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Conserved domains on  [gi|30694913|ref|NP_191463|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000098)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 142-488 5.50e-29

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 122.68  E-value: 5.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   142 FLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVE 221
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   222 GDKFKEAEEVFETLLDEKkspLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVP--QSTVTYNSLMSFETSYKEVS 299
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKN---VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVD 596

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   300 K---IYDQMQRSDIQ--PDVvsYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKS 374
Cdd:PLN03218  597 RakeVYQMIHEYNIKgtPEV--YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQD 674

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   375 MRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQ 454
Cdd:PLN03218  675 ARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNT 754

                         330       340       350
                  ....*....|....*....|....*....|....
gi 30694913   455 TILTTIMDASGRCKNFGSALGWYKEMESCGVPPD 488
Cdd:PLN03218  755 ITYSILLVASERKDDADVGLDLLSQAKEDGIKPN 788
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 142-488 5.50e-29

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 122.68  E-value: 5.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   142 FLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVE 221
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   222 GDKFKEAEEVFETLLDEKkspLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVP--QSTVTYNSLMSFETSYKEVS 299
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKN---VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVD 596

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   300 K---IYDQMQRSDIQ--PDVvsYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKS 374
Cdd:PLN03218  597 RakeVYQMIHEYNIKgtPEV--YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQD 674

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   375 MRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQ 454
Cdd:PLN03218  675 ARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNT 754

                         330       340       350
                  ....*....|....*....|....*....|....
gi 30694913   455 TILTTIMDASGRCKNFGSALGWYKEMESCGVPPD 488
Cdd:PLN03218  755 ITYSILLVASERKDDADVGLDLLSQAKEDGIKPN 788
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 312-360 3.13e-11

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 58.53  E-value: 3.13e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30694913   312 PDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFA 360
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 143-341 6.86e-10

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: 60.13  E-value: 6.86e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 143 LMLITAYGKLGNFNGAERVLSVLSKMGSTpNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVEG 222
Cdd:COG2956  80 LELAQDYLKAGLLDRAEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQG 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 223 DkFKEAEEVFETLLDEKKSPLKPdqkmYHMMIYMYKKAGNYEKARKVFSSMVGKGvPQSTVTYNSLMSFETSYKEVSKIY 302
Cdd:COG2956 159 D-YDEAIEALEKALKLDPDCARA----LLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEAL 232

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 30694913 303 DQMQR-SDIQPDVVSYALLIKAYGRARREEEALSVFEEML 341
Cdd:COG2956 233 ELLRKaLELDPSDDLLLALADLLERKEGLEAALALLERQL 272
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 420-453 4.11e-07

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 4.11e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30694913   420 VTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKAN 453
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 142-488 5.50e-29

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 122.68  E-value: 5.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   142 FLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVE 221
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCAR 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   222 GDKFKEAEEVFETLLDEKkspLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVP--QSTVTYNSLMSFETSYKEVS 299
Cdd:PLN03218  520 AGQVAKAFGAYGIMRSKN---VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPidPDHITVGALMKACANAGQVD 596

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   300 K---IYDQMQRSDIQ--PDVvsYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKS 374
Cdd:PLN03218  597 RakeVYQMIHEYNIKgtPEV--YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQD 674

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   375 MRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQ 454
Cdd:PLN03218  675 ARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNT 754

                         330       340       350
                  ....*....|....*....|....*....|....
gi 30694913   455 TILTTIMDASGRCKNFGSALGWYKEMESCGVPPD 488
Cdd:PLN03218  755 ITYSILLVASERKDDADVGLDLLSQAKEDGIKPN 788
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 142-466 3.16e-20

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 94.94  E-value: 3.16e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  142 FLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYGRGGKCNNAEAIFRRMqssgPEPSAITYQIILKTFV- 220
Cdd:PLN03081 227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGM----PEKTTVAWNSMLAGYAl 302

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  221 EGdkfkEAEEVFETLLDEKKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSLMSFETSYKEVSK 300
Cdd:PLN03081 303 HG----YSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMED 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  301 ---IYDQMQRSDIqpdvVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRR 377
Cdd:PLN03081 379 arnVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSE 454

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  378 D-RIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKvdgFEPNIVTYGTLIkgyaKANDVEKMME----VYEKMRLSGIK- 451
Cdd:PLN03081 455 NhRIKPRAMHYACMIELLGREGLLDEAYAMIRRAP---FKPTVNMWAALL----TACRIHKNLElgrlAAEKLYGMGPEk 527

                        330
                 ....*....|....*.
gi 30694913  452 -ANQTILTTIMDASGR 466
Cdd:PLN03081 528 lNNYVVLLNLYNSSGR 543
PLN03077 PLN03077
Protein ECB2; Provisional
 142-480 8.75e-15

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 77.58  E-value: 8.75e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  142 FLMLITAYGKLGNfngaerVLSVLSKMGSTpNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVE 221
Cdd:PLN03077 127 MLSMFVRFGELVH------AWYVFGKMPER-DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGG 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  222 GDKFKEAEEVFETLLdekKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVpqstVTYNSLMS--FETSY-KEV 298
Cdd:PLN03077 200 IPDLARGREVHAHVV---RFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDC----ISWNAMISgyFENGEcLEG 272

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  299 SKIYDQMQRSDIQPDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRrd 378
Cdd:PLN03077 273 LELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME-- 350

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  379 riFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQTILT 458
Cdd:PLN03077 351 --TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVAN 428

                        330       340
                 ....*....|....*....|..
gi 30694913  459 TIMDASGRCKNFGSALGWYKEM 480
Cdd:PLN03077 429 ALIEMYSKCKCIDKALEVFHNI 450
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 173-476 1.47e-13

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 73.75  E-value: 1.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  173 NVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVEGDKFKEAEEVFETLLdekKSPLKPDQKMYHM 252
Cdd:PLN03081 188 NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVL---KTGVVGDTFVSCA 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  253 MIYMYKKAGNYEKARKVFSSMVGKgvpqSTVTYNSLmsfetsykevskiydqmqrsdiqpdVVSYALlikaYGRArreEE 332
Cdd:PLN03081 265 LIDMYSKCGDIEDARCVFDGMPEK----TTVAWNSM-------------------------LAGYAL----HGYS---EE 308

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  333 ALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKV 412
Cdd:PLN03081 309 ALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR 388

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30694913  413 DgfepNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQTILTTIMDAsgrCKNFG-SALGW 476
Cdd:PLN03081 389 K----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSA---CRYSGlSEQGW 446
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 312-360 3.13e-11

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 58.53  E-value: 3.13e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30694913   312 PDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFA 360
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 382-431 9.62e-11

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 56.99  E-value: 9.62e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 30694913   382 PDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAK 431
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 138-523 1.30e-10

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 64.49  E-value: 1.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  138 SEIDFL-MLITAYGKLGNFNGAERVLSVLSKMgstpNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITY-QII 215
Cdd:PLN03077 220 LDVDVVnALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTItSVI 295

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  216 LKTFVEGDKfKEAEEVFETLLdekKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVpqstVTYNSLMS-FETS 294
Cdd:PLN03077 296 SACELLGDE-RLGREMHGYVV---KTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA----VSWTAMISgYEKN 367

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  295 Y--KEVSKIYDQMQRSDIQPDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVF 372
Cdd:PLN03077 368 GlpDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  373 KSMRRDrifpDLWSYTTMLSAY-VNASDMEgAEKFFKRIKVDgFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIK 451
Cdd:PLN03077 448 HNIPEK----DVISWTSIIAGLrLNNRCFE-ALIFFRQMLLT-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIG 521

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30694913  452 ANQTILTTIMDASGRCKNFGSALGWYKEMEScgvppDQKAKNVLLSLASTQDELEEAKEL------TGIRNETATIIA 523
Cdd:PLN03077 522 FDGFLPNALLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELfnrmveSGVNPDEVTFIS 594
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 333-482 2.41e-10

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: 60.49  E-value: 2.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   333 ALSVFEEMLDAGVRPTHKAYNILL----------DAFAISGMvEQAKTVFKSMRRDRIFPDLWSYTTMLSAYVNASDMEG 402
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLylcskaadatDLKPQLAA-DRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDL 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   403 AEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQTILTTIMDASGRCknfGSALGWYKEMES 482
Cdd:pfam17177 109 AFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKA---GRADKVYAYLHR 185
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 194-509 2.96e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 62.97  E-value: 2.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  194 EAIFRRMQSSGPEpSAITYQIilKTFVEGDKFKEAEEVFETLldEKKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSM 273
Cdd:PLN03081  75 DARLDDTQIRKSG-VSLCSQI--EKLVACGRHREALELFEIL--EAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHV 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  274 VGKGVPQSTVTYNSLMsfeTSYKEVSKIYDQMQRSDIQPD--VVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKA 351
Cdd:PLN03081 150 ESSGFEPDQYMMNRVL---LMHVKCGMLIDARRLFDEMPErnLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRT 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  352 YNILLDAFAISGMVEQAKTVFKSMRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKvdgfEPNIVTYGTLIKGYAK 431
Cdd:PLN03081 227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYAL 302

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30694913  432 ANDVEKMMEVYEKMRLSGIKANQTILTTIMDASGRCKNFGSALGWYKEMESCGVPPDQKAKNVLLSLASTQDELEEAK 509
Cdd:PLN03081 303 HGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDAR 380
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 143-341 6.86e-10

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: 60.13  E-value: 6.86e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 143 LMLITAYGKLGNFNGAERVLSVLSKMGSTpNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVEG 222
Cdd:COG2956  80 LELAQDYLKAGLLDRAEELLEKLLELDPD-DAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQG 158

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 223 DkFKEAEEVFETLLDEKKSPLKPdqkmYHMMIYMYKKAGNYEKARKVFSSMVGKGvPQSTVTYNSLMSFETSYKEVSKIY 302
Cdd:COG2956 159 D-YDEAIEALEKALKLDPDCARA----LLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEAL 232

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 30694913 303 DQMQR-SDIQPDVVSYALLIKAYGRARREEEALSVFEEML 341
Cdd:COG2956 233 ELLRKaLELDPSDDLLLALADLLERKEGLEAALALLERQL 272
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 300-359 7.84e-10

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: 55.06  E-value: 7.84e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   300 KIYDQMQRSDIQPDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAF 359
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 193-445 8.95e-10

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: 59.74  E-value: 8.95e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 193 AEAIFRRMQSSgpEPSAITYQIIL-KTFVEGDKFKEAEEVFETLLDekkspLKPDQKMYHMMI-YMYKKAGNYEKARKVF 270
Cdd:COG2956  27 AIDLLEEALEL--DPETVEAHLALgNLYRRRGEYDRAIRIHQKLLE-----RDPDRAEALLELaQDYLKAGLLDRAEELL 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 271 SSMVGKGvPQSTVTYNSLMSFETSYKEVSKIYDQMQR-SDIQPDVVSYALLI-KAYGRARREEEALSVFEEMLDAgvRPT 348
Cdd:COG2956 100 EKLLELD-PDDAEALRLLAEIYEQEGDWEKAIEVLERlLKLGPENAHAYCELaELYLEQGDYDEAIEALEKALKL--DPD 176

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 349 H-KAYNILLDAFAISGMVEQAKTVFKsmRRDRIFPDLWSYTTMLS-AYVNASDMEGAEKFFKRIKVDgfEPNIVTYGTLI 426
Cdd:COG2956 177 CaRALLLLAELYLEQGDYEEAIAALE--RALEQDPDYLPALPRLAeLYEKLGDPEEALELLRKALEL--DPSDDLLLALA 252

                       250
                ....*....|....*....
gi 30694913 427 KGYAKANDVEKMMEVYEKM 445
Cdd:COG2956 253 DLLERKEGLEAALALLERQ 271
PLN03077 PLN03077
Protein ECB2; Provisional
 145-497 1.52e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 61.02  E-value: 1.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  145 LITAYGKLGNFNGAErvlSVLSKMgSTPNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVEGDK 224
Cdd:PLN03077 329 LIQMYLSLGSWGEAE---KVFSRM-ETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGD 404

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  225 FKEAEEVFEtlLDEKKSpLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSL----MSFETSYkevsk 300
Cdd:PLN03077 405 LDVGVKLHE--LAERKG-LISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLrlnnRCFEALI----- 476

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  301 iYDQMQRSDIQPDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRRDri 380
Cdd:PLN03077 477 -FFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKD-- 553

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  381 fpdLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLS-GIKANQTILTT 459
Cdd:PLN03077 554 ---VVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKySITPNLKHYAC 630

                        330       340       350
                 ....*....|....*....|....*....|....*...
gi 30694913  460 IMDASGRCKNFGSALGWYKEMEscgVPPDQKAKNVLLS 497
Cdd:PLN03077 631 VVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLN 665
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 371-431 2.28e-09

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: 53.52  E-value: 2.28e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30694913   371 VFKSMRRDRIFPDLWSYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYAK 431
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 139-348 7.08e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 58.74  E-value: 7.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   139 EIDFLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMesygrgGKCNNAE------AIFRRMQSSGPEPSAITY 212
Cdd:PLN03218  649 EVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM------GACSNAKnwkkalELYEDIKSIKLRPTVSTM 722

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   213 QIILKTFVEGDKFKEAeevFETLLDEKKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSLmsfe 292
Cdd:PLN03218  723 NALITALCEGNQLPKA---LEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI---- 795

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30694913   293 tsykeVSKIYDQMQRSDIQPD-VVSYALlikayGRARREEE----ALSVFEEMLDAGVRPT 348
Cdd:PLN03218  796 -----TGLCLRRFEKACALGEpVVSFDS-----GRPQIENKwtswALMVYRETISAGTLPT 846
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 417-463 2.65e-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: 50.05  E-value: 2.65e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 30694913   417 PNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQTILTTIMDA 463
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 351-396 5.63e-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: 5.63e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30694913   351 AYNILLDAFAISGMVEQAKTVFKSMRRDRIFPDLWSYTTMLSAYVN 396
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 413-446 6.26e-08

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: 48.50  E-value: 6.26e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30694913   413 DGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMR 446
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 266-377 1.10e-07

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: 52.78  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   266 ARKVFSSMVGKGVPQSTVTYNSLM-------SFETSYKEVSkiydQMQRSDIQPDVVSYALLIKAYGRARREEEALSVFE 338
Cdd:pfam17177  74 GFEVFEAMKAQGVSPNEATYTAVArlaaakgDGDLAFDLVK----EMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEE 149

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 30694913   339 EMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRR 377
Cdd:pfam17177 150 HMLAHGVELEEPELAALLKVSAKAGRADKVYAYLHRLRD 188
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 257-511 1.45e-07

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 53.19  E-value: 1.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 257 YKKAGNYEKARKVFSSMVgKGVPQSTVTYNSLMSFETSYKEVSK---IYDQ-MQRSDIQPDVvsYALLIKAYGRARREEE 332
Cdd:COG2956  18 YLLNGQPDKAIDLLEEAL-ELDPETVEAHLALGNLYRRRGEYDRairIHQKlLERDPDRAEA--LLELAQDYLKAGLLDR 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 333 ALSVFEEMLDagVRPTH-KAYNILLDAFAISGMVEQAKTVFKsmRRDRIFPDLWSYTTMLS-AYVNASDMEGAEKFFKR- 409
Cdd:COG2956  95 AEELLEKLLE--LDPDDaEALRLLAEIYEQEGDWEKAIEVLE--RLLKLGPENAHAYCELAeLYLEQGDYDEAIEALEKa 170

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 410 IKVDgfePNIV-TYGTLIKGYAKANDVEKMMEVYEKMrLSGIKANQTILTTIMDASGRCKNFGSALGWYKEMESCGvpPD 488
Cdd:COG2956 171 LKLD---PDCArALLLLAELYLEQGDYEEAIAALERA-LEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD--PS 244

                       250       260
                ....*....|....*....|...
gi 30694913 489 QKAKNVLLSLASTQDELEEAKEL 511
Cdd:COG2956 245 DDLLLALADLLERKEGLEAALAL 267
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 172-219 2.92e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 47.36  E-value: 2.92e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 30694913   172 PNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTF 219
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 420-453 4.11e-07

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 46.29  E-value: 4.11e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30694913   420 VTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKAN 453
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 315-348 2.86e-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: 43.98  E-value: 2.86e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30694913   315 VSYALLIKAYGRARREEEALSVFEEMLDAGVRPT 348
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 420-450 6.27e-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: 42.84  E-value: 6.27e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30694913   420 VTYGTLIKGYAKANDVEKMMEVYEKMRLSGI 450
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 160-220 8.47e-06

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: 43.50  E-value: 8.47e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30694913   160 RVLSVLSKMGSTPNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFV 220
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 245-290 8.62e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.12  E-value: 8.62e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30694913   245 PDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSLMS 290
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILIN 46
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 281-326 1.34e-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: 42.35  E-value: 1.34e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30694913   281 STVTYNSLMS---FETSYKEVSKIYDQMQRSDIQPDVVSYALLIKAYGR 326
Cdd:pfam13041   2 DVVTYNTLINgycKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 405-465 1.68e-05

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 42.73  E-value: 1.68e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30694913   405 KFFKRIKVDGFEPNIVTYGTLIKGYAKANDVEKMMEVYEKMRLSGIKANQTILTTIMDASG 465
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 335-396 2.03e-05

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 42.35  E-value: 2.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30694913   335 SVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRRDRIFPDLWSYTTMLSAYVN 396
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 313-510 2.30e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 47.56  E-value: 2.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  313 DVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMrrdrifPD--LWSYTTM 390
Cdd:PLN03081 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEM------PErnLASWGTI 195

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  391 LSAYVNASDMEGAEKFFKRIKVDGFEPNIVTYGT-----------------------------------LIKGYAKANDV 435
Cdd:PLN03081 196 IGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVmlrasaglgsaragqqlhccvlktgvvgdtfvscaLIDMYSKCGDI 275

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30694913  436 EKMMEVYEKM-RLSGIKANQTILTTIMdaSGRCKnfgSALGWYKEMESCGVPPDQKAKNVLLSLASTQDELEEAKE 510
Cdd:PLN03081 276 EDARCVFDGMpEKTTVAWNSMLAGYAL--HGYSE---EALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQ 346
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 351-383 3.17e-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: 40.90  E-value: 3.17e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 30694913   351 AYNILLDAFAISGMVEQAKTVFKSMRRDRIFPD 383
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 386-419 5.08e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.08e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 30694913   386 SYTTMLSAYVNASDMEGAEKFFKRIKVDGFEPNI 419
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 315-345 7.22e-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: 7.22e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30694913   315 VSYALLIKAYGRARREEEALSVFEEMLDAGV 345
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 310-340 1.71e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 38.87  E-value: 1.71e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30694913   310 IQPDVVSYALLIKAYGRARREEEALSVFEEM 340
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 239-407 3.26e-04

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 42.38  E-value: 3.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   239 KKSPLKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSLMSF------------ETSYKEVSKIYDQMQ 306
Cdd:pfam17177   3 KKKGKQTPESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLcskaadatdlkpQLAADRGFEVFEAMK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   307 RSDIQPDVVSYALLIKAYGRARREEEALSVFEEMLDAGVRPTHKAYNILLDAFAISGMVEQAKTVFKSMRRDRIFPDLWS 386
Cdd:pfam17177  83 AQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPE 162

                         170       180
                  ....*....|....*....|.
gi 30694913   387 YTTMLSAYVNASDmegAEKFF 407
Cdd:pfam17177 163 LAALLKVSAKAGR---ADKVY 180
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 249-278 6.73e-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: 37.43  E-value: 6.73e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 30694913   249 MYHMMIYMYKKAGNYEKARKVFSSMVGKGV 278
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 175-209 1.34e-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: 1.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 30694913   175 ISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSA 209
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 137-185 1.64e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.95  E-value: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30694913   137 FSEIDFLMLITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYG 185
Cdd:pfam13812  13 LNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 168-200 1.85e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 36.17  E-value: 1.85e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 30694913   168 MGSTPNVISYTALMESYGRGGKCNNAEAIFRRM 200
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 385-415 1.88e-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: 1.88e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 30694913   385 WSYTTMLSAYVNASDMEGAEKFFKRIKVDGF 415
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 243-290 1.90e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.95  E-value: 1.90e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 30694913   243 LKPDQKMYHMMIYMYKKAGNYEKARKVFSSMVGKGVPQSTVTYNSLMS 290
Cdd:pfam13812  11 IQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 351-380 2.02e-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: 2.02e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 30694913   351 AYNILLDAFAISGMVEQAKTVFKSMRRDRI 380
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 295-409 2.12e-03

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


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 38.63  E-value: 2.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 295 YKEVSKIYDQMQRSDIQpDVVSYALLIKAYGRARREEEALSVFEEMLDagVRPTHK-AYNILLDAFAISGMVEQAKTVF- 372
Cdd:COG4783  20 YDEAEALLEKALELDPD-NPEAFALLGEILLQLGDLDEAIVLLHEALE--LDPDEPeARLNLGLALLKAGDYDEALALLe 96

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 30694913 373 KSMRRDRIFPDLWSYttMLSAYVNASDMEGAEKFFKR 409
Cdd:COG4783  97 KALKLDPEHPEAYLR--LARAYRALGRPDEAIAALEK 131
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 175-204 2.23e-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: 2.23e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 30694913   175 ISYTALMESYGRGGKCNNAEAIFRRMQSSG 204
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 249-278 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 30694913   249 MYHMMIYMYKKAGNYEKARKVFSSMVGKGV 278
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03077 PLN03077
Protein ECB2; Provisional
 141-450 2.36e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.99  E-value: 2.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  141 DFL--MLITAYGKLGNFNGAERVLSVLSKmgstpNVISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKT 218
Cdd:PLN03077 524 GFLpnALLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCA 598

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  219 FVEGDKFKEAEEVFETLldEKKSPLKPDQKMYHMMIYMYKKAGNYEKArkvfssmvgkgvpqstvtynslmsfetsykev 298
Cdd:PLN03077 599 CSRSGMVTQGLEYFHSM--EEKYSITPNLKHYACVVDLLGRAGKLTEA-------------------------------- 644

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913  299 skiYDQMQRSDIQPDVVSYALLIKAYgRARR-----EEEALSVFEemLDagvrPTHKAYNILL-DAFAISGMVEQAKTVF 372
Cdd:PLN03077 645 ---YNFINKMPITPDPAVWGALLNAC-RIHRhvelgELAAQHIFE--LD----PNSVGYYILLcNLYADAGKWDEVARVR 714

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30694913  373 KSMRRDRIFPDlwsyttmlsayVNASDMEGAEKFFKRIKVDGFEPNIVTYGTLIKGYakandvekmmevYEKMRLSGI 450
Cdd:PLN03077 715 KTMRENGLTVD-----------PGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGF------------YEKMKASGL 769
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 268-325 2.88e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 36.57  E-value: 2.88e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30694913   268 KVFSSMVGKGVPQSTVTYNSLMS---FETSYKEVSKIYDQMQRSDIQPDVVSYALLIKAYG 325
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHayaNVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 145-186 3.73e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.80  E-value: 3.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 30694913   145 LITAYGKLGNFNGAERVLSVLSKMGSTPNVISYTALMESYGR 186
Cdd:pfam13041   9 LINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 313-444 5.50e-03

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


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 37.48  E-value: 5.50e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913 313 DVVSYALLIKAYGRARREEEALSVFEEMLDAgvRPTHK-AYNILLDAFAISGMVEQAKTVF-KSMRRDrifPDLWSYTTM 390
Cdd:COG4783   3 CAEALYALAQALLLAGDYDEAEALLEKALEL--DPDNPeAFALLGEILLQLGDLDEAIVLLhEALELD---PDEPEARLN 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30694913 391 LS-AYVNASDMEGAEKFFKR-IKVDGFEPNIvtYGTLIKGYAKANDVEKMMEVYEK 444
Cdd:COG4783  78 LGlALLKAGDYDEALALLEKaLKLDPEHPEA--YLRLARAYRALGRPDEAIAALEK 131
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 430-508 6.99e-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: 38.15  E-value: 6.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30694913   430 AKANDVEKMMEVYEKMRLSGIKANQTILTTIM-------DASGRCKNFGSALGW--YKEMESCGVPPDQKAKNVLLSLAS 500
Cdd:pfam17177  22 SKHADATGALALYDAAKAEGVRLAQYHYNVLLylcskaaDATDLKPQLAADRGFevFEAMKAQGVSPNEATYTAVARLAA 101


                  ....*...
gi 30694913   501 TQDELEEA 508
Cdd:pfam17177 102 AKGDGDLA 109
 
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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