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Conserved domains on  [gi|334188141|ref|NP_199060|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 43-489 1.56e-95

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 308.32  E-value: 1.56e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  43 IRNAHKVFDEIPELDVISATAVIGRFVKESRHVEASQAFKRLLCLGIRPNEFTFGTVIGSSTTSRDVKLGKQLHCYALKM 122
Cdd:PLN03077 238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 123 GLASNVFVGSAVLNCYVKLSTLTDARRCFD--DTRDpnVVSITNLISGY------------------------------- 169
Cdd:PLN03077 318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSrmETKD--AVSWTAMISGYeknglpdkaletyalmeqdnvspdeitiasv 395

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 170 -------------LKKHEF--------------------------EEALSLFRAMPERSVVTWNAVIGGFSQTGRNEEAV 210
Cdd:PLN03077 396 lsacaclgdldvgVKLHELaerkglisyvvvanaliemyskckciDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL 475

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 211 NTFVDMLreGVVIPNESTFPCAITAISNIASHGAGKSIHACAIKfLGKRFNVFVWNSLISFYSKCGNMEdslLAFNKLEE 290
Cdd:PLN03077 476 IFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLR-TGIGFDGFLPNALLDLYVRCGRMN---YAWNQFNS 549

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 291 EQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdTNLRPNNVTILGVLFACNHAGLIQEGYMYFNKAVNDYD-DPNLlel 369
Cdd:PLN03077 550 HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSiTPNL--- 625

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 370 EHYACMVDMLSRSGRFKEAEELIKSMPLDPGIGFWKALLGGCQIHSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAME 449
Cdd:PLN03077 626 KHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG 705

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|
gi 334188141 450 NWQNVSLIRRKMKETGLKRFTGCSWIEVRDQIRVFVNADK 489
Cdd:PLN03077 706 KWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDE 745
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 43-489 1.56e-95

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 308.32  E-value: 1.56e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  43 IRNAHKVFDEIPELDVISATAVIGRFVKESRHVEASQAFKRLLCLGIRPNEFTFGTVIGSSTTSRDVKLGKQLHCYALKM 122
Cdd:PLN03077 238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 123 GLASNVFVGSAVLNCYVKLSTLTDARRCFD--DTRDpnVVSITNLISGY------------------------------- 169
Cdd:PLN03077 318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSrmETKD--AVSWTAMISGYeknglpdkaletyalmeqdnvspdeitiasv 395

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 170 -------------LKKHEF--------------------------EEALSLFRAMPERSVVTWNAVIGGFSQTGRNEEAV 210
Cdd:PLN03077 396 lsacaclgdldvgVKLHELaerkglisyvvvanaliemyskckciDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL 475

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 211 NTFVDMLreGVVIPNESTFPCAITAISNIASHGAGKSIHACAIKfLGKRFNVFVWNSLISFYSKCGNMEdslLAFNKLEE 290
Cdd:PLN03077 476 IFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLR-TGIGFDGFLPNALLDLYVRCGRMN---YAWNQFNS 549

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 291 EQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdTNLRPNNVTILGVLFACNHAGLIQEGYMYFNKAVNDYD-DPNLlel 369
Cdd:PLN03077 550 HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSiTPNL--- 625

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 370 EHYACMVDMLSRSGRFKEAEELIKSMPLDPGIGFWKALLGGCQIHSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAME 449
Cdd:PLN03077 626 KHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG 705

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|
gi 334188141 450 NWQNVSLIRRKMKETGLKRFTGCSWIEVRDQIRVFVNADK 489
Cdd:PLN03077 706 KWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDE 745
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 414-476 1.72e-17

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: 76.43  E-value: 1.72e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334188141  414 HSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAMENWQNVSLIRRKMKETGLKRFTGCSWIE 476
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
261-452 4.32e-09

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 57.32  E-value: 4.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 261 NVFVWNSLISFYSKCGNMEDSLLAFNK-LEEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL- 338
Cdd:COG0457    7 DAEAYNNLGLAYRRLGRYEEAIEDYEKaLELDPDDAEALYNLGLAYLRLGRYEEALADYEQALE---LDPDDAEALNNLg 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 339 FACNHAGLIQEGYMYFNKAVN-DYDDPNLleLEHYACmvdMLSRSGRFKEAEELIKsmpldpgigfwkallggcqihsnk 417
Cdd:COG0457   84 LALQALGRYEEALEDYDKALElDPDDAEA--LYNLGL---ALLELGRYDEAIEAYE------------------------ 134

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 334188141 418 rlaklaasKILELDPRDVSSYVMLSNAYSAMENWQ 452
Cdd:COG0457  135 --------RALELDPDDADALYNLGIALEKLGRYE 161
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 296-330 5.33e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.13  E-value: 5.33e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334188141  296 VSWNSMIWGYAHNGRGEEAVAMFEKMVKDtNLRPN 330
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKER-GIEPD 34
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 43-489 1.56e-95

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 308.32  E-value: 1.56e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  43 IRNAHKVFDEIPELDVISATAVIGRFVKESRHVEASQAFKRLLCLGIRPNEFTFGTVIGSSTTSRDVKLGKQLHCYALKM 122
Cdd:PLN03077 238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 123 GLASNVFVGSAVLNCYVKLSTLTDARRCFD--DTRDpnVVSITNLISGY------------------------------- 169
Cdd:PLN03077 318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSrmETKD--AVSWTAMISGYeknglpdkaletyalmeqdnvspdeitiasv 395

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 170 -------------LKKHEF--------------------------EEALSLFRAMPERSVVTWNAVIGGFSQTGRNEEAV 210
Cdd:PLN03077 396 lsacaclgdldvgVKLHELaerkglisyvvvanaliemyskckciDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL 475

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 211 NTFVDMLreGVVIPNESTFPCAITAISNIASHGAGKSIHACAIKfLGKRFNVFVWNSLISFYSKCGNMEdslLAFNKLEE 290
Cdd:PLN03077 476 IFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLR-TGIGFDGFLPNALLDLYVRCGRMN---YAWNQFNS 549

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 291 EQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdTNLRPNNVTILGVLFACNHAGLIQEGYMYFNKAVNDYD-DPNLlel 369
Cdd:PLN03077 550 HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVE-SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSiTPNL--- 625

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 370 EHYACMVDMLSRSGRFKEAEELIKSMPLDPGIGFWKALLGGCQIHSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAME 449
Cdd:PLN03077 626 KHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG 705

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|
gi 334188141 450 NWQNVSLIRRKMKETGLKRFTGCSWIEVRDQIRVFVNADK 489
Cdd:PLN03077 706 KWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDE 745
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 34-517 1.53e-92

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 296.78  E-value: 1.53e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  34 LVKHIDSDLIRNAHKVFDEIPELDVISATAVIGRFVKESRHVEASQAFKRLLCLGIRPNEFTFGTVIGSSTTSRDVKLGK 113
Cdd:PLN03081 165 LLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQ 244

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 114 QLHCYALKMGLASNVFVGSAVLNCYVKLSTLTDARRCFDdtrdpnvvsitnlisgylkkhefeealslfrAMPERSVVTW 193
Cdd:PLN03081 245 QLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFD-------------------------------GMPEKTTVAW 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 194 NAVIGGFSQTGRNEEAVNTFVDMLREGVVIpNESTFPCAITAISNIASHGAGKSIHACAIKFlGKRFNVFVWNSLISFYS 273
Cdd:PLN03081 294 NSMLAGYALHGYSEEALCLYYEMRDSGVSI-DQFTFSIMIRIFSRLALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYS 371

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 274 KCGNMEDSLLAFNKLEeeQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKDtNLRPNNVTILGVLFACNHAGLIQEGYMY 353
Cdd:PLN03081 372 KWGRMEDARNVFDRMP--RKNLISWNALIAGYGNHGRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEI 448

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 354 FNKAVNDYD-DPNLLeleHYACMVDMLSRSGRFKEAEELIKSMPLDPGIGFWKALLGGCQIHSNKRLAKLAASKILELDP 432
Cdd:PLN03081 449 FQSMSENHRiKPRAM---HYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGP 525

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 433 RDVSSYVMLSNAYSAMENWQNVSLIRRKMKETGLKRFTGCSWIEVRDQIRVFVNADKNNELKDEVYR----MLALVSQH- 507
Cdd:PLN03081 526 EKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQkldeLMKEISEYg 605

                        490
                 ....*....|..
gi 334188141 508 --LEENECWKDL 517
Cdd:PLN03081 606 yvAEENELLPDV 617
PLN03077 PLN03077
Protein ECB2; Provisional
 66-412 8.31e-28

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 118.03  E-value: 8.31e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  66 GRFVKESRHVEASQAFKrllclgIRPNEFTFGTVIGSSTTSRDVKLGKQLHCYALKMGLASNVFVGSAVLNCYVKLSTLT 145
Cdd:PLN03077  65 GQLEQALKLLESMQELR------VPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELV 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 146 DARRcfddtrdpnvvsitnlisgylkkhefeealsLFRAMPERSVVTWNAVIGGFSQTGRNEEAVNTFVDMLREGVViPN 225
Cdd:PLN03077 139 HAWY-------------------------------VFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVR-PD 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 226 ESTFPCAITAISNIASHGAGKSIHACAIKFlGKRFNVFVWNSLISFYSKCGNMEDSLLAFNKLeeEQRNIVSWNSMIWGY 305
Cdd:PLN03077 187 VYTFPCVLRTCGGIPDLARGREVHAHVVRF-GFELDVDVVNALITMYVKCGDVVSARLVFDRM--PRRDCISWNAMISGY 263

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 306 AHNGRGEEAVAMFEKMVKDTnLRPNNVTILGVLFACN-----------HAGLIQEGYMyfnkavndyddpnlLELEHYAC 374
Cdd:PLN03077 264 FENGECLEGLELFFTMRELS-VDPDLMTITSVISACEllgderlgremHGYVVKTGFA--------------VDVSVCNS 328

                        330       340       350
                 ....*....|....*....|....*....|....*...
gi 334188141 375 MVDMLSRSGRFKEAEELIKSMPLDPGIGfWKALLGGCQ 412
Cdd:PLN03077 329 LIQMYLSLGSWGEAEKVFSRMETKDAVS-WTAMISGYE 365
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 414-476 1.72e-17

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: 76.43  E-value: 1.72e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334188141  414 HSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAMENWQNVSLIRRKMKETGLKRFTGCSWIE 476
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
261-452 4.32e-09

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 57.32  E-value: 4.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 261 NVFVWNSLISFYSKCGNMEDSLLAFNK-LEEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL- 338
Cdd:COG0457    7 DAEAYNNLGLAYRRLGRYEEAIEDYEKaLELDPDDAEALYNLGLAYLRLGRYEEALADYEQALE---LDPDDAEALNNLg 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 339 FACNHAGLIQEGYMYFNKAVN-DYDDPNLleLEHYACmvdMLSRSGRFKEAEELIKsmpldpgigfwkallggcqihsnk 417
Cdd:COG0457   84 LALQALGRYEEALEDYDKALElDPDDAEA--LYNLGL---ALLELGRYDEAIEAYE------------------------ 134

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 334188141 418 rlaklaasKILELDPRDVSSYVMLSNAYSAMENWQ 452
Cdd:COG0457  135 --------RALELDPDDADALYNLGIALEKLGRYE 161
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 293-333 6.90e-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: 51.60  E-value: 6.90e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 334188141  293 RNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKDtNLRPNNVT 333
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKR-GVKPNVYT 40
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 79-388 9.28e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 58.35  E-value: 9.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141   79 QAFKRLLCLGIRPNEFTFGTVIGSstTSRDVKLGKQLHCYALKMglASNVFVGSAVLNCYVKLSTLTDA-RRCFD---DT 154
Cdd:PLN03218  493 EVFHEMVNAGVEANVHTFGALIDG--CARAGQVAKAFGAYGIMR--SKNVKPDRVVFNALISACGQSGAvDRAFDvlaEM 568

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  155 R------DPNVVSITNLISGYLKKHEFEEALSLFRAMPERSV----VTWNAVIGGFSQTGRNEEAVNTFVDMLREGVViP 224
Cdd:PLN03218  569 KaethpiDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIkgtpEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK-P 647

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  225 NESTFpcaiTAISNIASHgAGKSIHACAI----KFLGKRFNVFVWNSLISFYSKCGNMEDSLLAFNKLEEEQ-RNIVS-W 298
Cdd:PLN03218  648 DEVFF----SALVDVAGH-AGDLDKAFEIlqdaRKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKlRPTVStM 722

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141  299 NSMIWGYAHNGRGEEAVAMFEKMvKDTNLRPNNVTILGVLFACNHAGLIQEGYMYFNKAVNDYDDPNLLeleHYACMVDM 378
Cdd:PLN03218  723 NALITALCEGNQLPKALEVLSEM-KRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLV---MCRCITGL 798

                         330
                  ....*....|
gi 334188141  379 LSRsgRFKEA 388
Cdd:PLN03218  799 CLR--RFEKA 806
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 157-200 2.80e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 46.97  E-value: 2.80e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 334188141  157 PNVVSITNLISGYLKKHEFEEALSLFRAMPER----SVVTWNAVIGGF 200
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 ...
 188-229 2.85e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 46.97  E-value: 2.85e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 334188141  188 RSVVTWNAVIGGFSQTGRNEEAVNTFVDMLREGVViPNESTF 229
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVK-PNVYTY 41
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 305-453 7.72e-07

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 50.88  E-value: 7.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 305 YAHNGRGEEAVAMFEKMVKDTNLRPNNVTILGVLFAcnHAGLIQEGYMYFNKAVN-DYDDPNLLELehyacMVDMLSRSG 383
Cdd:COG2956   52 YRRRGEYDRAIRIHQKLLERDPDRAEALLELAQDYL--KAGLLDRAEELLEKLLElDPDDAEALRL-----LAEIYEQEG 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334188141 384 RFKEAEELIKSM-PLDPGIGFWKALLGGCQI-HSNKRLAKLAASKILELDPRDVSSYVMLSNAYSAMENWQN 453
Cdd:COG2956  125 DWEKAIEVLERLlKLGPENAHAYCELAELYLeQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEE 196
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 296-324 1.57e-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: 44.38  E-value: 1.57e-06
                          10        20
                  ....*....|....*....|....*....
gi 334188141  296 VSWNSMIWGYAHNGRGEEAVAMFEKMVKD 324
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEK 29
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
288-452 6.65e-06

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 47.69  E-value: 6.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 288 LEEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL-FACNHAGLIQEGYMYFNKAVNDydDPNL 366
Cdd:COG0457    1 LELDPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALE---LDPDDAEALYNLgLAYLRLGRYEEALADYEQALEL--DPDD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 367 LELehYACMVDMLSRSGRFKEAEELIKsmpldpgigfwkallggcqihsnkrlaklaasKILELDPRDVSSYVMLSNAYS 446
Cdd:COG0457   76 AEA--LNNLGLALQALGRYEEALEDYD--------------------------------KALELDPDDAEALYNLGLALL 121


                 ....*.
gi 334188141 447 AMENWQ 452
Cdd:COG0457  122 ELGRYD 127
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 272-399 1.40e-05

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: 44.80  E-value: 1.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 272 YSKCGNMEDSLLAFNK-LEEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL-FACNHAGLIQE 349
Cdd:COG4783   14 LLLAGDYDEAEALLEKaLELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALE---LDPDEPEARLNLgLALLKAGDYDE 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 334188141 350 GYMYFNKAVN-DYDDPNLLELehyacMVDMLSRSGRFKEAEELI-KSMPLDP 399
Cdd:COG4783   91 ALALLEKALKlDPEHPEAYLR-----LARAYRALGRPDEAIAALeKALELDP 137
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 261-452 2.41e-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: 46.26  E-value: 2.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 261 NVFVWNSLISFYSKCGNMEDSLLAFNKL-EEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVLF 339
Cdd:COG2956   41 TVEAHLALGNLYRRRGEYDRAIRIHQKLlERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLE---LDPDDAEALRLLA 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 340 ACnhagLIQEGYmyFNKAVNDYDDpnLLEL----EHYAC-MVDMLSRSGRFKEA-EELIKSMPLDPGigFWKALLGGCQI 413
Cdd:COG2956  118 EI----YEQEGD--WEKAIEVLER--LLKLgpenAHAYCeLAELYLEQGDYDEAiEALEKALKLDPD--CARALLLLAEL 187

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 334188141 414 HS---NKRLAKLAASKILELDPRDVSSYVMLSNAYSAMENWQ 452
Cdd:COG2956  188 YLeqgDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPE 229
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 296-330 5.33e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.13  E-value: 5.33e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 334188141  296 VSWNSMIWGYAHNGRGEEAVAMFEKMVKDtNLRPN 330
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKER-GIEPD 34
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 286-399 8.61e-05

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 42.30  E-value: 8.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 286 NKLEEEQRNIVSWNSMIWGYAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL-FACNHAGLIQEGYMYFNKAVN-DYDD 363
Cdd:COG4235    8 QALAANPNDAEGWLLLGRAYLRLGRYDEALAAYEKALR---LDPDNADALLDLaEALLAAGDTEEAEELLERALAlDPDN 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 334188141 364 PNLLELehyacMVDMLSRSGRFKEA----EELIKSMPLDP 399
Cdd:COG4235   85 PEALYL-----LGLAAFQQGDYAEAiaawQKLLALLPADA 119
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 305-463 2.51e-04

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 43.83  E-value: 2.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 305 YAHNGRGEEAVAMFEKMVKdtnLRPNNVTILGVL-FACNHAGLIQEGYMYFNKAVNDydDPNLLELehYACMVDMLSRSG 383
Cdd:COG3914   88 LQALGRYEEALALYRRALA---LNPDNAEALFNLgNLLLALGRLEEALAALRRALAL--NPDFAEA--YLNLGEALRRLG 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 384 RFKEAEELI-KSMPLDPGigFWKAL--LGGCQIHSNK-RLAKLAASKILELDPRDVSSYVMLSNAYSAMENWQNVSLIRR 459
Cdd:COG3914  161 RLEEAIAALrRALELDPD--NAEALnnLGNALQDLGRlEEAIAAYRRALELDPDNADAHSNLLFALRQACDWEVYDRFEE 238


                 ....
gi 334188141 460 KMKE 463
Cdd:COG3914  239 LLAA 242
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 191-221 2.56e-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: 38.22  E-value: 2.56e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334188141  191 VTWNAVIGGFSQTGRNEEAVNTFVDMLREGV 221
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 305-452 3.50e-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: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 305 YAHNGRGEEAVAMFEKMVKdtnLRPNNVTI---LGVLFAcnHAGLIQEGYMYFNKAVNDydDPNllELEHYACMVDMLSR 381
Cdd:COG4783   14 LLLAGDYDEAEALLEKALE---LDPDNPEAfalLGEILL--QLGDLDEAIVLLHEALEL--DPD--EPEARLNLGLALLK 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334188141 382 SGRFKEAEELIKsmpldpgigfwkallggcqihsnkrlaklaasKILELDPRDVSSYVMLSNAYSAMENWQ 452
Cdd:COG4783   85 AGDYDEALALLE--------------------------------KALKLDPEHPEAYLRLARAYRALGRPD 123
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 363-452 8.39e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.60  E-value: 8.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188141 363 DPNLLELehYACMVDMLSRSGRFKEAEE-LIKSMPLDPGIGFWKALLGGCQIHSNK-RLAKLAASKILELDPRDVSSYVM 440
Cdd:COG4235   13 NPNDAEG--WLLLGRAYLRLGRYDEALAaYEKALRLDPDNADALLDLAEALLAAGDtEEAEELLERALALDPDNPEALYL 90

                         90
                 ....*....|..
gi 334188141 441 LSNAYSAMENWQ 452
Cdd:COG4235   91 LGLAAFQQGDYA 102
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 261-307 2.61e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.80  E-value: 2.61e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334188141  261 NVFVWNSLISFYSKCGNMEDSLLAFNKLEEE--QRNIVSWNSMIWGYAH 307
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 57-100 5.35e-03

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 35.03  E-value: 5.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334188141   57 DVISATAVIGRFVKESRHVEASQAFKRLLCLGIRPNEFTFGTVI 100
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILI 45
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
379-452 1.00e-02

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 35.53  E-value: 1.00e-02
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334188141 379 LSRSGRFKEAEELI-KSMPLDPGIGFWKALLGGCQIhSNKRLAK-LAASKILELDPRDVSSYVMLSNAYSAMENWQ 452
Cdd:COG3063    2 YLKLGDLEEAEEYYeKALELDPDNADALNNLGLLLL-EQGRYDEaIALEKALKLDPNNAEALLNLAELLLELGDYD 76
 
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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