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Conserved domains on  [gi|15226463|ref|NP_179705|]
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Pentatricopeptide repeat (PPR-like) 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
26-584 2.02e-118

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 371.49  E-value: 2.02e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   26 ELSQAVSRLESLTQQGIRLPFDLLASLLQQCGDTKSLKQGKWIHRHLkitgFKRPNTL---LSNHLIGMYMKCGKPIDAC 102
Cdd:PLN03077  66 QLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRA----LSSHPSLgvrLGNAMLSMFVRFGELVHAW 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  103 KVFDQMHLRNLYSWNNMVSGYVKSGML----------------------------------------------------- 129
Cdd:PLN03077 142 YVFGKMPERDLFSWNVLVGGYAKAGYFdealclyhrmlwagvrpdvytfpcvlrtcggipdlargrevhahvvrfgfeld 221
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  130 -----------------VRARVVFDSMPERDVVSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKS 192
Cdd:PLN03077 222 vdvvnalitmyvkcgdvVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL 301
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  193 RQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMTVKDIHIWTTLISGY----------------- 255
Cdd:PLN03077 302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYeknglpdkaletyalme 381
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  256 ------------------AKLGDMEAAEKL-----------------------------------FCEMPEKNPVSWTAL 282
Cdd:PLN03077 382 qdnvspdeitiasvlsacACLGDLDVGVKLhelaerkglisyvvvanaliemyskckcidkalevFHNIPEKDVISWTSI 461
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  283 IAGYVRQGSGNRALDLFRKMIaLGVKPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSL 362
Cdd:PLN03077 462 IAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRM 540
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  363 EASERVFRICddKHDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFESMTVQ 442
Cdd:PLN03077 541 NYAWNQFNSH--EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEK 618
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  443 HGIVPDQEHYACLIDLLGRAGCFKELMRKIEEMPFEPDKHIWNAILGVCRIHGNEELGKKAADELIKLDPESSAPYILLS 522
Cdd:PLN03077 619 YSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLC 698
                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15226463  523 SIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIEIEKKVEAFTVSDGSHAHARkeEIYFILH 584
Cdd:PLN03077 699 NLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIK--EINTVLE 758
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
26-584 2.02e-118

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 371.49  E-value: 2.02e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   26 ELSQAVSRLESLTQQGIRLPFDLLASLLQQCGDTKSLKQGKWIHRHLkitgFKRPNTL---LSNHLIGMYMKCGKPIDAC 102
Cdd:PLN03077  66 QLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRA----LSSHPSLgvrLGNAMLSMFVRFGELVHAW 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  103 KVFDQMHLRNLYSWNNMVSGYVKSGML----------------------------------------------------- 129
Cdd:PLN03077 142 YVFGKMPERDLFSWNVLVGGYAKAGYFdealclyhrmlwagvrpdvytfpcvlrtcggipdlargrevhahvvrfgfeld 221
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  130 -----------------VRARVVFDSMPERDVVSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKS 192
Cdd:PLN03077 222 vdvvnalitmyvkcgdvVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL 301
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  193 RQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMTVKDIHIWTTLISGY----------------- 255
Cdd:PLN03077 302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYeknglpdkaletyalme 381
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  256 ------------------AKLGDMEAAEKL-----------------------------------FCEMPEKNPVSWTAL 282
Cdd:PLN03077 382 qdnvspdeitiasvlsacACLGDLDVGVKLhelaerkglisyvvvanaliemyskckcidkalevFHNIPEKDVISWTSI 461
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  283 IAGYVRQGSGNRALDLFRKMIaLGVKPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSL 362
Cdd:PLN03077 462 IAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRM 540
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  363 EASERVFRICddKHDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFESMTVQ 442
Cdd:PLN03077 541 NYAWNQFNSH--EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEK 618
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  443 HGIVPDQEHYACLIDLLGRAGCFKELMRKIEEMPFEPDKHIWNAILGVCRIHGNEELGKKAADELIKLDPESSAPYILLS 522
Cdd:PLN03077 619 YSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLC 698
                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15226463  523 SIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIEIEKKVEAFTVSDGSHAHARkeEIYFILH 584
Cdd:PLN03077 699 NLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIK--EINTVLE 758
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
494-556 9.15e-15

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: 69.11  E-value: 9.15e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15226463   494 HGNEELGKKAADELIKLDPESSAPYILLSSIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIE 556
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
381-412 5.25e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.25e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226463   381 WNTMISALAQHGLGHKALRMLDDMIKFRVQPN 412
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
220-305 8.91e-05

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 43.03  E-value: 8.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463 220 IIDAYAKCGQMESAKRCFD---EMTVKDIHIWTTLISGYAKLGDMEAAEKLF---CEMPEKNPVSWTALIAGYVRQGSGN 293
Cdd:COG5010  60 SDNLYNKLGDFEESLALLEqalQLDPNNPELYYNLALLYSRSGDKDEAKEYYekaLALSPDNPNAYSNLAALLLSLGQDD 139
                        90
                ....*....|..
gi 15226463 294 RALDLFRKMIAL 305
Cdd:COG5010 140 EAKAALQRALGT 151
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
26-584 2.02e-118

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 371.49  E-value: 2.02e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   26 ELSQAVSRLESLTQQGIRLPFDLLASLLQQCGDTKSLKQGKWIHRHLkitgFKRPNTL---LSNHLIGMYMKCGKPIDAC 102
Cdd:PLN03077  66 QLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRA----LSSHPSLgvrLGNAMLSMFVRFGELVHAW 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  103 KVFDQMHLRNLYSWNNMVSGYVKSGML----------------------------------------------------- 129
Cdd:PLN03077 142 YVFGKMPERDLFSWNVLVGGYAKAGYFdealclyhrmlwagvrpdvytfpcvlrtcggipdlargrevhahvvrfgfeld 221
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  130 -----------------VRARVVFDSMPERDVVSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKS 192
Cdd:PLN03077 222 vdvvnalitmyvkcgdvVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL 301
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  193 RQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMTVKDIHIWTTLISGY----------------- 255
Cdd:PLN03077 302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYeknglpdkaletyalme 381
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  256 ------------------AKLGDMEAAEKL-----------------------------------FCEMPEKNPVSWTAL 282
Cdd:PLN03077 382 qdnvspdeitiasvlsacACLGDLDVGVKLhelaerkglisyvvvanaliemyskckcidkalevFHNIPEKDVISWTSI 461
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  283 IAGYVRQGSGNRALDLFRKMIaLGVKPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSL 362
Cdd:PLN03077 462 IAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRM 540
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  363 EASERVFRICddKHDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFESMTVQ 442
Cdd:PLN03077 541 NYAWNQFNSH--EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEK 618
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  443 HGIVPDQEHYACLIDLLGRAGCFKELMRKIEEMPFEPDKHIWNAILGVCRIHGNEELGKKAADELIKLDPESSAPYILLS 522
Cdd:PLN03077 619 YSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLC 698
                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15226463  523 SIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIEIEKKVEAFTVSDGSHAHARkeEIYFILH 584
Cdd:PLN03077 699 NLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIK--EINTVLE 758
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
113-592 1.34e-104

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 331.06  E-value: 1.34e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  113 LYSWNNMVSGYVKSGMLVRARVVFDSMPERDVVSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKS 192
Cdd:PLN03081 158 QYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGL 237
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  193 RQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMtvkdihiwttlisgyaklgdmeaaeklfcemP 272
Cdd:PLN03081 238 GSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGM-------------------------------P 286
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  273 EKNPVSWTALIAGYVRQGSGNRALDLFRKMIALGVKPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSL 352
Cdd:PLN03081 287 EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTAL 366
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  353 IDMYSKSGSLEASERVFRICDDKhDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEG 432
Cdd:PLN03081 367 VDLYSKWGRMEDARNVFDRMPRK-NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQG 445
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  433 LRWFESMTVQHGIVPDQEHYACLIDLLGRAGCFKELMRKIEEMPFEPDKHIWNAILGVCRIHGNEELGKKAADELIKLDP 512
Cdd:PLN03081 446 WEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGP 525
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  513 ESSAPYILLSSIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIEIEKKVEAFTVSDGSHAHARkeEIYFILHNLAAVIEE 592
Cdd:PLN03081 526 EKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSR--EIYQKLDELMKEISE 603
PLN03077 PLN03077
Protein ECB2; Provisional
148-517 6.56e-33

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 134.59  E-value: 6.56e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  148 NTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKSRQLQLNRQAHGQVLvagflsnvvlscsiidayakc 227
Cdd:PLN03077  55 NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRAL--------------------- 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  228 gqmesakrcfDEMTVKDIHIWTTLISGYAKLGDMEAAEKLFCEMPEKNPVSWTALIAGYVRQGSGNRALDLFRKMIALGV 307
Cdd:PLN03077 114 ----------SSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGV 183
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  308 KPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSLEASERVFricdDK---HDCVFWNTM 384
Cdd:PLN03077 184 RPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF----DRmprRDCISWNAM 259
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463  385 ISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGlvEEGL-RWFESMTVQHGIVPDQEHYACLIDLLGRAG 463
Cdd:PLN03077 260 ISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLG--DERLgREMHGYVVKTGFAVDVSVCNSLIQMYLSLG 337
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15226463  464 CFKELMRKIEEMPFEpDKHIWNAILGVCRIHGneeLGKKAADELIKLDPESSAP 517
Cdd:PLN03077 338 SWGEAEKVFSRMETK-DAVSWTAMISGYEKNG---LPDKALETYALMEQDNVSP 387
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
494-556 9.15e-15

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: 69.11  E-value: 9.15e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15226463   494 HGNEELGKKAADELIKLDPESSAPYILLSSIYADHGKWELVEKLRGVMKKRRVNKEKAVSWIE 556
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
162-437 3.10e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.99  E-value: 3.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   162 EALWFYKEFRRSGIKfnefSFAGLLTACVKSRQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMT 241
Cdd:PLN03218  424 EAFRFAKLIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMV 499
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   242 VKDI----HIWTTLISGYAKLGDMEAAEKLFCEMPEKN--P--VSWTALIAGYVRQGSGNRALDLFRKMIALG--VKPEQ 311
Cdd:PLN03218  500 NAGVeanvHTFGALIDGCARAGQVAKAFGAYGIMRSKNvkPdrVVFNALISACGQSGAVDRAFDVLAEMKAEThpIDPDH 579
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   312 FTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSLEASERVFricDD------KHDCVFWNTMI 385
Cdd:PLN03218  580 ITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIY---DDmkkkgvKPDEVFFSALV 656
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15226463   386 SALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFE 437
Cdd:PLN03218  657 DVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYE 708
PLN03218 PLN03218
maturation of RBCL 1; Provisional
171-458 1.44e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 70.68  E-value: 1.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   171 RRSGIKFNEFSFAGLLTACVKSRQLQLNRQAHGQVLVAGFLSNVVLSCSIIDAYAKCGQMESAKRCFDEMTVKDIH---- 246
Cdd:PLN03218  464 QEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKpdrv 543
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   247 IWTTLISGYAKLGDMEAAEKLFCEM-PEKNP-----VSWTALIAGYVRQGSGNRALDLFRKMIALGVK--PEQFTFSSCL 318
Cdd:PLN03218  544 VFNALISACGQSGAVDRAFDVLAEMkAETHPidpdhITVGALMKACANAGQVDRAKEVYQMIHEYNIKgtPEVYTIAVNS 623
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   319 CASasIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSKSGSLEASERVFRI-------------------CDDKHDcv 379
Cdd:PLN03218  624 CSQ--KGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDarkqgiklgtvsysslmgaCSNAKN-- 699
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   380 fW----------------------NTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFE 437
Cdd:PLN03218  700 -WkkalelyediksiklrptvstmNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLS 778
                         330       340
                  ....*....|....*....|.
gi 15226463   438 SMTVQhGIVPDQEHYACLIDL 458
Cdd:PLN03218  779 QAKED-GIKPNLVMCRCITGL 798
PLN03218 PLN03218
maturation of RBCL 1; Provisional
279-515 2.72e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 69.91  E-value: 2.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   279 WTALIAGYVRQGSGNRALDLFRKMIALGVKPEQFTFSSCL--CASASIASLRHGKeiHGYMIRTNVRPNAIVISSLIDMY 356
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIdgCARAGQVAKAFGA--YGIMRSKNVKPDRVVFNALISAC 552
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   357 SKSGsleASERVFRICDD--------KHDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGL 428
Cdd:PLN03218  553 GQSG---AVDRAFDVLAEmkaethpiDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGD 629
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   429 VEEGLRWFESMTvQHGIVPDQEHYACLIDLLGRAGCFKELMRKIEEMP---FEPDKHIWNAILGVCRIHGNEELGKKAAD 505
Cdd:PLN03218  630 WDFALSIYDDMK-KKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARkqgIKLGTVSYSSLMGACSNAKNWKKALELYE 708
                         250
                  ....*....|..
gi 15226463   506 EL--IKLDPESS 515
Cdd:PLN03218  709 DIksIKLRPTVS 720
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
243-288 9.70e-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: 9.70e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226463   243 KDIHIWTTLISGYAKLGDMEAAEKLFCEMPEK----NPVSWTALIAGYVR 288
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 ...
379-425 4.09e-08

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 49.67  E-value: 4.09e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15226463   379 VFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSH 425
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
274-320 1.87e-07

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 47.74  E-value: 1.87e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15226463   274 KNPVSWTALIAGYVRQGSGNRALDLFRKMIALGVKPEQFTFSSCLCA 320
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
142-191 9.80e-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: 45.82  E-value: 9.80e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226463   142 RDVVSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVK 191
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
247-275 2.74e-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: 43.99  E-value: 2.74e-06
                          10        20
                  ....*....|....*....|....*....
gi 15226463   247 IWTTLISGYAKLGDMEAAEKLFCEMPEKN 275
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
145-175 1.76e-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: 41.68  E-value: 1.76e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226463   145 VSWNTMVIGYAQDGNLHEALWFYKEFRRSGI 175
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
219-257 2.06e-05

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 41.97  E-value: 2.06e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 15226463   219 SIIDAYAKCGQMESAKRCFDEMTVK----DIHIWTTLISGYAK 257
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
381-412 5.25e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.25e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226463   381 WNTMISALAQHGLGHKALRMLDDMIKFRVQPN 412
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
246-275 5.90e-05

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 40.52  E-value: 5.90e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226463   246 HIWTTLISGYAKLGDMEAAEKLFCEMPEKN 275
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERG 30
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
111-156 6.43e-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: 6.43e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226463   111 RNLYSWNNMVSGYVKSGMLVRARVVFDSMPER----DVVSWNTMVIGYAQ 156
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
379-409 7.31e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 40.14  E-value: 7.31e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226463   379 VFWNTMISALAQHGLGHKALRMLDDMIKFRV 409
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
277-309 8.49e-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: 39.75  E-value: 8.49e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 15226463   277 VSWTALIAGYVRQGSGNRALDLFRKMIALGVKP 309
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
220-305 8.91e-05

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 43.03  E-value: 8.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463 220 IIDAYAKCGQMESAKRCFD---EMTVKDIHIWTTLISGYAKLGDMEAAEKLF---CEMPEKNPVSWTALIAGYVRQGSGN 293
Cdd:COG5010  60 SDNLYNKLGDFEESLALLEqalQLDPNNPELYYNLALLYSRSGDKDEAKEYYekaLALSPDNPNAYSNLAALLLSLGQDD 139
                        90
                ....*....|..
gi 15226463 294 RALDLFRKMIAL 305
Cdd:COG5010 140 EAKAALQRALGT 151
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
277-307 9.08e-05

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 39.76  E-value: 9.08e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226463   277 VSWTALIAGYVRQGSGNRALDLFRKMIALGV 307
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
155-343 1.95e-04

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


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 43.15  E-value: 1.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   155 AQDGNLHEALWFYKEFRRSGIKFNEFSFAGLLTACVKSRQLQLNRQAHGqvLVAGFlsnvvlscsiiDAYAkcgQMESAK 234
Cdd:pfam17177  22 SKHADATGALALYDAAKAEGVRLAQYHYNVLLYLCSKAADATDLKPQLA--ADRGF-----------EVFE---AMKAQG 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   235 RCFDEMTVkdihiwTTLISGYAKLGDMEAAEKLFCEMPEKNPV----SWTALIAGYVRQGSGNRALDLFRKMIALGVKPE 310
Cdd:pfam17177  86 VSPNEATY------TAVARLAAAKGDGDLAFDLVKEMEAAGVSprlrSYSPALHAYCEAGDADKAYEVEEHMLAHGVELE 159
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 15226463   311 QFTFSSCLCASASIASlrhGKEIHGYM--IRTNVR 343
Cdd:pfam17177 160 EPELAALLKVSAKAGR---ADKVYAYLhrLRDAVR 191
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
145-179 2.25e-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: 38.59  E-value: 2.25e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15226463   145 VSWNTMVIGYAQDGNLHEALWFYKEFRRSGIKFNE 179
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
222-443 2.44e-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: 43.18  E-value: 2.44e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463 222 DAYAKCGQMESAKRCFDEMTVKD---IHIWTTLISGYAKLGDMEAAEKLF---CEMPEKNPVSWTALIAGYVRQGSGNRA 295
Cdd:COG2956  50 NLYRRRGEYDRAIRIHQKLLERDpdrAEALLELAQDYLKAGLLDRAEELLeklLELDPDDAEALRLLAEIYEQEGDWEKA 129
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463 296 LDLFRKMIALGVKPEQFtfsSCLCASAS---------IASLRHGKEIHgymiRTNVRPNAivisSLIDMYSKSGSLEASE 366
Cdd:COG2956 130 IEVLERLLKLGPENAHA---YCELAELYleqgdydeaIEALEKALKLD----PDCARALL----LLAELYLEQGDYEEAI 198
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15226463 367 RVFRIC--DDKHDCVFWNTMISALAQHGLGHKALRMLDDMIkfRVQPNRTTLVVILNACSHSGLVEEGLRWFESMTVQH 443
Cdd:COG2956 199 AALERAleQDPDYLPALPRLAELYEKLGDPEEALELLRKAL--ELDPSDDLLLALADLLERKEGLEAALALLERQLRRH 275
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
244-271 4.20e-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: 37.71  E-value: 4.20e-04
                          10        20
                  ....*....|....*....|....*...
gi 15226463   244 DIHIWTTLISGYAKLGDMEAAEKLFCEM 271
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
80-125 4.51e-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: 38.11  E-value: 4.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226463    80 PNTLLSNHLIGMYMKCGKPIDACKVFDQMHLR----NLYSWNNMVSGYVK 125
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
114-144 7.07e-04

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


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.06  E-value: 7.07e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226463   114 YSWNNMVSGYVKSGMLVRARVVFDSMPERDV 144
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
114-145 1.34e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 36.66  E-value: 1.34e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226463   114 YSWNNMVSGYVKSGMLVRARVVFDSMPERDVV 145
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
298-358 4.46e-03

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 35.80  E-value: 4.46e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15226463   298 LFRKMIALGVKPEQFTFSSCLCASASIASLRHGKEIHGYMIRTNVRPNAIVISSLIDMYSK 358
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PLN03218 PLN03218
maturation of RBCL 1; Provisional
375-491 5.10e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 39.86  E-value: 5.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226463   375 KHDCVFWNTMISALAQHGLGHKALRMLDDMIKFRVQPNRTTLVVILNACSHSGLVEEGLRWFESMTVQHgIVPDQEHYAC 454
Cdd:PLN03218  469 KADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKN-VKPDRVVFNA 547
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 15226463   455 LIDLLGRAGCFKELMRKIEEM-----PFEPDKHIWNAILGVC 491
Cdd:PLN03218  548 LISACGQSGAVDRAFDVLAEMkaethPIDPDHITVGALMKAC 589
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
219-245 5.80e-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: 5.80e-03
                          10        20
                  ....*....|....*....|....*..
gi 15226463   219 SIIDAYAKCGQMESAKRCFDEMTVKDI 245
Cdd:pfam01535   5 SLISGYCKNGKLEEALELFKEMKEKGI 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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