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Conserved domains on  [gi|564378538|ref|XP_006249060|]
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A-kinase anchor protein 17A isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 147-278 2.03e-43

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).


The actual alignment was detected with superfamily member cd12264:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 122  Bit Score: 152.43  E-value: 2.03e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 147 DTIHLQGLPCRWFAPRGgsggdeaggisspggiaSAERPSEALLRQAFGAFGEIRHVDIPMLDPY---LGEDGSHGGGGG 223
Cdd:cd12264    5 DTIHLEGLPCKWFAVPR-----------------SSDKPSENVLRKVFEKFGKIRNVDIPMLDPYrkeMDGNGFDTFSFG 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564378538 224 GRLRFEAYVQYRERDAYARAMAALRGAKLMFRGTDGKAVACGIKVTSDATQHLSE 278
Cdd:cd12264   68 GHLHFEAYVQYEEYDGFVKAMDALRGMKLMYKGEDGKALAANIKVDFDKTKHLSE 122
CCDC47 super family cl46382
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 251-326 1.30e-04

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


The actual alignment was detected with superfamily member pfam07946:

Pssm-ID: 480722  Cd Length: 323  Bit Score: 44.48  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  251 KLMFRGTDgkAVACGIKVTSDATQHL-----SEASIRRRQLERQKLQELEQRREEQKRKEREDEARR--RAGQRK--QRE 321
Cdd:pfam07946 239 QLVLYLID--KLAKRAKLRPEALKKAkktreEEIEKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKlsPEEQRKyeEKE 316


                  ....*
gi 564378538  322 AEQQQ 326
Cdd:pfam07946 317 RKKEQ 321
Smc super family cl34174
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 233-453 1.71e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


The actual alignment was detected with superfamily member COG1196:

Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.93  E-value: 1.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 233 QYRERDAYARAmAALRGAKLMFRGTDGKAVACGIKVTS-DATQHLSEASIRRRQLERQKLQE-----LEQRREEQKRKER 306
Cdd:COG1196  221 ELKELEAELLL-LKLRELEAELEELEAELEELEAELEElEAELAELEAELEELRLELEELELeleeaQAEEYELLAELAR 299

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 307 EDEARRRAGQRKQREAEQQQRARRREEKLRRREARQRARKRRGrrreeeeeeeeaepqpvlgREEEEGAEPRRLLLAQRN 386
Cdd:COG1196  300 LEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEEL-------------------EEELEEAEEELEEAEAEL 360

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564378538 387 LQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELRRQQEAELRRQREAELRRVEEEKRRALGLQ 453
Cdd:COG1196  361 AEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELE 427
 
Name Accession Description Interval E-value
RRM_AKAP17A cd12264
RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar ...
 147-278 2.03e-43

RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar proteins; This subfamily corresponds to the RRM domain of AKAP-17A, also termed 721P, or splicing factor, arginine/serine-rich 17A (SFRS17A). It was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor. It has been suggested that AKAP-17A is an alternative splicing factor and an SR-related splicing protein that interacts with the classical SR protein ASF/SF2 and the SR-related factor ZNF265. Additional studies have indicated that AKAP-17A is a dual-specific protein kinase A anchoring protein (AKAP) that can bind both type I and type II protein kinase A (PKA) with high affinity and co-localizes with the catalytic subunit of PKA in nuclear speckles as well as the splicing factor SC35 in splicing factor compartments. It is involved in regulation of pre-mRNA splicing possibly by docking a pool of PKA in splicing factor compartments. AKAP-17A contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409708 [Multi-domain]  Cd Length: 122  Bit Score: 152.43  E-value: 2.03e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 147 DTIHLQGLPCRWFAPRGgsggdeaggisspggiaSAERPSEALLRQAFGAFGEIRHVDIPMLDPY---LGEDGSHGGGGG 223
Cdd:cd12264    5 DTIHLEGLPCKWFAVPR-----------------SSDKPSENVLRKVFEKFGKIRNVDIPMLDPYrkeMDGNGFDTFSFG 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564378538 224 GRLRFEAYVQYRERDAYARAMAALRGAKLMFRGTDGKAVACGIKVTSDATQHLSE 278
Cdd:cd12264   68 GHLHFEAYVQYEEYDGFVKAMDALRGMKLMYKGEDGKALAANIKVDFDKTKHLSE 122
RRM smart00360
RNA recognition motif;
186-255 3.82e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.20  E-value: 3.82e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538   186 SEALLRQAFGAFGEIRHVDIPMldpylgedgshgGGGGGRLRFEAYVQYRERDAYARAMAALRGAKLMFR 255
Cdd:smart00360  12 TEEELRELFSKFGKVESVRLVR------------DKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR 69
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 251-326 1.30e-04

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 44.48  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  251 KLMFRGTDgkAVACGIKVTSDATQHL-----SEASIRRRQLERQKLQELEQRREEQKRKEREDEARR--RAGQRK--QRE 321
Cdd:pfam07946 239 QLVLYLID--KLAKRAKLRPEALKKAkktreEEIEKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKlsPEEQRKyeEKE 316


                  ....*
gi 564378538  322 AEQQQ 326
Cdd:pfam07946 317 RKKEQ 321
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 233-453 1.71e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.93  E-value: 1.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 233 QYRERDAYARAmAALRGAKLMFRGTDGKAVACGIKVTS-DATQHLSEASIRRRQLERQKLQE-----LEQRREEQKRKER 306
Cdd:COG1196  221 ELKELEAELLL-LKLRELEAELEELEAELEELEAELEElEAELAELEAELEELRLELEELELeleeaQAEEYELLAELAR 299

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 307 EDEARRRAGQRKQREAEQQQRARRREEKLRRREARQRARKRRGrrreeeeeeeeaepqpvlgREEEEGAEPRRLLLAQRN 386
Cdd:COG1196  300 LEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEEL-------------------EEELEEAEEELEEAEAEL 360

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564378538 387 LQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELRRQQEAELRRQREAELRRVEEEKRRALGLQ 453
Cdd:COG1196  361 AEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELE 427
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 282-445 1.76e-04

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 44.56  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  282 RRRQLERQKLQELEQRREEQKRKEREDEARRRAGQ---RKQR--EAEQQQRARRREEKLRRREARQRARKRRGRRREEEE 356
Cdd:pfam15709 354 RREQEEQRRLQQEQLERAEKMREELELEQQRRFEEirlRKQRleEERQRQEEEERKQRLQLQAAQERARQQQEEFRRKLQ 433

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  357 EEEEAEPQPVLGREEEEgaEPRRLLLAQRNLQSVRLIaallaraeaarrrqREQSEERR----RHAKEAELRRQQEAELR 432
Cdd:pfam15709 434 ELQRKKQQEEAERAEAE--KQRQKELEMQLAEEQKRL--------------MEMAEEERleyqRQKQEAEEKARLEAEER 497

                         170
                  ....*....|...
gi 564378538  433 RQREAELRRVEEE 445
Cdd:pfam15709 498 RQKEEEAARLALE 510
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 186-253 2.08e-04

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.91  E-value: 2.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564378538  186 SEALLRQAFGAFGEIRHVDIPmldpylgedgshgGGGGGRLRFEAYVQYRERDAYARAMAALRGAKLM 253
Cdd:pfam00076  11 TEEDLKDLFSKFGPIKSIRLV-------------RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
PTZ00121 PTZ00121
MAEBL; Provisional
 274-449 6.61e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 6.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  274 QHLSEASIRRRQLERQKLQEL----EQRREEQKRKEREDE--ARRRAGQRKQRE---AEQQQRARRREEKLRRREARQRA 344
Cdd:PTZ00121 1537 DEAKKAEEKKKADELKKAEELkkaeEKKKAEEAKKAEEDKnmALRKAEEAKKAEearIEEVMKLYEEEKKMKAEEAKKAE 1616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  345 RKRRGRRREEEEEEEEAEPQPVLGREEEEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELR 424
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

                         170       180
                  ....*....|....*....|....*
gi 564378538  425 RQQEAelrRQREAELRRVEEEKRRA 449
Cdd:PTZ00121 1697 EAEEA---KKAEELKKKEAEEKKKA 1718
 
Name Accession Description Interval E-value
RRM_AKAP17A cd12264
RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar ...
 147-278 2.03e-43

RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar proteins; This subfamily corresponds to the RRM domain of AKAP-17A, also termed 721P, or splicing factor, arginine/serine-rich 17A (SFRS17A). It was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor. It has been suggested that AKAP-17A is an alternative splicing factor and an SR-related splicing protein that interacts with the classical SR protein ASF/SF2 and the SR-related factor ZNF265. Additional studies have indicated that AKAP-17A is a dual-specific protein kinase A anchoring protein (AKAP) that can bind both type I and type II protein kinase A (PKA) with high affinity and co-localizes with the catalytic subunit of PKA in nuclear speckles as well as the splicing factor SC35 in splicing factor compartments. It is involved in regulation of pre-mRNA splicing possibly by docking a pool of PKA in splicing factor compartments. AKAP-17A contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409708 [Multi-domain]  Cd Length: 122  Bit Score: 152.43  E-value: 2.03e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 147 DTIHLQGLPCRWFAPRGgsggdeaggisspggiaSAERPSEALLRQAFGAFGEIRHVDIPMLDPY---LGEDGSHGGGGG 223
Cdd:cd12264    5 DTIHLEGLPCKWFAVPR-----------------SSDKPSENVLRKVFEKFGKIRNVDIPMLDPYrkeMDGNGFDTFSFG 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564378538 224 GRLRFEAYVQYRERDAYARAMAALRGAKLMFRGTDGKAVACGIKVTSDATQHLSE 278
Cdd:cd12264   68 GHLHFEAYVQYEEYDGFVKAMDALRGMKLMYKGEDGKALAANIKVDFDKTKHLSE 122
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 186-255 2.90e-05

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 42.66  E-value: 2.90e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 186 SEALLRQAFGAFGEIRHVDIPMldpylgedgshggGGGGRLRFEAYVQYRERDAYARAMAALRGAKLMFR 255
Cdd:cd00590   11 TEEDLRELFSKFGEVVSVRIVR-------------DRDGKSKGFAFVEFESPEDAEKALEALNGTELGGR 67
RRM smart00360
RNA recognition motif;
186-255 3.82e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.20  E-value: 3.82e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538   186 SEALLRQAFGAFGEIRHVDIPMldpylgedgshgGGGGGRLRFEAYVQYRERDAYARAMAALRGAKLMFR 255
Cdd:smart00360  12 TEEELRELFSKFGKVESVRLVR------------DKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR 69
CCDC47 pfam07946
PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of ...
 251-326 1.30e-04

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.


Pssm-ID: 462322  Cd Length: 323  Bit Score: 44.48  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  251 KLMFRGTDgkAVACGIKVTSDATQHL-----SEASIRRRQLERQKLQELEQRREEQKRKEREDEARR--RAGQRK--QRE 321
Cdd:pfam07946 239 QLVLYLID--KLAKRAKLRPEALKKAkktreEEIEKIKKAAEEERAEEAQEKKEEAKKKEREEKLAKlsPEEQRKyeEKE 316


                  ....*
gi 564378538  322 AEQQQ 326
Cdd:pfam07946 317 RKKEQ 321
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 233-453 1.71e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 44.93  E-value: 1.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 233 QYRERDAYARAmAALRGAKLMFRGTDGKAVACGIKVTS-DATQHLSEASIRRRQLERQKLQE-----LEQRREEQKRKER 306
Cdd:COG1196  221 ELKELEAELLL-LKLRELEAELEELEAELEELEAELEElEAELAELEAELEELRLELEELELeleeaQAEEYELLAELAR 299

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 307 EDEARRRAGQRKQREAEQQQRARRREEKLRRREARQRARKRRGrrreeeeeeeeaepqpvlgREEEEGAEPRRLLLAQRN 386
Cdd:COG1196  300 LEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEEL-------------------EEELEEAEEELEEAEAEL 360

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564378538 387 LQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELRRQQEAELRRQREAELRRVEEEKRRALGLQ 453
Cdd:COG1196  361 AEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELE 427
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 282-445 1.76e-04

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 44.56  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  282 RRRQLERQKLQELEQRREEQKRKEREDEARRRAGQ---RKQR--EAEQQQRARRREEKLRRREARQRARKRRGRRREEEE 356
Cdd:pfam15709 354 RREQEEQRRLQQEQLERAEKMREELELEQQRRFEEirlRKQRleEERQRQEEEERKQRLQLQAAQERARQQQEEFRRKLQ 433

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  357 EEEEAEPQPVLGREEEEgaEPRRLLLAQRNLQSVRLIaallaraeaarrrqREQSEERR----RHAKEAELRRQQEAELR 432
Cdd:pfam15709 434 ELQRKKQQEEAERAEAE--KQRQKELEMQLAEEQKRL--------------MEMAEEERleyqRQKQEAEEKARLEAEER 497

                         170
                  ....*....|...
gi 564378538  433 RQREAELRRVEEE 445
Cdd:pfam15709 498 RQKEEEAARLALE 510
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 186-253 2.08e-04

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.91  E-value: 2.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564378538  186 SEALLRQAFGAFGEIRHVDIPmldpylgedgshgGGGGGRLRFEAYVQYRERDAYARAMAALRGAKLM 253
Cdd:pfam00076  11 TEEDLKDLFSKFGPIKSIRLV-------------RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 282-448 3.56e-04

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 43.96  E-value: 3.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  282 RRRQLERQKLQELEqrREEQKRKEREDEARRRagqRKQREAEQQQrarrreeklrrrearqrarkrrgrrreeeeeeeea 361
Cdd:pfam17380 444 RAREMERVRLEEQE--RQQQVERLRQQEEERK---RKKLELEKEK----------------------------------- 483

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  362 epqpvlgREEEEGAEPRRLLLAQRNLQSVRLIAALLAR----AEAARRRQREQSEERRRHAKEAELRRQQEAELRRQREA 437
Cdd:pfam17380 484 -------RDRKRAEEQRRKILEKELEERKQAMIEEERKrkllEKEMEERQKAIYEEERRREAEEERRKQQEMEERRRIQE 556

                         170
                  ....*....|.
gi 564378538  438 ELRRVEEEKRR 448
Cdd:pfam17380 557 QMRKATEERSR 567
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 271-453 4.89e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.39  E-value: 4.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 271 DATQHLSEASIRRRQLERQKLQELEQRREEQKRKEREDEARRRAgqrKQREAEQQQRARRREEKLRRREARQRARKRRGR 350
Cdd:COG1196  285 EAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAEL---EEELEELEEELEELEEELEEAEEELEEAEAELA 361

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538 351 RREEEEEEEeaepqpvlgREEEEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELRRQQEAE 430
Cdd:COG1196  362 EAEEALLEA---------EAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAE 432

                        170       180
                 ....*....|....*....|...
gi 564378538 431 LRRQREAELRRVEEEKRRALGLQ 453
Cdd:COG1196  433 LEEEEEEEEEALEEAAEEEAELE 455
PTZ00121 PTZ00121
MAEBL; Provisional
 274-449 6.61e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 6.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  274 QHLSEASIRRRQLERQKLQEL----EQRREEQKRKEREDE--ARRRAGQRKQRE---AEQQQRARRREEKLRRREARQRA 344
Cdd:PTZ00121 1537 DEAKKAEEKKKADELKKAEELkkaeEKKKAEEAKKAEEDKnmALRKAEEAKKAEearIEEVMKLYEEEKKMKAEEAKKAE 1616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  345 RKRRGRRREEEEEEEEAEPQPVLGREEEEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRHAKEAELR 424
Cdd:PTZ00121 1617 EAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

                         170       180
                  ....*....|....*....|....*
gi 564378538  425 RQQEAelrRQREAELRRVEEEKRRA 449
Cdd:PTZ00121 1697 EAEEA---KKAEELKKKEAEEKKKA 1718
PTZ00121 PTZ00121
MAEBL; Provisional
 281-449 4.10e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 40.89  E-value: 4.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  281 IRRRQLERQKLQELEQRREEQKRKERE----DEARRRAGQRKQREaEQQQRARRREEKLRRREARQRARKRRGRRREEEE 356
Cdd:PTZ00121 1475 AKKKAEEAKKADEAKKKAEEAKKKADEakkaAEAKKKADEAKKAE-EAKKADEAKKAEEAKKADEAKKAEEKKKADELKK 1553

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  357 EEEEAEPQPVLGREEEEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRHAKEA-----ELRRqqEAEL 431
Cdd:PTZ00121 1554 AEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAkikaeELKK--AEEE 1631

                         170
                  ....*....|....*...
gi 564378538  432 RRQREAELRRVEEEKRRA 449
Cdd:PTZ00121 1632 KKKVEQLKKKEAEEKKKA 1649
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 287-326 4.66e-03

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 38.10  E-value: 4.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 564378538  287 ERQKLQELEQRREEQKRKEREDEARRRAGQRKQREAEQQQ 326
Cdd:pfam05672  18 EKRRQAREQREREEQERLEKEEEERLRKEELRRRAEEERA 57
PTZ00121 PTZ00121
MAEBL; Provisional
 281-449 5.75e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 40.12  E-value: 5.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  281 IRRRQLERQKLQEL----EQRREEQKRKERE----DEARRRAGQRKQ---REAEQQQRARRREEKLRRREARQRARKRRG 349
Cdd:PTZ00121 1502 AKKAAEAKKKADEAkkaeEAKKADEAKKAEEakkaDEAKKAEEKKKAdelKKAEELKKAEEKKKAEEAKKAEEDKNMALR 1581

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  350 RRREEEEEEEEAEPQPVLGREEEEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRhakeAELRRQQEA 429
Cdd:PTZ00121 1582 KAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKK----AEELKKAEE 1657

                         170       180
                  ....*....|....*....|
gi 564378538  430 ELRRQREAELRRVEEEKRRA 449
Cdd:PTZ00121 1658 ENKIKAAEEAKKAEEDKKKA 1677
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 287-453 9.78e-03

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 39.16  E-value: 9.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  287 ERQKLQELEQRREEQKRKEREDEARRRAGQRKQREAEQQQRARRREEKLRRREARQRARKRRGRRREEEEEEEEAEPQPV 366
Cdd:pfam15709 336 DRLRAERAEMRRLEVERKRREQEEQRRLQQEQLERAEKMREELELEQQRRFEEIRLRKQRLEEERQRQEEEERKQRLQLQ 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564378538  367 LGREE--EEGAEPRRLLLAQRNLQSVRLIAALLARAEAARRRQREQSEERRRHAKEAE------LRRQQEAELRRQREAE 438
Cdd:pfam15709 416 AAQERarQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELEMQLAEEQKRLMEMAEeerleyQRQKQEAEEKARLEAE 495

                         170
                  ....*....|....*
gi 564378538  439 LRRVEEEKRRALGLQ 453
Cdd:pfam15709 496 ERRQKEEEAARLALE 510
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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