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Conserved domains on  [gi|15228825|ref|NP_188906|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 12851728)

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
 214-558 1.64e-23

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 105.34  E-value: 1.64e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   214 AKSGKYNKAVDAFLEMEKSyGVKTDTIAMNSLMDALVKENSIEHAHEVF-LKLFDTIKPDARTFNILIHGFCKARKFDDA 292
Cdd:PLN03218  483 AKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAFGAYgIMRSKNVKPDRVVFNALISACGQSGAVDRA 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   293 RAMMDLMK--VTEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMK 370
Cdd:PLN03218  562 FDVLAEMKaeTHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK 641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   371 EDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAALHHSRDEMALRLLkrmEDEEGESCSPN 450
Cdd:PLN03218  642 KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELY---EDIKSIKLRPT 718

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   451 vetyapllkmcchkkkmkllgillhhmvkndvsidVSTYILLIRGLCMSGKVEEACLFFEEAVRKGMVPRDSTCKMLVDE 530
Cdd:PLN03218  719 -----------------------------------VSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVA 763

                         330       340
                  ....*....|....*....|....*...
gi 15228825   531 LEKKNMAEAKLKIqsLVQSKtmIDSHSP 558
Cdd:PLN03218  764 SERKDDADVGLDL--LSQAK--EDGIKP 787
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 167-192 5.12e-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: 34.74  E-value: 5.12e-03
                          10        20
                  ....*....|....*....|....*.
gi 15228825   167 HTYNAMVDVLGKCRNFDLMWELVNEM 192
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 214-558 1.64e-23

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 105.34  E-value: 1.64e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   214 AKSGKYNKAVDAFLEMEKSyGVKTDTIAMNSLMDALVKENSIEHAHEVF-LKLFDTIKPDARTFNILIHGFCKARKFDDA 292
Cdd:PLN03218  483 AKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAFGAYgIMRSKNVKPDRVVFNALISACGQSGAVDRA 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   293 RAMMDLMK--VTEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMK 370
Cdd:PLN03218  562 FDVLAEMKaeTHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK 641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   371 EDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAALHHSRDEMALRLLkrmEDEEGESCSPN 450
Cdd:PLN03218  642 KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELY---EDIKSIKLRPT 718

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   451 vetyapllkmcchkkkmkllgillhhmvkndvsidVSTYILLIRGLCMSGKVEEACLFFEEAVRKGMVPRDSTCKMLVDE 530
Cdd:PLN03218  719 -----------------------------------VSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVA 763

                         330       340
                  ....*....|....*....|....*...
gi 15228825   531 LEKKNMAEAKLKIqsLVQSKtmIDSHSP 558
Cdd:PLN03218  764 SERKDDADVGLDL--LSQAK--EDGIKP 787
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 306-355 1.67e-14

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: 67.77  E-value: 1.67e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15228825   306 PDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGK 355
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 344-378 4.00e-07

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: 46.29  E-value: 4.00e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15228825   344 VTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDA 378
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 211-438 8.30e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.80  E-value: 8.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825 211 RRLAKSGKYNKAVDAFLEMEKsygVKTDTI-AMNSLMDALVKENSIEHAHEVFLKLFDTIKPDARTFNILIHGFCKARKF 289
Cdd:COG2956  16 LNYLLNGQPDKAIDLLEEALE---LDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALLELAQDYLKAGLL 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825 290 DDARAM-MDLMKVTEFTPDVvtYTSFVEAYCKEGDFRRVNEMLEEMRENGcNPNVVTYTIVMHSLGKSKQVAEALGVYEK 368
Cdd:COG2956  93 DRAEELlEKLLELDPDDAEA--LRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAIEALEK 169

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15228825 369 -MKEDgcvPD-AKFYSSLIHILSKTGRFKDAAEIFEDMTNQGvRRDVLVYNTMISAALHHSRDEMALRLLKR 438
Cdd:COG2956 170 aLKLD---PDcARALLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEALELLRK 237
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 167-192 5.12e-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: 34.74  E-value: 5.12e-03
                          10        20
                  ....*....|....*....|....*.
gi 15228825   167 HTYNAMVDVLGKCRNFDLMWELVNEM 192
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 214-558 1.64e-23

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 105.34  E-value: 1.64e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   214 AKSGKYNKAVDAFLEMEKSyGVKTDTIAMNSLMDALVKENSIEHAHEVF-LKLFDTIKPDARTFNILIHGFCKARKFDDA 292
Cdd:PLN03218  483 AKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAFGAYgIMRSKNVKPDRVVFNALISACGQSGAVDRA 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   293 RAMMDLMK--VTEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMK 370
Cdd:PLN03218  562 FDVLAEMKaeTHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK 641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   371 EDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAALHHSRDEMALRLLkrmEDEEGESCSPN 450
Cdd:PLN03218  642 KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELY---EDIKSIKLRPT 718

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   451 vetyapllkmcchkkkmkllgillhhmvkndvsidVSTYILLIRGLCMSGKVEEACLFFEEAVRKGMVPRDSTCKMLVDE 530
Cdd:PLN03218  719 -----------------------------------VSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVA 763

                         330       340
                  ....*....|....*....|....*...
gi 15228825   531 LEKKNMAEAKLKIqsLVQSKtmIDSHSP 558
Cdd:PLN03218  764 SERKDDADVGLDL--LSQAK--EDGIKP 787
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 306-355 1.67e-14

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: 67.77  E-value: 1.67e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15228825   306 PDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGK 355
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 149-424 5.02e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 75.30  E-value: 5.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   149 AYGFFIWANSQTGYVhsghTYNAMVDVLGKCRNFDLMWELVNEMNKneESKLVTLD--TMSKVMRRLAKSGKYNKAVDAF 226
Cdd:PLN03218  529 AYGIMRSKNVKPDRV----VFNALISACGQSGAVDRAFDVLAEMKA--ETHPIDPDhiTVGALMKACANAGQVDRAKEVY 602

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   227 LEMEKsYGVKTD----TIAMNSLMdalvKENSIEHAHEVFLKLF-DTIKPDARTFNILIHGFCKARKFDDARAMMDLMKV 301
Cdd:PLN03218  603 QMIHE-YNIKGTpevyTIAVNSCS----QKGDWDFALSIYDDMKkKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK 677

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   302 TEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFY 381
Cdd:PLN03218  678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY 757

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 15228825   382 SSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAAL 424
Cdd:PLN03218  758 SILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCL 800
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 271-320 1.81e-11

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: 58.91  E-value: 1.81e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15228825   271 PDARTFNILIHGFCKARKFDDARAMMDLMKVTEFTPDVVTYTSFVEAYCK 320
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 341-390 6.34e-11

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: 57.37  E-value: 6.34e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15228825   341 PNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSK 390
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 238-285 2.46e-09

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: 53.14  E-value: 2.46e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15228825   238 DTIAMNSLMDALVKENSIEHAHEVFLKLFDT-IKPDARTFNILIHGFCK 285
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 299-355 2.54e-09

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: 53.52  E-value: 2.54e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15228825   299 MKVTEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGK 355
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 214-517 5.30e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 59.11  E-value: 5.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  214 AKSGKYNKAVDAFLEM-EKSygvktdTIAMNSLMDALVKENSIEHAHEVFLKLFDT-IKPDARTFNILIHGFCKARKFDD 291
Cdd:PLN03081 270 SKCGDIEDARCVFDGMpEKT------TVAWNSMLAGYALHGYSEEALCLYYEMRDSgVSIDQFTFSIMIRIFSRLALLEH 343

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  292 ARAMMDLMKVTEFTPDVVTYTSFVEAYCKEG---DFRRVNEMLEEMrengcnpNVVTYTIVMHSLGKSKQVAEALGVYEK 368
Cdd:PLN03081 344 AKQAHAGLIRTGFPLDIVANTALVDLYSKWGrmeDARNVFDRMPRK-------NLISWNALIAGYGNHGRGTKAVEMFER 416

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  369 MKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMT-NQGVRRDVLVYNTMISAALHHSRDEMALRLLKRmedeegESC 447
Cdd:PLN03081 417 MIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSeNHRIKPRAMHYACMIELLGREGLLDEAYAMIRR------APF 490

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  448 SPNVETYAPLLKMCCHKKKMKLLGILLHHMVKNDVSiDVSTYILLIRGLCMSGKVEEACLFFEEAVRKGM 517
Cdd:PLN03081 491 KPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPE-KLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGL 559
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 190-441 5.73e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 58.73  E-value: 5.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  190 NEMNKNEESKLVTLDTMSKVMRRLAKSGKYNKAVDAFLEMEKSYGVKTDTIAMNSLMDALVKENSIEHAHEVFLKLFDT- 268
Cdd:PLN03081  74 KDARLDDTQIRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSg 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  269 IKPDARTFNILIHGFCKARKFDDARAMMDLMkvteftPD--VVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTY 346
Cdd:PLN03081 154 FEPDQYMMNRVLLMHVKCGMLIDARRLFDEM------PErnLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTF 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  347 TIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTnqgvRRDVLVYNTMISAALHH 426
Cdd:PLN03081 228 VVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALH 303

                        250
                 ....*....|....*
gi 15228825  427 SRDEMALRLLKRMED 441
Cdd:PLN03081 304 GYSEEALCLYYEMRD 318
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 269-300 9.05e-09

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: 51.19  E-value: 9.05e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15228825   269 IKPDARTFNILIHGFCKARKFDDARAMMDLMK 300
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PLN03077 PLN03077
Protein ECB2; Provisional
 307-443 1.26e-08

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 57.94  E-value: 1.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  307 DVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKED-GCVPDAKFYSSLI 385
Cdd:PLN03077 553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVV 632

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15228825  386 HILSKTGRFKDAAEIFEDMTnqgVRRDVLVYNTMISAA-LHHSRD--EMALRLLKRMEDEE 443
Cdd:PLN03077 633 DLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACrIHRHVElgELAAQHIFELDPNS 690
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 263-393 6.01e-08

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: 53.55  E-value: 6.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   263 LKLFDTIKPD-----ARTFNILIHgFC----------KARKFDDARAMMDLMKVTEFTPDVVTYTSFVEAYCKEGDFRRV 327
Cdd:pfam17177  31 LALYDAAKAEgvrlaQYHYNVLLY-LCskaadatdlkPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15228825   328 NEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSKTGR 393
Cdd:pfam17177 110 FDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGR 175
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 355-458 3.64e-07

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: 51.24  E-value: 3.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   355 KSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSKTG---------RFKDAAEIFEDMTNQGVRRDVLVYNTMISAALH 425
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVSPNEATYTAVARLAAA 102

                          90       100       110
                  ....*....|....*....|....*....|...
gi 15228825   426 HSRDEMALRLLKRMEDeegESCSPNVETYAPLL 458
Cdd:pfam17177 103 KGDGDLAFDLVKEMEA---AGVSPRLRSYSPAL 132
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 344-378 4.00e-07

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: 46.29  E-value: 4.00e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15228825   344 VTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDA 378
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03077 PLN03077
Protein ECB2; Provisional
 234-386 5.56e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 52.54  E-value: 5.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  234 GVKTDTIAMNSLMDALVKENSIEHAhevfLKLFDTIKPDARTFNILIHGFCKARKFDDARAMMDLMKVTEFTPDVVTYTS 313
Cdd:PLN03077 519 GIGFDGFLPNALLDLYVRCGRMNYA----WNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFIS 594

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15228825  314 FVEAYCKEGDFRRVNEMLEEMREN-GCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDgcvPDAKFYSSLIH 386
Cdd:PLN03077 595 LLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKMPIT---PDPAVWGALLN 665
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 309-343 1.14e-06

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: 45.14  E-value: 1.14e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15228825   309 VTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNV 343
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 ...
 376-422 1.78e-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: 45.05  E-value: 1.78e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15228825   376 PDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISA 422
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 274-308 1.96e-06

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: 44.37  E-value: 1.96e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15228825   274 RTFNILIHGFCKARKFDDARAMMDLMKVTEFTPDV 308
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 306-335 5.75e-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: 5.75e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 15228825   306 PDVVTYTSFVEAYCKEGDFRRVNEMLEEMR 335
Cdd:pfam12854   5 PDVVTYNTLINGLCRAGRVDEAFELLDEME 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 211-438 8.30e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.80  E-value: 8.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825 211 RRLAKSGKYNKAVDAFLEMEKsygVKTDTI-AMNSLMDALVKENSIEHAHEVFLKLFDTIKPDARTFNILIHGFCKARKF 289
Cdd:COG2956  16 LNYLLNGQPDKAIDLLEEALE---LDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALLELAQDYLKAGLL 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825 290 DDARAM-MDLMKVTEFTPDVvtYTSFVEAYCKEGDFRRVNEMLEEMRENGcNPNVVTYTIVMHSLGKSKQVAEALGVYEK 368
Cdd:COG2956  93 DRAEELlEKLLELDPDDAEA--LRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAIEALEK 169

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15228825 369 -MKEDgcvPD-AKFYSSLIHILSKTGRFKDAAEIFEDMTNQGvRRDVLVYNTMISAALHHSRDEMALRLLKR 438
Cdd:COG2956 170 aLKLD---PDcARALLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEALELLRK 237
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 400-458 1.32e-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: 43.12  E-value: 1.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15228825   400 IFEDMTNQGVRRDVLVYNTMISAALHHSRDEMALRLLKRMEdEEGesCSPNVETYAPLL 458
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMK-KKG--IKPTLDTYNAIL 57
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 309-339 1.55e-05

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: 41.68  E-value: 1.55e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15228825   309 VTYTSFVEAYCKEGDFRRVNEMLEEMRENGC 339
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 330-385 2.75e-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: 2.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15228825   330 MLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLI 385
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 337-370 2.76e-05

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: 41.18  E-value: 2.76e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15228825   337 NGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMK 370
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 344-374 8.39e-05

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: 39.76  E-value: 8.39e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15228825   344 VTYTIVMHSLGKSKQVAEALGVYEKMKEDGC 374
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 365-422 1.20e-04

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: 40.42  E-value: 1.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15228825   365 VYEKMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISA 422
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 411-454 1.84e-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: 1.84e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15228825   411 RDVLVYNTMISAALHHSRDEMALRLLKRMEDeegESCSPNVETY 454
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKK---RGVKPNVYTY 41
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 485-531 2.13e-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: 2.13e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15228825   485 DVSTYILLIRGLCMSGKVEEACLFFEEAVRKGMVPRDSTCKMLVDEL 531
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 381-413 4.09e-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: 37.82  E-value: 4.09e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15228825   381 YSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDV 413
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 302-451 4.53e-04

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 42.94  E-value: 4.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  302 TEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGC-NPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKF 380
Cdd:PLN03081  81 TQIRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPfTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYM 160

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15228825  381 YSSLIHILSKTGRFKDAAEIFEDMTNqgvrRDVLVYNTMISAALHHSRDEMALRLLKRMEdEEGESCSPNV 451
Cdd:PLN03081 161 MNRVLLMHVKCGMLIDARRLFDEMPE----RNLASWGTIIGGLVDAGNYREAFALFREMW-EDGSDAEPRT 226
PLN03077 PLN03077
Protein ECB2; Provisional
 203-443 4.69e-04

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 43.30  E-value: 4.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  203 LDTMSKVMRRLAKSGKYNKAVDAFLEMEKsygvkTDTIAMNSLMDALVKENSIEHAHEVFLKLF-DTIKPDARTFNILIH 281
Cdd:PLN03077 222 VDVVNALITMYVKCGDVVSARLVFDRMPR-----RDCISWNAMISGYFENGECLEGLELFFTMReLSVDPDLMTITSVIS 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  282 --GFCKARKFddARAMMDLMKVTEFTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENgcnpNVVTYTIVMHSLGKSKQV 359
Cdd:PLN03077 297 acELLGDERL--GREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLP 370

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  360 AEALGVYEKMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAALHHSRDEMALRLLKRM 439
Cdd:PLN03077 371 DKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNI 450


                 ....
gi 15228825  440 EDEE 443
Cdd:PLN03077 451 PEKD 454
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 480-511 9.49e-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: 36.94  E-value: 9.49e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15228825   480 NDVSIDVSTYILLIRGLCMSGKVEEACLFFEE 511
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 488-519 1.08e-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: 36.66  E-value: 1.08e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15228825   488 TYILLIRGLCMSGKVEEACLFFEEAVRKGMVP 519
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 267-321 1.14e-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: 37.34  E-value: 1.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15228825   267 DTIKPDARTFNILIHGFCKARKFDDARAMMDLMKVTEFTPDVVTYTSFVEAYCKE 321
Cdd:pfam13812   9 DGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 275-300 1.35e-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: 1.35e-03
                          10        20
                  ....*....|....*....|....*.
gi 15228825   275 TFNILIHGFCKARKFDDARAMMDLMK 300
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMK 27
PLN03077 PLN03077
Protein ECB2; Provisional
 272-439 3.03e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.60  E-value: 3.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  272 DARTFNILIHGFCKARKFDDARAMMDLMKvtefTPDVVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMH 351
Cdd:PLN03077 322 DVSVCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLS 397

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825  352 SLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTnqgvRRDVLVYNTMISAALHHSRDEM 431
Cdd:PLN03077 398 ACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIP----EKDVISWTSIIAGLRLNNRCFE 473


                 ....*...
gi 15228825  432 ALRLLKRM 439
Cdd:PLN03077 474 ALIFFRQM 481
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 167-192 5.12e-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: 34.74  E-value: 5.12e-03
                          10        20
                  ....*....|....*....|....*.
gi 15228825   167 HTYNAMVDVLGKCRNFDLMWELVNEM 192
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEM 26
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 487-517 6.46e-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: 34.36  E-value: 6.46e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15228825   487 STYILLIRGLCMSGKVEEACLFFEEAVRKGM 517
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 381-409 6.99e-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: 34.36  E-value: 6.99e-03
                          10        20
                  ....*....|....*....|....*....
gi 15228825   381 YSSLIHILSKTGRFKDAAEIFEDMTNQGV 409
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 325-409 8.62e-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: 37.76  E-value: 8.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15228825   325 RRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYEKMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDM 404
Cdd:pfam17177  72 DRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHM 151


                  ....*
gi 15228825   405 TNQGV 409
Cdd:pfam17177 152 LAHGV 156
 
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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