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Conserved domains on  [gi|15220095|ref|NP_178143|]
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PENTATRICOPEPTIDE REPEAT 596 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 340-501 1.50e-06

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


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 50.11  E-value: 1.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 340 ARHYSGAGLKDKAEKVLKEMEGESlEANRRAFKDLLSIYASLGREDE----VKRIWKICESKPYFEESLAaiQAFGKLNK 415
Cdd:COG2956  83 AQDYLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKaievLERLLKLGPENAHAYCELA--ELYLEQGD 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 416 VQEAEAIFEKIVKMDRRaSSSTYSVLLRVYVDHKMLSKGKDLVKRMAESGcRIEATTWDALIKLYVEAGEVEKADSLLDK 495
Cdd:COG2956 160 YDEAIEALEKALKLDPD-CARALLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEALELLRK 237


                ....*.
gi 15220095 496 ASKQSH 501
Cdd:COG2956 238 ALELDP 243
PPR_3 super family cl37870
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 250-309 1.04e-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.


The actual alignment was detected with superfamily member pfam13812:

Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 40.42  E-value: 1.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15220095   250 LVFNKMKDLGFPLSGFTCDQMLLLHKRIDRKKIA-DVLLLMEKENIKPSLLTYKILIDVKG 309
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLAlEIFERMKKKGIKPTLDTYNAILGVIG 61
 
Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 340-501 1.50e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 50.11  E-value: 1.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 340 ARHYSGAGLKDKAEKVLKEMEGESlEANRRAFKDLLSIYASLGREDE----VKRIWKICESKPYFEESLAaiQAFGKLNK 415
Cdd:COG2956  83 AQDYLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKaievLERLLKLGPENAHAYCELA--ELYLEQGD 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 416 VQEAEAIFEKIVKMDRRaSSSTYSVLLRVYVDHKMLSKGKDLVKRMAESGcRIEATTWDALIKLYVEAGEVEKADSLLDK 495
Cdd:COG2956 160 YDEAIEALEKALKLDPD-CARALLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEALELLRK 237


                ....*.
gi 15220095 496 ASKQSH 501
Cdd:COG2956 238 ALELDP 243
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 250-309 1.04e-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: 40.42  E-value: 1.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15220095   250 LVFNKMKDLGFPLSGFTCDQMLLLHKRIDRKKIA-DVLLLMEKENIKPSLLTYKILIDVKG 309
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLAlEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 437-468 9.81e-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: 33.97  E-value: 9.81e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15220095   437 TYSVLLRVYVDHKMLSKGKDLVKRMAESGCRI 468
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 340-501 1.50e-06

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 50.11  E-value: 1.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 340 ARHYSGAGLKDKAEKVLKEMEGESlEANRRAFKDLLSIYASLGREDE----VKRIWKICESKPYFEESLAaiQAFGKLNK 415
Cdd:COG2956  83 AQDYLKAGLLDRAEELLEKLLELD-PDDAEALRLLAEIYEQEGDWEKaievLERLLKLGPENAHAYCELA--ELYLEQGD 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220095 416 VQEAEAIFEKIVKMDRRaSSSTYSVLLRVYVDHKMLSKGKDLVKRMAESGcRIEATTWDALIKLYVEAGEVEKADSLLDK 495
Cdd:COG2956 160 YDEAIEALEKALKLDPD-CARALLLLAELYLEQGDYEEAIAALERALEQD-PDYLPALPRLAELYEKLGDPEEALELLRK 237


                ....*.
gi 15220095 496 ASKQSH 501
Cdd:COG2956 238 ALELDP 243
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 250-309 1.04e-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: 40.42  E-value: 1.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15220095   250 LVFNKMKDLGFPLSGFTCDQMLLLHKRIDRKKIA-DVLLLMEKENIKPSLLTYKILIDVKG 309
Cdd:pfam13812   1 SILREMVRDGIQLNVNTYTHLLHAYANVGNLKLAlEIFERMKKKGIKPTLDTYNAILGVIG 61
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 437-468 9.81e-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: 33.97  E-value: 9.81e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15220095   437 TYSVLLRVYVDHKMLSKGKDLVKRMAESGCRI 468
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
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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