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Conserved domains on  [gi|18415979|ref|NP_568214|]
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Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000279)

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

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
SCOP:  4001344

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PPR_2 super family cl38385
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
193-238 3.18e-06

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


The actual alignment was detected with superfamily member pfam13041:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.89  E-value: 3.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18415979   193 ITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCA 238
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
139-286 1.98e-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: 42.79  E-value: 1.98e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979 139 IDAAERYFE-GLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESDSLTFGAitYNEMMTLYMSVGQVEKvpeVIEV 217
Cdd:COG2956  58 YDRAIRIHQkLLERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEA--LRLLAEIYEQEGDWEK---AIEV 132
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18415979 218 LKQ-KKVSPDIFTYNLWLSSCAATFN-----IDELRKILEEMRHDASSnegwvrYIDLTSIYINSSRVTNAESTL 286
Cdd:COG2956 133 LERlLKLGPENAHAYCELAELYLEQGdydeaIEALEKALKLDPDCARA------LLLLAELYLEQGDYEEAIAAL 201
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
193-238 3.18e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.89  E-value: 3.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18415979   193 ITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCA 238
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
139-286 1.98e-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: 42.79  E-value: 1.98e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979 139 IDAAERYFE-GLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESDSLTFGAitYNEMMTLYMSVGQVEKvpeVIEV 217
Cdd:COG2956  58 YDRAIRIHQkLLERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEA--LRLLAEIYEQEGDWEK---AIEV 132
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18415979 218 LKQ-KKVSPDIFTYNLWLSSCAATFN-----IDELRKILEEMRHDASSnegwvrYIDLTSIYINSSRVTNAESTL 286
Cdd:COG2956 133 LERlLKLGPENAHAYCELAELYLEQGdydeaIEALEKALKLDPDCARA------LLLLAELYLEQGDYEEAIAAL 201
PLN03218 PLN03218
maturation of RBCL 1; Provisional
116-256 9.75e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 41.40  E-value: 9.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979   116 HEESKISDADYASRI--DLISK------VFG---IDAA------ERYFEGLDIDSKT-----AETYTSLLHAYAASKQTE 173
Cdd:PLN03218  622 NSCSQKGDWDFALSIydDMKKKgvkpdeVFFsalVDVAghagdlDKAFEILQDARKQgiklgTVSYSSLMGACSNAKNWK 701
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979   174 RAEALFKRIiESDSLTFGAITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCAATFNIDELRKILEEM 253
Cdd:PLN03218  702 KALELYEDI-KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780

                  ...
gi 18415979   254 RHD 256
Cdd:PLN03218  781 KED 783
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
193-238 3.18e-06

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


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 43.89  E-value: 3.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18415979   193 ITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCA 238
Cdd:pfam13041   4 VTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
180-237 1.32e-04

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


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 39.65  E-value: 1.32e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 18415979   180 KRIIESDSLTFGAITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSC 237
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVI 60
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
139-286 1.98e-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: 42.79  E-value: 1.98e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979 139 IDAAERYFE-GLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESDSLTFGAitYNEMMTLYMSVGQVEKvpeVIEV 217
Cdd:COG2956  58 YDRAIRIHQkLLERDPDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEA--LRLLAEIYEQEGDWEK---AIEV 132
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18415979 218 LKQ-KKVSPDIFTYNLWLSSCAATFN-----IDELRKILEEMRHDASSnegwvrYIDLTSIYINSSRVTNAESTL 286
Cdd:COG2956 133 LERlLKLGPENAHAYCELAELYLEQGdydeaIEALEKALKLDPDCARA------LLLLAELYLEQGDYEEAIAAL 201
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
140-210 2.59e-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: 42.41  E-value: 2.59e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18415979 140 DAAERYF-EGLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESDSLTFGAitYNEMMTLYMSVGQVEK 210
Cdd:COG2956  25 DKAIDLLeEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEA--LLELAQDYLKAGLLDR 94
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
140-186 2.99e-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: 40.37  E-value: 2.99e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 18415979 140 DAAERYFE-GLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESD 186
Cdd:COG4235  34 DEALAAYEkALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALD 81
PLN03218 PLN03218
maturation of RBCL 1; Provisional
116-256 9.75e-04

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 41.40  E-value: 9.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979   116 HEESKISDADYASRI--DLISK------VFG---IDAA------ERYFEGLDIDSKT-----AETYTSLLHAYAASKQTE 173
Cdd:PLN03218  622 NSCSQKGDWDFALSIydDMKKKgvkpdeVFFsalVDVAghagdlDKAFEILQDARKQgiklgTVSYSSLMGACSNAKNWK 701
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979   174 RAEALFKRIiESDSLTFGAITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCAATFNIDELRKILEEM 253
Cdd:PLN03218  702 KALELYEDI-KSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA 780

                  ...
gi 18415979   254 RHD 256
Cdd:PLN03218  781 KED 783
PLN03077 PLN03077
Protein ECB2; Provisional
159-282 2.21e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 40.22  E-value: 2.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18415979  159 YTSLLHAYAASKQTERAEALFKRIIESDsltfgAITYNEMMTLYMSVGQVEKVPEVIEVLKQKKVSPDIFTYNLWLSSCA 238
Cdd:PLN03077 326 CNSLIQMYLSLGSWGEAEKVFSRMETKD-----AVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACA 400
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 18415979  239 ATFNIDELRKIleemrHDASSNEGWVRYI----DLTSIYINSSRVTNA 282
Cdd:PLN03077 401 CLGDLDVGVKL-----HELAERKGLISYVvvanALIEMYSKCKCIDKA 443
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
140-186 9.67e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 35.15  E-value: 9.67e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 18415979 140 DAAERYFEGLDIDSKTAETYTSLLHAYAASKQTERAEALFKRIIESD 186
Cdd:COG3063  43 DEAIALEKALKLDPNNAEALLNLAELLLELGDYDEALAYLERALELD 89
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
140-210 9.96e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 35.15  E-value: 9.96e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18415979 140 DAAERYFE-GLDIDSKTAETYTSLLHAYAASKQTERAEAlFKRIIESDSLTfgAITYNEMMTLYMSVGQVEK 210
Cdd:COG3063   9 EEAEEYYEkALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDPNN--AEALLNLAELLLELGDYDE 77
 
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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