NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|8810476|gb|AAF80137|]
View 

Contains similarity to a hypothetical protein F24K9.13 gi|6006885 from Arabidopsis thaliana gb|AC008153 and contains multiple PPR PF|01535 repeats [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
24-557 3.79e-121

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 377.27  E-value: 3.79e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    24 QQVHAKVIIHGFEDEVVLGSSLTNAYIQSNRLDFATSSFNRIPcwKRNRHSWNTILSGYSKSKTCcySDVLLLYNRMRRH 103
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP--RRDCISWNAMISGYFENGEC--LEGLELFFTMREL 282
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   104 CDGVDSFNLVFAIKACVGLGLLENGILIHGLAMKNGLDKDDYVAPSLVEMYAQLGTMESAQKVFDEIPVRNSVLWGVLMK 183
Cdd:PLN03077 283 SVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMIS 362
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   184 GYLKYSKDPEVFRLFCLMRDTGLALDALTLICLVKACGNVFAGKVGKCVHGVSIRRSFIDQSdYLQASIIDMYVKCRLLD 263
Cdd:PLN03077 363 GYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYV-VVANALIEMYSKCKCID 441
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   264 NARKLFETSVDRNVVMWTTLISGFAKCERAVEAFDLFRQMLReSILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGI 343
Cdd:PLN03077 442 KALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI 520
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   344 EMDAVNFTSFIDMYARCGNIQMARTVFDMMpERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSAC 423
Cdd:PLN03077 521 GFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   424 SHSGNVKEGWKQFESMTRDYGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMPVKPMASAWGALLSACRIHKEVDLAGEI 503
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 8810476   504 AEKLLSMEPEKSSVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATEV 557
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEV 733
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
24-557 3.79e-121

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 377.27  E-value: 3.79e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    24 QQVHAKVIIHGFEDEVVLGSSLTNAYIQSNRLDFATSSFNRIPcwKRNRHSWNTILSGYSKSKTCcySDVLLLYNRMRRH 103
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP--RRDCISWNAMISGYFENGEC--LEGLELFFTMREL 282
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   104 CDGVDSFNLVFAIKACVGLGLLENGILIHGLAMKNGLDKDDYVAPSLVEMYAQLGTMESAQKVFDEIPVRNSVLWGVLMK 183
Cdd:PLN03077 283 SVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMIS 362
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   184 GYLKYSKDPEVFRLFCLMRDTGLALDALTLICLVKACGNVFAGKVGKCVHGVSIRRSFIDQSdYLQASIIDMYVKCRLLD 263
Cdd:PLN03077 363 GYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYV-VVANALIEMYSKCKCID 441
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   264 NARKLFETSVDRNVVMWTTLISGFAKCERAVEAFDLFRQMLReSILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGI 343
Cdd:PLN03077 442 KALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI 520
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   344 EMDAVNFTSFIDMYARCGNIQMARTVFDMMpERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSAC 423
Cdd:PLN03077 521 GFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   424 SHSGNVKEGWKQFESMTRDYGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMPVKPMASAWGALLSACRIHKEVDLAGEI 503
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 8810476   504 AEKLLSMEPEKSSVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATEV 557
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEV 733
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
494-556 2.30e-11

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: 59.09  E-value: 2.30e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 8810476    494 HKEVDLAGEIAEKLLSMEPEKSSVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATE 556
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
379-413 2.32e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.37  E-value: 2.32e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 8810476    379 ISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNS 413
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
24-557 3.79e-121

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 377.27  E-value: 3.79e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    24 QQVHAKVIIHGFEDEVVLGSSLTNAYIQSNRLDFATSSFNRIPcwKRNRHSWNTILSGYSKSKTCcySDVLLLYNRMRRH 103
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP--RRDCISWNAMISGYFENGEC--LEGLELFFTMREL 282
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   104 CDGVDSFNLVFAIKACVGLGLLENGILIHGLAMKNGLDKDDYVAPSLVEMYAQLGTMESAQKVFDEIPVRNSVLWGVLMK 183
Cdd:PLN03077 283 SVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMIS 362
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   184 GYLKYSKDPEVFRLFCLMRDTGLALDALTLICLVKACGNVFAGKVGKCVHGVSIRRSFIDQSdYLQASIIDMYVKCRLLD 263
Cdd:PLN03077 363 GYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYV-VVANALIEMYSKCKCID 441
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   264 NARKLFETSVDRNVVMWTTLISGFAKCERAVEAFDLFRQMLReSILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGI 343
Cdd:PLN03077 442 KALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI 520
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   344 EMDAVNFTSFIDMYARCGNIQMARTVFDMMpERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSAC 423
Cdd:PLN03077 521 GFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   424 SHSGNVKEGWKQFESMTRDYGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMPVKPMASAWGALLSACRIHKEVDLAGEI 503
Cdd:PLN03077 600 SRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELA 679
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 8810476   504 AEKLLSMEPEKSSVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATEV 557
Cdd:PLN03077 680 AQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEV 733
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
116-558 4.13e-112

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 349.17  E-value: 4.13e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   116 IKACVGLGLLENGILIHGLAMKNGLDKDDYVAPSLVEMYAQLGTMESAQKVFDEIPVRNSVLWGVLMKGYLKYSKDPEVF 195
Cdd:PLN03081 130 VEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAF 209
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   196 RLFCLMRDTGLALDALTLICLVKACGNVFAGKVGKCVHGVSIRRSFIDQSdYLQASIIDMYVKCRLLDNARKLFETSVDR 275
Cdd:PLN03081 210 ALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDT-FVSCALIDMYSKCGDIEDARCVFDGMPEK 288
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   276 NVVMWTTLISGFAKCERAVEAFDLFRQMLRESILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGIEMDAVNFTSFID 355
Cdd:PLN03081 289 TTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVD 368
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   356 MYARCGNIQMARTVFDMMPERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSACSHSGNVKEGWKQ 435
Cdd:PLN03081 369 LYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEI 448
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   436 FESMTRDYGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMPVKPMASAWGALLSACRIHKEVDLAGEIAEKLLSMEPEKS 515
Cdd:PLN03081 449 FQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKL 528
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|...
gi 8810476   516 SVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATEVG 558
Cdd:PLN03081 529 NNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVK 571
PLN03077 PLN03077
Protein ECB2; Provisional
173-491 1.75e-35

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 141.91  E-value: 1.75e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   173 RNSVLWGVLMKGYLKyskdpEVFRLFCLMRDTGLALDALTLICLVKACGNVFAGKVGKCVHGVSIRrSFIDQSDYLQASI 252
Cdd:PLN03077  54 SNSQLRALCSHGQLE-----QALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS-SHPSLGVRLGNAM 127
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   253 IDMYVKCRLLDNARKLFETSVDRNVVMWTTLISGFAKCERAVEAFDLFRQMLRESILPNQCTLAAILVSCSSLGSLRHGK 332
Cdd:PLN03077 128 LSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGR 207
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   333 SVHGYMIRNGIEMDAVNFTSFIDMYARCGNIQMARTVFDMMPERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPN 412
Cdd:PLN03077 208 EVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPD 287
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 8810476   413 SVTFVSLLSACSHSGNVKEGwKQFESMTRDYGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMPVKPMASaWGALLSAC 491
Cdd:PLN03077 288 LMTITSVISACELLGDERLG-REMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVS-WTAMISGY 364
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
270-494 3.70e-26

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 113.04  E-value: 3.70e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   270 ETSVDRNVVMWTTLISGFAKCERAVEAFDLFRQM-LRESILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGIEMDAV 348
Cdd:PLN03081  80 DTQIRKSGVSLCSQIEKLVACGRHREALELFEILeAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQY 159
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476   349 NFTSFIDMYARCGNIQMARTVFDMMPERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSACSHSGN 428
Cdd:PLN03081 160 MMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGS 239
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 8810476   429 VKEGwKQFESMTRDYGVVpEEEHYAC-MVDLLGRAGEIGEAKSFIDNMPVKPMAsAWGALLSACRIH 494
Cdd:PLN03081 240 ARAG-QQLHCCVLKTGVV-GDTFVSCaLIDMYSKCGDIEDARCVFDGMPEKTTV-AWNSMLAGYALH 303
PLN03218 PLN03218
maturation of RBCL 1; Provisional
278-510 1.85e-19

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 92.63  E-value: 1.85e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    278 VMWTTLISGFAKCERAVEAFDLFRQMLRESILPNQCTLAAILVSCSSLGSLRHGKSVHGYMIRNGIEMDAVNFTSFIDMY 357
Cdd:PLN03218  473 KLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISAC 552
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    358 ARCGNIQMARTVF-DMMPERNVI-----SWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSACSHSGNVKE 431
Cdd:PLN03218  553 GQSGAVDRAFDVLaEMKAETHPIdpdhiTVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDF 632
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    432 GWKQFESMTRDyGVVPEEEHYACMVDLLGRAGEIGEAKSFIDNMP---VKPMASAWGALLSACRIHKEVDLAGEIAEKLL 508
Cdd:PLN03218  633 ALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARkqgIKLGTVSYSSLMGACSNAKNWKKALELYEDIK 711

                  ..
gi 8810476    509 SM 510
Cdd:PLN03218  712 SI 713
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
494-556 2.30e-11

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: 59.09  E-value: 2.30e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 8810476    494 HKEVDLAGEIAEKLLSMEPEKSSVYVLLSNIYADAGMWEMVNCVRRKMGIKGYRKHVGQSATE 556
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
376-425 4.65e-11

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 57.76  E-value: 4.65e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 8810476    376 RNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSACSH 425
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
273-509 7.23e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 65.28  E-value: 7.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    273 VDRNVVMWTTLISGFAK--------------------------------CER--AVE-AFDLFRQMLRES--ILPNQCTL 315
Cdd:PLN03218  503 VEANVHTFGALIDGCARagqvakafgaygimrsknvkpdrvvfnalisaCGQsgAVDrAFDVLAEMKAEThpIDPDHITV 582
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    316 AAILVSCSSLGSLRHGKSVHGYMIRNGIEMDAVNFTSFIDMYARCGNIQMARTVFDMMPERNV----ISWSSMINAFGIN 391
Cdd:PLN03218  583 GALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVkpdeVFFSALVDVAGHA 662
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    392 GLFEEALDCFHKMKSQNVVPNSVTFVSLLSACSHSGNVKEGWKQFESMtRDYGVVPEEEHYACMVDLLGRAGEIGEAKSF 471
Cdd:PLN03218  663 GDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI-KSIKLRPTVSTMNALITALCEGNQLPKALEV 741
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 8810476    472 IDNMP---VKPMASAWGALLSACRIHKEVDLAGEIAEKLLS 509
Cdd:PLN03218  742 LSEMKrlgLCPNTITYSILLVASERKDDADVGLDLLSQAKE 782
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
275-314 3.57e-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: 46.97  E-value: 3.57e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 8810476    275 RNVVMWTTLISGFAKCERAVEAFDLFRQMLRESILPNQCT 314
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
379-413 2.32e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.37  E-value: 2.32e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 8810476    379 ISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNS 413
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
379-409 1.50e-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: 1.50e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 8810476    379 ISWSSMINAFGINGLFEEALDCFHKMKSQNV 409
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
397-529 4.10e-05

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 45.08  E-value: 4.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    397 ALDCFHKMKSQNVVPNSVTFVSLLSACSHSGNVKEGWKQ---------FESMTRDyGVVPEEEHYACMVDLLGRAGEIGE 467
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQlaadrgfevFEAMKAQ-GVSPNEATYTAVARLAAAKGDGDL 108
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 8810476    468 AKSFIDNMPVK---PMASAWGALLSACRIHKEVDLAGEIAEKLLS--MEPEKSSVYVLLsNIYADAG 529
Cdd:pfam17177 109 AFDLVKEMEAAgvsPRLRSYSPALHAYCEAGDADKAYEVEEHMLAhgVELEEPELAALL-KVSAKAG 174
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
338-391 1.08e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 40.42  E-value: 1.08e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 8810476    338 MIRNGIEMDAVNFTSFIDMYARCGNIQMARTVFDMMPER----NVISWSSMINAFGIN 391
Cdd:pfam13812   6 MVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKgikpTLDTYNAILGVIGGR 63
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
278-308 1.14e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 39.37  E-value: 1.14e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 8810476    278 VMWTTLISGFAKCERAVEAFDLFRQMLRESI 308
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
278-311 1.46e-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: 38.98  E-value: 1.46e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 8810476    278 VMWTTLISGFAKCERAVEAFDLFRQMLRESILPN 311
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
273-303 1.53e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 38.87  E-value: 1.53e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 8810476    273 VDRNVVMWTTLISGFAKCERAVEAFDLFRQM 303
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03218 PLN03218
maturation of RBCL 1; Provisional
343-500 4.40e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 43.33  E-value: 4.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    343 IEMDAVNFTSFIDMYARCGNIQMARTVFDMMPERNVISWSSMINAFGINGLFEEALDCFHKMKSQNVVPNSVTFVSLLSA 422
Cdd:PLN03218  402 LDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLIST 481
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8810476    423 CSHSGNVKEGWKQFESMTrDYGVVPEEEHYACMVDLLGRAGEIgeAKSF-----IDNMPVKPMASAWGALLSACRIHKEV 497
Cdd:PLN03218  482 CAKSGKVDAMFEVFHEMV-NAGVEANVHTFGALIDGCARAGQV--AKAFgaygiMRSKNVKPDRVVFNALISACGQSGAV 558

                  ...
gi 8810476    498 DLA 500
Cdd:PLN03218  559 DRA 561
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH
HHS Vulnerability Disclosure