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Conserved domains on  [gi|15238925|ref|NP_199046|]
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Pentatricopeptide repeat (PPR-like) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13595575)

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
 365-688 5.53e-38

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 152.34  E-value: 5.53e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   365 MEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDR 444
Cdd:PLN03218  463 VQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDR 542

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   445 QFYNVVIDTFGKFNCLDHAMTTFDRMLSEG--IEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMER---RGCLPCattYNI 519
Cdd:PLN03218  543 VVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEyniKGTPEV---YTI 619

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   520 MINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQRGL 599
Cdd:PLN03218  620 AVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   600 SEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEE 679
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQ 779


                  ....*....
gi 15238925   680 MIMSGCKPD 688
Cdd:PLN03218  780 AKEDGIKPN 788
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 341-386 1.95e-12

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: 62.00  E-value: 1.95e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15238925   341 AYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVN 386
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 199-242 3.11e-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.


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 44.66  E-value: 3.11e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSL 242
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 309-351 4.54e-05

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: 41.19  E-value: 4.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15238925   309 SIISALADSGRTLEAEALFEELRQSGIKPRTRAYNALLKGYVK 351
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 365-688 5.53e-38

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 152.34  E-value: 5.53e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   365 MEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDR 444
Cdd:PLN03218  463 VQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDR 542

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   445 QFYNVVIDTFGKFNCLDHAMTTFDRMLSEG--IEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMER---RGCLPCattYNI 519
Cdd:PLN03218  543 VVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEyniKGTPEV---YTI 619

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   520 MINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQRGL 599
Cdd:PLN03218  620 AVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   600 SEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEE 679
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQ 779


                  ....*....
gi 15238925   680 MIMSGCKPD 688
Cdd:PLN03218  780 AKEDGIKPN 788
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 477-524 4.21e-13

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: 63.92  E-value: 4.21e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15238925   477 PDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLPCATTYNIMINSY 524
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 341-386 1.95e-12

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: 62.00  E-value: 1.95e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15238925   341 AYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVN 386
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 480-512 1.21e-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: 48.22  E-value: 1.21e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   480 VTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLP 512
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 199-242 3.11e-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: 44.66  E-value: 3.11e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSL 242
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 279-537 5.42e-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: 48.57  E-value: 5.42e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 279 FAKSGDPSKALQLLgmAQATGLSAKTA-TLVSIISALADSGRTLEAEALFEELRQSGIKpRTRAYNALLKGYVKTGPLKD 357
Cdd:COG2956  18 YLLNGQPDKAIDLL--EEALELDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPD-RAEALLELAQDYLKAGLLDR 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 358 AESMVSEMEKRGVSpDEHTYSLLIDAYVNAGRWESARIVLKEMEAgdVQPNSFVFSRLLAG-FRDRGEWQKTFQVLKemK 436
Cdd:COG2956  95 AEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLK--LGPENAHAYCELAElYLEQGDYDEAIEALE--K 169

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 437 SIGVKPDRQFYNVVI-DTFGKFNCLDHAMTTFDRMLSegIEPDRV-TWNTLIDCHCKHGRHIVAEEMFEAMERRGclPCA 514
Cdd:COG2956 170 ALKLDPDCARALLLLaELYLEQGDYEEAIAALERALE--QDPDYLpALPRLAELYEKLGDPEEALELLRKALELD--PSD 245

                       250       260
                ....*....|....*....|...
gi 15238925 515 TTYNIMINSYGDQERWDDMKRLL 537
Cdd:COG2956 246 DLLLALADLLERKEGLEAALALL 268
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 340-374 7.04e-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: 43.21  E-value: 7.04e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15238925   340 RAYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDE 374
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 ...
 309-351 4.54e-05

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: 41.19  E-value: 4.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15238925   309 SIISALADSGRTLEAEALFEELRQSGIKPRTRAYNALLKGYVK 351
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 199-231 4.68e-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: 40.90  E-value: 4.68e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSD 231
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 365-688 5.53e-38

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 152.34  E-value: 5.53e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   365 MEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDR 444
Cdd:PLN03218  463 VQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDR 542

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   445 QFYNVVIDTFGKFNCLDHAMTTFDRMLSEG--IEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMER---RGCLPCattYNI 519
Cdd:PLN03218  543 VVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEyniKGTPEV---YTI 619

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   520 MINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQRGL 599
Cdd:PLN03218  620 AVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKN 699

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   600 SEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEE 679
Cdd:PLN03218  700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQ 779


                  ....*....
gi 15238925   680 MIMSGCKPD 688
Cdd:PLN03218  780 AKEDGIKPN 788
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 199-597 1.11e-33

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 138.86  E-value: 1.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSLTRSNKIDSvmLLRLYKEIERDKLELDVQLVNDIIMG 278
Cdd:PLN03218  439 TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDA--MFEVFHEMVNAGVEANVHTFGALIDG 516

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   279 FAKSGDPSKALQLLGMaqatglsaktatlvsiisaladsgrtleaealfeeLRQSGIKPRTRAYNALLKGYVKTGPLKDA 358
Cdd:PLN03218  517 CARAGQVAKAFGAYGI-----------------------------------MRSKNVKPDRVVFNALISACGQSGAVDRA 561

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   359 ESMVSEM--EKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMK 436
Cdd:PLN03218  562 FDVLAEMkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK 641

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   437 SIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLPCATT 516
Cdd:PLN03218  642 KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVST 721

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   517 YNIMINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQ 596
Cdd:PLN03218  722 MNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLR 801


                  .
gi 15238925   597 R 597
Cdd:PLN03218  802 R 802
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 255-663 2.65e-29

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 124.21  E-value: 2.65e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  255 RLYKEIERDKLELDVQLVNDIIMGFAKSGDPSKALQLL-GMAQATGLSAKTatlvsIISALADSGRTLEAEALFEELRQS 333
Cdd:PLN03081 144 AVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFdEMPERNLASWGT-----IIGGLVDAGNYREAFALFREMWED 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  334 GIKPRTRAYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEM-EAGDVQPNSfvf 412
Cdd:PLN03081 219 GSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMpEKTTVAWNS--- 295

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  413 srLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHCKH 492
Cdd:PLN03081 296 --MLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKW 373

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  493 GRHIVAEEMFEAMERRgclpcattyniminsygdqerwddmkrllgkmksqgilpNVVTHTTLVDVYGKSGRFNDAIECL 572
Cdd:PLN03081 374 GRMEDARNVFDRMPRK---------------------------------------NLISWNALIAGYGNHGRGTKAVEMF 414

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  573 EEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSD-GLKPSLLALNSLINAFGEDRRDAEAFAvlqYMKENGVK 651
Cdd:PLN03081 415 ERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENhRIKPRAMHYACMIELLGREGLLDEAYA---MIRRAPFK 491

                        410
                 ....*....|..
gi 15238925  652 PDVVTYTTLMKA 663
Cdd:PLN03081 492 PTVNMWAALLTA 503
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 335-708 2.16e-27

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 118.83  E-value: 2.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   335 IKPRTRAYNALLKgyvkTGPLKDAESMVSEMEKRG-VSPDEHTYSLLIDAYVNAGRWESARIVLKEMEagdvQPNSFVFS 413
Cdd:PLN03218  370 SPEYIDAYNRLLR----DGRIKDCIDLLEDMEKRGlLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIR----NPTLSTFN 441

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   414 RLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHCKHG 493
Cdd:PLN03218  442 MLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAG 521

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   494 RHIVAEEMFEAMERRGCLPCATTYNIMINSYGDQERWDDMKRLLGKMKSQG--ILPNVVTHTTLVDVYGKSGRFNDAIEC 571
Cdd:PLN03218  522 QVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEV 601

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   572 LEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVK 651
Cdd:PLN03218  602 YQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15238925   652 PDVVTYTTLMKALIRVDKFQKVPVVYEEMIMSGCKPDRKARSMLRSALRYMKQTLRA 708
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKA 738
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 298-666 2.85e-25

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 111.50  E-value: 2.85e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  298 TGLSAKTATLVSIISALADSGRTLEAEALFEELR------------------------------------QSGIKPRTRA 341
Cdd:PLN03081  81 TQIRKSGVSLCSQIEKLVACGRHREALELFEILEagcpftlpastydalveacialksircvkavywhveSSGFEPDQYM 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  342 YNALLKGYVKTGPLKDAESMVSEMEKRgvspDEHTYSLLIDAYVNAGRWESARIVLKEM--EAGDVQPNSFVFS-RLLAG 418
Cdd:PLN03081 161 MNRVLLMHVKCGMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMweDGSDAEPRTFVVMlRASAG 236

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  419 FRD-RGEWQKTFQVLKemksIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMlsegIEPDRVTWNTLIDCHCKHGRHIV 497
Cdd:PLN03081 237 LGSaRAGQQLHCCVLK----TGVVGDTFVSCALIDMYSKCGDIEDARCVFDGM----PEKTTVAWNSMLAGYALHGYSEE 308

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  498 AEEMFEAMERRGCLPCATTYNIMINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKS 577
Cdd:PLN03081 309 ALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR 388

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  578 VGLkpssTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKEN-GVKPDVVT 656
Cdd:PLN03081 389 KNL----ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENhRIKPRAMH 464

                        410
                 ....*....|
gi 15238925  657 YTTLMKALIR 666
Cdd:PLN03081 465 YACMIELLGR 474
PLN03077 PLN03077
Protein ECB2; Provisional
 199-700 9.77e-21

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 97.61  E-value: 9.77e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSLTrsnkidSVMLLRLYKEIE----RDKLELDVQLVND 274
Cdd:PLN03077 154 SWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCG------GIPDLARGREVHahvvRFGFELDVDVVNA 227

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  275 IIMGFAKSGDPSKALQLL-GMAQATGLSAKtatlvSIISALADSGRTLEAEALFEELRQSGIKPRTRAYNALLKGYVKTG 353
Cdd:PLN03077 228 LITMYVKCGDVVSARLVFdRMPRRDCISWN-----AMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLG 302

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  354 PLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVqpnsFVFSRLLAGFRDRGEWQKTFQVLK 433
Cdd:PLN03077 303 DERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA----VSWTAMISGYEKNGLPDKALETYA 378

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  434 EMKSIGVKPDR-----------------------------------QFYNVVIDTFGKFNCLDHAMTTFDRMlsegIEPD 478
Cdd:PLN03077 379 LMEQDNVSPDEitiasvlsacaclgdldvgvklhelaerkglisyvVVANALIEMYSKCKCIDKALEVFHNI----PEKD 454

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  479 RVTWNTLIDCHCKHGRHIVAEEMFEAM------------------ERRGCLPCATTynimINSYGdqerwddmkrLLGKM 540
Cdd:PLN03077 455 VISWTSIIAGLRLNNRCFEALIFFRQMlltlkpnsvtliaalsacARIGALMCGKE----IHAHV----------LRTGI 520

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  541 KSQGILPNvvthtTLVDVYGKSGRFNDAIE--CLEEmKSVGlkpsstMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPS 618
Cdd:PLN03077 521 GFDGFLPN-----ALLDLYVRCGRMNYAWNqfNSHE-KDVV------SWNILLTGYVAHGKGSMAVELFNRMVESGVNPD 588

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  619 LLALNSLINAFGEDRRDAEAFAVLQYMKEN-GVKPDVVTYTTLMKALIRVDKFQKVPVVYEEMIMsgcKPDRKARSMLRS 697
Cdd:PLN03077 589 EVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYACVVDLLGRAGKLTEAYNFINKMPI---TPDPAVWGALLN 665


                 ...
gi 15238925  698 ALR 700
Cdd:PLN03077 666 ACR 668
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 169-708 2.78e-15

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 79.92  E-value: 2.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   169 LYSILIHALGRSEKLYEAF--LLSQKQTLTPL-----TYNALIGACARNNDIEKALNLiakmrqdgYQSdfvnyslviqs 241
Cdd:PLN03218  544 VFNALISACGQSGAVDRAFdvLAEMKAETHPIdpdhiTVGALMKACANAGQVDRAKEV--------YQM----------- 604

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   242 ltrsnkidsvmllrlykeierdkleldvqlvndiimgfaksgdpskalqllgmaqatglsaktatlvsiisaladsgrtl 321
Cdd:PLN03218      --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   322 eaealfeeLRQSGIKPRTRAYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEME 401
Cdd:PLN03218  605 --------IHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDAR 676

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   402 AGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVT 481
Cdd:PLN03218  677 KQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTIT 756

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   482 WNTLidchckhgrhivaeemFEAMERRgclpcattyniminsyGDQERWDDmkrLLGKMKSQGILPNVVTHTTLVD---- 557
Cdd:PLN03218  757 YSIL----------------LVASERK----------------DDADVGLD---LLSQAKEDGIKPNLVMCRCITGlclr 801

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   558 ------------VYGKSGRF-------NDAIECLEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPS 618
Cdd:PLN03218  802 rfekacalgepvVSFDSGRPqienkwtSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQK 881

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   619 LLALNSLINAFGEdrRDAEAFAVLQYMKENGVKPDVvtyttlmkalirvdKFQKVPVVYEEMIMsgckPDRKARSMLRSA 698
Cdd:PLN03218  882 QSNLSTLVDGFGE--YDPRAFSLLEEAASLGVVPSV--------------SFKKSPIVIDAEEL----PVFAAEVYLLTI 941

                         570
                  ....*....|
gi 15238925   699 LRYMKQTLRA 708
Cdd:PLN03218  942 LKGLKHRLAA 951
PLN03077 PLN03077
Protein ECB2; Provisional
 188-586 4.59e-15

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 79.12  E-value: 4.59e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  188 LLSQKQTLTPLTYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSLTRSNKIDsvMLLRLYKEIERDKLEL 267
Cdd:PLN03077 345 VFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLD--VGVKLHELAERKGLIS 422

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  268 DVQLVNDIIMGFAKSGDPSKALQ-----------------------------LLGMAQATG-LSAKTATLVSIISALAD- 316
Cdd:PLN03077 423 YVVVANALIEMYSKCKCIDKALEvfhnipekdviswtsiiaglrlnnrcfeaLIFFRQMLLtLKPNSVTLIAALSACARi 502

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  317 ----SGRTLEAEALFEELRQSGIKPrtrayNALLKGYVKTGPLKDAESMVSEMEKrgvspDEHTYSLLIDAYVNAGRWES 392
Cdd:PLN03077 503 galmCGKEIHAHVLRTGIGFDGFLP-----NALLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSM 572

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  393 ARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMK-SIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMl 471
Cdd:PLN03077 573 AVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEeKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM- 651

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  472 seGIEPDRVTWNTLIDChCKHGRHI-----VAEEMFEaMErrgclPCATTYNIMI-NSYGDQERWDDMKRLLGKMKSQGI 545
Cdd:PLN03077 652 --PITPDPAVWGALLNA-CRIHRHVelgelAAQHIFE-LD-----PNSVGYYILLcNLYADAGKWDEVARVRKTMRENGL 722

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15238925  546 lpNVVTHTTLVDVYGKSGRF-------------NDAIECL-EEMKSVGL--KPSSTM 586
Cdd:PLN03077 723 --TVDPGCSWVEVKGKVHAFltddeshpqikeiNTVLEGFyEKMKASGLagSESSSM 777
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 477-524 4.21e-13

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: 63.92  E-value: 4.21e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15238925   477 PDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLPCATTYNIMINSY 524
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 341-386 1.95e-12

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: 62.00  E-value: 1.95e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 15238925   341 AYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVN 386
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 343-664 3.23e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 69.88  E-value: 3.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  343 NALLKGYVKTGPLKDAESMVSEMEKRgvspDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFS---RLLAGF 419
Cdd:PLN03077 125 NAMLSMFVRFGELVHAWYVFGKMPER----DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPcvlRTCGGI 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  420 RDrgeWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEgiepDRVTWNTLIDCHCKHGRHIVAE 499
Cdd:PLN03077 201 PD---LARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGL 273

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  500 EMFEAME-----------------------------------RRGCLPCATTYNIMINSYGDQERWDDMKRLLGKMKSQg 544
Cdd:PLN03077 274 ELFFTMRelsvdpdlmtitsvisacellgderlgremhgyvvKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK- 352

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  545 ilpNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPSLLALNS 624
Cdd:PLN03077 353 ---DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANA 429

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 15238925  625 LINAFGEDRRDAEAFAVLQYMKENgvkpDVVTYTTLMKAL 664
Cdd:PLN03077 430 LIEMYSKCKCIDKALEVFHNIPEK----DVISWTSIIAGL 465
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 535-597 4.49e-11

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: 58.52  E-value: 4.49e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238925   535 RLLGKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQR 597
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 547-596 1.07e-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: 56.99  E-value: 1.07e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15238925   547 PNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQ 596
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 ...
 617-664 2.51e-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: 2.51e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15238925   617 PSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKAL 664
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 512-561 2.59e-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: 2.59e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15238925   512 PCATTYNIMINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGK 561
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 280-432 1.69e-09

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: 58.18  E-value: 1.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   280 AKSGDPSKALQLLGMAQATGLSAKT---ATLVSIISALADSGRTLEAEAL------FEELRQSGIKPRTRAYNALLKGYV 350
Cdd:pfam17177  22 SKHADATGALALYDAAKAEGVRLAQyhyNVLLYLCSKAADATDLKPQLAAdrgfevFEAMKAQGVSPNEATYTAVARLAA 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   351 KTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQ 430
Cdd:pfam17177 102 AKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYA 181


                  ..
gi 15238925   431 VL 432
Cdd:pfam17177 182 YL 183
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 467-684 1.73e-09

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 61.04  E-value: 1.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  467 FDRMLSEGIEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLpcatTYNIMINSYGDQERWDDMKRLLGKMksQGIL 546
Cdd:PLN03081 146 YWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLA----SWGTIIGGLVDAGNYREAFALFREM--WEDG 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925  547 PNVVTHTTLVDVYGKSG----RFNDAIECLeeMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTsdglKPSLLAL 622
Cdd:PLN03081 220 SDAEPRTFVVMLRASAGlgsaRAGQQLHCC--VLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAW 293

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238925  623 NSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEEMIMSG 684
Cdd:PLN03081 294 NSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTG 355
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 447-491 2.22e-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: 50.44  E-value: 2.22e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 15238925   447 YNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHCK 491
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 326-386 2.59e-08

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: 50.82  E-value: 2.59e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238925   326 LFEELRQSGIKPRTRAYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVN 386
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 572-630 5.09e-08

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: 50.05  E-value: 5.09e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15238925   572 LEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPSLLALNSLINAFG 630
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 473-506 5.83e-08

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: 48.88  E-value: 5.83e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15238925   473 EGIEPDRVTWNTLIDCHCKHGRHIVAEEMFEAME 506
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 ...
 480-510 9.63e-08

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: 48.23  E-value: 9.63e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15238925   480 VTWNTLIDCHCKHGRHIVAEEMFEAMERRGC 510
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 480-512 1.21e-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: 48.22  E-value: 1.21e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   480 VTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLP 512
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 652-688 3.01e-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: 47.36  E-value: 3.01e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 15238925   652 PDVVTYTTLMKALIRVDKFQKVPVVYEEMIMSGCKPD 688
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPN 37
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 323-442 3.14e-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: 51.63  E-value: 3.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   323 AEALFEELRQSGIKPRTRAYNALLkgYV-----------KTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWE 391
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLL--YLcskaadatdlkPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGD 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15238925   392 SARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKP 442
Cdd:pfam17177 108 LAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 544-576 3.14e-07

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: 46.96  E-value: 3.14e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   544 GILPNVVTHTTLVDVYGKSGRFNDAIECLEEMK 576
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 396-456 3.38e-07

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: 47.74  E-value: 3.38e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238925   396 VLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGK 456
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 607-663 4.31e-07

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: 47.35  E-value: 4.31e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15238925   607 FRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMKENGVKPDVVTYTTLMKA 663
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 516-549 5.09e-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: 5.09e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15238925   516 TYNIMINSYGDQERWDDMKRLLGKMKSQGILPNV 549
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 372-419 5.59e-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: 46.59  E-value: 5.59e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15238925   372 PDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGF 419
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 467-526 3.01e-06

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: 45.04  E-value: 3.01e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   467 FDRMLSEGIEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLPCATTYNIMINSYGD 526
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 199-242 3.11e-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: 44.66  E-value: 3.11e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSDFVNYSLVIQSL 242
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 550-584 5.25e-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: 43.60  E-value: 5.25e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15238925   550 VTHTTLVDVYGKSGRFNDAIECLEEMKSVGLKPSS 584
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 279-537 5.42e-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: 48.57  E-value: 5.42e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 279 FAKSGDPSKALQLLgmAQATGLSAKTA-TLVSIISALADSGRTLEAEALFEELRQSGIKpRTRAYNALLKGYVKTGPLKD 357
Cdd:COG2956  18 YLLNGQPDKAIDLL--EEALELDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPD-RAEALLELAQDYLKAGLLDR 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 358 AESMVSEMEKRGVSpDEHTYSLLIDAYVNAGRWESARIVLKEMEAgdVQPNSFVFSRLLAG-FRDRGEWQKTFQVLKemK 436
Cdd:COG2956  95 AEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLK--LGPENAHAYCELAElYLEQGDYDEAIEALE--K 169

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 437 SIGVKPDRQFYNVVI-DTFGKFNCLDHAMTTFDRMLSegIEPDRV-TWNTLIDCHCKHGRHIVAEEMFEAMERRGclPCA 514
Cdd:COG2956 170 ALKLDPDCARALLLLaELYLEQGDYEEAIAALERALE--QDPDYLpALPRLAELYEKLGDPEEALELLRKALELD--PSD 245

                       250       260
                ....*....|....*....|...
gi 15238925 515 TTYNIMINSYGDQERWDDMKRLL 537
Cdd:COG2956 246 DLLLALADLLERKEGLEAALALL 268
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 340-374 7.04e-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: 43.21  E-value: 7.04e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15238925   340 RAYNALLKGYVKTGPLKDAESMVSEMEKRGVSPDE 374
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 379-643 8.13e-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: 48.19  E-value: 8.13e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 379 LLIDAYVNAGRWESARIVLKEMEAGDvqPNSFVFSRLLAG-FRDRGEWQKTFQVLKEMksIGVKPDRQFYNVVI-DTFGK 456
Cdd:COG2956  13 FKGLNYLLNGQPDKAIDLLEEALELD--PETVEAHLALGNlYRRRGEYDRAIRIHQKL--LERDPDRAEALLELaQDYLK 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 457 FNCLDHAMTTFDRMLSEGIEpDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGcLPCATTYNIMINSYGDQERWDDMKRL 536
Cdd:COG2956  89 AGLLDRAEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAIEA 166

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 537 LGKMksQGILPN-VVTHTTLVDVYGKSGRFNDAIECLEEMksVGLKPSST-MYNALINAYAQRGLSEQAVNAFRvmTSDG 614
Cdd:COG2956 167 LEKA--LKLDPDcARALLLLAELYLEQGDYEEAIAALERA--LEQDPDYLpALPRLAELYEKLGDPEEALELLR--KALE 240

                       250       260
                ....*....|....*....|....*....
gi 15238925 615 LKPSLLALNSLINAFGEDRRDAEAFAVLQ 643
Cdd:COG2956 241 LDPSDDLLLALADLLERKEGLEAALALLE 269
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 655-688 1.36e-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: 42.44  E-value: 1.36e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15238925   655 VTYTTLMKALIRVDKFQKVPVVYEEMIMSGCKPD 688
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 407-456 1.60e-05

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: 1.60e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15238925   407 PNSFVFSRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGK 456
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 430-602 1.92e-05

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: 46.24  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   430 QVLKEMKSIGVKPDRQFYNVVI---------DTFGKFNCLDHAMTTFDRMLSEGIEPDrvtwntlidchckhgrhivaEE 500
Cdd:pfam17177  32 ALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPN--------------------EA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   501 MFEAMERRgclpCATTyniminsyGDQERWDDMKRllgKMKSQGILPNVVTHTTLVDVYGKSGRFNDAIECLEEMKSVGL 580
Cdd:pfam17177  92 TYTAVARL----AAAK--------GDGDLAFDLVK---EMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGV 156

                         170       180
                  ....*....|....*....|..
gi 15238925   581 KPSSTMYNALINAYAQRGLSEQ 602
Cdd:pfam17177 157 ELEEPELAALLKVSAKAGRADK 178
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 309-351 4.54e-05

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: 41.19  E-value: 4.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15238925   309 SIISALADSGRTLEAEALFEELRQSGIKPRTRAYNALLKGYVK 351
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 199-231 4.68e-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: 40.90  E-value: 4.68e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDGYQSD 231
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 360-422 5.23e-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: 41.57  E-value: 5.23e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238925   360 SMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDR 422
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 368-401 5.36e-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: 40.79  E-value: 5.36e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15238925   368 RGVSPDEHTYSLLIDAYVNAGRWESARIVLKEME 401
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 ...
 199-227 6.46e-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: 40.53  E-value: 6.46e-05
                          10        20
                  ....*....|....*....|....*....
gi 15238925   199 TYNALIGACARNNDIEKALNLIAKMRQDG 227
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 341-370 1.25e-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: 39.37  E-value: 1.25e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15238925   341 AYNALLKGYVKTGPLKDAESMVSEMEKRGV 370
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 447-478 1.38e-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: 39.36  E-value: 1.38e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15238925   447 YNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPD 478
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 641-689 1.57e-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: 40.03  E-value: 1.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15238925   641 VLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEEMIMSGCKPDR 689
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTL 50
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 548-643 1.69e-04

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 44.98  E-value: 1.69e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 548 NVVTHTTLVDVYGKSGRFNDAIECLEemKSVGLKPSST-MYNALINAYAQRGLSEQAVNAFRVMTSdgLKPSLL-ALNSL 625
Cdd:COG3914 111 NAEALFNLGNLLLALGRLEEALAALR--RALALNPDFAeAYLNLGEALRRLGRLEEAIAALRRALE--LDPDNAeALNNL 186

                        90
                ....*....|....*...
gi 15238925 626 INAFGEDRRDAEAFAVLQ 643
Cdd:COG3914 187 GNALQDLGRLEEAIAAYR 204
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 484-622 1.76e-04

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: 43.54  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   484 TLIDChCKHGRHIVAEEMFEAMERRGCLPCATTYNIMIN--SYGD-------QERWDDMKRLLGKMKSQGILPNVVTHTT 554
Cdd:pfam17177  17 QLDKC-SKHADATGALALYDAAKAEGVRLAQYHYNVLLYlcSKAAdatdlkpQLAADRGFEVFEAMKAQGVSPNEATYTA 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238925   555 LVDVYGKSGRFNDAIECLEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPS---LLAL 622
Cdd:pfam17177  96 VARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEepeLAAL 166
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 550-580 1.96e-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: 38.99  E-value: 1.96e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15238925   550 VTHTTLVDVYGKSGRFNDAIECLEEMKSVGL 580
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 501-561 2.45e-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: 39.65  E-value: 2.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238925   501 MFEAMERRGCLPCATTYNIMINSYGDQERWDDMKRLLGKMKSQGILPNVVTHTTLVDVYGK 561
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 431-486 3.04e-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: 39.26  E-value: 3.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15238925   431 VLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLI 486
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 516-545 4.74e-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: 37.83  E-value: 4.74e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15238925   516 TYNIMINSYGDQERWDDMKRLLGKMKSQGI 545
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 567-673 5.15e-04

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: 42.00  E-value: 5.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   567 DAIECLEEMKSVGLKPSSTMYNALINAYAQRGLSEQAVNAFRVMTSDGLKPSLLALNSLINAFGEDRRDAEAFAVLQYMK 646
Cdd:pfam17177  73 RGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHML 152

                          90       100
                  ....*....|....*....|....*..
gi 15238925   647 ENGVKPDVVTYTTLMKALIRVDKFQKV 673
Cdd:pfam17177 153 AHGVELEEPELAALLKVSAKAGRADKV 179
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 375-409 8.25e-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: 37.43  E-value: 8.25e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15238925   375 HTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNS 409
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 568-687 8.52e-04

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: 41.23  E-value: 8.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   568 AIECLEEMKSVGLKPSSTMYNALIN-----AYAQRGLSEQAV-NAFRV---MTSDGLKPSLLALNSLINAFGEDRRDAEA 638
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYlcskaADATDLKPQLAAdRGFEVfeaMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 15238925   639 FAVLQYMKENGVKPDVVTYTTLMKALIRVDKFQKVPVVYEEMIMSGCKP 687
Cdd:pfam17177 110 FDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 623-654 9.85e-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: 37.05  E-value: 9.85e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15238925   623 NSLINAFGEDRRDAEAFAVLQYMKENGVKPDV 654
Cdd:TIGR00756   4 NTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 586-618 1.34e-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: 1.34e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   586 MYNALINAYAQRGLSEQAVNAFRVMTSDGLKPS 618
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 586-615 2.26e-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: 35.90  E-value: 2.26e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 15238925   586 MYNALINAYAQRGLSEQAVNAFRVMTSDGL 615
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 351-507 2.35e-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: 40.07  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   351 KTGPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAG---------RWESARIVLKEMEAGDVQPNSFVFS---RLLAG 418
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVSPNEATYTavaRLAAA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925   419 FRDRGEwqkTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHCKHGRhivA 498
Cdd:pfam17177 103 KGDGDL---AFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGR---A 176


                  ....*....
gi 15238925   499 EEMFEAMER 507
Cdd:pfam17177 177 DKVYAYLHR 185
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 283-387 3.56e-03

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 40.28  E-value: 3.56e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 283 GDPSKALQLLGMAQATGLSAKTATLVSIISALADSGRTLEAEALFEELRQSGikPR-TRAYNALLKGYVKTGPLKDAESM 361
Cdd:COG3071  64 GDYERRDEYLAQALELAPEAELAVLLTRAELLLDQGQAEQALATLEALRAGA--PRhPQVLRLLLQAYRQLGDWEELLEL 141

                        90       100
                ....*....|....*....|....*.
gi 15238925 362 VSEMEKRGVSPDEHTYSLLIDAYVNA 387
Cdd:COG3071 142 LPALRKHKALSAEEAQALERRAYLGL 167
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 376-401 4.20e-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: 4.20e-03
                          10        20
                  ....*....|....*....|....*.
gi 15238925   376 TYSLLIDAYVNAGRWESARIVLKEME 401
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMK 27
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 508-541 4.98e-03

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: 35.01  E-value: 4.98e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15238925   508 RGCLPCATTYNIMINSYGDQERWDDMKRLLGKMK 541
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 334-366 8.82e-03

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: 34.24  E-value: 8.82e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   334 GIKPRTRAYNALLKGYVKTGPLKDAESMVSEME 366
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 579-611 8.82e-03

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: 34.24  E-value: 8.82e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15238925   579 GLKPSSTMYNALINAYAQRGLSEQAVNAFRVMT 611
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
548-643 9.57e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 38.45  E-value: 9.57e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238925 548 NVVTHTTLVDVYGKSGRFNDAIECLEemKSVGLKPS-STMYNALINAYAQRGLSEQAVNAF-RVMTsdgLKPSL-LALNS 624
Cdd:COG0457   7 DAEAYNNLGLAYRRLGRYEEAIEDYE--KALELDPDdAEALYNLGLAYLRLGRYEEALADYeQALE---LDPDDaEALNN 81

                        90
                ....*....|....*....
gi 15238925 625 LINAFGEDRRDAEAFAVLQ 643
Cdd:COG0457  82 LGLALQALGRYEEALEDYD 100
 
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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