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Conserved domains on  [gi|1780590970|emb|VYS65105|]
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unnamed protein product [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1002420)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 131-324 2.03e-20

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.79  E-value: 2.03e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  131 YGTPRSA------VSFNALLNACLHSKNFDKVPQLFDEIPQRYNKIIPDKISYGILIKSYCDSGTPEKAIEIMRQMQGKG 204
Cdd:PLN03218   530 YGIMRSKnvkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYN 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  205 MEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCELDNAAYNVRIMSA-QKESPERVKELIEEMSSMGLKPDTISYNY 283
Cdd:PLN03218   610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAgHAGDLDKAFEILQDARKQGIKLGTVSYSS 689

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1780590970  284 LMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLC 324
Cdd:PLN03218   690 LMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 105-147 1.19e-04

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 1.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYGTPRSAVSFNALLNAC 147
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 131-324 2.03e-20

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.79  E-value: 2.03e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  131 YGTPRSA------VSFNALLNACLHSKNFDKVPQLFDEIPQRYNKIIPDKISYGILIKSYCDSGTPEKAIEIMRQMQGKG 204
Cdd:PLN03218   530 YGIMRSKnvkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYN 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  205 MEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCELDNAAYNVRIMSA-QKESPERVKELIEEMSSMGLKPDTISYNY 283
Cdd:PLN03218   610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAgHAGDLDKAFEILQDARKQGIKLGTVSYSS 689

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1780590970  284 LMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLC 324
Cdd:PLN03218   690 LMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 276-324 1.24e-10

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 56.22  E-value: 1.24e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1780590970 276 PDTISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLC 324
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 279-313 2.10e-05

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 41.29  E-value: 2.10e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1780590970 279 ISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNA 313
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 105-147 1.19e-04

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 1.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYGTPRSAVSFNALLNAC 147
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 105-132 8.70e-03

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 33.58  E-value: 8.70e-03
                          10        20
                  ....*....|....*....|....*...
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYG 132
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERG 30
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 131-324 2.03e-20

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 93.79  E-value: 2.03e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  131 YGTPRSA------VSFNALLNACLHSKNFDKVPQLFDEIPQRYNKIIPDKISYGILIKSYCDSGTPEKAIEIMRQMQGKG 204
Cdd:PLN03218   530 YGIMRSKnvkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYN 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  205 MEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCELDNAAYNVRIMSA-QKESPERVKELIEEMSSMGLKPDTISYNY 283
Cdd:PLN03218   610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAgHAGDLDKAFEILQDARKQGIKLGTVSYSS 689

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1780590970  284 LMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLC 324
Cdd:PLN03218   690 LMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 101-239 1.58e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.52  E-value: 1.58e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  101 EEPFYSTLIRSYGQASMFNHAMRTFEQMDQYGTPRSAVSFNALLNACLHSKNFDKVPQLFDEIpqRYNKIIPDKISYGIL 180
Cdd:PLN03218   648 DEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI--KSIKLRPTVSTMNAL 725

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1780590970  181 IKSYCDSGTPEKAIEIMRQMQGKGMEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKG 239
Cdd:PLN03218   726 ITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDG 784
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 160-345 5.36e-11

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 64.51  E-value: 5.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 160 FDEIPQRynkiipDKISYGILIKSYCDSGTPEKAIEIMRQMQGKGMEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKG 239
Cdd:PLN03081  282 FDGMPEK------TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTG 355

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 240 CELDNAAYNVRI-MSAQKESPERVKELIEEMSSMGLkpdtISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRT 318
Cdd:PLN03081  356 FPLDIVANTALVdLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLA 431

                         170       180
                  ....*....|....*....|....*..
gi 1780590970 319 LIFHLCYSRLYEQGYAIFKKSVYMHKI 345
Cdd:PLN03081  432 VLSACRYSGLSEQGWEIFQSMSENHRI 458
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 276-324 1.24e-10

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 56.22  E-value: 1.24e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1780590970 276 PDTISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLC 324
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 97-377 2.75e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.59  E-value: 2.75e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970   97 PKIKEEPFYSTLIRSYGQASMFNHAMRTFEQMDQYGT-PRSAVSFNALLNAClhsKNFDKVPQLFdeipqRYNKIIPD-K 174
Cdd:PLN03218   365 SGKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLlDMDKIYHAKFFKAC---KKQRAVKEAF-----RFAKLIRNpT 436

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  175 IS-YGILIKSYCDSGTPEKAIEIMRQMQGKGMEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCE---------LDN 244
Cdd:PLN03218   437 LStFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEanvhtfgalIDG 516

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  245 -----------AAYNvrIMSAQKESPERV--KELIEEMSSMG------------------LKPDTISYNYLMTAYCERGM 293
Cdd:PLN03218   517 caragqvakafGAYG--IMRSKNVKPDRVvfNALISACGQSGavdrafdvlaemkaethpIDPDHITVGALMKACANAGQ 594

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  294 LDEAKKVYEGLEGNNCAPNAATFrTLIFHLCySRLYEQGYAIfkkSVY--MHKI---PDFNTLKHLVVGLVENKKRDDAK 368
Cdd:PLN03218   595 VDRAKEVYQMIHEYNIKGTPEVY-TIAVNSC-SQKGDWDFAL---SIYddMKKKgvkPDEVFFSALVDVAGHAGDLDKAF 669


                   ....*....
gi 1780590970  369 GLIRTVKKK 377
Cdd:PLN03218   670 EILQDARKQ 678
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 208-249 4.00e-08

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 49.28  E-value: 4.00e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1780590970 208 TTIAFTTILSSLYKKGELEVADNLWNEMVKKGCELDNAAYNV 249
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTI 43
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 135-186 1.31e-07

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 47.74  E-value: 1.31e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1780590970 135 RSAVSFNALLNACLHSKNFDKVPQLFDEIPQRynKIIPDKISYGILIKSYCD 186
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKR--GVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 46-353 4.07e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.16  E-value: 4.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970  46 PDKALKIYANVSDHSASPvssryaQELTVRR-LAKCRRFSDIETLIESHkndpkikeepfystlirsygqasmfnhamrt 124
Cdd:PLN03077  370 PDKALETYALMEQDNVSP------DEITIASvLSACACLGDLDVGVKLH------------------------------- 412

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 125 fEQMDQYGTPRSAVSFNALLNACLHSKNFDKVPQLFDEIPQRynkiipDKISYGILIKSYCDSGTPEKAIEIMRQMQGKg 204
Cdd:PLN03077  413 -ELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK------DVISWTSIIAGLRLNNRCFEALIFFRQMLLT- 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 205 MEVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCELD----NAAYNVRIMSAQKESPervkelIEEMSSMglKPDTIS 280
Cdd:PLN03077  485 LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDgflpNALLDLYVRCGRMNYA------WNQFNSH--EKDVVS 556

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1780590970 281 YNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLIFHLCYSRLYEQGYAIFKK-SVYMHKIPDfntLKH 353
Cdd:PLN03077  557 WNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSmEEKYSITPN---LKH 627
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 272-302 4.19e-06

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 43.10  E-value: 4.19e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1780590970 272 MGLKPDTISYNYLMTAYCERGMLDEAKKVYE 302
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLD 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 172-221 9.53e-06

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 42.35  E-value: 9.53e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1780590970 172 PDKISYGILIKSYCDSGTPEKAIEIMRQMQGKGMEVTTIAFTTILSSLYK 221
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 265-320 1.96e-05

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 41.96  E-value: 1.96e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1780590970 265 LIEEMSSMGLKPDTISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAATFRTLI 320
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 279-313 2.10e-05

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 41.29  E-value: 2.10e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1780590970 279 ISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNA 313
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03077 PLN03077
Protein ECB2; Provisional
 159-315 1.18e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 44.46  E-value: 1.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 159 LFDEIPQRynkiipDKISYGILIKSYCDSGTPEKAIEIMRQMQGKGMEVTTIAFTTILSSLYKKGELEVADNLWNEMVKK 238
Cdd:PLN03077  244 VFDRMPRR------DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT 317

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1780590970 239 GCELDNAAYNVRI-MSAqkeSPERVKELIEEMSSMGLKpDTISYNYLMTAYCERGMLDEAKKVYEGLEGNNCAPNAAT 315
Cdd:PLN03077  318 GFAVDVSVCNSLIqMYL---SLGSWGEAEKVFSRMETK-DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEIT 391
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 105-147 1.19e-04

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 39.27  E-value: 1.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYGTPRSAVSFNALLNAC 147
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 172-200 2.15e-04

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 38.10  E-value: 2.15e-04
                          10        20
                  ....*....|....*....|....*....
gi 1780590970 172 PDKISYGILIKSYCDSGTPEKAIEIMRQM 200
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 105-373 2.15e-04

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 43.32  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYGTPRSAVSFNALLNACLHSKNFDKVPQLFDEIPQRYnKIIPDKISYGILIKSY 184
Cdd:PLN03081  394 WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENH-RIKPRAMHYACMIELL 472

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 185 CDSGTPEKAIEIMRQMQGKgmeVTTIAFTTILSSLYKKGELEVADNLWNEMVKKGCE-LDNAA--YNVRIMSAQKESPER 261
Cdd:PLN03081  473 GREGLLDEAYAMIRRAPFK---PTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEkLNNYVvlLNLYNSSGRQAEAAK 549

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 262 VkelIEEMSSMGLKpdtisynylMTAYCErgMLDEAKKVYEGLEGNNCAP-NAATFRTLifHLCYSRLYEQGYAIFKKsv 340
Cdd:PLN03081  550 V---VETLKRKGLS---------MHPACT--WIEVKKQDHSFFSGDRLHPqSREIYQKL--DELMKEISEYGYVAEEN-- 611

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1780590970 341 ymHKIPDFNTLKHLVVGLVENKKRDDAKGLIRT 373
Cdd:PLN03081  612 --ELLPDVDEDEEKVSGRYHSEKLAIAFGLINT 642
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 175-205 5.21e-04

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.06  E-value: 5.21e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1780590970 175 ISYGILIKSYCDSGTPEKAIEIMRQMQGKGM 205
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 210-243 7.88e-04

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 7.88e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1780590970 210 IAFTTILSSLYKKGELEVADNLWNEMVKKGCELD 243
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 279-309 1.12e-03

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 36.29  E-value: 1.12e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1780590970 279 ISYNYLMTAYCERGMLDEAKKVYEGLEGNNC 309
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 175-209 2.35e-03

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 2.35e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1780590970 175 ISYGILIKSYCDSGTPEKAIEIMRQMQGKGMEVTT 209
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 210-240 2.58e-03

PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 35.13  E-value: 2.58e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1780590970 210 IAFTTILSSLYKKGELEVADNLWNEMVKKGC 240
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 234-291 5.02e-03

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 35.41  E-value: 5.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1780590970 234 EMVKKGCELDNAAYNVRI-MSAQKESPERVKELIEEMSSMGLKPDTISYNYLMTAYCER 291
Cdd:pfam13812   5 EMVRDGIQLNVNTYTHLLhAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 123-223 8.05e-03

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 37.38  E-value: 8.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1780590970 123 RTFEQMDQYGTPRSAVSFNALLNACLHSKNFDKVpqlFDEIPQRYNKIIPDKI-SYGILIKSYCDSGTPEKAIEIMRQMQ 201
Cdd:pfam17177  76 EVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA---FDLVKEMEAAGVSPRLrSYSPALHAYCEAGDADKAYEVEEHML 152

                          90       100
                  ....*....|....*....|..
gi 1780590970 202 GKGMEVTTIAFTTILSSLYKKG 223
Cdd:pfam17177 153 AHGVELEEPELAALLKVSAKAG 174
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 105-132 8.70e-03

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 33.58  E-value: 8.70e-03
                          10        20
                  ....*....|....*....|....*...
gi 1780590970 105 YSTLIRSYGQASMFNHAMRTFEQMDQYG 132
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERG 30
 
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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