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Conserved domains on  [gi|15233440|ref|NP_195326|]
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cold shock domain protein 1 [Arabidopsis thaliana]

Protein Classification

cold shock domain-containing protein; zinc finger CCHC domain-containing protein( domain architecture ID 13626150)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation| zinc finger CCHC (ZCCHC) domain-containing protein with a retrotransposon gag domain, contains a zinc knuckle or a zinc binding motif, CX2CX4HX4C, where X can be any amino acid, and may bind single-stranded RNA; similar to Pyrenophora graminea gag protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 134-297 1.80e-35

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 124.92  E-value: 1.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  134 CYNCGDTGHFARDCTSAGNGDQRGATKggndgCYTCGDVGHVARDCTQKSVGNGDQrgavkggndGCYTCGDVGHFARDC 213
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARP-----CYKCGEPGHLSRECPSAPGGRGER---------SCYNCGKTGHLSREC 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  214 TQkvaagnvRSGGGGSGTCYSCGGVGHIARDCATKRQPSRG---CYQCGGSGHLARDCDQRGSGGGGnDNACYKCGKEGH 290
Cdd:PTZ00368  69 PE-------APPGSGPRSCYNCGQTGHISRECPNRAKGGAArraCYNCGGEGHISRDCPNAGKRPGG-DKTCYNCGQTGH 140


                 ....*..
gi 15233440  291 FARECSS 297
Cdd:PTZ00368 141 LSRDCPD 147
CSD pfam00313
'Cold-shock' DNA-binding domain;
12-77 2.42e-27

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 2.42e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15233440    12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGsDGKTKAVNVTAP 77
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 134-297 1.80e-35

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 124.92  E-value: 1.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  134 CYNCGDTGHFARDCTSAGNGDQRGATKggndgCYTCGDVGHVARDCTQKSVGNGDQrgavkggndGCYTCGDVGHFARDC 213
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARP-----CYKCGEPGHLSRECPSAPGGRGER---------SCYNCGKTGHLSREC 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  214 TQkvaagnvRSGGGGSGTCYSCGGVGHIARDCATKRQPSRG---CYQCGGSGHLARDCDQRGSGGGGnDNACYKCGKEGH 290
Cdd:PTZ00368  69 PE-------APPGSGPRSCYNCGQTGHISRECPNRAKGGAArraCYNCGGEGHISRDCPNAGKRPGG-DKTCYNCGQTGH 140


                 ....*..
gi 15233440  291 FARECSS 297
Cdd:PTZ00368 141 LSRDCPD 147
CSD pfam00313
'Cold-shock' DNA-binding domain;
12-77 2.42e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 2.42e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15233440    12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGsDGKTKAVNVTAP 77
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
12-76 2.13e-24

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 93.34  E-value: 2.13e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15233440  12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKtKAVNVTA 76
Cdd:COG1278   3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGP-QAVNVRV 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 12-75 2.82e-24

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 93.03  E-value: 2.82e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15233440  12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGsDGKTKAVNVT 75
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG-DKGPQAVNVR 64
cspE PRK09507
cold shock-like protein CspE;
13-76 7.17e-21

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 84.32  E-value: 7.17e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15233440   13 GKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTkAVNVTA 76
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPS-AANVIA 68
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 102-263 2.03e-18

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 81.05  E-value: 2.03e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 102 CYNCGELGHISKDCGIGGgggggerrsrggegCYNCGDTGHFARDCTSAGNgdqrgatkggndgCYTCGDVGHVARDCTQ 181
Cdd:COG5082  63 CFNCGQNGHLRRDCPHSI--------------CYNCSWDGHRSNHCPKPKK-------------CYNCGETGHLSRDCNP 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 182 ksvgNGDQRGAvkggndgCYTCGDVGHFARDCTQ--KVAAGNVRSGGGGSGTCYSCGGVGHIARDCaTKRQPSRGCYQCG 259
Cdd:COG5082 116 ----SKDQQKS-------CFDCNSTRHSSEDCPSiwKHYVLNNGDGHPIKKFCYSCGSAGHFGDDC-KEPRSSRVPYVCG 183


                ....
gi 15233440 260 GSGH 263
Cdd:COG5082 184 KKGY 187
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 12-77 2.85e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 71.86  E-value: 2.85e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15233440     12 TGKVNWFNasKGYGFITPDDGSVELFVHQSSIVSeGYRSLTVGDAVEFAITQGSD-GKTKAVNVTAP 77
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPEGgEKPEAENVVKL 64
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 134-149 8.40e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 33.27  E-value: 8.40e-03
                          10
                  ....*....|....*.
gi 15233440   134 CYNCGDTGHFARDCTS 149
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 134-297 1.80e-35

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 124.92  E-value: 1.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  134 CYNCGDTGHFARDCTSAGNGDQRGATKggndgCYTCGDVGHVARDCTQKSVGNGDQrgavkggndGCYTCGDVGHFARDC 213
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARP-----CYKCGEPGHLSRECPSAPGGRGER---------SCYNCGKTGHLSREC 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  214 TQkvaagnvRSGGGGSGTCYSCGGVGHIARDCATKRQPSRG---CYQCGGSGHLARDCDQRGSGGGGnDNACYKCGKEGH 290
Cdd:PTZ00368  69 PE-------APPGSGPRSCYNCGQTGHISRECPNRAKGGAArraCYNCGGEGHISRDCPNAGKRPGG-DKTCYNCGQTGH 140


                 ....*..
gi 15233440  291 FARECSS 297
Cdd:PTZ00368 141 LSRDCPD 147
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 102-268 2.62e-33

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 119.53  E-value: 2.62e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  102 CYNCGELGHISKDCGIGGGGGGGERRSrggegCYNCGDTGHFARDCTSAgngdqrgATKGGNDGCYTCGDVGHVARDCTQ 181
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARP-----CYKCGEPGHLSRECPSA-------PGGRGERSCYNCGKTGHLSRECPE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  182 KSVGNGDQRgavkggndgCYTCGDVGHFARDCTqkvaagNVRSGGGGSGTCYSCGGVGHIARDCATKRQPSRG---CYQC 258
Cdd:PTZ00368  71 APPGSGPRS---------CYNCGQTGHISRECP------NRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGdktCYNC 135

                        170
                 ....*....|
gi 15233440  259 GGSGHLARDC 268
Cdd:PTZ00368 136 GQTGHLSRDC 145
CSD pfam00313
'Cold-shock' DNA-binding domain;
12-77 2.42e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 2.42e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15233440    12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGsDGKTKAVNVTAP 77
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 102-248 5.78e-25

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 97.57  E-value: 5.78e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440  102 CYNCGELGHISKDCgigggggGGERRSRGGEGCYNCGDTGHFARDCTSAgngdqrgATKGGNDGCYTCGDVGHVARDCTQ 181
Cdd:PTZ00368  30 CYKCGEPGHLSREC-------PSAPGGRGERSCYNCGKTGHLSRECPEA-------PPGSGPRSCYNCGQTGHISRECPN 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15233440  182 KSVGNGDQRgavkggndGCYTCGDVGHFARDCTqkvaagNVRSGGGGSGTCYSCGGVGHIARDCATK 248
Cdd:PTZ00368  96 RAKGGAARR--------ACYNCGGEGHISRDCP------NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
CspC COG1278
Cold shock protein, CspA family [Transcription];
12-76 2.13e-24

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 93.34  E-value: 2.13e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15233440  12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKtKAVNVTA 76
Cdd:COG1278   3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGP-QAVNVRV 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 12-75 2.82e-24

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 93.03  E-value: 2.82e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15233440  12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGsDGKTKAVNVT 75
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG-DKGPQAVNVR 64
cspE PRK09507
cold shock-like protein CspE;
13-76 7.17e-21

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 84.32  E-value: 7.17e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15233440   13 GKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTkAVNVTA 76
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPS-AANVIA 68
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 102-263 2.03e-18

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 81.05  E-value: 2.03e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 102 CYNCGELGHISKDCGIGGgggggerrsrggegCYNCGDTGHFARDCTSAGNgdqrgatkggndgCYTCGDVGHVARDCTQ 181
Cdd:COG5082  63 CFNCGQNGHLRRDCPHSI--------------CYNCSWDGHRSNHCPKPKK-------------CYNCGETGHLSRDCNP 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 182 ksvgNGDQRGAvkggndgCYTCGDVGHFARDCTQ--KVAAGNVRSGGGGSGTCYSCGGVGHIARDCaTKRQPSRGCYQCG 259
Cdd:COG5082 116 ----SKDQQKS-------CFDCNSTRHSSEDCPSiwKHYVLNNGDGHPIKKFCYSCGSAGHFGDDC-KEPRSSRVPYVCG 183


                ....
gi 15233440 260 GSGH 263
Cdd:COG5082 184 KKGY 187
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
10-76 1.13e-17

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 75.78  E-value: 1.13e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15233440   10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTkAVNVTA 76
Cdd:PRK10354   4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPA-AGNVTS 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 10-75 2.81e-17

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 74.80  E-value: 2.81e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15233440   10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTKAVNVT 75
Cdd:PRK09890   4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVT 69
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 154-296 5.98e-17

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 77.20  E-value: 5.98e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 154 DQRGATKGGNDGCYTCGDVGHVARDCTQksvgngdqrgavkggnDGCYTCGDVGHFARDCTQKVaagnvrsggggsgTCY 233
Cdd:COG5082  51 EDVSAIREENPVCFNCGQNGHLRRDCPH----------------SICYNCSWDGHRSNHCPKPK-------------KCY 101

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 234 SCGGVGHIARDCATKRQPSRGCYQCGGSGHLARDCDQRGSGGGGNDN-------ACYKCGKEGHFARECS 296
Cdd:COG5082 102 NCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGdghpikkFCYSCGSAGHFGDDCK 171
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 9-76 1.33e-16

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 72.79  E-value: 1.33e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15233440    9 ARSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTkAVNVTA 76
Cdd:PRK10943   2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPA-AVNVTA 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 12-77 2.85e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 71.86  E-value: 2.85e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15233440     12 TGKVNWFNasKGYGFITPDDGSVELFVHQSSIVSeGYRSLTVGDAVEFAITQGSD-GKTKAVNVTAP 77
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVSPEGgEKPEAENVVKL 64
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 231-298 1.77e-14

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 69.45  E-value: 1.77e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15233440  231 TCYSCGGVGHIARDCATKRQP----SRGCYQCGGSGHLARDCDQRGSGGGgnDNACYKCGKEGHFARECSSV 298
Cdd:PTZ00368   2 VCYRCGGVGHQSRECPNSAPAgaakARPCYKCGEPGHLSRECPSAPGGRG--ERSCYNCGKTGHLSRECPEA 71
PRK09937 PRK09937
cold shock-like protein CspD;
13-74 1.70e-13

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 64.37  E-value: 1.70e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15233440   13 GKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTKAVNV 74
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 12-74 5.37e-13

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 63.15  E-value: 5.37e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15233440   12 TGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTKAVNV 74
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIV 65
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 200-298 4.90e-11

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 60.63  E-value: 4.90e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233440 200 CYTCGDVGHFARDCTQKVaagnvrsggggsgtCYSCGGVGHIARDCATKRQpsrgCYQCGGSGHLARDCDQRGSGGggnd 279
Cdd:COG5082  63 CFNCGQNGHLRRDCPHSI--------------CYNCSWDGHRSNHCPKPKK----CYNCGETGHLSRDCNPSKDQQ---- 120

                        90
                ....*....|....*....
gi 15233440 280 NACYKCGKEGHFARECSSV 298
Cdd:COG5082 121 KSCFDCNSTRHSSEDCPSI 139
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 10-71 2.30e-05

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 41.81  E-value: 2.30e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15233440   10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTKA 71
Cdd:PRK15463   4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAA 65
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 10-71 8.66e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 37.39  E-value: 8.66e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15233440   10 RSTGKVNWFNASKGYGFITPDDGSVELFVHQSSIVSEGYRSLTVGDAVEFAITQGSDGKTKA 71
Cdd:PRK15464   4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAA 65
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 134-149 8.40e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 33.27  E-value: 8.40e-03
                          10
                  ....*....|....*.
gi 15233440   134 CYNCGDTGHFARDCTS 149
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
 
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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