NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|449460882|ref|XP_004148173|]
View 

calcium homeostasis endoplasmic reticulum protein [Cucumis sativus]

Protein Classification

SWAP and CTD_bind domain-containing protein( domain architecture ID 10652740)

SWAP and CTD_bind domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 280-402 2.86e-25

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


:

Pssm-ID: 461442  Cd Length: 117  Bit Score: 100.75  E-value: 2.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882  280 LNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNIDeSEKQLHIIYLVNDILFESMMRRINskdldNEALAF 359
Cdd:pfam04818   3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAK-PEKKLHLLYLANDVLQNSRKKGKS-----EFADAF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 449460882  360 EPVLGSMLARVYHNpqMKEESQLKLQKLVQFWASKEIYDQDTI 402
Cdd:pfam04818  77 EPVLPEAFASAYKK--CDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 133-182 6.91e-14

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


:

Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 66.46  E-value: 6.91e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 449460882   133 IDKLVEYIIKNGPEFESMIREKQQDNPAYGFLF-GGEGQSYYRYKLWLMTR 182
Cdd:smart00648   4 IDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
PHA03378 super family cl33729
EBNA-3B; Provisional
 446-574 8.77e-03

EBNA-3B; Provisional


The actual alignment was detected with superfamily member PHA03378:

Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.28  E-value: 8.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 446 QWQPDRQGAIPSFPDQEHPDKAVSSGQALPRSVTPQQFLPSTIPTAAFVSSiPLPTSVQPPNQQPNAqLMPPQPAavgek 525
Cdd:PHA03378 688 QWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPA-AAPGRARPPAAAPGR-ARPPAAA----- 760

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 449460882 526 lpPYPLFPPGLIPGMVRKMQIGSGVPYSPMSPLDIPTVIPPSTISPSEV 574
Cdd:PHA03378 761 --PGRARPPAAAPGAPTPQPPPQAPPAPQQRPRGAPTPQPPPQAGPTSM 807
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 280-402 2.86e-25

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 100.75  E-value: 2.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882  280 LNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNIDeSEKQLHIIYLVNDILFESMMRRINskdldNEALAF 359
Cdd:pfam04818   3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAK-PEKKLHLLYLANDVLQNSRKKGKS-----EFADAF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 449460882  360 EPVLGSMLARVYHNpqMKEESQLKLQKLVQFWASKEIYDQDTI 402
Cdd:pfam04818  77 EPVLPEAFASAYKK--CDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 133-182 6.91e-14

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 66.46  E-value: 6.91e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 449460882   133 IDKLVEYIIKNGPEFESMIREKQQDNPAYGFLF-GGEGQSYYRYKLWLMTR 182
Cdd:smart00648   4 IDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 133-178 3.26e-13

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.


Pssm-ID: 460339 [Multi-domain]  Cd Length: 52  Bit Score: 64.46  E-value: 3.26e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 449460882  133 IDKLVEYIIKNGPEFESMIREKQQDNPAYGFLFGGEGQ--SYYRYKLW 178
Cdd:pfam01805   3 IKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPDDPlhAYYRWKLE 50
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 280-406 1.20e-10

CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins; Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340800  Cd Length: 127  Bit Score: 59.54  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 280 LNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNI-DESEKQLHIIYLVNDILFESMMRRInSKDLDnealA 358
Cdd:cd17003    4 FISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSsVNSRRKLLLIYLANDVVQQAKAKKK-TEFID----A 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 449460882 359 FEPVLGSMLARVYhnPQMKEESQLKLQKLVQFWASKEIYDQDTINALE 406
Cdd:cd17003   79 FSKVLPEVLEKIY--PSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIE 124
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
279-408 4.27e-06

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 46.50  E-value: 4.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882   279 ELNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIfNIDESEKQLHIIYLVNDILFesmmrriNSKD-LDNEAL 357
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYI-KKAPVPRKLPLLYLLDSIVQ-------NSKRkYGSEFG 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 449460882   358 -AFEPVLGSMLARVYHNPQMKEESQLKlqKLVQFWASKEIYDQDTINALEGE 408
Cdd:smart00582  73 dELGPVFQDALRRVLGAAPEELKKKIR--RLLNIWEERGIFPPEVLRPLREK 122
PHA03378 PHA03378
EBNA-3B; Provisional
 446-574 8.77e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.28  E-value: 8.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 446 QWQPDRQGAIPSFPDQEHPDKAVSSGQALPRSVTPQQFLPSTIPTAAFVSSiPLPTSVQPPNQQPNAqLMPPQPAavgek 525
Cdd:PHA03378 688 QWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPA-AAPGRARPPAAAPGR-ARPPAAA----- 760

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 449460882 526 lpPYPLFPPGLIPGMVRKMQIGSGVPYSPMSPLDIPTVIPPSTISPSEV 574
Cdd:PHA03378 761 --PGRARPPAAAPGAPTPQPPPQAPPAPQQRPRGAPTPQPPPQAGPTSM 807
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 280-402 2.86e-25

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 100.75  E-value: 2.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882  280 LNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNIDeSEKQLHIIYLVNDILFESMMRRINskdldNEALAF 359
Cdd:pfam04818   3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAK-PEKKLHLLYLANDVLQNSRKKGKS-----EFADAF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 449460882  360 EPVLGSMLARVYHNpqMKEESQLKLQKLVQFWASKEIYDQDTI 402
Cdd:pfam04818  77 EPVLPEAFASAYKK--CDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 133-182 6.91e-14

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 66.46  E-value: 6.91e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 449460882   133 IDKLVEYIIKNGPEFESMIREKQQDNPAYGFLF-GGEGQSYYRYKLWLMTR 182
Cdd:smart00648   4 IDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 133-178 3.26e-13

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.


Pssm-ID: 460339 [Multi-domain]  Cd Length: 52  Bit Score: 64.46  E-value: 3.26e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 449460882  133 IDKLVEYIIKNGPEFESMIREKQQDNPAYGFLFGGEGQ--SYYRYKLW 178
Cdd:pfam01805   3 IKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPDDPlhAYYRWKLE 50
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 280-406 1.20e-10

CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins; Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340800  Cd Length: 127  Bit Score: 59.54  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 280 LNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNI-DESEKQLHIIYLVNDILFESMMRRInSKDLDnealA 358
Cdd:cd17003    4 FISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSsVNSRRKLLLIYLANDVVQQAKAKKK-TEFID----A 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 449460882 359 FEPVLGSMLARVYhnPQMKEESQLKLQKLVQFWASKEIYDQDTINALE 406
Cdd:cd17003   79 FSKVLPEVLEKIY--PSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIE 124
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 284-407 2.72e-07

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 49.89  E-value: 2.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 284 LSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIFNIDeSEKQLHIIYLVNDILFESmmRRINSKDLDNEalaFEPVL 363
Cdd:cd16981    8 LRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAK-PERKLTLLYLANDVLQNS--RRKGAPEFVEA---FKKVL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 449460882 364 GSMLARVYHNPQmkEESQLKLQKLVQFWASKEIYDQDTINALEG 407
Cdd:cd16981   82 PEALALVRSEGD--ESVRKKVLRVLNIWEERNVFGSEFLAELRA 123
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
279-408 4.27e-06

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 46.50  E-value: 4.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882   279 ELNNVLSNLTGAKESIKGAKTWFMQRSPFAPAMAEALRDMIfNIDESEKQLHIIYLVNDILFesmmrriNSKD-LDNEAL 357
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYI-KKAPVPRKLPLLYLLDSIVQ-------NSKRkYGSEFG 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 449460882   358 -AFEPVLGSMLARVYHNPQMKEESQLKlqKLVQFWASKEIYDQDTINALEGE 408
Cdd:smart00582  73 dELGPVFQDALRRVLGAAPEELKKKIR--RLLNIWEERGIFPPEVLRPLREK 122
PHA03378 PHA03378
EBNA-3B; Provisional
 446-574 8.77e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.28  E-value: 8.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449460882 446 QWQPDRQGAIPSFPDQEHPDKAVSSGQALPRSVTPQQFLPSTIPTAAFVSSiPLPTSVQPPNQQPNAqLMPPQPAavgek 525
Cdd:PHA03378 688 QWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPA-AAPGRARPPAAAPGR-ARPPAAA----- 760

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 449460882 526 lpPYPLFPPGLIPGMVRKMQIGSGVPYSPMSPLDIPTVIPPSTISPSEV 574
Cdd:PHA03378 761 --PGRARPPAAAPGAPTPQPPPQAPPAPQQRPRGAPTPQPPPQAGPTSM 807
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH