSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFAGEE 1587
Cdd:cd12713    1 SSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFASEE 80

                 ....*...
gi 33413425 1588 EVNRFLAQ 1595
Cdd:cd12713   81 EVNRFLAQ 88

UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins; TNRC6C is one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 33413425  941 SRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEK 978
Cdd:cd14283    1 SRLLKQLTDMGFKREPAEEALKSNNMNLEQAVSALLSK 38

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   250 GLSPGNPATGNSNSGFSQGNGDTVNSALSAKQNGSSSAVQKEGSG-GNAWDSGPPAGPGILA---WGRGSGN---NGVGN 322
Cdd:NF033849  294 SESTGQSSSVGTSESQSHGTTEGTSTTDSSSHSQSSSYNVSSGTGvSSSHSDGTSQSTSISHsesSSESTGTsvgHSTSS 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   323 IHSGAWGHpSRSTSNGVNGEWG---KPPNQHSNS-DINGKGSTGW---ESPSVTSQNPTVQPGGEHMNSWAKAASSGTTA 395
Cdd:NF033849  374 SVSSSESS-SRSSSSGVSGGFSggiAGGGVTSEGlGASQGGSEGWgsgDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSS 452

                         170       180
                  ....*....|....*....|....*.
gi 33413425   396 SEGSSDGSGN-HNEGSTGREGTGEGR 420
Cdd:NF033849  453 GQADSVSQGTsWSEGTGTSQGQSVGT 478

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                           10        20
                   ....*....|....*....|....*....
gi 33413425    944 IKQLTDMGFPREPAEEALKSNNMNLDQAM 972
Cdd:pfam00627    6 IQRLVEMGFDREQVREALRATGNNVERAA 34

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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   1516 LVLRNLTPQIDGSTLRTLCLQHGPLITFHL-----NLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTIL 1580
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C); This subgroup corresponds to the RRM of TNRC6C, one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425 1508 TSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFAGEE 1587
Cdd:cd12713    1 SSGRTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFASEE 80

                 ....*...
gi 33413425 1588 EVNRFLAQ 1595
Cdd:cd12713   81 EVNRFLAQ 88

RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B); This subgroup corresponds to the RRM of TNRC6B, one of three GW182 paralogs in mammalian genomes. It is involved in miRNA-mediated mRNA degradation. TNRC6B is composed of an N-terminal glycine/tryptophan (G/W)-rich region; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. TNRC6B directly interacts with Argonaute (Ago) proteins through its N-terminal glycine/tryptophan (G/W)-rich region that is called Ago protein-binding domain. TNRC6B is enriched in P-bodies and its Q-rich domain is responsible for P-body localization. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half of TNRC6B comprising an RRM domain exerts a strong translation inhibition potential, which does not require either association with Agos or localization to P-bodies.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425 1513 SSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFAGEEEVNRF 1592
Cdd:cd12712    1 SYWLVLHNLTPQIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATEEEVSRY 80

                 ...
gi 33413425 1593 LAQ 1595
Cdd:cd12712   81 FAQ 83

M domain of GW182;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   1020 KDGGLVEEPTPsPFLPSPSLKLPLS---HSALPSQALGGIASGLGMQNLNSSRQIPS----------GNLGMFGNSGAAQ 1086
Cdd:pfam12938    1 KSGGFAGGRYP-FLGAQPSLSFPPNnlmMGGLGGQALGGGGGNPNMAALNSQKYLSQggghgvafqgGPQGVGGSSGAAV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   1087 ARTMQQPPQPPVQPLNSSQPSLRAQVPQFLSPQVQAQLLQFAAKNIGLNPALLTSPINPQHMTMLNQLY----QLQLAyq 1162
Cdd:pfam12938   80 ARGQQQPNPPSVQPLNSSQASLRAQQPSGQQLRMLVQQIQLAVQNGFLNHQILTQPLAPQTLNLLNQLLnaikQLQAA-- 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   1163 rlqiqqQMLQAQRNVSGSMRQQEQQVArtITNLQQQIQQHQRQLA--QALLVKQPPPPPPPPHLSLHPSA-----GKSAM 1235
Cdd:pfam12938  158 ------QQSLARRGVGGNANQMQQNVA--INKYKQQIQQLQNQIAaqQAIYVKQQQQQQNSQQQQQPPPHpgghpNASGN 229

                          250
                   ....*....|....
gi 33413425   1236 DSFPSHPQTPGLPD 1249
Cdd:pfam12938  230 DYFRSHDDISGLQG 243

Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425    828 DNGTAAWGKPPSSGSGWGDHPAEPPVAFGRAGAPVAASALCKPASKSMQEGWGSGGDEMNLSTSQWEDEE--GDVWNNAA 905
Cdd:pfam10427   28 DNGTAAWGHPNNSGPGWGGGRNEPSVVTGWGDDSHGAPNLSKPGSKSSQSNWGDDKDEGSLGQNSWSDEDsyGGGWGNKQ 107

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 33413425    906 --SQESTSSCSSWGNAPKKGLQkgMKTSGKQDEAW 938
Cdd:pfam10427  108 sqLSTSSGNSSGWGNASKKGMQ--MVDGGDLGSEW 140

UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains.

                         10        20        30
                 ....*....|....*....|....*....|
gi 33413425  944 IKQLTDMGFPREPAEEALKSNNMNLDQAMS 973
Cdd:cd14270    1 LAQLVEMGFSREQARRALRATNGDVEAAVE 30

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   250 GLSPGNPATGNSNSGFSQGNGDTVNSALSAKQNGSSSAVQKEGSG-GNAWDSGPPAGPGILA---WGRGSGN---NGVGN 322
Cdd:NF033849  294 SESTGQSSSVGTSESQSHGTTEGTSTTDSSSHSQSSSYNVSSGTGvSSSHSDGTSQSTSISHsesSSESTGTsvgHSTSS 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33413425   323 IHSGAWGHpSRSTSNGVNGEWG---KPPNQHSNS-DINGKGSTGW---ESPSVTSQNPTVQPGGEHMNSWAKAASSGTTA 395
Cdd:NF033849  374 SVSSSESS-SRSSSSGVSGGFSggiAGGGVTSEGlGASQGGSEGWgsgDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSS 452

                         170       180
                  ....*....|....*....|....*.
gi 33413425   396 SEGSSDGSGN-HNEGSTGREGTGEGR 420
Cdd:NF033849  453 GQADSVSQGTsWSEGTGTSQGQSVGT 478

UBA domain found in a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE) and similar proteins; P. Yoelii ubiquitin-conjugating enzyme and other uncharacterized family members show high sequence similarity to the human Huntingtin interacting protein-2 (HIP2) which belongs to a class II E2 ubiquitin-conjugating enzyme family. These proteins may play roles in the ubiquitin-mediated protein degradation pathway. They all contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 33413425  944 IKQLTDMGFPREPAEEALKSNNMNLDQAMSALL 976
Cdd:cd14314    5 IKKLLEMGFPRDQARKALEKNGWDETLALNTLL 37

UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.

                         10        20        30
                 ....*....|....*....|....*....|....
gi 33413425  944 IKQLTDMGFPREPAEEALKSNNMNLDQAMSALLE 977
Cdd:cd14306    1 VAKLMELGFPEEDCIRALRACGGNVEEAANWLLE 34

UBA domain found in Drosophila melanogaster protein Gawky (GW) and similar proteins; GW is the D. melanogaster GW182 homolog (dGW182) which belongs to the GW182 protein family. The GW182 proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. They are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The GW182 proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. In addition to a G/W repeats region, a Q-rich region, and a RRM domain, GW also contains a ubiquitin-associated domain (UBA).

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 33413425  941 SRLIKQLTDMGFPREPAEEALKSNNMNLDQAMSAL 975
Cdd:cd14284    1 SKQFRILSEMGFKKEDVENALRSANMNMEEALEIL 35

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 33413425  942 RLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALL 976
Cdd:cd14282    4 KALRHITEMGFSKEAARQALMDNNNNLEAALNFLL 38

UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 33413425  940 MSRLIKQLTDMGFPREPAEEALK-SNNMNLDQAMSALLEKKVDVD 983
Cdd:cd14295    1 DQELVAQLMEMGFPKVRAEKALFfTQNKGLEEAMEWLEEHSEDAD 45

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                           10        20
                   ....*....|....*....|....*....
gi 33413425    944 IKQLTDMGFPREPAEEALKSNNMNLDQAM 972
Cdd:pfam00627    6 IQRLVEMGFDREQVREALRATGNNVERAA 34

UBA domain found in Schizosaccharomyces pombe UBA domain-containing protein mud1 and similar proteins; Schizosaccharomyces pombe mud1 is an ortholog of the Saccharomyces cerevisiae DNA-damage response protein Ddi1. S. cerevisiae Ddi1, also called v-SNARE-master 1 (Vsm1), belongs to a family of proteins known as the ubiquitin receptors which can bind ubiquitinated substrates and the proteasome. It is involved in the degradation of the F-box protein Ufo1, involved in the G1/S transition. It also participates in Mec1-mediated degradation of Ho endonuclease. Both S. pombe mud1 and S. cerevisiae Ddi1 contain an N-terminal ubiquitin-like (UBL) domain, an aspartyl protease-like domain, and a C-terminal ubiquitin-associated (UBA) domain. S. pombe mud1 binds to K48-linked polyubiquitin (polyUb) through UBA domain.

                         10        20        30
                 ....*....|....*....|....*....|....
gi 33413425  943 LIKQLTDMGFPREPAEEALKSNNMNLDQAMSALL 976
Cdd:cd14308    3 KVRQLVDMGFTPTDAGRALKAANGDVTVAAEWLL 36

UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins; UBXN1, also called SAPK substrate protein 1 (SAKS1) or UBA/UBX 33.3 kDa protein, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (UBX) domain. It binds polyubiquitin and valosin-containing protein (VCP), and has been identified as a substrate for stress-activated protein kinases (SAPKs). Moreover, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and may be involved in the Ub-proteasome proteolytic pathways. In addition, UBXN1 can associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domain.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 33413425  944 IKQLTDMGFPREPAEEAL-KSNNMNLDQAMSALLE 977
Cdd:cd14302    3 LQTLIEMGFSRNRAEKALaKTGNQGVEAAMEWLLA 37

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 33413425  944 IKQLTDMGFPREPAEEALKSNNMNLDQAMSALLEK 978
Cdd:cd14307    4 VASLLEMGIPREVAIEALRETNGDVEAAANYIFSN 38

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins; UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5. It has similar domain architecture, but functions differently from USP5 in cellular deubiquitination processes. It exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin in a non-activation manner. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.

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gi 33413425  943 LIKQLTDMGFPREPAEEAL-KSNNMNLDQAMSALLEKKVDVD 983
Cdd:cd14294    3 VVSQLAEMGFPLEACRKAVyHTNNSGLEAAMNWIMEHMDDPD 44

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.

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gi 33413425 1516 LVLRNLTPQIDGSTLRTLCLQHGPLITFHL-----NLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFA 1584
Cdd:cd12414    2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIpkkpdGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75

UBA domain found in Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins; UbcD4, also called ubiquitin carrier protein or ubiquitin-protein ligase, is a class II E2 ubiquitin-conjugating enzyme encoded by Drosophila E2 gene which is only expressed in pole cells in embryos. It is a putative E2 enzyme homologous to the Huntingtin interacting protein-2 (HIP2) of human. UbcD4 specifically interacts with the polyubiquitin-binding subunit of the proteasome. It contains a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain.

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gi 33413425  944 IKQLTDMGFPREPAEEALKSNNMNLDQAMSALL 976
Cdd:cd14391    4 IRQLMDMGFDEHKARVALSSHNWDLEKATESLF 36

UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.

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gi 33413425  943 LIKQLTDMGFPREPAEEAL-KSNNMNLDQAMSALLEKKVDVD 983
Cdd:cd14290    6 LLKELEAMGFPRARAVRALhHTGNTSVEAAVNWIVEHENDPD 47