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Conserved domains on  [gi|449455158|ref|XP_004145320|]
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pentatricopeptide repeat-containing protein At2g29760, chloroplastic [Cucumis sativus]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 42-731 0e+00

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 542.13  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  42 KEVHARMLRTGLFFDPFSASKLFTASAlsSFSTLDYARNLFDQIPQPNLYTWNTLIRAYASSSDPFQSFVIFLDLLDKCE 121
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYV--KCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSV 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 122 DlPNKFTFPFVIKAASELKASRVGTAVHGMAIKLSFGMDLYILNSLVRFYGACGDLSMAERLFKGISCKDVVSWNSMISA 201
Cdd:PLN03077 285 D-PDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 202 FAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDA 281
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 282 QKLFDEMPERDVFSWTIMLDGYakmgdydaaRLvfnampvkeiaawnvlisayeqNGKPKEALAIFNELQLSkiAKPDEV 361
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGL---------RL----------------------NNRCFEALIFFRQMLLT--LKPNSV 490

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 362 TLVSTLSACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFySVEERDVYVWSAMIAGLGMHGR 441
Cdd:PLN03077 491 TLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGK 569

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 442 GKAAIDLFFEMQEAKVKPNSVTFTNVLCACSHAGLVDEGRVFFHEMEPVYGVVPEMKHYACMVDILGRAGFLEEAMELIN 521
Cdd:PLN03077 570 GSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN 649

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 522 EMSTTPSASVWGALLGACSLHMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKTGRWEKVSELRKLMRDTELKKEPGCS 601
Cdd:PLN03077 650 KMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCS 729

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 602 SIEANGNVHEFLVGDNTHPLSSNIYSKLEEIATKLKSVGYEPNKSHLLQliEEDDLKEQALSLHSEKLAIAFGLVTLAPS 681
Cdd:PLN03077 730 WVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMD--EIEVSKDDIFCGHSERLAIAFGLINTVPG 807

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|
gi 449455158 682 QPIRVVKNLRICGDCHAFAKLVSRVYDRDILLRDRYRFHHFRDGHCSCMD 731
Cdd:PLN03077 808 MPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 42-731 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 542.13  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  42 KEVHARMLRTGLFFDPFSASKLFTASAlsSFSTLDYARNLFDQIPQPNLYTWNTLIRAYASSSDPFQSFVIFLDLLDKCE 121
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYV--KCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSV 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 122 DlPNKFTFPFVIKAASELKASRVGTAVHGMAIKLSFGMDLYILNSLVRFYGACGDLSMAERLFKGISCKDVVSWNSMISA 201
Cdd:PLN03077 285 D-PDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 202 FAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDA 281
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 282 QKLFDEMPERDVFSWTIMLDGYakmgdydaaRLvfnampvkeiaawnvlisayeqNGKPKEALAIFNELQLSkiAKPDEV 361
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGL---------RL----------------------NNRCFEALIFFRQMLLT--LKPNSV 490

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 362 TLVSTLSACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFySVEERDVYVWSAMIAGLGMHGR 441
Cdd:PLN03077 491 TLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGK 569

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 442 GKAAIDLFFEMQEAKVKPNSVTFTNVLCACSHAGLVDEGRVFFHEMEPVYGVVPEMKHYACMVDILGRAGFLEEAMELIN 521
Cdd:PLN03077 570 GSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN 649

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 522 EMSTTPSASVWGALLGACSLHMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKTGRWEKVSELRKLMRDTELKKEPGCS 601
Cdd:PLN03077 650 KMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCS 729

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 602 SIEANGNVHEFLVGDNTHPLSSNIYSKLEEIATKLKSVGYEPNKSHLLQliEEDDLKEQALSLHSEKLAIAFGLVTLAPS 681
Cdd:PLN03077 730 WVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMD--EIEVSKDDIFCGHSERLAIAFGLINTVPG 807

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|
gi 449455158 682 QPIRVVKNLRICGDCHAFAKLVSRVYDRDILLRDRYRFHHFRDGHCSCMD 731
Cdd:PLN03077 808 MPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 640-733 3.63e-37

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 134.09  E-value: 3.63e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  640 GYEPNKSHLLQLIEEDDlKEQALSLHSEKLAIAFGLVTLAPSQPIRVVKNLRICGDCHAFAKLVSRVYDRDILLRDRYRF 719
Cdd:pfam14432   1 GYVPDLKFVLHDVDEEE-KKQLLHGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIFGREIVVRDASRF 79

                          90
                  ....*....|....
gi 449455158  720 HHFRDGHCSCMDYW 733
Cdd:pfam14432  80 HHFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 193-227 4.61e-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: 4.61e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 449455158  193 VSWNSMISAFAQGNCPEDALELFLKMERENVMPNS 227
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 271-350 8.64e-04

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


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.18  E-value: 8.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 271 MYTKCGSVDDAQKLFDEMPERD---VFSWTIMLDGYAKMGDYDAARLVFN---AMPVKEIAAWNVLISAYEQNGKPKEAL 344
Cdd:COG4783   13 ALLLAGDYDEAEALLEKALELDpdnPEAFALLGEILLQLGDLDEAIVLLHealELDPDEPEARLNLGLALLKAGDYDEAL 92


                 ....*.
gi 449455158 345 AIFNEL 350
Cdd:COG4783   93 ALLEKA 98
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 42-731 0e+00

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 542.13  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  42 KEVHARMLRTGLFFDPFSASKLFTASAlsSFSTLDYARNLFDQIPQPNLYTWNTLIRAYASSSDPFQSFVIFLDLLDKCE 121
Cdd:PLN03077 207 REVHAHVVRFGFELDVDVVNALITMYV--KCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSV 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 122 DlPNKFTFPFVIKAASELKASRVGTAVHGMAIKLSFGMDLYILNSLVRFYGACGDLSMAERLFKGISCKDVVSWNSMISA 201
Cdd:PLN03077 285 D-PDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISG 363

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 202 FAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDA 281
Cdd:PLN03077 364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKA 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 282 QKLFDEMPERDVFSWTIMLDGYakmgdydaaRLvfnampvkeiaawnvlisayeqNGKPKEALAIFNELQLSkiAKPDEV 361
Cdd:PLN03077 444 LEVFHNIPEKDVISWTSIIAGL---------RL----------------------NNRCFEALIFFRQMLLT--LKPNSV 490

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 362 TLVSTLSACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFySVEERDVYVWSAMIAGLGMHGR 441
Cdd:PLN03077 491 TLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHGK 569

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 442 GKAAIDLFFEMQEAKVKPNSVTFTNVLCACSHAGLVDEGRVFFHEMEPVYGVVPEMKHYACMVDILGRAGFLEEAMELIN 521
Cdd:PLN03077 570 GSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN 649

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 522 EMSTTPSASVWGALLGACSLHMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKTGRWEKVSELRKLMRDTELKKEPGCS 601
Cdd:PLN03077 650 KMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCS 729

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 602 SIEANGNVHEFLVGDNTHPLSSNIYSKLEEIATKLKSVGYEPNKSHLLQliEEDDLKEQALSLHSEKLAIAFGLVTLAPS 681
Cdd:PLN03077 730 WVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMD--EIEVSKDDIFCGHSERLAIAFGLINTVPG 807

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|
gi 449455158 682 QPIRVVKNLRICGDCHAFAKLVSRVYDRDILLRDRYRFHHFRDGHCSCMD 731
Cdd:PLN03077 808 MPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 128-733 4.01e-146

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 443.16  E-value: 4.01e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 128 TFPFVIKAASELKASRVGTAVHGMAIKLSFGMDLYILNSLVRFYGACGDLSMAERLFKGISCKDVVSWNSMISAFAQGNC 207
Cdd:PLN03081 125 TYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGN 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 208 PEDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDE 287
Cdd:PLN03081 205 YREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDG 284

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 288 MPErdvfswtimldgyakmgdydaarlvfnampvKEIAAWNVLISAYEQNGKPKEALAIFNELQLSKIAKpDEVTLVSTL 367
Cdd:PLN03081 285 MPE-------------------------------KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSI-DQFTFSIMI 332

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 368 SACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFYSVEERDVYVWSAMIAGLGMHGRGKAAID 447
Cdd:PLN03081 333 RIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVE 412

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 448 LFFEMQEAKVKPNSVTFTNVLCACSHAGLVDEGRVFFHEMEPVYGVVPEMKHYACMVDILGRAGFLEEAMELINEMSTTP 527
Cdd:PLN03081 413 MFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKP 492

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 528 SASVWGALLGACSLHMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKTGRWEKVSELRKLMRDTELKKEPGCSSIEANG 607
Cdd:PLN03081 493 TVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKK 572

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 608 NVHEFLVGDNTHPLSSNIYSKLEEIATKLKSVGYEPNKSHLLQLIEEDDlKEQALSLHSEKLAIAFGLVTLAPSQPIRVV 687
Cdd:PLN03081 573 QDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDE-EKVSGRYHSEKLAIAFGLINTSEWTPLQIT 651

                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*.
gi 449455158 688 KNLRICGDCHAFAKLVSRVYDRDILLRDRYRFHHFRDGHCSCMDYW 733
Cdd:PLN03081 652 QSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 640-733 3.63e-37

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 134.09  E-value: 3.63e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  640 GYEPNKSHLLQLIEEDDlKEQALSLHSEKLAIAFGLVTLAPSQPIRVVKNLRICGDCHAFAKLVSRVYDRDILLRDRYRF 719
Cdd:pfam14432   1 GYVPDLKFVLHDVDEEE-KKQLLHGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIFGREIVVRDASRF 79

                          90
                  ....*....|....
gi 449455158  720 HHFRDGHCSCMDYW 733
Cdd:pfam14432  80 HHFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 209-591 1.87e-34

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 141.14  E-value: 1.87e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 209 EDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEM 288
Cdd:PLN03077  68 EQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKM 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 289 PERDVFSWtimldgyakmgdydaarlvfnampvkeiaawNVLISAYEQNGKPKEALAIFNELQLSKIaKPDEVTLVSTLS 368
Cdd:PLN03077 148 PERDLFSW-------------------------------NVLVGGYAKAGYFDEALCLYHRMLWAGV-RPDVYTFPCVLR 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 369 ACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFYSVEERDVYVWSAMIAGLGMHGRGKAAIDL 448
Cdd:PLN03077 196 TCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLEL 275

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 449 FFEMQEAKVKPNSVTFTNVLCAC-----------------------------------SHAGLVDEGRVFFHEMEpvygv 493
Cdd:PLN03077 276 FFTMRELSVDPDLMTITSVISACellgderlgremhgyvvktgfavdvsvcnsliqmyLSLGSWGEAEKVFSRME----- 350

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 494 VPEMKHYACMVDILGRAGFLEEAMELINEM---STTPSASVWGALLGAC----SLHMNVELGELAsdqllklEPRNHGAI 566
Cdd:PLN03077 351 TKDAVSWTAMISGYEKNGLPDKALETYALMeqdNVSPDEITIASVLSACaclgDLDVGVKLHELA-------ERKGLISY 423

                        410       420
                 ....*....|....*....|....*....
gi 449455158 567 VLLSN----IYAKTGRWEKVSELRKLMRD 591
Cdd:PLN03077 424 VVVANalieMYSKCKCIDKALEVFHNIPE 452
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 542-604 2.87e-19

E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466580 [Multi-domain]  Cd Length: 63  Bit Score: 82.21  E-value: 2.87e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 449455158  542 HMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKTGRWEKVSELRKLMRDTELKKEPGCSSIE 604
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 209-548 2.91e-18

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 89.94  E-value: 2.91e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  209 EDALElFLKMERENVMpNSVTMVgvLSACAKKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEM 288
Cdd:PLN03218  423 KEAFR-FAKLIRNPTL-STFNML--MSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEM 498

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  289 P----ERDVFSWTIMLDGYAKMGDYDAARLVFNAMPVKEI----AAWNVLISAYEQNGKPKEALAIFNELQL-SKIAKPD 359
Cdd:PLN03218  499 VnagvEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKAeTHPIDPD 578

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  360 EVTLVSTLSACAQLGAIDLGGWIHVYIKREGI--VLNCHLISslVDMYAKCGSLEKALEVFYSVEERDV----YVWSAMI 433
Cdd:PLN03218  579 HITVGALMKACANAGQVDRAKEVYQMIHEYNIkgTPEVYTIA--VNSCSQKGDWDFALSIYDDMKKKGVkpdeVFFSALV 656

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  434 AGLGMHGRGKAAIDLFFEMQEAKVKPNSVTFTNVLCACSHAGLVDEGRVFFHEMEPVyGVVPEMKHYACMVDILGRAGFL 513
Cdd:PLN03218  657 DVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQL 735

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 449455158  514 EEAMELINEMST---TPSASVWGALLGACSLHMNVELG 548
Cdd:PLN03218  736 PKALEVLSEMKRlglCPNTITYSILLVASERKDDADVG 773
PLN03077 PLN03077
Protein ECB2; Provisional
 337-536 1.95e-12

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 70.65  E-value: 1.95e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 337 NGKPKEALAIFNELQLSKIAkPDEVTLVSTLSACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALE 416
Cdd:PLN03077  64 HGQLEQALKLLESMQELRVP-VDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWY 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 417 VFYSVEERDVYVWSAMIAGLGMHGRGKAAIDLFFEMQEAKVKPNSVTFTNVLCACshAGLVD--EGR-VFFHEMEpvYGV 493
Cdd:PLN03077 143 VFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTC--GGIPDlaRGReVHAHVVR--FGF 218

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 449455158 494 VPEMKHYACMVDILGRAGFLEEAMELINEMSTTPSASvWGALL 536
Cdd:PLN03077 219 ELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCIS-WNAMI 260
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 157-480 1.02e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 68.75  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  157 FGMDLYILNSLVRFYGACGDLSMA-ERLFKGisckDVVSWNSMISAFAQGNCPEDALELFLKMERENVMPNSVTMVGVLS 235
Cdd:PLN03218  440 FNMLMSVCASSQDIDGALRVLRLVqEAGLKA----DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALID 515

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  236 ACAK--KLDLEFGRWvcSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEMPER------DVFSWTIMLDGYAKMG 307
Cdd:PLN03218  516 GCARagQVAKAFGAY--GIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEthpidpDHITVGALMKACANAG 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  308 DYDAARLVFNAMPVKEI----AAWNVLISAYEQNGKPKEALAIFNELqLSKIAKPDEVTLVSTLSACAQLGAIDLGGWIH 383
Cdd:PLN03218  594 QVDRAKEVYQMIHEYNIkgtpEVYTIAVNSCSQKGDWDFALSIYDDM-KKKGVKPDEVFFSALVDVAGHAGDLDKAFEIL 672

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  384 VYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFYSVE----ERDVYVWSAMIAGLGMHGRGKAAIDLFFEMQEAKVKP 459
Cdd:PLN03218  673 QDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKsiklRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCP 752

                         330       340
                  ....*....|....*....|.
gi 449455158  460 NSVTFTNVLCACSHAGLVDEG 480
Cdd:PLN03218  753 NTITYSILLVASERKDDADVG 773
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 367-557 3.17e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 63.74  E-value: 3.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  367 LSACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFYSVE----ERDVYVWSAMIAGLGMHGRG 442
Cdd:PLN03218  444 MSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVnagvEANVHTFGALIDGCARAGQV 523

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  443 KAAIDLFFEMQEAKVKPNSVTFTNVLCACSHAGLVDegRVF--FHEMEP-VYGVVPEMKHYACMVDILGRAGFLEEAME- 518
Cdd:PLN03218  524 AKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVD--RAFdvLAEMKAeTHPIDPDHITVGALMKACANAGQVDRAKEv 601

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 449455158  519 --LINEMSTTPSASVWGALLGACSLHMNVELGELASDQLLK 557
Cdd:PLN03218  602 yqMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK 642
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 190-239 5.36e-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: 5.36e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 449455158  190 KDVVSWNSMISAFAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACAK 239
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 ...
 424-473 5.40e-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: 52.37  E-value: 5.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 449455158  424 RDVYVWSAMIAGLGMHGRGKAAIDLFFEMQEAKVKPNSVTFTNVLCACSH 473
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 90-468 7.40e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.51  E-value: 7.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158   90 LYTwnTLIRAYASSSDPFQSFVIFLDLlDKCEDLPNKFTFPFVIKAASelKASRVGTA--VHGMAIKLSFGMDLYILNSL 167
Cdd:PLN03218  474 LYT--TLISTCAKSGKVDAMFEVFHEM-VNAGVEANVHTFGALIDGCA--RAGQVAKAfgAYGIMRSKNVKPDRVVFNAL 548

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  168 VrfyGACGDLSMAERLFKGIS---------CKDVVSWNSMISAFAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACA 238
Cdd:PLN03218  549 I---SACGQSGAVDRAFDVLAemkaethpiDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCS 625

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  239 KKLDLEFGRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEMPERDV----FSWTIMLDGYAKMGDYDAARL 314
Cdd:PLN03218  626 QKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIklgtVSYSSLMGACSNAKNWKKALE 705

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  315 VFNA------MPVkeIAAWNVLISAY-EQNGKPKeALAIFNELQLSKIaKPDEVTLVSTLSACAQLGAIDLGGWIHVYIK 387
Cdd:PLN03218  706 LYEDiksiklRPT--VSTMNALITALcEGNQLPK-ALEVLSEMKRLGL-CPNTITYSILLVASERKDDADVGLDLLSQAK 781

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  388 REGIVLN---CHLISSL-VDMYAKCGSLEKALEVFYSVEERDVYVWSAMiaglgmhgrgkaAIDLFFEMQEAKVKPNSVT 463
Cdd:PLN03218  782 EDGIKPNlvmCRCITGLcLRRFEKACALGEPVVSFDSGRPQIENKWTSW------------ALMVYRETISAGTLPTMEV 849


                  ....*
gi 449455158  464 FTNVL 468
Cdd:PLN03218  850 LSQVL 854
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 265-305 1.57e-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: 51.21  E-value: 1.57e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 449455158  265 CNAMLDMYTKCGSVDDAQKLFDEMPER----DVFSWTIMLDGYAK 305
Cdd:pfam13041   6 YNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 324-372 4.32e-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: 44.28  E-value: 4.32e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 449455158  324 IAAWNVLISAYEQNGKPKEALAIFNELQLSKIaKPDEVTLVSTLSACAQ 372
Cdd:pfam13041   3 VVTYNTLINGYCKKGKVEEAFKLFNEMKKRGV-KPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 193-223 5.52e-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: 43.22  E-value: 5.52e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 449455158  193 VSWNSMISAFAQGNCPEDALELFLKMERENV 223
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 193-227 4.61e-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: 4.61e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 449455158  193 VSWNSMISAFAQGNCPEDALELFLKMERENVMPNS 227
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 427-461 6.31e-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: 6.31e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 449455158  427 YVWSAMIAGLGMHGRGKAAIDLFFEMQEAKVKPNS 461
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
Eplus_motif pfam20430
E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins ...
 609-636 9.27e-05

E+ motif; This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif, precedes the DYW domain and, although their role is not clear, they are essential in th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.


Pssm-ID: 466579 [Multi-domain]  Cd Length: 28  Bit Score: 39.95  E-value: 9.27e-05
                          10        20
                  ....*....|....*....|....*...
gi 449455158  609 VHEFLVGDNTHPLSSNIYSKLEEIATKL 636
Cdd:pfam20430   1 THTFFAGDKSHPESKQIYEKLSDLTQRI 28
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 291-334 2.29e-04

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: 39.27  E-value: 2.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 449455158  291 RDVFSWTIMLDGYAKMGDYDAARLVFNAMPVKEIAA----WNVLISAY 334
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPnvytYTILINGL 48
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 267-598 3.73e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.92  E-value: 3.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  267 AMLDMytKCGSVDDAQKLFDEMPERDVFSWTIML---DGYAKMGD-YDAARLVFNAMPV--KEIAAWNVLISAYEQNGKP 340
Cdd:TIGR02917 506 ARIDI--QEGNPDDAIQRFEKVLTIDPKNLRAILalaGLYLRTGNeEEAVAWLEKAAELnpQEIEPALALAQYYLGKGQL 583

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  341 KEALAIFNELQLskiAKPDEVTLVSTLsACAQLGAIDLGGWIHVYIKREGIVLNCHLISSLV-DMYAKCGSLEKALEVFY 419
Cdd:TIGR02917 584 KKALAILNEAAD---AAPDSPEAWLML-GRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLaDAYAVMKNYAKAITSLK 659

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  420 SVEERDVYVWSAMI--AGLGMH-GRGKAAIDLFFEMQEAKVKpnsvtftnvlcacSHAGLVDEGRVFFHEMEPVygvvpe 496
Cdd:TIGR02917 660 RALELKPDNTEAQIglAQLLLAaKRTESAKKIAKSLQKQHPK-------------AALGFELEGDLYLRQKDYP------ 720

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  497 mkhyacmvdilgragflEEAMELINEMSTTPSASVWGALLGACSLHMNVELGELASDQLLKLEPRNHGAIVLLSNIYAKT 576
Cdd:TIGR02917 721 -----------------AAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQ 783

                         330       340
                  ....*....|....*....|...
gi 449455158  577 GRWEK-VSELRKLmrdteLKKEP 598
Cdd:TIGR02917 784 KDYDKaIKHYQTV-----VKKAP 801
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 326-355 6.84e-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: 37.44  E-value: 6.84e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 449455158  326 AWNVLISAYEQNGKPKEALAIFNELQLSKI 355
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 271-350 8.64e-04

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


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.18  E-value: 8.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 271 MYTKCGSVDDAQKLFDEMPERD---VFSWTIMLDGYAKMGDYDAARLVFN---AMPVKEIAAWNVLISAYEQNGKPKEAL 344
Cdd:COG4783   13 ALLLAGDYDEAEALLEKALELDpdnPEAFALLGEILLQLGDLDEAIVLLHealELDPDEPEARLNLGLALLKAGDYDEAL 92


                 ....*.
gi 449455158 345 AIFNEL 350
Cdd:COG4783   93 ALLEKA 98
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 278-425 1.81e-03

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: 40.87  E-value: 1.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158 278 VDDAQKLFDEMPERDVFsWTIMLDGYAKMGDYDAARLVFNAM----PvKEIAAWNVLISAYEQNGKPKEALAIFNE-LQL 352
Cdd:COG2956  130 IEVLERLLKLGPENAHA-YCELAELYLEQGDYDEAIEALEKAlkldP-DCARALLLLAELYLEQGDYEEAIAALERaLEQ 207

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 449455158 353 SkiakPDEVTLVSTLSAC-AQLGaiDLGGWIHVYIKREGIVLNCHLISSLVDMYAKCGSLEKALEVFYSVEERD 425
Cdd:COG2956  208 D----PDYLPALPRLAELyEKLG--DPEEALELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQLRRH 275
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 265-293 1.85e-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: 1.85e-03
                          10        20
                  ....*....|....*....|....*....
gi 449455158  265 CNAMLDMYTKCGSVDDAQKLFDEMPERDV 293
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 256-288 2.77e-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: 35.78  E-value: 2.77e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 449455158  256 KGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEM 288
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 294-324 3.45e-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: 35.51  E-value: 3.45e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 449455158  294 FSWTIMLDGYAKMGDYDAARLVFNAMPVKEI 324
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 427-457 5.29e-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: 35.13  E-value: 5.29e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 449455158  427 YVWSAMIAGLGMHGRGKAAIDLFFEMQEAKV 457
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 402-524 5.41e-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: 38.92  E-value: 5.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449455158  402 VDMYAKCGSLEKALEVFYSVEERDV----YVWSAMI-----AGLGMHGRGKAAIDLFFE----MQEAKVKPNSVTFTNVL 468
Cdd:pfam17177  18 LDKCSKHADATGALALYDAAKAEGVrlaqYHYNVLLylcskAADATDLKPQLAADRGFEvfeaMKAQGVSPNEATYTAVA 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 449455158  469 CACSHAGLVDEGRVFFHEMEpVYGVVPEMKHYACMVDILGRAGFLEEAMELINEMS 524
Cdd:pfam17177  98 RLAAAKGDGDLAFDLVKEME-AAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHML 152
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 294-324 5.56e-03

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 34.75  E-value: 5.56e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 449455158  294 FSWTIMLDGYAKMGDYDAARLVFNAMPVKEI 324
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
 
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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