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Conserved domains on  [gi|332661361|gb|AEE86761|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000225)

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

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

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 48-691 1.31e-166

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 494.77  E-value: 1.31e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  48 VERLCRANRFGEAIDVLcgqKLLReavqlLGRAKKPPASTYCNLIQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRLL 127
Cdd:PLN03081  94 IEKLVACGRHREALELF---EILE-----AGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVL 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 128 RMYAKCGSLVDARKVFDEMPNRDLCSWNVMVNGYAEVGLLEEARKLFDEMTEKDSyswtamvtgyvkkdqpeealvlysl 207
Cdd:PLN03081 166 LMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGS------------------------- 220

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 208 mqrvpNSRPNIFTVSIAVAAAAAVkcIRRGKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIVEKDVVSW 287
Cdd:PLN03081 221 -----DAEPRTFVVMLRASAGLGS--ARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAW 293

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 288 TSMIDRYFKSSRWREGFSLFSELVGSCERPNEYTFAGVLNACADLTTEELGKQVHGYMTRVGFDPYSFASSSLVDMYTKC 367
Cdd:PLN03081 294 NSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKW 373

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 368 GNIESAKHVVDGCPKPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSIT 447
Cdd:PLN03081 374 GRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMS 453

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 448 EKHRLSHTSDHYTCLVDLLARSGRFEQLKSVISEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVT 527
Cdd:PLN03081 454 ENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVV 533

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 528 MANIYAAAGKWEEEGKMRKRMQEIGVTKRPGSSWTEIKRKRHVFIAADTSHPMYNQIVEFLRELRKKMKEEGYVPATSLV 607
Cdd:PLN03081 534 LLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENEL 613

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 608 LHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFHCFENGQCSC 687
Cdd:PLN03081 614 LPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSC 693


                 ....
gi 332661361 688 GDYW 691
Cdd:PLN03081 694 GDYW 697
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 48-691 1.31e-166

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 494.77  E-value: 1.31e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  48 VERLCRANRFGEAIDVLcgqKLLReavqlLGRAKKPPASTYCNLIQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRLL 127
Cdd:PLN03081  94 IEKLVACGRHREALELF---EILE-----AGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVL 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 128 RMYAKCGSLVDARKVFDEMPNRDLCSWNVMVNGYAEVGLLEEARKLFDEMTEKDSyswtamvtgyvkkdqpeealvlysl 207
Cdd:PLN03081 166 LMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGS------------------------- 220

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 208 mqrvpNSRPNIFTVSIAVAAAAAVkcIRRGKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIVEKDVVSW 287
Cdd:PLN03081 221 -----DAEPRTFVVMLRASAGLGS--ARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAW 293

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 288 TSMIDRYFKSSRWREGFSLFSELVGSCERPNEYTFAGVLNACADLTTEELGKQVHGYMTRVGFDPYSFASSSLVDMYTKC 367
Cdd:PLN03081 294 NSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKW 373

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 368 GNIESAKHVVDGCPKPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSIT 447
Cdd:PLN03081 374 GRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMS 453

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 448 EKHRLSHTSDHYTCLVDLLARSGRFEQLKSVISEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVT 527
Cdd:PLN03081 454 ENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVV 533

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 528 MANIYAAAGKWEEEGKMRKRMQEIGVTKRPGSSWTEIKRKRHVFIAADTSHPMYNQIVEFLRELRKKMKEEGYVPATSLV 607
Cdd:PLN03081 534 LLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENEL 613

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 608 LHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFHCFENGQCSC 687
Cdd:PLN03081 614 LPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSC 693


                 ....
gi 332661361 688 GDYW 691
Cdd:PLN03081 694 GDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 599-691 3.71e-40

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


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 142.18  E-value: 3.71e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  599 GYVPATSLVLHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFH 678
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 332661361  679 CFENGQCSCGDYW 691
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 397-540 9.42e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.80  E-value: 9.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 397 QNGQPDEALKYFDLLLKSgtKPDHVTFVNVLS-ACTHAGLVEKGLEFFYSITEKHrlSHTSDHYTCLVDLLARSGRFEQL 475
Cdd:COG2956   54 RRGEYDRAIRIHQKLLER--DPDRAEALLELAqDYLKAGLLDRAEELLEKLLELD--PDDAEALRLLAEIYEQEGDWEKA 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 332661361 476 KSVISEM-PMKPSKFLWASVLGgcSTY---GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG2956  130 IEVLERLlKLGPENAHAYCELA--ELYleqGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 386-419 2.96e-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: 41.29  E-value: 2.96e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 332661361  386 VSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPD 419
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 48-691 1.31e-166

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 494.77  E-value: 1.31e-166
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  48 VERLCRANRFGEAIDVLcgqKLLReavqlLGRAKKPPASTYCNLIQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRLL 127
Cdd:PLN03081  94 IEKLVACGRHREALELF---EILE-----AGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVL 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 128 RMYAKCGSLVDARKVFDEMPNRDLCSWNVMVNGYAEVGLLEEARKLFDEMTEKDSyswtamvtgyvkkdqpeealvlysl 207
Cdd:PLN03081 166 LMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGS------------------------- 220

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 208 mqrvpNSRPNIFTVSIAVAAAAAVkcIRRGKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIVEKDVVSW 287
Cdd:PLN03081 221 -----DAEPRTFVVMLRASAGLGS--ARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAW 293

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 288 TSMIDRYFKSSRWREGFSLFSELVGSCERPNEYTFAGVLNACADLTTEELGKQVHGYMTRVGFDPYSFASSSLVDMYTKC 367
Cdd:PLN03081 294 NSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKW 373

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 368 GNIESAKHVVDGCPKPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSIT 447
Cdd:PLN03081 374 GRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMS 453

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 448 EKHRLSHTSDHYTCLVDLLARSGRFEQLKSVISEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVT 527
Cdd:PLN03081 454 ENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVV 533

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 528 MANIYAAAGKWEEEGKMRKRMQEIGVTKRPGSSWTEIKRKRHVFIAADTSHPMYNQIVEFLRELRKKMKEEGYVPATSLV 607
Cdd:PLN03081 534 LLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENEL 613

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 608 LHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFHCFENGQCSC 687
Cdd:PLN03081 614 LPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSC 693


                 ....
gi 332661361 688 GDYW 691
Cdd:PLN03081 694 GDYW 697
PLN03077 PLN03077
Protein ECB2; Provisional
 62-689 1.21e-154

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 468.95  E-value: 1.21e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  62 DVLCG----QKLLREAVQLLGR----AKKPPASTYCNLIQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRLLRMYAKC 133
Cdd:PLN03077 156 NVLVGgyakAGYFDEALCLYHRmlwaGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKC 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 134 GSLVDARKVFDEMPNRDLCSWNVMVNGYAE-------------------------------------------------- 163
Cdd:PLN03077 236 GDVVSARLVFDRMPRRDCISWNAMISGYFEngecleglelfftmrelsvdpdlmtitsvisacellgderlgremhgyvv 315

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 164 --------------------VGLLEEARKLFDEMTEKDSYSWTAMVTGYVKKDQPEEALVLYSLMQrVPNSRPNIFTVSI 223
Cdd:PLN03077 316 ktgfavdvsvcnsliqmylsLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALME-QDNVSPDEITIAS 394

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 224 AVAAAAAVKCIRRGKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIVEKDVVSWTSMIDRYFKSSRWREG 303
Cdd:PLN03077 395 VLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEA 474

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 304 FSLFSELVGSCeRPNEYTFAGVLNACADLTTEELGKQVHGYMTRVGFDPYSFASSSLVDMYTKCGNIESAKHVVDGCPKp 383
Cdd:PLN03077 475 LIFFRQMLLTL-KPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEK- 552

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 384 DLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSITEKHRLSHTSDHYTCLV 463
Cdd:PLN03077 553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVV 632

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 464 DLLARSGRFEQLKSVISEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEEEGK 543
Cdd:PLN03077 633 DLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVAR 712

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 544 MRKRMQEIGVTKRPGSSWTEIKRKRHVFIAADTSHPMYNQIVEFLRELRKKMKEEGYVPATSLVLHDVEdEQKEENLVYH 623
Cdd:PLN03077 713 VRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIE-VSKDDIFCGH 791

                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332661361 624 SEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFHCFENGQCSCGD 689
Cdd:PLN03077 792 SERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 599-691 3.71e-40

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


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 142.18  E-value: 3.71e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  599 GYVPATSLVLHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHGAIKFISNITKRKITVRDSTRFH 678
Cdd:pfam14432   1 GYVPDLRFVLHDVDDEEKKQLLCGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIRGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 332661361  679 CFENGQCSCGDYW 691
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 501-563 3.74e-16

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: 72.96  E-value: 3.74e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332661361  501 YGNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEEEGKMRKRMQEIGVTKRPGSSWTE 563
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 18-507 7.53e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.59  E-value: 7.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361   18 KRNLSSFHASLKRFSDKKFFNPnhedggvVVERLCRANRFGEAIDVL----------------------C-GQKLLREAV 74
Cdd:PLN03218  354 ENSLAAYNGGVSGKRKSPEYID-------AYNRLLRDGRIKDCIDLLedmekrglldmdkiyhakffkaCkKQRAVKEAF 426

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361   75 QLLGRAKKPPASTYCNLIQVCSQTRALEEGKKVHEHIRTSGFVPGIVIWNRLLRMYAKCGSlVDAR-KVFDEMPNrdlcs 153
Cdd:PLN03218  427 RFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGK-VDAMfEVFHEMVN----- 500

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  154 wnvmvngyAEVglleearklfdemtEKDSYSWTAMVTGYVKKDQPEEALVLYSLMqRVPNSRPniftvsiavaaaaavkc 233
Cdd:PLN03218  501 --------AGV--------------EANVHTFGALIDGCARAGQVAKAFGAYGIM-RSKNVKP----------------- 540

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  234 irrgkeihghivragldsDEVLWSSLMDMYGKCGCIDEArniFDkiVEKDVVSWTSMIDryfkssrwregfslfselvgs 313
Cdd:PLN03218  541 ------------------DRVVFNALISACGQSGAVDRA---FD--VLAEMKAETHPID--------------------- 576

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  314 cerPNEYTFAGVLNACADLTTEELGKQV----HGYMTRVGFDPYSFASSSlvdmYTKCGNIESAKHVVDGCPK----PDL 385
Cdd:PLN03218  577 ---PDHITVGALMKACANAGQVDRAKEVyqmiHEYNIKGTPEVYTIAVNS----CSQKGDWDFALSIYDDMKKkgvkPDE 649

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  386 VSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFYSItEKHRLSHTSDHYTCLVDL 465
Cdd:PLN03218  650 VFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI-KSIKLRPTVSTMNALITA 728

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*
gi 332661361  466 LARSGRFEQLKSVISEMP---MKPSKFLWASVLGGCSTYGNIDLA 507
Cdd:PLN03218  729 LCEGNQLPKALEVLSEMKrlgLCPNTITYSILLVASERKDDADVG 773
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 383-430 7.09e-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: 51.98  E-value: 7.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 332661361  383 PDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSAC 430
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGL 48
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 149-194 2.69e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 50.44  E-value: 2.69e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332661361  149 RDLCSWNVMVNGYAEVGLLEEARKLFDEMTEK----DSYSWTAMVTGYVK 194
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 ...
 282-331 1.26e-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: 48.51  E-value: 1.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 332661361  282 KDVVSWTSMIDRYFKSSRWREGFSLFSELVGSCERPNEYTFAGVLNACAD 331
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 381-644 7.29e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 52.57  E-value: 7.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  381 PKPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSACTHAGLVEKGLEFFysitekHRLS------- 453
Cdd:PLN03218  433 RNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVF------HEMVnagvean 506

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  454 -HTsdhYTCLVDLLARSGRFEQ---LKSVISEMPMKPSKFLWASVLGGCSTYGNID-----LAEEAAqELFKIEPENpVT 524
Cdd:PLN03218  507 vHT---FGALIDGCARAGQVAKafgAYGIMRSKNVKPDRVVFNALISACGQSGAVDrafdvLAEMKA-ETHPIDPDH-IT 581

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361  525 YVTMANIYAAAGKWEEEGKMRKRMQEIGVTKRPgsswteikrkrHVFIAADTSHpmyNQI--VEFLRELRKKMKEEGYVP 602
Cdd:PLN03218  582 VGALMKACANAGQVDRAKEVYQMIHEYNIKGTP-----------EVYTIAVNSC---SQKgdWDFALSIYDDMKKKGVKP 647

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 332661361  603 atslvlhdveDEQKEENLV---YHSEKLAVAFAILSTEEGTAIKV 644
Cdd:PLN03218  648 ----------DEVFFSALVdvaGHAGDLDKAFEILQDARKQGIKL 682
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 118-162 9.71e-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: 9.71e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 332661361  118 PGIVIWNRLLRMYAKCGSLVDARKVFDEMPNR----DLCSWNVMVNGYA 162
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLC 49
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 153-180 7.64e-06

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 42.84  E-value: 7.64e-06
                          10        20
                  ....*....|....*....|....*...
gi 332661361  153 SWNVMVNGYAEVGLLEEARKLFDEMTEK 180
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEK 29
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 397-540 9.42e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 47.80  E-value: 9.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 397 QNGQPDEALKYFDLLLKSgtKPDHVTFVNVLS-ACTHAGLVEKGLEFFYSITEKHrlSHTSDHYTCLVDLLARSGRFEQL 475
Cdd:COG2956   54 RRGEYDRAIRIHQKLLER--DPDRAEALLELAqDYLKAGLLDRAEELLEKLLELD--PDDAEALRLLAEIYEQEGDWEKA 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 332661361 476 KSVISEM-PMKPSKFLWASVLGgcSTY---GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG2956  130 IEVLERLlKLGPENAHAYCELA--ELYleqGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 386-415 1.01e-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: 42.45  E-value: 1.01e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 332661361  386 VSWTSLIGGCAQNGQPDEALKYFDLLLKSG 415
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 386-419 2.96e-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: 41.29  E-value: 2.96e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 332661361  386 VSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPD 419
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 180-223 6.24e-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: 40.81  E-value: 6.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 332661361  180 KDSYSWTAMVTGYVKKDQPEEALVLYSLMQRVpNSRPNIFTVSI 223
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKR-GVKPNVYTYTI 43
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 397-540 8.41e-05

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 45.11  E-value: 8.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 397 QNGQPDEALKYFDLLLKsgTKPDHVT-FVNVLSACTHAGLVEKGLEFFysiTEKHRLSHTSDHYTC-LVDLLARSGRFEQ 474
Cdd:COG2956   88 KAGLLDRAEELLEKLLE--LDPDDAEaLRLLAEIYEQEGDWEKAIEVL---ERLLKLGPENAHAYCeLAELYLEQGDYDE 162

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332661361 475 ----LKSVISEMPmkpsKFLWASVLGGcSTY---GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG2956  163 aieaLEKALKLDP----DCARALLLLA-ELYleqGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEE 230
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 152-181 1.80e-04

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 38.98  E-value: 1.80e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 332661361  152 CSWNVMVNGYAEVGLLEEARKLFDEMTEKD 181
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERG 30
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 150-178 4.03e-04

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 38.10  E-value: 4.03e-04
                          10        20
                  ....*....|....*....|....*....
gi 332661361  150 DLCSWNVMVNGYAEVGLLEEARKLFDEMT 178
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEME 34
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 502-540 4.65e-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: 40.95  E-value: 4.65e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 332661361 502 GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG4783   18 GDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDE 56
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 382-430 5.29e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 38.49  E-value: 5.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 332661361  382 KPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGTKPDHVTFVNVLSAC 430
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 254-284 6.71e-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: 6.71e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332661361  254 VLWSSLMDMYGKCGCIDEARNIFDKIVEKDV 284
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
502-540 8.13e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.00  E-value: 8.13e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 332661361 502 GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG3063    6 GDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDE 44
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 459-540 9.61e-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: 9.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 459 YTCLVDLLARSGRFEQLKSVISE-MPMKPSKFLWASVLGgcSTY---GNIDLAEEAAQELFKIEPENPVTYVTMANIYAA 534
Cdd:COG4783   41 FALLGEILLQLGDLDEAIVLLHEaLELDPDEPEARLNLG--LALlkaGDYDEALALLEKALKLDPEHPEAYLRLARAYRA 118


                 ....*.
gi 332661361 535 AGKWEE 540
Cdd:COG4783  119 LGRPDE 124
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 397-540 9.98e-04

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 41.64  E-value: 9.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332661361 397 QNGQPDEALKYFDLLLK--SGTKPDHVTFVNVLSActhAGLVEKGLEFFysiteKHRLSHTSDHYTCLVDL---LARSGR 471
Cdd:COG2956   20 LNGQPDKAIDLLEEALEldPETVEAHLALGNLYRR---RGEYDRAIRIH-----QKLLERDPDRAEALLELaqdYLKAGL 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332661361 472 FEQ----LKSVISEMPMKPSkfLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEE 540
Cdd:COG2956   92 LDRaeelLEKLLELDPDDAE--ALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDE 162
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 183-210 2.00e-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: 2.00e-03
                          10        20
                  ....*....|....*....|....*...
gi 332661361  183 YSWTAMVTGYVKKDQPEEALVLYSLMQR 210
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKE 28
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 121-151 2.85e-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: 35.52  E-value: 2.85e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 332661361  121 VIWNRLLRMYAKCGSLVDARKVFDEMPNRDL 151
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 502-552 3.20e-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: 40.10  E-value: 3.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 332661361 502 GNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAGKWEEEGKMRKRMQEIG 552
Cdd:COG2956   90 GLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG 140
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 254-285 3.85e-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: 3.85e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 332661361  254 VLWSSLMDMYGKCGCIDEARNIFDKIVEKDVV 285
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 378-409 7.41e-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: 34.63  E-value: 7.41e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 332661361  378 DGCpKPDLVSWTSLIGGCAQNGQPDEALKYFD 409
Cdd:pfam12854   1 KGL-KPDVVTYNTLINGLCRAGRVDEAFELLD 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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