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Conserved domains on  [gi|15227724|ref|NP_178481|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000225)

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

Gene Ontology:  GO:0003723|GO:0009451
PubMed:  24471833|19004664

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
60-630 8.80e-170

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 500.55  E-value: 8.80e-170
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   60 DSATYSELIKCCISNRAVHEGNLICRHLYFNGHRPMMFLVNVLINMYVKFNLLNDAHQLFDQMPQRNVISWTTMISAYSK 139
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVD 201
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  140 CKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDVRM---LHCGIIKEGLESDVFVRSALIDVFAKLGEPEDALSV 216
Cdd:PLN03081 202 AGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAgqqLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV 281
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  217 FDEMVTGDAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLTSVLRACTGLALLELGMQAHVHIVK--YDQDLI 294
Cdd:PLN03081 282 FDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRtgFPLDIV 361
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  295 LNNALVDMYCKCGSLEDALRVFNQMKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVLFACSHAGL 374
Cdd:PLN03081 362 ANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGL 441
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  375 LEDGWYYFRSMKKLYGIDPVREHYGCMIDLLGKAGKLDDAVKLLNEMECEPDAVTWRTLLGACRVQRNMVLAEYAAKKVI 454
Cdd:PLN03081 442 SEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLY 521
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  455 ALDPEDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKKEPGCSWIEVNKQIHAFIIGDNSHPQIVEVSKKLNQLIHRL 534
Cdd:PLN03081 522 GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEI 601
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  535 TGIGYVPETNFVLQDLEGEQMEDSLRHHSEKLALAFGLMTLPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPI 614
Cdd:PLN03081 602 SEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDAS 681
                        570
                 ....*....|....*.
gi 15227724  615 RYHHFQDGKCSCGDYW 630
Cdd:PLN03081 682 RFHHFKLGKCSCGDYW 697
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
60-630 8.80e-170

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 500.55  E-value: 8.80e-170
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   60 DSATYSELIKCCISNRAVHEGNLICRHLYFNGHRPMMFLVNVLINMYVKFNLLNDAHQLFDQMPQRNVISWTTMISAYSK 139
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVD 201
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  140 CKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDVRM---LHCGIIKEGLESDVFVRSALIDVFAKLGEPEDALSV 216
Cdd:PLN03081 202 AGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAgqqLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV 281
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  217 FDEMVTGDAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLTSVLRACTGLALLELGMQAHVHIVK--YDQDLI 294
Cdd:PLN03081 282 FDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRtgFPLDIV 361
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  295 LNNALVDMYCKCGSLEDALRVFNQMKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVLFACSHAGL 374
Cdd:PLN03081 362 ANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGL 441
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  375 LEDGWYYFRSMKKLYGIDPVREHYGCMIDLLGKAGKLDDAVKLLNEMECEPDAVTWRTLLGACRVQRNMVLAEYAAKKVI 454
Cdd:PLN03081 442 SEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLY 521
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  455 ALDPEDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKKEPGCSWIEVNKQIHAFIIGDNSHPQIVEVSKKLNQLIHRL 534
Cdd:PLN03081 522 GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEI 601
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  535 TGIGYVPETNFVLQDLEGEQMEDSLRHHSEKLALAFGLMTLPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPI 614
Cdd:PLN03081 602 SEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDAS 681
                        570
                 ....*....|....*.
gi 15227724  615 RYHHFQDGKCSCGDYW 630
Cdd:PLN03081 682 RFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
538-630 3.56e-40

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: 141.79  E-value: 3.56e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   538 GYVPETNFVLQDLEGEQMEDSLRHHSEKLALAFGLMTLPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPIRYH 617
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80
                          90
                  ....*....|...
gi 15227724   618 HFQDGKCSCGDYW 630
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
325-358 4.76e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 43.60  E-value: 4.76e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227724   325 ITWSTMISGLAQNGYSQEALKLFERMKSSGTKPN 358
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
286-482 1.78e-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: 47.03  E-value: 1.78e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 286 IVKYDQDLI-LNNALVDMYCKCGSLEDALRVFNQMKERDVITWSTMIsGLAQ----NGYSQEALKLFER-MKSSGTKPNY 359
Cdd:COG2956  34 ALELDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALL-ELAQdylkAGLLDRAEELLEKlLELDPDDAEA 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 360 ITIVGVLFAcsHAGLLEDGWYYFRsmkKLYGIDPVREHYGCMI-DLLGKAGKLDDAVKLLNE-MECEPDAVTWRTLLGAC 437
Cdd:COG2956 113 LRLLAEIYE--QEGDWEKAIEVLE---RLLKLGPENAHAYCELaELYLEQGDYDEAIEALEKaLKLDPDCARALLLLAEL 187
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 15227724 438 RVQR-NMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEE 482
Cdd:COG2956 188 YLEQgDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALE 233
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
60-630 8.80e-170

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 500.55  E-value: 8.80e-170
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   60 DSATYSELIKCCISNRAVHEGNLICRHLYFNGHRPMMFLVNVLINMYVKFNLLNDAHQLFDQMPQRNVISWTTMISAYSK 139
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVD 201
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  140 CKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDVRM---LHCGIIKEGLESDVFVRSALIDVFAKLGEPEDALSV 216
Cdd:PLN03081 202 AGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAgqqLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV 281
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  217 FDEMVTGDAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLTSVLRACTGLALLELGMQAHVHIVK--YDQDLI 294
Cdd:PLN03081 282 FDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRtgFPLDIV 361
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  295 LNNALVDMYCKCGSLEDALRVFNQMKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVLFACSHAGL 374
Cdd:PLN03081 362 ANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGL 441
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  375 LEDGWYYFRSMKKLYGIDPVREHYGCMIDLLGKAGKLDDAVKLLNEMECEPDAVTWRTLLGACRVQRNMVLAEYAAKKVI 454
Cdd:PLN03081 442 SEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLY 521
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  455 ALDPEDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKKEPGCSWIEVNKQIHAFIIGDNSHPQIVEVSKKLNQLIHRL 534
Cdd:PLN03081 522 GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEI 601
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  535 TGIGYVPETNFVLQDLEGEQMEDSLRHHSEKLALAFGLMTLPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPI 614
Cdd:PLN03081 602 SEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDAS 681
                        570
                 ....*....|....*.
gi 15227724  615 RYHHFQDGKCSCGDYW 630
Cdd:PLN03081 682 RFHHFKLGKCSCGDYW 697
PLN03077 PLN03077
Protein ECB2; Provisional
100-628 2.87e-144

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 440.06  E-value: 2.87e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  100 NVLINMYVKFNLLNDAHQLFDQMPQRNVISWTTMISAYSKCKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDVR 179
Cdd:PLN03077 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLD 406
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  180 M---LHCGIIKEGLESDVFVRSALIDVFAKLGEPEDALSVFDEMVTGDAIVWNSIIGGFAQNSRSDVALELFKRMKrAGF 256
Cdd:PLN03077 407 VgvkLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTL 485
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  257 IAEQATLTSVLRACTGLALLELGMQAHVHIVK--YDQDLILNNALVDMYCKCGSLEDALRVFNqMKERDVITWSTMISGL 334
Cdd:PLN03077 486 KPNSVTLIAALSACARIGALMCGKEIHAHVLRtgIGFDGFLPNALLDLYVRCGRMNYAWNQFN-SHEKDVVSWNILLTGY 564
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  335 AQNGYSQEALKLFERMKSSGTKPNYITIVGVLFACSHAGLLEDGWYYFRSMKKLYGIDPVREHYGCMIDLLGKAGKLDDA 414
Cdd:PLN03077 565 VAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEA 644
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  415 VKLLNEMECEPDAVTWRTLLGACRVQRNMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKK 494
Cdd:PLN03077 645 YNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTV 724
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724  495 EPGCSWIEVNKQIHAFIIGDNSHPQIVEVSKKLNQLIHRLTGIGYVPETNFVLQDLEGEQmEDSLRHHSEKLALAFGLMT 574
Cdd:PLN03077 725 DPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIEVSK-DDIFCGHSERLAIAFGLIN 803
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15227724  575 LPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPIRYHHFQDGKCSCGD 628
Cdd:PLN03077 804 TVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
538-630 3.56e-40

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: 141.79  E-value: 3.56e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   538 GYVPETNFVLQDLEGEQMEDSLRHHSEKLALAFGLMTLPIEKVIRIRKNLRICGDCHVFCKLASKLEIRSIVIRDPIRYH 617
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80
                          90
                  ....*....|...
gi 15227724   618 HFQDGKCSCGDYW 630
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
442-502 6.74e-20

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: 83.75  E-value: 6.74e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15227724   442 NMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKKEPGCSWIE 502
Cdd:pfam20431   3 NVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
130-437 1.19e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 71.45  E-value: 1.19e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   130 WTTMISAYSKCKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDVRMLH--CGI-IKEGLESDVFVRSALIDVFAK 206
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFgaYGImRSKNVKPDRVVFNALISACGQ 554
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   207 LGEPEDALSVFDEM------VTGDAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLTSVLRACTglallelgm 280
Cdd:PLN03218  555 SGAVDRAFDVLAEMkaethpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCS--------- 625
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   281 qahvhivkydqdlilnnalvdmycKCGSLEDALRVFNQMKERDV----ITWSTMISGLAQNGYSQEALKLFERMKSSGTK 356
Cdd:PLN03218  626 ------------------------QKGDWDFALSIYDDMKKKGVkpdeVFFSALVDVAGHAGDLDKAFEILQDARKQGIK 681
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   357 PNYITIVGVLFACSHAGLLEDGWYYFRSMKKLyGIDPVREHYGCMIDLLGKAGKLDDAVKLLNEME----CePDAVTWRT 432
Cdd:PLN03218  682 LGTVSYSSLMGACSNAKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQLPKALEVLSEMKrlglC-PNTITYSI 759

                  ....*
gi 15227724   433 LLGAC 437
Cdd:PLN03218  760 LLVAS 764
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
125-172 2.93e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.83  E-value: 2.93e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15227724   125 RNVISWTTMISAYSKCKIHQKALELLVLMLRDNVRPNVYTYSSVLRSC 172
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03218 PLN03218
maturation of RBCL 1; Provisional
112-493 3.15e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 63.36  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   112 LNDAHQLFDQMPQRNVISWTTMISA--YSKCKIhQKALELLVLMLRDNVRPNVYTYSSVLRSCNGMSDV----RMLHcgI 185
Cdd:PLN03218  386 IKDCIDLLEDMEKRGLLDMDKIYHAkfFKACKK-QRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIdgalRVLR--L 462
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   186 IKE-GLESDVFVRSALIDVFAKLGEPEDALSVFDEMVTG--DAIV--WNSIIGGFAqnsrsdvalelfkrmkRAGFIAEQ 260
Cdd:PLN03218  463 VQEaGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAgvEANVhtFGALIDGCA----------------RAGQVAKA 526
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   261 ATLTSVLRACTglallelgmqahvhiVKYDQdlILNNALVDMYCKCGSLEDALRVFNQMKER------DVITWSTMISGL 334
Cdd:PLN03218  527 FGAYGIMRSKN---------------VKPDR--VVFNALISACGQSGAVDRAFDVLAEMKAEthpidpDHITVGALMKAC 589
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   335 AQNGYSQEALKLFERMKSSGTK--PNYITIVgvLFACSHAGLLEDGWYYFRSMKKLyGIDPVREHYGCMIDLLGKAGKLD 412
Cdd:PLN03218  590 ANAGQVDRAKEVYQMIHEYNIKgtPEVYTIA--VNSCSQKGDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLD 666
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   413 DAVKLLNEMECE---PDAVTWRTLLGACRVQRN--MVLAEYAAKKVIALDPEdAGTYTLLSNIYANSQKWDSVEEIRTRM 487
Cdd:PLN03218  667 KAFEILQDARKQgikLGTVSYSSLMGACSNAKNwkKALELYEDIKSIKLRPT-VSTMNALITALCEGNQLPKALEVLSEM 745

                  ....*.
gi 15227724   488 RDRGIK 493
Cdd:PLN03218  746 KRLGLC 751
PLN03218 PLN03218
maturation of RBCL 1; Provisional
304-573 2.04e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 60.66  E-value: 2.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   304 CKC-GSLEDALRVFNQMKERDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPN---YITIVGvlfACSHAGLLEDGW 379
Cdd:PLN03218  416 CKKqRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADcklYTTLIS---TCAKSGKVDAMF 492
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   380 YYFRSMKKLyGIDPVREHYGCMIDLLGKAGKLDDAVK---LLNEMECEPDAVTWRTLLGAC----RVQRNM-VLAEYAAK 451
Cdd:PLN03218  493 EVFHEMVNA-GVEANVHTFGALIDGCARAGQVAKAFGaygIMRSKNVKPDRVVFNALISACgqsgAVDRAFdVLAEMKAE 571
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   452 KViALDPeDAGTYTLLSNIYANSQKWDSVEEIRTRMRDRGIKKEPGCSWIEVnkqihafiigdNSHPQIVEVSKKLnqLI 531
Cdd:PLN03218  572 TH-PIDP-DHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAV-----------NSCSQKGDWDFAL--SI 636
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 15227724   532 HR-LTGIGYVPETNFV--LQDLEGeqmedslrhHSEKLALAFGLM 573
Cdd:PLN03218  637 YDdMKKKGVKPDEVFFsaLVDVAG---------HAGDLDKAFEIL 672
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
297-336 3.35e-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: 52.75  E-value: 3.35e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15227724   297 NALVDMYCKCGSLEDALRVFNQMKER----DVITWSTMISGLAQ 336
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
30-360 6.06e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.12  E-value: 6.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724    30 LSEFTRL----CYQRDLPRAMKAMDSLQSHGLWADSATYSELIKCCISNRAV-------HE-------------GNLI-- 83
Cdd:PLN03218  437 LSTFNMLmsvcASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVdamfevfHEmvnagveanvhtfGALIdg 516
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724    84 CRHLyfnGHRPMMF-LVNVLINMYVK-----FNLLNDA-------HQLFDQMPQRNV---------ISWTTMISAYSKCK 141
Cdd:PLN03218  517 CARA---GQVAKAFgAYGIMRSKNVKpdrvvFNALISAcgqsgavDRAFDVLAEMKAethpidpdhITVGALMKACANAG 593
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   142 IHQKALELLVLMLRDNVR--PNVYTysSVLRSCNGMSDV---RMLHCGIIKEGLESDVFVRSALIDVFAKLGEPEDALSV 216
Cdd:PLN03218  594 QVDRAKEVYQMIHEYNIKgtPEVYT--IAVNSCSQKGDWdfaLSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEI 671
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   217 FDEMVTG----DAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLtsvlractglallelgmqahvhivkydqd 292
Cdd:PLN03218  672 LQDARKQgiklGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTM----------------------------- 722
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15227724   293 lilnNALVDMYCKCGSLEDALRVFNQMKER----DVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYI 360
Cdd:PLN03218  723 ----NALITALCEGNQLPKALEVLSEMKRLglcpNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLV 790
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
322-361 1.95e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.44  E-value: 1.95e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15227724   322 RDVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYIT 361
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYT 40
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
398-437 7.78e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 48.90  E-value: 7.78e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15227724   398 YGCMIDLLGKAGKLDDAVKLLNEME---CEPDAVTWRTLLGAC 437
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKkrgVKPNVYTYTILINGL 48
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
325-354 5.85e-07

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: 45.92  E-value: 5.85e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 15227724   325 ITWSTMISGLAQNGYSQEALKLFERMKSSG 354
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
325-358 4.76e-06

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 43.60  E-value: 4.76e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227724   325 ITWSTMISGLAQNGYSQEALKLFERMKSSGTKPN 358
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 ...
100-139 1.07e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 42.74  E-value: 1.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15227724   100 NVLINMYVKFNLLNDAHQLFDQMPQR----NVISWTTMISAYSK 139
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
321-351 1.24e-05

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 42.33  E-value: 1.24e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227724   321 ERDVITWSTMISGLAQNGYSQEALKLFERMK 351
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
286-482 1.78e-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: 47.03  E-value: 1.78e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 286 IVKYDQDLI-LNNALVDMYCKCGSLEDALRVFNQMKERDVITWSTMIsGLAQ----NGYSQEALKLFER-MKSSGTKPNY 359
Cdd:COG2956  34 ALELDPETVeAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALL-ELAQdylkAGLLDRAEELLEKlLELDPDDAEA 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 360 ITIVGVLFAcsHAGLLEDGWYYFRsmkKLYGIDPVREHYGCMI-DLLGKAGKLDDAVKLLNE-MECEPDAVTWRTLLGAC 437
Cdd:COG2956 113 LRLLAEIYE--QEGDWEKAIEVLE---RLLKLGPENAHAYCELaELYLEQGDYDEAIEALEKaLKLDPDCARALLLLAEL 187
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 15227724 438 RVQR-NMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEE 482
Cdd:COG2956 188 YLEQgDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALE 233
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
224-270 2.54e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 41.97  E-value: 2.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15227724   224 DAIVWNSIIGGFAQNSRSDVALELFKRMKRAGFIAEQATLTSVLRAC 270
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
390-422 3.66e-05

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 40.79  E-value: 3.66e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15227724   390 GIDPVREHYGCMIDLLGKAGKLDDAVKLLNEME 422
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
226-256 5.86e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.14  E-value: 5.86e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227724   226 IVWNSIIGGFAQNSRSDVALELFKRMKRAGF 256
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
307-483 9.96e-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: 44.72  E-value: 9.96e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 307 GSLEDALRVFNQMKERD---VITWSTMISGLAQNGYSQEALKLFER-MKSSGTKPNYITIVGVLFAcsHAGLLEDGWYYF 382
Cdd:COG2956  22 GQPDKAIDLLEEALELDpetVEAHLALGNLYRRRGEYDRAIRIHQKlLERDPDRAEALLELAQDYL--KAGLLDRAEELL 99
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 383 rsmKKLYGIDPVR-EHYGCMIDLLGKAGKLDDAVKLLNEM-ECEPDAVTWRTLLGACRVQRNMV-LAEYAAKKVIALDPE 459
Cdd:COG2956 100 ---EKLLELDPDDaEALRLLAEIYEQEGDWEKAIEVLERLlKLGPENAHAYCELAELYLEQGDYdEAIEALEKALKLDPD 176
                       170       180
                ....*....|....*....|....
gi 15227724 460 DAGTYTLLSNIYANSQKWDSVEEI 483
Cdd:COG2956 177 CARALLLLAELYLEQGDYEEAIAA 200
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
371-483 1.41e-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: 42.64  E-value: 1.41e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 371 HAGLLEDGWYYFRSMKKLYGIDPVREHYGCMIDLLGKAGKLDDAVKLLNE-MECEPDAVTWRTLLGACRVQR-NMVLAEY 448
Cdd:COG5010  30 ALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQaLQLDPNNPELYYNLALLYSRSgDKDEAKE 109
                        90       100       110
                ....*....|....*....|....*....|....*
gi 15227724 449 AAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEEI 483
Cdd:COG5010 110 YYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAA 144
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
297-320 1.45e-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: 39.25  E-value: 1.45e-04
                          10        20
                  ....*....|....*....|....
gi 15227724   297 NALVDMYCKCGSLEDALRVFNQMK 320
Cdd:pfam12854  11 NTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
297-324 1.58e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 38.99  E-value: 1.58e-04
                          10        20
                  ....*....|....*....|....*...
gi 15227724   297 NALVDMYCKCGSLEDALRVFNQMKERDV 324
Cdd:pfam01535   4 NSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
383-490 2.88e-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: 41.33  E-value: 2.88e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 383 RSMKKLYGIDPVREH-YGCMIDLLGKAGKLDDAVKLLNE-MECEPDAVTWRTLLGACRVQRNMV-LAEYAAKKVIALDPE 459
Cdd:COG4783  25 ALLEKALELDPDNPEaFALLGEILLQLGDLDEAIVLLHEaLELDPDEPEARLNLGLALLKAGDYdEALALLEKALKLDPE 104
                        90       100       110
                ....*....|....*....|....*....|.
gi 15227724 460 DAGTYTLLSNIYANSQKWDSVEEIRTRMRDR 490
Cdd:COG4783 105 HPEAYLRLARAYRALGRPDEAIAALEKALEL 135
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
297-324 3.48e-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: 38.21  E-value: 3.48e-04
                          10        20
                  ....*....|....*....|....*...
gi 15227724   297 NALVDMYCKCGSLEDALRVFNQMKERDV 324
Cdd:TIGR00756   4 NTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
124-175 6.09e-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: 38.49  E-value: 6.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15227724   124 QRNVISWTTMISAYSKCKIHQKALELLVLMLRDNVRPNVYTYSSVLRSCNGM 175
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
404-507 7.58e-04

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: 39.99  E-value: 7.58e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 404 LLGKA----GKLDDAVKLLNE-MECEPDAVTWRTLLGACRVQRNMV-LAEYAAKKVIALDPEDAGTYTLLSNIYANSQKW 477
Cdd:COG4235  22 LLGRAylrlGRYDEALAAYEKaLRLDPDNADALLDLAEALLAAGDTeEAEELLERALALDPDNPEALYLLGLAAFQQGDY 101
                        90       100       110
                ....*....|....*....|....*....|
gi 15227724 478 DSVEEIRTRMRDRGIKKEPgcsWIEVNKQI 507
Cdd:COG4235 102 AEAIAAWQKLLALLPADAP---ARLLEASI 128
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
404-496 9.32e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 38.61  E-value: 9.32e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724 404 LLGKAGKLDDAVKLLNE-MECEPDAVTWRTLLGACRVQRNMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEe 482
Cdd:COG3063   1 LYLKLGDLEEAEEYYEKaLELDPDNADALNNLGLLLLEQGRYDEAIALEKALKLDPNNAEALLNLAELLLELGDYDEAL- 79
                        90
                ....*....|....
gi 15227724 483 irtRMRDRGIKKEP 496
Cdd:COG3063  80 ---AYLERALELDP 90
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
398-427 9.86e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 37.05  E-value: 9.86e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15227724   398 YGCMIDLLGKAGKLDDAVKLLNEME---CEPDA 427
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKergIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
226-256 1.07e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 1.07e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227724   226 IVWNSIIGGFAQNSRSDVALELFKRMKRAGF 256
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
314-369 1.39e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 37.34  E-value: 1.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227724   314 RVFNQMKER----DVITWSTMISGLAQNGYSQEALKLFERMKSSGTKPNYITIVGVLFAC 369
Cdd:pfam13812   1 SILREMVRDgiqlNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
128-162 2.10e-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: 35.89  E-value: 2.10e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15227724   128 ISWTTMISAYSKCKIHQKALELLVLMLRDNVRPNV 162
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 ...
398-422 3.10e-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: 35.52  E-value: 3.10e-03
                          10        20
                  ....*....|....*....|....*
gi 15227724   398 YGCMIDLLGKAGKLDDAVKLLNEME 422
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMK 27
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
416-483 3.10e-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: 38.06  E-value: 3.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15227724 416 KLLNEMECEPDAVTWRTLLG-ACRVQRNMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWDSVEEI 483
Cdd:COG4235   5 RLRQALAANPNDAEGWLLLGrAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEEL 73
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
128-158 3.39e-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: 35.52  E-value: 3.39e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15227724   128 ISWTTMISAYSKCKIHQKALELLVLMLRDNV 158
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
404-478 4.05e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 39.22  E-value: 4.05e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15227724 404 LLGKAGKLDDAVKLLNE-MECEPD-AVTWRTLLGACRVQRNMVLAEYAAKKVIALDPEDAGTYTLLSNIYANSQKWD 478
Cdd:COG0457  17 AYRRLGRYEEAIEDYEKaLELDPDdAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYE 93
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
198-221 4.93e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 34.75  E-value: 4.93e-03
                          10        20
                  ....*....|....*....|....
gi 15227724   198 SALIDVFAKLGEPEDALSVFDEMV 221
Cdd:pfam01535   4 NSLISGYCKNGKLEEALELFKEMK 27
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
193-237 5.32e-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: 35.42  E-value: 5.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 15227724   193 DVFVRSALIDVFAKLGEPEDALSVFDEM----VTGDAIVWNSIIGGFAQ 237
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMkkrgVKPNVYTYTILINGLCK 50
 
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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