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Conserved domains on  [gi|15227144|ref|NP_179798|]
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pentatricopeptide (PPR) repeat-containing protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 36-784 0e+00

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 543.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   36 VHCRVIKSGLMFSVYLMNNLMNVYSKTGYALHARKLFDEMPLRTAFSWNTVLSAYSKRGdmdstceFFDQLpqrdsvswt 115
Cdd:PLN03077 108 VCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAG-------YFDEA--------- 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  116 tmivgyknIGQYHKairvmgdMVKEGIEPTQFTLTNVLASVAATRCMETGKKVHSFIVKLGLRGNVSVSNSLLNMYAKCG 195
Cdd:PLN03077 172 --------LCLYHR-------MLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCG 236

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  196 DPMMAKFVFDRMVVRDISSWNAMIA------------------------------------------------------- 220
Cdd:PLN03077 237 DVVSARLVFDRMPRRDCISWNAMISgyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvk 316

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  221 ---------------LHMQVGQMDLAMAQFEQMAERDIVTWNSMISGFNQRGYDLRALDIFSKMLRDSLlSPDRFTLASV 285
Cdd:PLN03077 317 tgfavdvsvcnsliqMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNV-SPDEITIASV 395

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  286 LSACANLEKLCIGKQIHSHIVTTGFDISGIVLNALISMYSRCGGVEtarrlieqrgtkdlkiegftalldgyiklgdmnQ 365
Cdd:PLN03077 396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCID---------------------------------K 442

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  366 AKNIFVSLKDRDVVAWTAMIVGYEQHGSYGEAINLFRSMVGGGQrPNSYTLAAMLSVASSLASLSHGKQIHGSAVKSGEI 445
Cdd:PLN03077 443 ALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIG 521

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  446 YSVSVSNALITMYAKAGNITSASRAFDLirCERDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSAC 525
Cdd:PLN03077 522 FDGFLPNALLDLYVRCGRMNYAWNQFNS--HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  526 THAGLVNQGRQYFDMMKDVDKIIPTLSHYACMVDLFGRAGLLQEAQEFIEKMPIEPDVVTWGSLLSACRVHKNIDLGKVA 605
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  606 AERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGFSWIEVKHKVHVFGVEDGTHPEKNEIYMTMKK 685
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEG 759

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  686 IWDEIKKMGYVPDTASVLHDLEEEvKEQILRHHSEKLAIAFGLISTPDKTTLRIMKNLRVCNDCHTAIKFISKLVGREII 765
Cdd:PLN03077 760 FYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREIS 838

                        810
                 ....*....|....*....
gi 15227144  766 VRDTTRFHHFKDGFCSCRD 784
Cdd:PLN03077 839 VRDTEQFHHFKDGECSCGD 857
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 36-784 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 543.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   36 VHCRVIKSGLMFSVYLMNNLMNVYSKTGYALHARKLFDEMPLRTAFSWNTVLSAYSKRGdmdstceFFDQLpqrdsvswt 115
Cdd:PLN03077 108 VCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAG-------YFDEA--------- 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  116 tmivgyknIGQYHKairvmgdMVKEGIEPTQFTLTNVLASVAATRCMETGKKVHSFIVKLGLRGNVSVSNSLLNMYAKCG 195
Cdd:PLN03077 172 --------LCLYHR-------MLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCG 236

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  196 DPMMAKFVFDRMVVRDISSWNAMIA------------------------------------------------------- 220
Cdd:PLN03077 237 DVVSARLVFDRMPRRDCISWNAMISgyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvk 316

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  221 ---------------LHMQVGQMDLAMAQFEQMAERDIVTWNSMISGFNQRGYDLRALDIFSKMLRDSLlSPDRFTLASV 285
Cdd:PLN03077 317 tgfavdvsvcnsliqMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNV-SPDEITIASV 395

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  286 LSACANLEKLCIGKQIHSHIVTTGFDISGIVLNALISMYSRCGGVEtarrlieqrgtkdlkiegftalldgyiklgdmnQ 365
Cdd:PLN03077 396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCID---------------------------------K 442

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  366 AKNIFVSLKDRDVVAWTAMIVGYEQHGSYGEAINLFRSMVGGGQrPNSYTLAAMLSVASSLASLSHGKQIHGSAVKSGEI 445
Cdd:PLN03077 443 ALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIG 521

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  446 YSVSVSNALITMYAKAGNITSASRAFDLirCERDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSAC 525
Cdd:PLN03077 522 FDGFLPNALLDLYVRCGRMNYAWNQFNS--HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  526 THAGLVNQGRQYFDMMKDVDKIIPTLSHYACMVDLFGRAGLLQEAQEFIEKMPIEPDVVTWGSLLSACRVHKNIDLGKVA 605
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  606 AERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGFSWIEVKHKVHVFGVEDGTHPEKNEIYMTMKK 685
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEG 759

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  686 IWDEIKKMGYVPDTASVLHDLEEEvKEQILRHHSEKLAIAFGLISTPDKTTLRIMKNLRVCNDCHTAIKFISKLVGREII 765
Cdd:PLN03077 760 FYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREIS 838

                        810
                 ....*....|....*....
gi 15227144  766 VRDTTRFHHFKDGFCSCRD 784
Cdd:PLN03077 839 VRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 694-786 6.61e-49

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 167.21  E-value: 6.61e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   694 GYVPDTASVLHDLEEEVKEQILRHHSEKLAIAFGLISTPDKTTLRIMKNLRVCNDCHTAIKFISKLVGREIIVRDTTRFH 773
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 15227144   774 HFKDGFCSCRDYW 786
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
479-638 1.08e-05

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 47.69  E-value: 1.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 479 DTVSWTSMIIALAQHGHAEEALELFETMLMegLRPDH-ITYVGVFSACTHAGLVNQGRQYFDMmkdVDKIIPTLSH-YAC 556
Cdd:COG0457   7 DAEAYNNLGLAYRRLGRYEEAIEDYEKALE--LDPDDaEALYNLGLAYLRLGRYEEALADYEQ---ALELDPDDAEaLNN 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 557 MVDLFGRAGLLQEAQEFIEK-MPIEPDVV-TWGSLLSACRVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWE 634
Cdd:COG0457  82 LGLALQALGRYEEALEDYDKaLELDPDDAeALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYE 161


                ....
gi 15227144 635 EAAK 638
Cdd:COG0457 162 EALE 165
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 481-514 6.56e-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: 40.52  E-value: 6.56e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227144   481 VSWTSMIIALAQHGHAEEALELFETMLMEGLRPD 514
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 36-784 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 543.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   36 VHCRVIKSGLMFSVYLMNNLMNVYSKTGYALHARKLFDEMPLRTAFSWNTVLSAYSKRGdmdstceFFDQLpqrdsvswt 115
Cdd:PLN03077 108 VCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAG-------YFDEA--------- 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  116 tmivgyknIGQYHKairvmgdMVKEGIEPTQFTLTNVLASVAATRCMETGKKVHSFIVKLGLRGNVSVSNSLLNMYAKCG 195
Cdd:PLN03077 172 --------LCLYHR-------MLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCG 236

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  196 DPMMAKFVFDRMVVRDISSWNAMIA------------------------------------------------------- 220
Cdd:PLN03077 237 DVVSARLVFDRMPRRDCISWNAMISgyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvk 316

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  221 ---------------LHMQVGQMDLAMAQFEQMAERDIVTWNSMISGFNQRGYDLRALDIFSKMLRDSLlSPDRFTLASV 285
Cdd:PLN03077 317 tgfavdvsvcnsliqMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNV-SPDEITIASV 395

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  286 LSACANLEKLCIGKQIHSHIVTTGFDISGIVLNALISMYSRCGGVEtarrlieqrgtkdlkiegftalldgyiklgdmnQ 365
Cdd:PLN03077 396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCID---------------------------------K 442

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  366 AKNIFVSLKDRDVVAWTAMIVGYEQHGSYGEAINLFRSMVGGGQrPNSYTLAAMLSVASSLASLSHGKQIHGSAVKSGEI 445
Cdd:PLN03077 443 ALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIG 521

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  446 YSVSVSNALITMYAKAGNITSASRAFDLirCERDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSAC 525
Cdd:PLN03077 522 FDGFLPNALLDLYVRCGRMNYAWNQFNS--HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  526 THAGLVNQGRQYFDMMKDVDKIIPTLSHYACMVDLFGRAGLLQEAQEFIEKMPIEPDVVTWGSLLSACRVHKNIDLGKVA 605
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  606 AERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGFSWIEVKHKVHVFGVEDGTHPEKNEIYMTMKK 685
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEG 759

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  686 IWDEIKKMGYVPDTASVLHDLEEEvKEQILRHHSEKLAIAFGLISTPDKTTLRIMKNLRVCNDCHTAIKFISKLVGREII 765
Cdd:PLN03077 760 FYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREIS 838

                        810
                 ....*....|....*....
gi 15227144  766 VRDTTRFHHFKDGFCSCRD 784
Cdd:PLN03077 839 VRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 181-786 5.11e-156

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 470.51  E-value: 5.11e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  181 VSVSNSLLNMYAKCGDPMMAKFVFDRMVVR----DISSWNAMIALHMQVGQMDLAMAQFEQMAERDIVTWNSMISGFNQR 256
Cdd:PLN03081 123 ASTYDALVEACIALKSIRCVKAVYWHVESSgfepDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDA 202

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  257 GYDLRALDIFSKMLRDSLLSPDRfTLASVLSACANLEKLCIGKQIHSHIVTTGFDISGIVLNALISMYSRCGGVETARRl 336
Cdd:PLN03081 203 GNYREAFALFREMWEDGSDAEPR-TFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARC- 280

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  337 ieqrgtkdlkiegftalldgyiklgdmnqaknIFVSLKDRDVVAWTAMIVGYEQHGSYGEAINLFRSMVGGGQRPNSYTL 416
Cdd:PLN03081 281 --------------------------------VFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTF 328

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  417 AAMLSVASSLASLSHGKQIHGSAVKSGEIYSVSVSNALITMYAKAGNITSASRAFDLIRcERDTVSWTSMIIALAQHGHA 496
Cdd:PLN03081 329 SIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-RKNLISWNALIAGYGNHGRG 407

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  497 EEALELFETMLMEGLRPDHITYVGVFSACTHAGLVNQGRQYFDMMKDVDKIIPTLSHYACMVDLFGRAGLLQEAQEFIEK 576
Cdd:PLN03081 408 TKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRR 487

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  577 MPIEPDVVTWGSLLSACRVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGFSW 656
Cdd:PLN03081 488 APFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTW 567

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  657 IEVKHKVHVFGVEDGTHPEKNEIYMTMKKIWDEIKKMGYVPDTASVLHDLEEEVKEQILRHHSEKLAIAFGLISTPDKTT 736
Cdd:PLN03081 568 IEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTP 647

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|
gi 15227144  737 LRIMKNLRVCNDCHTAIKFISKLVGREIIVRDTTRFHHFKDGFCSCRDYW 786
Cdd:PLN03081 648 LQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 694-786 6.61e-49

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 167.21  E-value: 6.61e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   694 GYVPDTASVLHDLEEEVKEQILRHHSEKLAIAFGLISTPDKTTLRIMKNLRVCNDCHTAIKFISKLVGREIIVRDTTRFH 773
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 15227144   774 HFKDGFCSCRDYW 786
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 596-658 5.78e-16

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: 72.58  E-value: 5.78e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15227144   596 HKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGFSWIE 658
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03077 PLN03077
Protein ECB2; Provisional
 391-730 2.95e-15

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 80.28  E-value: 2.95e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  391 HGSYGEAINLFRSMVGGGQRPNSYTLAAMLSVASSLASLSHGKQIHGSAVKSGEIYSVSVSNALITMYAKAGNITSASRA 470
Cdd:PLN03077  64 HGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYV 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  471 FDLIRcERDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSACTHAGLVNQGRQY------FDMMKDV 544
Cdd:PLN03077 144 FGKMP-ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVhahvvrFGFELDV 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  545 DKIIPTLSHYAcmvdlfgRAGLLQEAQEFIEKMP----------------------------------IEPDVVTWGSLL 590
Cdd:PLN03077 223 DVVNALITMYV-------KCGDVVSARLVFDRMPrrdciswnamisgyfengecleglelfftmrelsVDPDLMTITSVI 295

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144  591 SACRVHKNIDLGK-VAAERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMkdgrvKKEQGFSWIEVkhkvhVFGVE 669
Cdd:PLN03077 296 SACELLGDERLGReMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRM-----ETKDAVSWTAM-----ISGYE 365

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15227144  670 DGTHPEKN-EIYMTMkkiwdeiKKMGYVPD---TASVLH------DLEEEVKEQilrhhseKLAIAFGLIS 730
Cdd:PLN03077 366 KNGLPDKAlETYALM-------EQDNVSPDeitIASVLSacaclgDLDVGVKLH-------ELAERKGLIS 422
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 447-654 2.15e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 64.51  E-value: 2.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   447 SVSVSNALITMYAKAGNITSASRAFDLIRcER----DTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVF 522
Cdd:PLN03218  436 TLSTFNMLMSVCASSQDIDGALRVLRLVQ-EAglkaDCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI 514

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   523 SACTHAGLVNQGRQYFDMM--KDV--DKIIPTLSHYACmvdlfGRAGLLQEAQEFIEKM-----PIEPDVVTWGSLLSAC 593
Cdd:PLN03218  515 DGCARAGQVAKAFGAYGIMrsKNVkpDRVVFNALISAC-----GQSGAVDRAFDVLAEMkaethPIDPDHITVGALMKAC 589

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15227144   594 ----------RVHKNIDLGKVAAerllllEPEnsgAYSALANLYSACGKWEEAAKIRKSMKDGRVKKEQGF 654
Cdd:PLN03218  590 anagqvdrakEVYQMIHEYNIKG------TPE---VYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVF 651
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 453-598 1.48e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 61.82  E-value: 1.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   453 ALITMYAKAGNITSASRAFDLIRCER---DTVSWTSMIIALAQHGHAEEALELFETMLMEG--LRPDHITYVGVFSACTH 527
Cdd:PLN03218  512 ALIDGCARAGQVAKAFGAYGIMRSKNvkpDRVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACAN 591

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   528 AGLVNQGRQYFDMM--------------------------------KDVDK--IIPTLSHYACMVDLFGRAGLLQEAQEF 573
Cdd:PLN03218  592 AGQVDRAKEVYQMIheynikgtpevytiavnscsqkgdwdfalsiyDDMKKkgVKPDEVFFSALVDVAGHAGDLDKAFEI 671

                         170       180
                  ....*....|....*....|....*...
gi 15227144   574 IEKMP---IEPDVVTWGSLLSACRVHKN 598
Cdd:PLN03218  672 LQDARkqgIKLGTVSYSSLMGACSNAKN 699
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 478-525 7.39e-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: 51.98  E-value: 7.39e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15227144   478 RDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYVGVFSAC 525
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 266-602 1.09e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 58.74  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   266 FSKMLRDSLLSpdrfTLASVLSACANLEKLCIGKQIHSHIVTTGFDISGIVLNALISMYSRCGGVETARRLIEQRGTKDL 345
Cdd:PLN03218  428 FAKLIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGV 503

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   346 K--IEGFTALLDGYIKLGDMNQAKNIFVSLKDRDV----VAWTAMIVGYEQHGSYGEAINLFRSMVGGGQ--RPNSYTLA 417
Cdd:PLN03218  504 EanVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHpiDPDHITVG 583

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   418 AMLSVASSLASLSHGKQ----IHGSAVK-SGEIYSVSVSNAlitmyAKAGNITSASRAFDLIRceRDTVS----WTSMII 488
Cdd:PLN03218  584 ALMKACANAGQVDRAKEvyqmIHEYNIKgTPEVYTIAVNSC-----SQKGDWDFALSIYDDMK--KKGVKpdevFFSALV 656

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   489 ALAQH-GHAEEALELFETMLMEGLRPDHITYVGVFSACTHAGLVNQGRQYFDMMKDVdKIIPTLSHYACMVDLFGRAGLL 567
Cdd:PLN03218  657 DVAGHaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQL 735

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 15227144   568 QEAQEFIEKMP---IEPDVVTWGSLLSACRVHKNIDLG 602
Cdd:PLN03218  736 PKALEVLSEMKrlgLCPNTITYSILLVASERKDDADVG 773
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 143-525 3.46e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 57.19  E-value: 3.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   143 EPTQFTLTNVLASVAATRCMETGKKVHSFIVKLGLRGNVSVSNSLLNMYAKCG--DPMMAkfVFDRMVVRDIS----SWN 216
Cdd:PLN03218  434 NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGkvDAMFE--VFHEMVNAGVEanvhTFG 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   217 AMIALHMQVGQMDLAMAQFEQMAERDI----VTWNSMISGFNQRGYDLRALDIFSKMLRDSL-LSPDRFTLASVLSACAN 291
Cdd:PLN03218  512 ALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHpIDPDHITVGALMKACAN 591

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   292 LEKLCIGKQIHSHIvtTGFDISGI--VLNALISMYSRCGGVETARRLIEQRGTKDLKIEG--FTALLDGYIKLGDMNQAK 367
Cdd:PLN03218  592 AGQVDRAKEVYQMI--HEYNIKGTpeVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEvfFSALVDVAGHAGDLDKAF 669

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   368 NIFVSLKDRDV----VAWTAMIVGYEQHGSYGEAINLFRSMVGGGQRPnsytlaamlsvasslaslshgkqihgsavksg 443
Cdd:PLN03218  670 EILQDARKQGIklgtVSYSSLMGACSNAKNWKKALELYEDIKSIKLRP-------------------------------- 717

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144   444 eiySVSVSNALITMYAKAGNITSA----SRAFDLIRCErDTVSWTSMIIALAQHGHAEEALELFETMLMEGLRPDHITYV 519
Cdd:PLN03218  718 ---TVSTMNALITALCEGNQLPKAlevlSEMKRLGLCP-NTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793


                  ....*.
gi 15227144   520 GVFSAC 525
Cdd:PLN03218  794 CITGLC 799
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 109-150 1.10e-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: 48.90  E-value: 1.10e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 15227144   109 RDSVSWTTMIVGYKNIGQYHKAIRVMGDMVKEGIEPTQFTLT 150
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYT 42
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 210-253 1.24e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 45.82  E-value: 1.24e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15227144   210 RDISSWNAMIALHMQVGQMDLAMAQFEQMAER----DIVTWNSMISGF 253
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 ...
 376-415 1.24e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 45.82  E-value: 1.24e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15227144   376 RDVVAWTAMIVGYEQHGSYGEAINLFRSMVGGGQRPNSYT 415
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
479-638 1.08e-05

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 47.69  E-value: 1.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 479 DTVSWTSMIIALAQHGHAEEALELFETMLMegLRPDH-ITYVGVFSACTHAGLVNQGRQYFDMmkdVDKIIPTLSH-YAC 556
Cdd:COG0457   7 DAEAYNNLGLAYRRLGRYEEAIEDYEKALE--LDPDDaEALYNLGLAYLRLGRYEEALADYEQ---ALELDPDDAEaLNN 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 557 MVDLFGRAGLLQEAQEFIEK-MPIEPDVV-TWGSLLSACRVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWE 634
Cdd:COG0457  82 LGLALQALGRYEEALEDYDKaLELDPDDAeALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYE 161


                ....
gi 15227144 635 EAAK 638
Cdd:COG0457 162 EALE 165
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 316-577 1.42e-05

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.42  E-value: 1.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 316 VLNALISMYSRCGGVETARRLIEQrgTKDLKIEGFTALL---DGYIKLGDMNQAKNIF---VSLKDRDVVAWTAMIVGYE 389
Cdd:COG2956  44 AHLALGNLYRRRGEYDRAIRIHQK--LLERDPDRAEALLelaQDYLKAGLLDRAEELLeklLELDPDDAEALRLLAEIYE 121

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 390 QHGSYGEAINLFRSMVG-GGQRPNSYTLAAMLsvasslaslshgkqihgsavksgeiysvsvsnalitmYAKAGNITSAS 468
Cdd:COG2956 122 QEGDWEKAIEVLERLLKlGPENAHAYCELAEL-------------------------------------YLEQGDYDEAI 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 469 RAFD-LIRCERDTV-SWTSMIIALAQHGHAEEALELFETMLmeGLRPDHITYVGVFSACTHAglVNQGRQYFDMMKDVDK 546
Cdd:COG2956 165 EALEkALKLDPDCArALLLLAELYLEQGDYEEAIAALERAL--EQDPDYLPALPRLAELYEK--LGDPEEALELLRKALE 240

                       250       260       270
                ....*....|....*....|....*....|.
gi 15227144 547 IIPTLSHYACMVDLFGRAGLLQEAQEFIEKM 577
Cdd:COG2956 241 LDPSDDLLLALADLLERKEGLEAALALLERQ 271
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 481-511 2.50e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 41.68  E-value: 2.50e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227144   481 VSWTSMIIALAQHGHAEEALELFETMLMEGL 511
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 481-514 6.56e-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: 40.52  E-value: 6.56e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227144   481 VSWTSMIIALAQHGHAEEALELFETMLMEGLRPD 514
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 487-638 2.10e-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: 2.10e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 487 IIALAQHGHAEEALELFETMLmeGLRPDHityvgvfsactHAGLVNQGRQYFDMmkdvdkiiptlshyacmvdlfgraGL 566
Cdd:COG3914  85 ALLLQALGRYEEALALYRRAL--ALNPDN-----------AEALFNLGNLLLAL------------------------GR 127

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15227144 567 LQEAQEFIEK-MPIEPD-VVTWGSLLSACRVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAK 638
Cdd:COG3914 128 LEEALAALRRaLALNPDfAEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNALQDLGRLEEAIA 201
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 112-145 2.89e-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: 38.59  E-value: 2.89e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227144   112 VSWTTMIVGYKNIGQYHKAIRVMGDMVKEGIEPT 145
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 ...
 78-121 3.14e-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: 38.88  E-value: 3.14e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15227144    78 RTAFSWNTVLSAYSKRGDMDSTCEFFDQLPQR----DSVSWTTMIVGY 121
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
605-644 3.91e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 40.15  E-value: 3.91e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15227144 605 AAERLLLLEPENSGAYSALANLYSACGKWEEAAKIRKSMK 644
Cdd:COG3063  14 YYEKALELDPDNADALNNLGLLLLEQGRYDEAIALEKALK 53
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 112-142 1.83e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 36.29  E-value: 1.83e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227144   112 VSWTTMIVGYKNIGQYHKAIRVMGDMVKEGI 142
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 ...
 244-274 2.68e-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: 2.68e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227144   244 VTWNSMISGFNQRGYDLRALDIFSKMLRDSL 274
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 453-638 2.79e-03

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: 40.48  E-value: 2.79e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 453 ALITMYAKAGNITSASRAFDLIRcERDTVSWTSMIiALAQ----HGHAEEALELFETMLmeGLRPDHItyvgvfSACTH- 527
Cdd:COG2956  47 ALGNLYRRRGEYDRAIRIHQKLL-ERDPDRAEALL-ELAQdylkAGLLDRAEELLEKLL--ELDPDDA------EALRLl 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 528 AGLVNQGRQY---FDMMKDVDKIIPTLSHYAC-MVDLFGRAGLLQEAQEFIEK-MPIEPDVVtwGSLLSACRVHknIDLG 602
Cdd:COG2956 117 AEIYEQEGDWekaIEVLERLLKLGPENAHAYCeLAELYLEQGDYDEAIEALEKaLKLDPDCA--RALLLLAELY--LEQG 192

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 15227144 603 KVAA-----ERLLLLEPENSGAYSALANLYSACGKWEEAAK 638
Cdd:COG2956 193 DYEEaiaalERALEQDPDYLPALPRLAELYEKLGDPEEALE 233
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 494-639 3.74e-03

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: 40.10  E-value: 3.74e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 494 GHAEEALELFETMLmeGLRPDHIT-YVGVFSACTHAGLVNQGRQYFDMMKDVDKiiPTLSHYACMVDLFGRAGLLQEAQE 572
Cdd:COG2956  56 GEYDRAIRIHQKLL--ERDPDRAEaLLELAQDYLKAGLLDRAEELLEKLLELDP--DDAEALRLLAEIYEQEGDWEKAIE 131

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15227144 573 FIEKM-PIEPDVVTWGSLLSAC-RVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAKI 639
Cdd:COG2956 132 VLERLlKLGPENAHAYCELAELyLEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAA 200
TPR_17 pfam13431
Tetratricopeptide repeat;
605-636 4.49e-03

Tetratricopeptide repeat;


Pssm-ID: 433201 [Multi-domain]  Cd Length: 34  Bit Score: 35.21  E-value: 4.49e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15227144   605 AAERLLLLEPENSGAYSALANLYSACGKWEEA 636
Cdd:pfam13431   1 LYLKALELDPNNADAYYNLAVLLLELGQSETA 32
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 48-92 4.62e-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: 4.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15227144    48 SVYLMNNLMNVYSKTGYALHARKLFDEMPLR----TAFSWNTVLSAYSK 92
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 592-644 5.77e-03

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: 37.86  E-value: 5.77e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15227144 592 ACRVHKNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAK-IRKSMK 644
Cdd:COG4783  13 ALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVlLHEALE 66
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 563-644 6.60e-03

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: 37.86  E-value: 6.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227144 563 RAGLLQEAQEFIEK-MPIEPDVVTWGSLLSACRVH-KNIDLGKVAAERLLLLEPENSGAYSALANLYSACGKWEEAAKI- 639
Cdd:COG4783  16 LAGDYDEAEALLEKaLELDPDNPEAFALLGEILLQlGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALl 95


                ....*
gi 15227144 640 RKSMK 644
Cdd:COG4783  96 EKALK 100
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 476-506 8.26e-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: 34.63  E-value: 8.26e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227144   476 CERDTVSWTSMIIALAQHGHAEEALELFETM 506
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
 
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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