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Conserved domains on  [gi|332640272|gb|AEE73793|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13595554)

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
PLN03077 super family cl33629
Protein ECB2; Provisional
 149-901 2.45e-157

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 483.20  E-value: 2.45e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 149 NSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDTDVVAASALLDMYAKG 228
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 229 KRFVESLRVFQGIPEKNSVSWSAIIAGCVQNNLLSLALKFFKEMqkVNAGVSQSIYA--SVLRSCAALSELRLGGQLHAH 306
Cdd:PLN03077 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRM--LWAGVRPDVYTfpCVLRTCGGIPDLARGREVHAH 212

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 307 ALKSDFAADGIVRTATLDMYAKCDNMQDAQILFDNSENLNRQSYNAMITGYSQEEHGFKALLLFHRLMSSGLGFDEISLS 386
Cdd:PLN03077 213 VVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 387 GVFRACALVKGLSEGLQIYGLAIKSSLSLDVCVANAAIDMYGKCQALAEAFRVFDEMRRRDAVSWNAIIAAHEQNGKGYE 466
Cdd:PLN03077 293 SVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDK 372

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 467 TLFLFVSMLRSRIEPDEFTFGSILKACTG-GSLGYGMEIHSSIVKSGMASNSSVGCSLIDMYSKCGMIEEAEKIHsRFFQ 545
Cdd:PLN03077 373 ALETYALMEQDNVSPDEITIASVLSACAClGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF-HNIP 451

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 546 RANVsgtmeelekmhnkrlqemcVSWNSIISGYVMKEQSEDAqMLFTRMMEMGITPDKFTYATVLDTCANLASAGLGKQI 625
Cdd:PLN03077 452 EKDV-------------------ISWTSIIAGLRLNNRCFEA-LIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEI 511

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 626 HAQVIKKELQSDVYICSTLVDMYSKCGDLHDSRLMFeKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHV 705
Cdd:PLN03077 512 HAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEV 590

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 706 TFISILRACAHMGLIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMPFEADDVIWRTLLGVCTIH 785
Cdd:PLN03077 591 TFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIH 670

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 786 RnNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVELKDELHVFLVGDKAHPR 865
Cdd:PLN03077 671 R-HVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQ 749

                        730       740       750       760
                 ....*....|....*....|....*....|....*....|
gi 332640272 866 WEEIYEELGLIYSEMKP----FDDSSFVRGVEVEEEDQWC 901
Cdd:PLN03077 750 IKEINTVLEGFYEKMKAsglaGSESSSMDEIEVSKDDIFC 789
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 112-155 2.18e-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: 48.13  E-value: 2.18e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332640272  112 RDVVSWNKMINGYSKSNDMFKANSFFNMMPVR----DVVSWNSMLSGY 155
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 81-126 4.86e-03

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: 35.80  E-value: 4.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332640272   81 PTTFVLNCLLQVYTNSRDFVSASMVFDKMPLR----DVVSWNKMINGYSK 126
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 149-901 2.45e-157

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 483.20  E-value: 2.45e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 149 NSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDTDVVAASALLDMYAKG 228
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 229 KRFVESLRVFQGIPEKNSVSWSAIIAGCVQNNLLSLALKFFKEMqkVNAGVSQSIYA--SVLRSCAALSELRLGGQLHAH 306
Cdd:PLN03077 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRM--LWAGVRPDVYTfpCVLRTCGGIPDLARGREVHAH 212

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 307 ALKSDFAADGIVRTATLDMYAKCDNMQDAQILFDNSENLNRQSYNAMITGYSQEEHGFKALLLFHRLMSSGLGFDEISLS 386
Cdd:PLN03077 213 VVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 387 GVFRACALVKGLSEGLQIYGLAIKSSLSLDVCVANAAIDMYGKCQALAEAFRVFDEMRRRDAVSWNAIIAAHEQNGKGYE 466
Cdd:PLN03077 293 SVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDK 372

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 467 TLFLFVSMLRSRIEPDEFTFGSILKACTG-GSLGYGMEIHSSIVKSGMASNSSVGCSLIDMYSKCGMIEEAEKIHsRFFQ 545
Cdd:PLN03077 373 ALETYALMEQDNVSPDEITIASVLSACAClGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF-HNIP 451

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 546 RANVsgtmeelekmhnkrlqemcVSWNSIISGYVMKEQSEDAqMLFTRMMEMGITPDKFTYATVLDTCANLASAGLGKQI 625
Cdd:PLN03077 452 EKDV-------------------ISWTSIIAGLRLNNRCFEA-LIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEI 511

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 626 HAQVIKKELQSDVYICSTLVDMYSKCGDLHDSRLMFeKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHV 705
Cdd:PLN03077 512 HAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEV 590

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 706 TFISILRACAHMGLIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMPFEADDVIWRTLLGVCTIH 785
Cdd:PLN03077 591 TFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIH 670

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 786 RnNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVELKDELHVFLVGDKAHPR 865
Cdd:PLN03077 671 R-HVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQ 749

                        730       740       750       760
                 ....*....|....*....|....*....|....*....|
gi 332640272 866 WEEIYEELGLIYSEMKP----FDDSSFVRGVEVEEEDQWC 901
Cdd:PLN03077 750 IKEINTVLEGFYEKMKAsglaGSESSSMDEIEVSKDDIFC 789
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 787-848 2.75e-18

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 79.51  E-value: 2.75e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332640272  787 NNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVE 848
Cdd:pfam20431   2 SNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
678-825 1.41e-08

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.55  E-value: 1.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 678 GYAHHGKG--EEAIQLFERMIleNIKPNHVTFISIL-RACAHMGLIDKGLEYFymmKRDYGLDPQLPH-YSNMVDILGKS 753
Cdd:COG0457   15 GLAYRRLGryEEAIEDYEKAL--ELDPDDAEALYNLgLAYLRLGRYEEALADY---EQALELDPDDAEaLNNLGLALQAL 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332640272 754 GKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEK 825
Cdd:COG0457   90 GRYEEALEDYDKaLELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEE 162
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 112-155 2.18e-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: 48.13  E-value: 2.18e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332640272  112 RDVVSWNKMINGYSKSNDMFKANSFFNMMPVR----DVVSWNSMLSGY 155
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 670-703 3.16e-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: 47.06  E-value: 3.16e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 332640272  670 VTWNAMICGYAHHGKGEEAIQLFERMILENIKPN 703
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 ...
 81-126 4.86e-03

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: 35.80  E-value: 4.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332640272   81 PTTFVLNCLLQVYTNSRDFVSASMVFDKMPLR----DVVSWNKMINGYSK 126
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 149-901 2.45e-157

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 483.20  E-value: 2.45e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 149 NSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDTDVVAASALLDMYAKG 228
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 229 KRFVESLRVFQGIPEKNSVSWSAIIAGCVQNNLLSLALKFFKEMqkVNAGVSQSIYA--SVLRSCAALSELRLGGQLHAH 306
Cdd:PLN03077 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRM--LWAGVRPDVYTfpCVLRTCGGIPDLARGREVHAH 212

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 307 ALKSDFAADGIVRTATLDMYAKCDNMQDAQILFDNSENLNRQSYNAMITGYSQEEHGFKALLLFHRLMSSGLGFDEISLS 386
Cdd:PLN03077 213 VVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 387 GVFRACALVKGLSEGLQIYGLAIKSSLSLDVCVANAAIDMYGKCQALAEAFRVFDEMRRRDAVSWNAIIAAHEQNGKGYE 466
Cdd:PLN03077 293 SVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDK 372

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 467 TLFLFVSMLRSRIEPDEFTFGSILKACTG-GSLGYGMEIHSSIVKSGMASNSSVGCSLIDMYSKCGMIEEAEKIHsRFFQ 545
Cdd:PLN03077 373 ALETYALMEQDNVSPDEITIASVLSACAClGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF-HNIP 451

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 546 RANVsgtmeelekmhnkrlqemcVSWNSIISGYVMKEQSEDAqMLFTRMMEMGITPDKFTYATVLDTCANLASAGLGKQI 625
Cdd:PLN03077 452 EKDV-------------------ISWTSIIAGLRLNNRCFEA-LIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEI 511

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 626 HAQVIKKELQSDVYICSTLVDMYSKCGDLHDSRLMFeKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHV 705
Cdd:PLN03077 512 HAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEV 590

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 706 TFISILRACAHMGLIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMPFEADDVIWRTLLGVCTIH 785
Cdd:PLN03077 591 TFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIH 670

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 786 RnNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVELKDELHVFLVGDKAHPR 865
Cdd:PLN03077 671 R-HVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQ 749

                        730       740       750       760
                 ....*....|....*....|....*....|....*....|
gi 332640272 866 WEEIYEELGLIYSEMKP----FDDSSFVRGVEVEEEDQWC 901
Cdd:PLN03077 750 IKEINTVLEGFYEKMKAsglaGSESSSMDEIEVSKDDIFC 789
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 391-881 2.91e-113

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 362.65  E-value: 2.91e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 391 ACALVKGLSEGLQIYGLAIKSSLSLDVCVANAAIDMYGKCQALAEAFRVFDEMRRRDAVSWNAIIAAHEQNGKGYETLFL 470
Cdd:PLN03081 132 ACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFAL 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 471 FVSMLRSRIEPDEFTFGSILKACTG-GSLGYGMEIHSSIVKSGMASNSSVGCSLIDMYSKCGMIEEAEKIhsrffqranv 549
Cdd:PLN03081 212 FREMWEDGSDAEPRTFVVMLRASAGlGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV---------- 281

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 550 sgtmeeLEKMHNKRLqemcVSWNSIISGYVMKEQSEDAQMLFTRMMEMGITPDKFTYATVLDTCANLASAGLGKQIHAQV 629
Cdd:PLN03081 282 ------FDGMPEKTT----VAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGL 351

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 630 IKKELQSDVYICSTLVDMYSKCGDLHDSRLMFEKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHVTFIS 709
Cdd:PLN03081 352 IRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLA 431

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 710 ILRACAHMGLIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMPFEADDVIWRTLLGVCTIHRnNV 789
Cdd:PLN03081 432 VLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHK-NL 510

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 790 EVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVELKDELHVFLVGDKAHPRWEEI 869
Cdd:PLN03081 511 ELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREI 590

                        490
                 ....*....|..
gi 332640272 870 YEELGLIYSEMK 881
Cdd:PLN03081 591 YQKLDELMKEIS 602
PLN03077 PLN03077
Protein ECB2; Provisional
 54-457 1.27e-56

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 210.09  E-value: 1.27e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  54 VFKECAKQGALELGKQAHAHMIISGFRPTTFVLNCLLQVYTNSRDFVSASMVFDKMPLRDVVSWNKMINGYSKsndmfka 133
Cdd:PLN03077 294 VISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK------- 366

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 134 nsffnmmpvrdvvswnsmlsgylqNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDT 213
Cdd:PLN03077 367 ------------------------NGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLIS 422

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 214 DVVAASALLDMYAKGKRFVESLRVFQGIPEKNSVSWSAIIAGCVQNNLLSLALKFFKEMqKVNAGVSQSIYASVLRSCAA 293
Cdd:PLN03077 423 YVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQM-LLTLKPNSVTLIAALSACAR 501

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 294 LSELRLGGQLHAHALKSDFAADGIVRTATLDMYAKCDNMQDAQILFdNSENLNRQSYNAMITGYSQEEHGFKALLLFHRL 373
Cdd:PLN03077 502 IGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRM 580

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 374 MSSGLGFDEISLSGVFRACALVKGLSEGLQIY-----GLAIKSSLSLDVCVanaaIDMYGKCQALAEAFRVFDEMR-RRD 447
Cdd:PLN03077 581 VESGVNPDEVTFISLLCACSRSGMVTQGLEYFhsmeeKYSITPNLKHYACV----VDLLGRAGKLTEAYNFINKMPiTPD 656

                        410
                 ....*....|
gi 332640272 448 AVSWNAIIAA 457
Cdd:PLN03077 657 PAVWGALLNA 666
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 179-560 8.37e-47

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 178.91  E-value: 8.37e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 179 DGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDTDVVAASALLDMYAKGKRFVESLRVFQGIPEKNSVSWSAIIAGCVQ 258
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVD 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 259 NNLLSLALKFFKEMQKVNAGVSQSIYASVLRSCAALSELRLGGQLHAHALKSDFAADGIVRTATLDMYAKCDNMQDAQIL 338
Cdd:PLN03081 202 AGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV 281

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 339 FDNSENLNRQSYNAMITGYSQEEHGFKALLLFHRLMSSGLGFDEISLSGVFRACALVKGLSEGLQIYGLAIKSSLSLDVC 418
Cdd:PLN03081 282 FDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIV 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 419 VANAAIDMYGKCQALAEAFRVFDEMRRRDAVSWNAIIAAHEQNGKGYETLFLFVSMLRSRIEPDEFTFGSILKACT-GGS 497
Cdd:PLN03081 362 ANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRySGL 441

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332640272 498 LGYGMEIHSSIVKS-GMASNSSVGCSLIDMYSKCGMIEEAEKIHSR--FFQRANVSGTMEELEKMH 560
Cdd:PLN03081 442 SEQGWEIFQSMSENhRIKPRAMHYACMIELLGREGLLDEAYAMIRRapFKPTVNMWAALLTACRIH 507
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 117-437 1.69e-43

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 168.90  E-value: 1.69e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 117 WNKMINGYSKSNDMFKANSFFNMMPVRDVVSWNSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDT 196
Cdd:PLN03081 161 MNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSA 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 197 SLGMQIHGIVVRVGCDTDVVAASALLDMYAKGKRFVESLRVFQGIPEKNSVSWSAIIAGCVQNNLLSLALKFFKEMQKVN 276
Cdd:PLN03081 241 RAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSG 320

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 277 AGVSQSIYASVLRSCAALSELRLGGQLHAHALKSDFAADGIVRTATLDMYAKCDNMQDAQILFDNSENLNRQSYNAMITG 356
Cdd:PLN03081 321 VSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAG 400

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 357 YSQEEHGFKALLLFHRLMSSGLGFDEISLSGVFRACALvKGLSE-GLQIYGL-----AIKSSLSLDVCVanaaIDMYGKC 430
Cdd:PLN03081 401 YGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRY-SGLSEqGWEIFQSmsenhRIKPRAMHYACM----IELLGRE 475


                 ....*..
gi 332640272 431 QALAEAF 437
Cdd:PLN03081 476 GLLDEAY 482
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 12-292 9.72e-26

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 113.81  E-value: 9.72e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  12 RSVVSFNRCLTEKISY-RRVPSFSYFTDFLNQVNSVSTTNFSFVFKECAKQGALELGKQAHAHMIISGFRPTTFVLNCLL 90
Cdd:PLN03081 187 RNLASWGTIIGGLVDAgNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALI 266

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  91 QVYTNSRDFVSASMVFDKMPLRDVVSWNKMINGYSksndmfkansffnmmpvrdvvswnsmLSGYlqngeSLKSIEVFVD 170
Cdd:PLN03081 267 DMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYA--------------------------LHGY-----SEEALCLYYE 315

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 171 MGREGIEFDGRTFAIILKVCSFLEDTSLGMQIHGIVVRVGCDTDVVAASALLDMYAKGKRFVESLRVFQGIPEKNSVSWS 250
Cdd:PLN03081 316 MRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWN 395

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 332640272 251 AIIAGCVQNNLLSLALKFFKEMQKVNAGVSQSIYASVLRSCA 292
Cdd:PLN03081 396 ALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACR 437
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 787-848 2.75e-18

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 79.51  E-value: 2.75e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332640272  787 NNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLKKEPGCSWVE 848
Cdd:pfam20431   2 SNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 51-261 1.22e-14

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 78.37  E-value: 1.22e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  51 FSFVFKECAKQGALELGKQAHAHMIISGFrpttfvlncllqvytnsrdfvsasmvfdkmPLrDVVSWNKMINGYSKSNDM 130
Cdd:PLN03081 328 FSIMIRIFSRLALLEHAKQAHAGLIRTGF------------------------------PL-DIVANTALVDLYSKWGRM 376

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 131 FKANSFFNMMPVRDVVSWNSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVCSFLEDTSLGMQI-------H 203
Cdd:PLN03081 377 EDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIfqsmsenH 456

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332640272 204 GIVVRV---GCDTDVVAASALLDmyakgkrfvESLRVFQGIPEKNSVS-WSAIIAGC-VQNNL 261
Cdd:PLN03081 457 RIKPRAmhyACMIELLGREGLLD---------EAYAMIRRAPFKPTVNmWAALLTACrIHKNL 510
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 540-839 2.60e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 74.14  E-value: 2.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  540 HSRFFQRANVSGTMEELEK----MHNKRLQemcvSWNSIISGYVMKEQSEDAQMLFTRMMEMGITPDKFTYATVLDTCAN 615
Cdd:PLN03218  409 HAKFFKACKKQRAVKEAFRfaklIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAK 484

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  616 LASAGLGKQIHAQVIKKELQSDVYICSTLVDMYSKCGDLHDS----RLMFEKSLRRDFVTWNAMICGYAHHGKGEEAIQL 691
Cdd:PLN03218  485 SGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAfgayGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDV 564

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  692 FERMILEN--IKPNHVTFISILRACAHMGLIDKGLEYFYMMkRDYGLDPQLPHYSNMVDILGKSGKVKRALELIREMP-- 767
Cdd:PLN03218  565 LAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMI-HEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKkk 643

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 332640272  768 -FEADDVIWRTLLGVCTiHRNNVEVA----EEATAALLRLdpqDSSAYTLLSNVYADAGMWEKVSDLRRNMRGFKLK 839
Cdd:PLN03218  644 gVKPDEVFFSALVDVAG-HAGDLDKAfeilQDARKQGIKL---GTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 670-716 2.01e-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: 62.38  E-value: 2.01e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 332640272  670 VTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHVTFISILRACAH 716
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 569-615 1.59e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 54.29  E-value: 1.59e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 332640272  569 VSWNSIISGYVMKEQSEDAQMLFTRMMEMGITPDKFTYATVLDTCAN 615
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
678-825 1.41e-08

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.55  E-value: 1.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 678 GYAHHGKG--EEAIQLFERMIleNIKPNHVTFISIL-RACAHMGLIDKGLEYFymmKRDYGLDPQLPH-YSNMVDILGKS 753
Cdd:COG0457   15 GLAYRRLGryEEAIEDYEKAL--ELDPDDAEALYNLgLAYLRLGRYEEALADY---EQALELDPDDAEaLNNLGLALQAL 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332640272 754 GKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEK 825
Cdd:COG0457   90 GRYEEALEDYDKaLELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEE 162
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 369-647 2.95e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 57.96  E-value: 2.95e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  369 LFHRLMSSGLGFDEISLSGVFRACALVKGLSEGLQIYGLAIKSSLSLDVCVANAAIDMYGKCQALAEAFRVFDEMRRR-- 446
Cdd:PLN03218  494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEth 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  447 ----DAVSWNAIIAAHEQNGKGYETLFLFVSMLRSRIE--PDEFTFGsiLKACT-GGSLGYGMEIHSSIVKSGMASNSSV 519
Cdd:PLN03218  574 pidpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKgtPEVYTIA--VNSCSqKGDWDFALSIYDDMKKKGVKPDEVF 651

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  520 GCSLIDMYSKCGMIEEAEKIhsrfFQRANVSGT-----------------------MEELEKMHNKRLQEMCVSWNSIIS 576
Cdd:PLN03218  652 FSALVDVAGHAGDLDKAFEI----LQDARKQGIklgtvsysslmgacsnaknwkkaLELYEDIKSIKLRPTVSTMNALIT 727

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 332640272  577 GYVMKEQSEDAQMLFTRMMEMGITPDKFTYATVLDTCANLASAGLGKQIHAQVIKKELQSDVYICSTLVDM 647
Cdd:PLN03218  728 ALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL 798
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 112-155 2.18e-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: 48.13  E-value: 2.18e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332640272  112 RDVVSWNKMINGYSKSNDMFKANSFFNMMPVR----DVVSWNSMLSGY 155
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 ...
 143-190 2.92e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 47.74  E-value: 2.92e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332640272  143 RDVVSWNSMLSGYLQNGESLKSIEVFVDMGREGIEFDGRTFAIILKVC 190
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 670-703 3.16e-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: 47.06  E-value: 3.16e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 332640272  670 VTWNAMICGYAHHGKGEEAIQLFERMILENIKPN 703
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 661-874 5.48e-07

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: 52.04  E-value: 5.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 661 FEKSLRRD---FVTWNAMICGYAHHGKGEEAIQLFERMIleNIKPNHVTFISIL-RACAHMGLIDKGLEYFymmKRDYGL 736
Cdd:COG2956   31 LEEALELDpetVEAHLALGNLYRRRGEYDRAIRIHQKLL--ERDPDRAEALLELaQDYLKAGLLDRAEELL---EKLLEL 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 737 DPQLPH-YSNMVDILGKSGKVKRALELIREM-PFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLS 814
Cdd:COG2956  106 DPDDAEaLRLLAEIYEQEGDWEKAIEVLERLlKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKLDPDCARALLLLA 185

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 332640272 815 NVYADAGMWEK-VSDLRRnmrgfKLKKEPGCSwvelkdelhvflvgdKAHPRWEEIYEELG 874
Cdd:COG2956  186 ELYLEQGDYEEaIAALER-----ALEQDPDYL---------------PALPRLAELYEKLG 226
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 446-493 7.79e-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: 7.79e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332640272  446 RDAVSWNAIIAAHEQNGKGYETLFLFVSMLRSRIEPDEFTFGSILKAC 493
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 578-825 1.48e-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: 50.88  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 578 YVMKEQSEDAQMLFTRMMEmgITPDkftYATVLDTCANLASAgLGK-----QIHAQVIKKELQSDVYiCSTLVDMYSKCG 652
Cdd:COG2956   18 YLLNGQPDKAIDLLEEALE--LDPE---TVEAHLALGNLYRR-RGEydraiRIHQKLLERDPDRAEA-LLELAQDYLKAG 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 653 DLHDSRLMFEKSLR---RDFVTWNAMICGYAHHGKGEEAIQLFERmiLENIKPNHVTFISIL-RACAHMGLIDKGLEYFy 728
Cdd:COG2956   91 LLDRAEELLEKLLEldpDDAEALRLLAEIYEQEGDWEKAIEVLER--LLKLGPENAHAYCELaELYLEQGDYDEAIEAL- 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 729 mmKRDYGLDPQLPHYS-NMVDILGKSGKVKRALELIREMP-FEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQD 806
Cdd:COG2956  168 --EKALKLDPDCARALlLLAELYLEQGDYEEAIAALERALeQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSD 245

                        250
                 ....*....|....*....
gi 332640272 807 SsAYTLLSNVYADAGMWEK 825
Cdd:COG2956  246 D-LLLALADLLERKEGLEA 263
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 670-700 1.72e-06

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: 45.15  E-value: 1.72e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332640272  670 VTWNAMICGYAHHGKGEEAIQLFERMILENI 700
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
648-820 5.53e-06

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 48.85  E-value: 5.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 648 YSKCGDLHDSRLMFEKSLR---RDFVTWNAMICGYAHHGKGEEAIQLFERmILEnIKPNHV-TFISILRACAHMGLIDKG 723
Cdd:COG0457   52 YLRLGRYEEALADYEQALEldpDDAEALNNLGLALQALGRYEEALEDYDK-ALE-LDPDDAeALYNLGLALLELGRYDEA 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 724 LEYFymmKRDYGLDPQLPH-YSNMVDILGKSGKVKRALELIREMPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRL 802
Cdd:COG0457  130 IEAY---ERALELDPDDADaLYNLGIALEKLGRYEEALELLEKLEAAALAALLAAALGEAALALAAAEVLLALLLALEQA 206

                        170
                 ....*....|....*...
gi 332640272 803 DPQDSSAYTLLSNVYADA 820
Cdd:COG0457  207 LRKKLAILTLAALAELLL 224
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 683-831 4.36e-05

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


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 47.30  E-value: 4.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 683 GKGEEAIQLFERMIleNIKPNHVTFISIL-RACAHMGLIDKGLEYFYMMKRdygLDPQLPH-YSNMVDILGKSGKVKRAL 760
Cdd:COG3914   92 GRYEEALALYRRAL--ALNPDNAEALFNLgNLLLALGRLEEALAALRRALA---LNPDFAEaYLNLGEALRRLGRLEEAI 166

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332640272 761 ELIREM-PFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEKVSDLRR 831
Cdd:COG3914  167 AALRRAlELDPDNAEALNNLGNALQDLGRLEEAIAAYRRALELDPDNADAHSNLLFALRQACDWEVYDRFEE 238
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 660-717 7.25e-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: 7.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 332640272  660 MFEKSLRRDFVTWNAMICGYAHHGKGEEAIQLFERMILENIKPNHVTFISILRACAHM 717
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 736-825 9.94e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 43.26  E-value: 9.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 736 LDPQLPH-YSNMVDILGKSGKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLL 813
Cdd:COG4783   33 LDPDNPEaFALLGEILLQLGDLDEAIVLLHEaLELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRL 112

                         90
                 ....*....|..
gi 332640272 814 SNVYADAGMWEK 825
Cdd:COG4783  113 ARAYRALGRPDE 124
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 749-834 1.83e-04

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 42.49  E-value: 1.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 749 ILGKSGKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEK-V 826
Cdd:COG4783   13 ALLLAGDYDEAEALLEKaLELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEaL 92


                 ....*...
gi 332640272 827 SDLRRNMR 834
Cdd:COG4783   93 ALLEKALK 100
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 679-765 2.61e-04

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 42.25  E-value: 2.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 679 YAHHGKGEEAIQLFERMIleNIKPNHVTFISIL-RACAHMGLIDKGLEYFymmKRDYGLDPQLPH-YSNMVDILGKSGKV 756
Cdd:COG5010   64 YNKLGDFEESLALLEQAL--QLDPNNPELYYNLaLLYSRSGDKDEAKEYY---EKALALSPDNPNaYSNLAALLLSLGQD 138


                 ....*....
gi 332640272 757 KRALELIRE 765
Cdd:COG5010  139 DEAKAALQR 147
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 610-783 5.23e-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: 42.38  E-value: 5.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  610 LDTCANLASAGLGKQIHAQVIKKELQSDVYICSTLVDMYSKCGDlhDSRLMFEKSLRRDFvtwnamicgyahhgkgeeai 689
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAAD--ATDLKPQLAADRGF-------------------- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  690 QLFERMILENIKPNHVTFISILRACAHMGLIDkglEYFYMMK--RDYGLDPQLPHYSNMVDILGKSGKVKRALELIREM- 766
Cdd:pfam17177  76 EVFEAMKAQGVSPNEATYTAVARLAAAKGDGD---LAFDLVKemEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMl 152

                         170       180
                  ....*....|....*....|..
gi 332640272  767 -----PFEADDVIwrtLLGVCT 783
Cdd:pfam17177 153 ahgveLEEPELAA---LLKVSA 171
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 146-176 6.45e-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: 6.45e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332640272  146 VSWNSMLSGYLQNGESLKSIEVFVDMGREGI 176
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 569-599 7.19e-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: 7.19e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332640272  569 VSWNSIISGYVMKEQSEDAQMLFTRMMEMGI 599
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 663-695 7.71e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.71  E-value: 7.71e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 332640272  663 KSLRRDFVTWNAMICGYAHHGKGEEAIQLFERM 695
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 244-274 9.57e-04

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 37.73  E-value: 9.57e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332640272  244 KNSVSWSAIIAGCVQNNLLSLALKFFKEMQK 274
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKK 31
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 757-829 1.42e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.60  E-value: 1.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 757 KRALELirempfEADDVIWRTLLGVCTIHRNNVEVAEEATAALLRLDPQDSSAYTLLSNVYADAG-------MWEKVSDL 829
Cdd:COG4235   41 EKALRL------DPDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGdyaeaiaAWQKLLAL 114
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 569-602 4.00e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 4.00e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 332640272  569 VSWNSIISGYVMKEQSEDAQMLFTRMMEMGITPD 602
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 710-839 4.09e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.79  E-value: 4.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272 710 ILRACAHMGLIDKGLEYFYMMKRDYGLDPQLPHYSNMVDILGKSGKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNN 788
Cdd:COG5010   24 VEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQaLQLDPNNPELYYNLALLYSRSGD 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 332640272 789 VEVAEEATAALLRLDPQDSSAYTLLSNVYADAGMWEK-VSDLRRNMRGFKLK 839
Cdd:COG5010  104 KDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEaKAALQRALGTSPLK 155
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
749-825 4.40e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 37.46  E-value: 4.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 332640272 749 ILGKSGKVKRALELIRE-MPFEADDVIWRTLLGVCTIHRNNVEVAEEATAALlRLDPQDSSAYTLLSNVYADAGMWEK 825
Cdd:COG3063    1 LYLKLGDLEEAEEYYEKaLELDPDNADALNNLGLLLLEQGRYDEAIALEKAL-KLDPNNAEALLNLAELLLELGDYDE 77
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 392-541 4.41e-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: 39.69  E-value: 4.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  392 CALVKGLSEGLQIYGLAIKSSLSLD---------VCVANAAIDMYGKCQALAEAFRVFDEMrRRDAVSWN-------AII 455
Cdd:pfam17177  21 CSKHADATGALALYDAAKAEGVRLAqyhynvllyLCSKAADATDLKPQLAADRGFEVFEAM-KAQGVSPNeatytavARL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332640272  456 AAHEQNGkgyETLFLFVS-MLRSRIEPDEFTFGSILKA-CTGGSLGYGMEIHSSIVKSGMASNSSVGCSLIDMYSKCGmi 533
Cdd:pfam17177 100 AAAKGDG---DLAFDLVKeMEAAGVSPRLRSYSPALHAyCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAG-- 174


                  ....*...
gi 332640272  534 eEAEKIHS 541
Cdd:pfam17177 175 -RADKVYA 181
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 691-752 4.83e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.18  E-value: 4.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332640272  691 LFERMILENIKPNHVTFISILRACAHMGLIDKGLEYFYMMKRDyGLDPQLPHYSNMVDILGK 752
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKK-GIKPTLDTYNAILGVIGG 62
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 81-126 4.86e-03

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: 35.80  E-value: 4.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332640272   81 PTTFVLNCLLQVYTNSRDFVSASMVFDKMPLR----DVVSWNKMINGYSK 126
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 115-145 4.94e-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: 4.94e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332640272  115 VSWNKMINGYSKSNDMFKANSFFNMMPVRDV 145
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 438-495 5.83e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.18  E-value: 5.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332640272  438 RVFDEMRRR----DAVSWNAIIAAHEQNGKGYETLFLFVSMLRSRIEPDEFTFGSILKACTG 495
Cdd:pfam13812   1 SILREMVRDgiqlNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 247-274 6.01e-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: 6.01e-03
                          10        20
                  ....*....|....*....|....*...
gi 332640272  247 VSWSAIIAGCVQNNLLSLALKFFKEMQK 274
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKE 28
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
 854-880 8.50e-03

E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif, precedes the DYW domain and, although their role is not clear, they are essential in th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466579 [Multi-domain]  Cd Length: 28  Bit Score: 34.56  E-value: 8.50e-03
                          10        20
                  ....*....|....*....|....*..
gi 332640272  854 HVFLVGDKAHPRWEEIYEELGLIYSEM 880
Cdd:pfam20430   2 YTFFAGDKSHPESKQIYEKLSDLTQRI 28
 
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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