NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1063681488|ref|NP_001321602|]
View 

Tetratricopeptide repeat (TPR)-like superfamily 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

 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
 14-635 3.43e-179

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 530.19  E-value: 3.43e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  14 ALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKVFDKSPH 93
Cdd:PLN03077  171 ALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  94 RDVVSYTALIKG-------------------------------------------------------------------- 105
Cdd:PLN03077  251 RDCISWNAMISGyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvktgfavdvsvcnsli 330

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 106 --YASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQ 183
Cdd:PLN03077  331 qmYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVK 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 184 VHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGEtPND 263
Cdd:PLN03077  411 LHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNS 489

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 264 VTMLSILPACAHLGAIDIGRWIHVYIDKrlKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSiLHKSLSSWNAMIFGFAM 343
Cdd:PLN03077  490 VTLIAALSACARIGALMCGKEIHAHVLR--TGIGFDGFLPNALLDLYVRCGRMNYAWNQFNS-HEKDVVSWNILLTGYVA 566

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 344 HGRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEAEE 423
Cdd:PLN03077  567 HGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYN 646

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 424 MINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVP 503
Cdd:PLN03077  647 FINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDP 726

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 504 GCSSIEIDSVVHEFIIGDKFHPRNREIYGMLEEMEVLLEKAGFVPDTSEVLQEMEEEwKEGALRHHSEKLAIAFGLISTK 583
Cdd:PLN03077  727 GCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTV 805

                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063681488 584 PGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFHHFRDGVCSCND 635
Cdd:PLN03077  806 PGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 14-635 3.43e-179

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 530.19  E-value: 3.43e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  14 ALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKVFDKSPH 93
Cdd:PLN03077  171 ALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  94 RDVVSYTALIKG-------------------------------------------------------------------- 105
Cdd:PLN03077  251 RDCISWNAMISGyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvktgfavdvsvcnsli 330

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 106 --YASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQ 183
Cdd:PLN03077  331 qmYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVK 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 184 VHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGEtPND 263
Cdd:PLN03077  411 LHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNS 489

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 264 VTMLSILPACAHLGAIDIGRWIHVYIDKrlKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSiLHKSLSSWNAMIFGFAM 343
Cdd:PLN03077  490 VTLIAALSACARIGALMCGKEIHAHVLR--TGIGFDGFLPNALLDLYVRCGRMNYAWNQFNS-HEKDVVSWNILLTGYVA 566

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 344 HGRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEAEE 423
Cdd:PLN03077  567 HGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYN 646

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 424 MINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVP 503
Cdd:PLN03077  647 FINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDP 726

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 504 GCSSIEIDSVVHEFIIGDKFHPRNREIYGMLEEMEVLLEKAGFVPDTSEVLQEMEEEwKEGALRHHSEKLAIAFGLISTK 583
Cdd:PLN03077  727 GCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTV 805

                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063681488 584 PGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFHHFRDGVCSCND 635
Cdd:PLN03077  806 PGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 545-637 1.35e-38

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: 137.55  E-value: 1.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 545 GFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLISTKPGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFH 624
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1063681488 625 HFRDGVCSCNDYW 637
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 128-162 8.24e-08

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 48.61  E-value: 8.24e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063681488 128 VSWNAMISGYAETGNYKEALELFKDMMKTNVRPDE 162
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 64-270 3.26e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 49.34  E-value: 3.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  64 DLYVHTSLISMYVQNGRLEDAHKVFDK----SPHRDVVsYTALIKGYASRGYIENAQKLFD---EIPVKDVVSWNAMISG 136
Cdd:COG2956    41 TVEAHLALGNLYRRRGEYDRAIRIHQKllerDPDRAEA-LLELAQDYLKAGLLDRAEELLEkllELDPDDAEALRLLAEI 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 137 YAETGNYKEALELFKDMMKTNvrPDESTMVTVVSACAQS-----GSIELGRQVhLWIDDHGFGSNLkivnALIDLYSKCG 211
Cdd:COG2956   120 YEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEqgdydEAIEALEKA-LKLDPDCARALL----LLAELYLEQG 192

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063681488 212 ELETACGLFERLPYKD---VISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSIL 270
Cdd:COG2956   193 DYEEAIAALERALEQDpdyLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLALADL 254
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 14-635 3.43e-179

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 530.19  E-value: 3.43e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  14 ALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKVFDKSPH 93
Cdd:PLN03077  171 ALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  94 RDVVSYTALIKG-------------------------------------------------------------------- 105
Cdd:PLN03077  251 RDCISWNAMISGyfengecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvvktgfavdvsvcnsli 330

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 106 --YASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQ 183
Cdd:PLN03077  331 qmYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVK 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 184 VHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGEtPND 263
Cdd:PLN03077  411 LHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLK-PNS 489

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 264 VTMLSILPACAHLGAIDIGRWIHVYIDKrlKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSiLHKSLSSWNAMIFGFAM 343
Cdd:PLN03077  490 VTLIAALSACARIGALMCGKEIHAHVLR--TGIGFDGFLPNALLDLYVRCGRMNYAWNQFNS-HEKDVVSWNILLTGYVA 566

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 344 HGRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEAEE 423
Cdd:PLN03077  567 HGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYN 646

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 424 MINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVP 503
Cdd:PLN03077  647 FINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDP 726

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 504 GCSSIEIDSVVHEFIIGDKFHPRNREIYGMLEEMEVLLEKAGFVPDTSEVLQEMEEEwKEGALRHHSEKLAIAFGLISTK 583
Cdd:PLN03077  727 GCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIEVS-KDDIFCGHSERLAIAFGLINTV 805

                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063681488 584 PGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFHHFRDGVCSCND 635
Cdd:PLN03077  806 PGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 32-637 2.64e-164

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 486.69  E-value: 2.64e-164
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  32 TFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAhkvfdksphrdvvsytalikgyasrgy 111
Cdd:PLN03081  125 TYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDA--------------------------- 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 112 ienaQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDH 191
Cdd:PLN03081  178 ----RRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKT 253

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 192 GFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSILP 271
Cdd:PLN03081  254 GVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIR 333

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 272 ACAHLGAIDIGRWIHVYIDKR---LKGVTNasslrTSLIDMYAKCGDIEAAHQVFNSILHKSLSSWNAMIFGFAMHGRAD 348
Cdd:PLN03081  334 IFSRLALLEHAKQAHAGLIRTgfpLDIVAN-----TALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGT 408

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 349 ASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEAEEMINMM 428
Cdd:PLN03081  409 KAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRA 488

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 429 EMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVPGCSSI 508
Cdd:PLN03081  489 PFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWI 568

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 509 EIDSVVHEFIIGDKFHPRNREIYGMLEEMEVLLEKAGFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLISTKPGTKL 588
Cdd:PLN03081  569 EVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPL 648

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*....
gi 1063681488 589 TIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFHHFRDGVCSCNDYW 637
Cdd:PLN03081  649 QITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 545-637 1.35e-38

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: 137.55  E-value: 1.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 545 GFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLISTKPGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFH 624
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1063681488 625 HFRDGVCSCNDYW 637
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 131-388 1.74e-38

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 152.31  E-value: 1.74e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 131 NAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDLYSKC 210
Cdd:PLN03077   55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRF 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 211 GELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSILPACAHLGAIDIGRWIHVYID 290
Cdd:PLN03077  135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVV 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 291 KRlkGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSILHKSLSSWNAMIFGFAMHGRADASFDLFSRMRKIGIQPDDITFV 370
Cdd:PLN03077  215 RF--GFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTIT 292

                         250
                  ....*....|....*...
gi 1063681488 371 GLLSACSHSGMLDLGRHI 388
Cdd:PLN03077  293 SVISACELLGDERLGREM 310
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 447-509 4.90e-23

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: 92.61  E-value: 4.90e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063681488 447 HGNVELGESFAENLIKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVPGCSSIE 509
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 26-411 1.58e-22

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 103.03  E-value: 1.58e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488   26 LLPNS--YTFPFVLKSCAKSKAFKEGQQIHGHVLKLGCDLDLYVHTSLISMYVQNGRLEDAHKVFdkspHRDVVS----- 98
Cdd:PLN03218   431 LIRNPtlSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVF----HEMVNAgvean 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488   99 ---YTALIKGYASRGYIENAQKLFDEIPVKDV----VSWNAMISGYAETGNYKEALELFKDMM--KTNVRPDESTMVTVV 169
Cdd:PLN03218   507 vhtFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKaeTHPIDPDHITVGALM 586

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  170 SACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLferlpYKDviswntliggythmnlykeall 249
Cdd:PLN03218   587 KACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI-----YDD---------------------- 639

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  250 lfqeMLRSGETPNDVTMLSILPACAHLGAIDIGrwIHVYIDKRLKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSI--- 326
Cdd:PLN03218   640 ----MKKKGVKPDEVFFSALVDVAGHAGDLDKA--FEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIksi 713

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  327 -LHKSLSSWNAMIFGFAMHGRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDyKMTPKLEHY 405
Cdd:PLN03218   714 kLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED-GIKPNLVMC 792


                   ....*.
gi 1063681488  406 GCMIDL 411
Cdd:PLN03218   793 RCITGL 798
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 79-380 1.31e-14

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 77.61  E-value: 1.31e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488   79 GRLEDAHKVFDKSPHRDV-----VSYTALIKGYASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKDM 153
Cdd:PLN03218   384 GRIKDCIDLLEDMEKRGLldmdkIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLV 463

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  154 MKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDV----I 229
Cdd:PLN03218   464 QEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrV 543

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  230 SWNTLIGGYTHMNLYKEALLLFQEMlrSGET----PNDVTMLSILPACAHLGAIDigRWIHVYIDKRLKGVTNASSLRTS 305
Cdd:PLN03218   544 VFNALISACGQSGAVDRAFDVLAEM--KAEThpidPDHITVGALMKACANAGQVD--RAKEVYQMIHEYNIKGTPEVYTI 619

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  306 LIDMYAKCGDIEAAHQVFNSILHKSLSSwNAMIFG----FAMH-GRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSG 380
Cdd:PLN03218   620 AVNSCSQKGDWDFALSIYDDMKKKGVKP-DEVFFSalvdVAGHaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAK 698
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 125-174 5.89e-12

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 60.45  E-value: 5.89e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063681488 125 KDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQ 174
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 226-275 1.46e-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: 53.91  E-value: 1.46e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063681488 226 KDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSILPACAH 275
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 265-500 3.00e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 60.28  E-value: 3.00e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  265 TMLsiLPACAHLGAIDIGRWIHVYIDKRlkGVTNASSLRTSLIDMYAKCGDIEAAHQVF----NSILHKSLSSWNAMIFG 340
Cdd:PLN03218   441 NML--MSVCASSQDIDGALRVLRLVQEA--GLKADCKLYTTLISTCAKSGKVDAMFEVFhemvNAGVEANVHTFGALIDG 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  341 FAMHGRADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDykMTPklehygcmIDllghsglfke 420
Cdd:PLN03218   517 CARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAE--THP--------ID---------- 576

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  421 aeeminmmemePDGVIWCSLLKACKMHGNV----ELGESFAENLIKIEPEnpgSYVLLSNIYASAGRWNEVAKTRALLND 496
Cdd:PLN03218   577 -----------PDHITVGALMKACANAGQVdrakEVYQMIHEYNIKGTPE---VYTIAVNSCSQKGDWDFALSIYDDMKK 642


                   ....
gi 1063681488  497 KGMK 500
Cdd:PLN03218   643 KGVK 646
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 333-378 5.53e-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: 49.28  E-value: 5.53e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063681488 333 SWNAMIFGFAMHGRADASFDLFSRMRKIGIQPDDITFVGLLSACSH 378
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 128-162 8.24e-08

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 48.61  E-value: 8.24e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063681488 128 VSWNAMISGYAETGNYKEALELFKDMMKTNVRPDE 162
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 94-138 4.04e-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: 4.04e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063681488  94 RDVVSYTALIKGYASRGYIENAQKLFDEIPVK----DVVSWNAMISGYA 138
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLC 49
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 128-155 1.00e-06

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 45.15  E-value: 1.00e-06
                          10        20
                  ....*....|....*....|....*...
gi 1063681488 128 VSWNAMISGYAETGNYKEALELFKDMMK 155
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKE 28
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 64-270 3.26e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 49.34  E-value: 3.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  64 DLYVHTSLISMYVQNGRLEDAHKVFDK----SPHRDVVsYTALIKGYASRGYIENAQKLFD---EIPVKDVVSWNAMISG 136
Cdd:COG2956    41 TVEAHLALGNLYRRRGEYDRAIRIHQKllerDPDRAEA-LLELAQDYLKAGLLDRAEELLEkllELDPDDAEALRLLAEI 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 137 YAETGNYKEALELFKDMMKTNvrPDESTMVTVVSACAQS-----GSIELGRQVhLWIDDHGFGSNLkivnALIDLYSKCG 211
Cdd:COG2956   120 YEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEqgdydEAIEALEKA-LKLDPDCARALL----LLAELYLEQG 192

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063681488 212 ELETACGLFERLPYKD---VISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSIL 270
Cdd:COG2956   193 DYEEAIAALERALEQDpdyLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLALADL 254
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 229-258 3.92e-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: 40.91  E-value: 3.92e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1063681488 229 ISWNTLIGGYTHMNLYKEALLLFQEMLRSG 258
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 69-107 4.59e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 41.19  E-value: 4.59e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063681488  69 TSLISMYVQNGRLEDAHKVFDK------SPhrDVVSYTALIKGYA 107
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEmkkrgvKP--NVYTYTILINGLC 49
PLN03077 PLN03077
Protein ECB2; Provisional
 1-228 6.18e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 46.38  E-value: 6.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488   1 MFRGHALSSDPVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEG-QQIHGHVLKLGCDLDLYVHTSLISMYVQNG 79
Cdd:PLN03077  560 LLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGlEYFHSMEEKYSITPNLKHYACVVDLLGRAG 639

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  80 RLEDAHKVFDKSPHR-DVVSYTALIKGYASRGYIE----NAQKLFdEIPVKDVVSWNAMISGYAETGNYKEALELFKdMM 154
Cdd:PLN03077  640 KLTEAYNFINKMPITpDPAVWGALLNACRIHRHVElgelAAQHIF-ELDPNSVGYYILLCNLYADAGKWDEVARVRK-TM 717

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063681488 155 KTNvrpdestMVTVVSACAQsgsIELGRQVHLWIDDHGFGSNLKIVNALID-LYSKCGELETACGLFERLPYKDV 228
Cdd:PLN03077  718 REN-------GLTVDPGCSW---VEVKGKVHAFLTDDESHPQIKEINTVLEgFYEKMKASGLAGSESSSMDEIEV 782
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 229-263 7.66e-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: 40.13  E-value: 7.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063681488 229 ISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPND 263
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
67-253 8.80e-05

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 44.61  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  67 VHTSLISMYVQNGRLEDAHKVFDKS----PhRDVVSYTALIKGYASRGYIENAQKLFD---EIPVKDVVSWNAMISGYAE 139
Cdd:COG0457    10 AYNNLGLAYRRLGRYEEAIEDYEKAleldP-DDAEALYNLGLAYLRLGRYEEALADYEqalELDPDDAEALNNLGLALQA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 140 TGNYKEALELFKDmmktnvrpdestmvtvvsacaqsgSIELGRQvhlwiddhgfgsNLKIVNALIDLYSKCGELETACGL 219
Cdd:COG0457    89 LGRYEEALEDYDK------------------------ALELDPD------------DAEALYNLGLALLELGRYDEAIEA 132

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1063681488 220 FER---LPYKDVISWNTLIGGYTHMNLYKEALLLFQE 253
Cdd:COG0457   133 YERaleLDPDDADALYNLGIALEKLGRYEEALELLEK 169
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 95-121 1.85e-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: 1.85e-04
                          10        20
                  ....*....|....*....|....*..
gi 1063681488  95 DVVSYTALIKGYASRGYIENAQKLFDE 121
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 332-362 4.02e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.83  E-value: 4.02e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063681488 332 SSWNAMIFGFAMHGRADASFDLFSRMRKIGI 362
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 126-153 4.44e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.71  E-value: 4.44e-04
                          10        20
                  ....*....|....*....|....*...
gi 1063681488 126 DVVSWNAMISGYAETGNYKEALELFKDM 153
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 137-383 6.20e-04

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: 42.02  E-value: 6.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 137 YAETGNYKEALELFKDMMKTNvrPD-ESTMVTVVSACAQSGSIELGRQVHLWIDDHGfGSNLKIVNALIDLYSKCGELET 215
Cdd:COG2956    18 YLLNGQPDKAIDLLEEALELD--PEtVEAHLALGNLYRRRGEYDRAIRIHQKLLERD-PDRAEALLELAQDYLKAGLLDR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 216 ACGLFERL---PYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGetPNDVTMLSILpACAHLGAIDIGRWIHvYIDKR 292
Cdd:COG2956    95 AEELLEKLlelDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCEL-AELYLEQGDYDEAIE-ALEKA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 293 LKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSIL---HKSLSSWNAMIFGFAMHGRADASFDLFsrMRKIGIQPDDITF 369
Cdd:COG2956   171 LKLDPDCARALLLLAELYLEQGDYEEAIAALERALeqdPDYLPALPRLAELYEKLGDPEEALELL--RKALELDPSDDLL 248

                         250
                  ....*....|....
gi 1063681488 370 VGLLSACSHSGMLD 383
Cdd:COG2956   249 LALADLLERKEGLE 262
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 60-90 6.51e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.33  E-value: 6.51e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063681488  60 GCDLDLYVHTSLISMYVQNGRLEDAHKVFDK 90
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 117-172 1.06e-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: 37.72  E-value: 1.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 117 KLFDEIPVK----DVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSAC 172
Cdd:pfam13812   1 SILREMVRDgiqlNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 291-406 1.84e-03

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 40.07  E-value: 1.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488 291 KRLKGVTNASSLRTSLiDMYAKCGDIEAAHQV---------------FNSILHksLSSWNAMIFGFAMHGRADASFDLFS 355
Cdd:pfam17177   3 KKKGKQTPESELRFQL-DKCSKHADATGALALydaakaegvrlaqyhYNVLLY--LCSKAADATDLKPQLAADRGFEVFE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063681488 356 RMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQdYKMTPKLEHYG 406
Cdd:pfam17177  80 AMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEA-AGVSPRLRSYS 129
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 97-127 2.27e-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: 2.27e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063681488  97 VSYTALIKGYASRGYIENAQKLFDEIPVKDV 127
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 333-366 2.69e-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: 2.69e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1063681488 333 SWNAMIFGFAMHGRADASFDLFSRMRKIGIQPDD 366
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 74-174 6.26e-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: 37.29  E-value: 6.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  74 MYVQNGRLEDAHKVFDK----SPhRDVVSYTALIKGYASRGYIENAQKLFDEI----PvKDVVSWNAMISGYAETGNYKE 145
Cdd:COG4235    26 AYLRLGRYDEALAAYEKalrlDP-DNADALLDLAEALLAAGDTEEAEELLERAlaldP-DNPEALYLLGLAAFQQGDYAE 103

                          90       100
                  ....*....|....*....|....*....
gi 1063681488 146 ALELFKDMMKTNvrPDESTMVTVVSACAQ 174
Cdd:COG4235   104 AIAAWQKLLALL--PADAPARLLEASIAE 130
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
64-151 6.42e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 38.83  E-value: 6.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681488  64 DLYVHTSLISMYVQNGRLEDAHKVFDKS----PhRDVVSYTALIKGYASRGYIENAQKLFD---EIPVKDVVSWNAMISG 136
Cdd:COG0457    41 DAEALYNLGLAYLRLGRYEEALADYEQAleldP-DDAEALNNLGLALQALGRYEEALEDYDkalELDPDDAEALYNLGLA 119

                          90
                  ....*....|....*
gi 1063681488 137 YAETGNYKEALELFK 151
Cdd:COG0457   120 LLELGRYDEAIEAYE 134
 
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