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Conserved domains on  [gi|9558596|gb|AAF88159|]
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Contains similarity to a hypothetical protein T3P18.15 gi|5454201 from Arabidopsis thaliana BAC T3P18 gb|AC005698 and contains multiple PPR PF|01535 repeats [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
 161-504 4.47e-26

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 113.05  E-value: 4.47e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    161 SGKVrqfDLAWHLIDLMKSRNVEISIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRkrrASEA 240
Cdd:PLN03218  485 SGKV---DAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ---SGAV 558

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    241 QSFFDSLKDR------FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIE--PNVYTysIVIDALCRCGQISRAHDV 312
Cdd:PLN03218  559 DRAFDVLAEMkaethpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKgtPEVYT--IAVNSCSQKGDWDFALSI 636

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    313 FADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCE 392
Cdd:PLN03218  637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    393 VNASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLV 472
Cdd:PLN03218  717 PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT 796

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 9558596    473 TM-------FCGMGHWNNAYKLFKEMVEEKCLTPSLSLY 504
Cdd:PLN03218  797 GLclrrfekACALGEPVVSFDSGRPQIENKWTSWALMVY 835
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 161-504 4.47e-26

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 113.05  E-value: 4.47e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    161 SGKVrqfDLAWHLIDLMKSRNVEISIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRkrrASEA 240
Cdd:PLN03218  485 SGKV---DAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ---SGAV 558

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    241 QSFFDSLKDR------FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIE--PNVYTysIVIDALCRCGQISRAHDV 312
Cdd:PLN03218  559 DRAFDVLAEMkaethpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKgtPEVYT--IAVNSCSQKGDWDFALSI 636

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    313 FADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCE 392
Cdd:PLN03218  637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    393 VNASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLV 472
Cdd:PLN03218  717 PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT 796

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 9558596    473 TM-------FCGMGHWNNAYKLFKEMVEEKCLTPSLSLY 504
Cdd:PLN03218  797 GLclrrfekACALGEPVVSFDSGRPQIENKWTSWALMVY 835
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 253-302 2.21e-17

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: 75.86  E-value: 2.21e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9558596    253 PDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCR 302
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 291-325 2.46e-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: 47.06  E-value: 2.46e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    291 YTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNA 325
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 161-504 4.47e-26

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 113.05  E-value: 4.47e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    161 SGKVrqfDLAWHLIDLMKSRNVEISIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRkrrASEA 240
Cdd:PLN03218  485 SGKV---DAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ---SGAV 558

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    241 QSFFDSLKDR------FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIE--PNVYTysIVIDALCRCGQISRAHDV 312
Cdd:PLN03218  559 DRAFDVLAEMkaethpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKgtPEVYT--IAVNSCSQKGDWDFALSI 636

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    313 FADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCE 392
Cdd:PLN03218  637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    393 VNASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLV 472
Cdd:PLN03218  717 PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT 796

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 9558596    473 TM-------FCGMGHWNNAYKLFKEMVEEKCLTPSLSLY 504
Cdd:PLN03218  797 GLclrrfekACALGEPVVSFDSGRPQIENKWTSWALMVY 835
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 251-532 3.80e-23

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 104.19  E-value: 3.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    251 FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNN 330
Cdd:PLN03218  468 LKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNA 547

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    331 LMRVHVKAGRTEKVLQVYNQMKKLG--CEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKK 408
Cdd:PLN03218  548 LISACGQSGAVDRAFDVLAEMKAEThpIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK 627

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    409 RDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNNAYKLF 488
Cdd:PLN03218  628 GDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELY 707

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 9558596    489 KEMVEEKcLTPSLSLYEMVLAQLRRAGQLKKHEELVEKMIQKGL 532
Cdd:PLN03218  708 EDIKSIK-LRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGL 750
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 253-302 2.21e-17

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: 75.86  E-value: 2.21e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9558596    253 PDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCR 302
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 ...
 323-372 1.04e-14

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: 68.16  E-value: 1.04e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9558596    323 PNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEAHCR 372
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 116-527 2.32e-13

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 72.96  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   116 CVIEKCGsvrhGIPlhqslaffNWATSRDDYDHKSPHPY-------NEMIDLSGKVRQFDLAWHLIDLMKSRNVeISiet 188
Cdd:PLN03077 192 CVLRTCG----GIP--------DLARGREVHAHVVRFGFeldvdvvNALITMYVKCGDVVSARLVFDRMPRRDC-IS--- 255

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   189 FTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISN---LSRKRRASEAQSFfdSLKDRFEPDVIVYTNLVRGW 265
Cdd:PLN03077 256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAcelLGDERLGREMHGY--VVKTGFAVDVSVCNSLIQMY 333

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   266 CRAGEISEAEKVFKEMKLAgiepNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRTEKVL 345
Cdd:PLN03077 334 LSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGV 409

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   346 QVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKC----------EVNASTFNTI--FRYIEKKRDVNG 413
Cdd:PLN03077 410 KLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDViswtsiiaglRLNNRCFEALifFRQMLLTLKPNS 489

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   414 -----------------------AHRMYSKM------------MEAKC-------------EPNTVTYNILMRMFVGSKS 445
Cdd:PLN03077 490 vtliaalsacarigalmcgkeihAHVLRTGIgfdgflpnalldLYVRCgrmnyawnqfnshEKDVVSWNILLTGYVAHGK 569

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   446 TDMVLKMKKEMDDKEVEPNVNTYrllVTMFCGM---GHWNNAYKLFKEMVEEKCLTPSLSLYEMVLAQLRRAGQLKKHEE 522
Cdd:PLN03077 570 GSMAVELFNRMVESGVNPDEVTF---ISLLCACsrsGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYN 646


                 ....*
gi 9558596   523 LVEKM 527
Cdd:PLN03077 647 FINKM 651
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 288-337 3.52e-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: 61.23  E-value: 3.52e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9558596    288 PNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVK 337
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 ...
 358-403 1.15e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 56.60  E-value: 1.15e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 9558596    358 PDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFR 403
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 ...
 394-440 4.81e-10

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 55.06  E-value: 4.81e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 9558596    394 NASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMF 440
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 157-389 6.23e-10

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 61.81  E-value: 6.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   157 MIDLSGKVRQFDLAWHLIDLMKsrnvEISIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRKRR 236
Cdd:PLN03081 265 LIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLAL 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   237 ASEAQSFFDSLKDR-FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAgiepNVYTYSIVIDALCRCGQISRAHDVFAD 315
Cdd:PLN03081 341 LEHAKQAHAGLIRTgFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFER 416

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9558596   316 MLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKK-LGCEPDTITYNFLIEAHCRDENLENAVkvlnTMIKK 389
Cdd:PLN03081 417 MIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEnHRIKPRAMHYACMIELLGREGLLDEAY----AMIRR 487
PLN03077 PLN03077
Protein ECB2; Provisional
 155-359 8.83e-10

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 61.40  E-value: 8.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   155 NEMIDLSGKVRQFDLAWHLIDLMKSrnveiSIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRK 234
Cdd:PLN03077 528 NALLDLYVRCGRMNYAWNQFNSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRS 602

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   235 RRASEAQSFFDSLKDRFE--PDVIVYTNLVRGWCRAGEISEAEKVFKEMKlagIEPNVYTYSIVIDAlCRC------GQI 306
Cdd:PLN03077 603 GMVTQGLEYFHSMEEKYSitPNLKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNA-CRIhrhvelGEL 678

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9558596   307 SRAHdVFAdmLDSGCAPNAITFNNLmrvHVKAGRTEKVLQVYNQMKKLGCEPD 359
Cdd:PLN03077 679 AAQH-IFE--LDPNSVGYYILLCNL---YADAGKWDEVARVRKTMRENGLTVD 725
PLN03077 PLN03077
Protein ECB2; Provisional
 212-494 1.38e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 61.02  E-value: 1.38e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   212 MEDYGCVPDK--IAFSIVISNLSRKRRASEAQSFFDSLKDRFEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPN 289
Cdd:PLN03077 444 LEVFHNIPEKdvISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFD 523

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   290 VYTYSIVIDALCRCGQISRAHDVFadmldSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEA 369
Cdd:PLN03077 524 GFLPNALLDLYVRCGRMNYAWNQF-----NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCA 598

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   370 HCRDENLENAVKVLNTMIKKKCEV-NASTFNTIFRYIEKKRDVNGAHRMYSKMmeaKCEPNTVTYNILM-------RMFV 441
Cdd:PLN03077 599 CSRSGMVTQGLEYFHSMEEKYSITpNLKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWGALLnacrihrHVEL 675

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9558596   442 GSKSTDMVLKMKKEmddkevepNVNTYRLLVTMFCGMGHWNNAYKLFKEMVEE 494
Cdd:PLN03077 676 GELAAQHIFELDPN--------SVGYYILLCNLYADAGKWDEVARVRKTMREN 720
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 252-344 1.83e-09

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: 57.79  E-value: 1.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    252 EPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNL 331
Cdd:pfam17177  87 SPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAAL 166

                          90
                  ....*....|...
gi 9558596    332 MRVHVKAGRTEKV 344
Cdd:pfam17177 167 LKVSAKAGRADKV 179
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 428-476 3.27e-09

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 52.75  E-value: 3.27e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 9558596    428 PNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFC 476
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PLN03077 PLN03077
Protein ECB2; Provisional
 252-461 8.33e-09

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 58.32  E-value: 8.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   252 EPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVidaLCRCGQI---SRAHDVFADMLDSGCAPNAITF 328
Cdd:PLN03077 149 ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCV---LRTCGGIpdlARGREVHAHVVRFGFELDVDVV 225

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   329 NNLMRVHVKAGRTEKVLQVYNQMKKLgcepDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKK 408
Cdd:PLN03077 226 NALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL 301

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 9558596   409 RDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEV 461
Cdd:PLN03077 302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA 354
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 355-386 1.23e-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: 50.42  E-value: 1.23e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 9558596    355 GCEPDTITYNFLIEAHCRDENLENAVKVLNTM 386
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 266-532 1.89e-08

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 57.19  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    266 CRA-GEISEAEKVFKEMKlagiEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRTEKV 344
Cdd:PLN03218  416 CKKqRAVKEAFRFAKLIR----NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAM 491

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    345 LQVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIfryIEKKRDVNGAHRMYSKMMEA 424
Cdd:PLN03218  492 FEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNAL---ISACGQSGAVDRAFDVLAEM 568

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    425 KCE-----PNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNNAYKLFKEMvEEKCLTP 499
Cdd:PLN03218  569 KAEthpidPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDM-KKKGVKP 647

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 9558596    500 SlslyEMVLAQL----RRAGQLKKHEELVEKMIQKGL 532
Cdd:PLN03218  648 D----EVFFSALvdvaGHAGDLDKAFEILQDARKQGI 680
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 276-337 1.95e-08

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: 50.82  E-value: 1.95e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9558596    276 KVFKEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVK 337
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 251-282 2.28e-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: 49.65  E-value: 2.28e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 9558596    251 FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMK 282
Cdd:pfam12854   3 LKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 285-316 4.43e-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: 48.88  E-value: 4.43e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 9558596    285 GIEPNVYTYSIVIDALCRCGQISRAHDVFADM 316
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 312-369 8.38e-08

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: 49.28  E-value: 8.38e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9558596    312 VFADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITYNFLIEA 369
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 267-382 2.06e-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: 51.63  E-value: 2.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    267 RAGEISEAEKVFKEMKLAGIEPNVYTYSIVI---------DALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVK 337
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAA 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 9558596    338 AGRTEKVLQVYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKV 382
Cdd:pfam17177 103 KGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEV 147
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 242-299 2.07e-07

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: 48.12  E-value: 2.07e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 9558596    242 SFFDSLKDR-FEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDA 299
Cdd:pfam13812   1 SILREMVRDgIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGV 59
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 291-325 2.46e-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: 47.06  E-value: 2.46e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    291 YTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNA 325
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 326-360 2.77e-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: 46.68  E-value: 2.77e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    326 ITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDT 360
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 256-290 6.19e-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: 45.91  E-value: 6.19e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    256 IVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNV 290
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 193-533 7.55e-07

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 51.79  E-value: 7.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   193 IRRYVRAGLASEAVHCFnRMEDYGC---VPDKIAFSIVISNLSRKRRASEAQSFFDSLKDRFEPDVIVYTNLVRGWCRAG 269
Cdd:PLN03081  94 IEKLVACGRHREALELF-EILEAGCpftLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCG 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   270 EISEAEKVFKEMKlagiEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYN 349
Cdd:PLN03081 173 MLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHC 248

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   350 QMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKkcevNASTFNTIFR------YIEKkrdvngAHRMYSKMME 423
Cdd:PLN03081 249 CVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEK----TTVAWNSMLAgyalhgYSEE------ALCLYYEMRD 318

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   424 AKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNNAYKLFKEMVEEKCLTpslsl 503
Cdd:PLN03081 319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLIS----- 393

                        330       340       350
                 ....*....|....*....|....*....|
gi 9558596   504 YEMVLAQLRRAGQLKKHEELVEKMIQKGLV 533
Cdd:PLN03081 394 WNALIAGYGNHGRGTKAVEMFERMIAEGVA 423
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 185-233 8.47e-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: 45.82  E-value: 8.47e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 9558596    185 SIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSR 233
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 239-536 1.56e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 51.02  E-value: 1.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   239 EAQSFFDSLKdrfEPDVIVYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLD 318
Cdd:PLN03081 277 DARCVFDGMP---EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIR 353

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   319 SGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKlgcePDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTF 398
Cdd:PLN03081 354 TGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTF 429

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   399 NTIFRYIEKKRDVNGAHRMYSKMMEA-KCEPNTVTYNILMRMFVGSKSTDMVLKMKKemdDKEVEPNVNTYRLLVTMfCG 477
Cdd:PLN03081 430 LAVLSACRYSGLSEQGWEIFQSMSENhRIKPRAMHYACMIELLGREGLLDEAYAMIR---RAPFKPTVNMWAALLTA-CR 505

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9558596   478 MgHWN------NAYKLFKeMVEEKcltpsLSLYEMVLAQLRRAGQLKKHEELVEKMIQKGLVARP 536
Cdd:PLN03081 506 I-HKNlelgrlAAEKLYG-MGPEK-----LNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHP 563
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 277-369 3.79e-06

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: 47.78  E-value: 3.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    277 VFKEMKLAGIEPNVYTYSIVIDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGC 356
Cdd:pfam17177  77 VFEAMKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGV 156

                          90
                  ....*....|...
gi 9558596    357 EPDTITYNFLIEA 369
Cdd:pfam17177 157 ELEEPELAALLKV 169
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 188-220 1.04e-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: 42.44  E-value: 1.04e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 9558596    188 TFTILIRRYVRAGLASEAVHCFNRMEDYGCVPD 220
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 154-198 1.06e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 42.74  E-value: 1.06e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 9558596    154 YNEMIDLSGKVRQFDLAWHLIDLMKSRNVEISIETFTILIRRYVR 198
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 347-401 1.42e-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: 1.42e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 9558596    347 VYNQMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTI 401
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAI 56
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 350-528 2.58e-05

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 45.47  E-value: 2.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    350 QMKKLGCEPDTITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKKRDVNGAH---------RMYSK 420
Cdd:pfam17177   1 QRKKKGKQTPESELRFQLDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKpqlaadrgfEVFEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    421 MMEAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNNAYKlfkemVEEKCLTPS 500
Cdd:pfam17177  81 MKAQGVSPNEATYTAVARLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYE-----VEEHMLAHG 155

                         170       180       190
                  ....*....|....*....|....*....|..
gi 9558596    501 LSLYEM-VLAQLR---RAGQLKKHEELVEKMI 528
Cdd:pfam17177 156 VELEEPeLAALLKvsaKAGRADKVYAYLHRLR 187
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 256-286 2.95e-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: 2.95e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 9558596    256 IVYTNLVRGWCRAGEISEAEKVFKEMKLAGI 286
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 157-355 3.53e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 46.79  E-value: 3.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   157 MIDLSGKVRQFDLAWHLIDLMKSRNVeISietFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRKRR 236
Cdd:PLN03081 366 LVDLYSKWGRMEDARNVFDRMPRKNL-IS---WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGL 441

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   237 ASEAQSFFDSLKD--RFEPDVIVYTNLVRGWCRAGEISEAekvFKEMKLAGIEPNVYTYSIVIDAlCRCGQISRAHDVFA 314
Cdd:PLN03081 442 SEQGWEIFQSMSEnhRIKPRAMHYACMIELLGREGLLDEA---YAMIRRAPFKPTVNMWAALLTA-CRIHKNLELGRLAA 517

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 9558596   315 DMLdSGCAPNAI-TFNNLMRVHVKAGRTEKVLQVYNQMKKLG 355
Cdd:PLN03081 518 EKL-YGMGPEKLnNYVVLLNLYNSSGRQAEAAKVVETLKRKG 558
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 291-321 8.18e-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: 39.76  E-value: 8.18e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 9558596    291 YTYSIVIDALCRCGQISRAHDVFADMLDSGC 321
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 459-492 9.56e-05

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 39.64  E-value: 9.56e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 9558596    459 KEVEPNVNTYRLLVTMFCGMGHWNNAYKLFKEMV 492
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 326-356 1.22e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 39.37  E-value: 1.22e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 9558596    326 ITFNNLMRVHVKAGRTEKVLQVYNQMKKLGC 356
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 407-533 1.94e-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: 42.77  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    407 KKRDVNGAHRMYSKMMEAKCEPNTVTYNILMrmFVGSKSTDMVLKMK-----------KEMDDKEVEPNVNTYRLLVTMF 475
Cdd:pfam17177  23 KHADATGALALYDAAKAEGVRLAQYHYNVLL--YLCSKAADATDLKPqlaadrgfevfEAMKAQGVSPNEATYTAVARLA 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9558596    476 CGMGHWNNAYKLFKEMVEEKcLTPSLSLYEMVLAQLRRAGQLKKHEELVEKMIQKGLV 533
Cdd:pfam17177 101 AAKGDGDLAFDLVKEMEAAG-VSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVE 157
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 381-442 2.33e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 39.26  E-value: 2.33e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9558596    381 KVLNTMIKKKCEVNASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVG 442
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 451-508 3.38e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.88  E-value: 3.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9558596    451 KMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNNAYKLFKEMVEEKClTPSLSLYEMVL 508
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGI-KPTLDTYNAIL 57
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 361-395 5.85e-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: 5.85e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    361 ITYNFLIEAHCRDENLENAVKVLNTMIKKKCEVNA 395
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 188-217 6.31e-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: 37.06  E-value: 6.31e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 9558596    188 TFTILIRRYVRAGLASEAVHCFNRMEDYGC 217
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 297-449 7.50e-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: 41.23  E-value: 7.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    297 IDALCRCGQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRT---------EKVLQVYNQMKKLGCEPDTITYNFLI 367
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADAtdlkpqlaaDRGFEVFEAMKAQGVSPNEATYTAVA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596    368 EAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNTVTYNILMRMFVGSKSTD 447
Cdd:pfam17177  98 RLAAAKGDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRAD 177


                  ..
gi 9558596    448 MV 449
Cdd:pfam17177 178 KV 179
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 463-496 1.04e-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: 36.96  E-value: 1.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 9558596    463 PNVNTYRLLVTMFCGMGHWNNAYKLFKEMVEEKC 496
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGV 34
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 427-478 1.25e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 37.34  E-value: 1.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9558596    427 EPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGM 478
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 361-391 1.43e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 36.29  E-value: 1.43e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 9558596    361 ITYNFLIEAHCRDENLENAVKVLNTMIKKKC 391
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PRK15174 PRK15174
Vi polysaccharide transport protein VexE;
252-347 1.51e-03

Vi polysaccharide transport protein VexE;


Pssm-ID: 185096 [Multi-domain]  Cd Length: 656  Bit Score: 41.27  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9558596   252 EPDVI-VYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVidALCRCGQISRAHDVFADMLDSGCAPNAITFNN 330
Cdd:PRK15174 140 FSGNSqIFALHLRTLVLMDKELQAISLARTQAQEVPPRGDMIATCL--SFLNKSRLPEDHDLARALLPFFALERQESAGL 217

                         90
                 ....*....|....*..
gi 9558596   331 LMRVHVKAGRTEKVLQV 347
Cdd:PRK15174 218 AVDTLCAVGKYQEAIQT 234
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 173-229 2.33e-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: 2.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9558596    173 LIDLMKSRNVEISIETFTILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVIS 229
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILG 58
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 431-465 2.39e-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: 35.51  E-value: 2.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9558596    431 VTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNV 465
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 397-430 6.45e-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: 34.35  E-value: 6.45e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 9558596    397 TFNTIFRYIEKKRDVNGAHRMYSKMMEAKCEPNT 430
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
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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