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Conserved domains on  [gi|2047905266|gb|KAG6578521|]
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Pentatricopeptide repeat-containing protein, mitochondrial, partial [Cucurbita argyrosperma subsp. sororia]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 10015785)

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
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 443-609 9.90e-05

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 45.64  E-value: 9.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  443 SRTGKSDEANDFMNGLEASGCNPDNKTWASLIEGLCAAGDLAMASDCIHKMVEKgDVSSAGYALDLIINAYCQKRRETDA 522
Cdd:PLN03218   483 AKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALISACGQSGAVDRA 561

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  523 SHLLSDL-VDGKQLKPWHSTYKALINKLLQRGEFKEALKLLGMMRNHEFPPFIEPF---ISYVSKSGTSDDAIGFLKAMT 598
Cdd:PLN03218   562 FDVLAEMkAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYtiaVNSCSQKGDWDFALSIYDDMK 641

                          170
                   ....*....|.
gi 2047905266  599 SKRFPSTSVFL 609
Cdd:PLN03218   642 KKGVKPDEVFF 652
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 292-323 2.88e-03

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


:

Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 2.88e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2047905266 292 TYNAMARVLGREDCIDRFWKVVDEMRSHGYEM 323
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 443-609 9.90e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 45.64  E-value: 9.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  443 SRTGKSDEANDFMNGLEASGCNPDNKTWASLIEGLCAAGDLAMASDCIHKMVEKgDVSSAGYALDLIINAYCQKRRETDA 522
Cdd:PLN03218   483 AKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALISACGQSGAVDRA 561

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  523 SHLLSDL-VDGKQLKPWHSTYKALINKLLQRGEFKEALKLLGMMRNHEFPPFIEPF---ISYVSKSGTSDDAIGFLKAMT 598
Cdd:PLN03218   562 FDVLAEMkAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYtiaVNSCSQKGDWDFALSIYDDMK 641

                          170
                   ....*....|.
gi 2047905266  599 SKRFPSTSVFL 609
Cdd:PLN03218   642 KKGVKPDEVFF 652
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 479-656 1.87e-03

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 40.87  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266 479 AAGDLAMASDCIHKMVEKGDvsSAGYALDLIINAYCQKRRETDASHLLSDLVDGKQLKPWHSTYKALInkLLQRGEFKEA 558
Cdd:COG2956    88 KAGLLDRAEELLEKLLELDP--DDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAEL--YLEQGDYDEA 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266 559 LKLLGMMRNHEfPPFIEPFISYV---SKSGTSDDAIGFLKAMTSKRFPSTSVFLHLFEAFFQAGRHGDAQDFLSKCPSDI 635
Cdd:COG2956   164 IEALEKALKLD-PDCARALLLLAelyLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD 242

                         170       180
                  ....*....|....*....|....
gi 2047905266 636 RNHADVLNL---FYSMKPVEAAAS 656
Cdd:COG2956   243 PSDDLLLALadlLERKEGLEAALA 266
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 292-323 2.88e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 2.88e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2047905266 292 TYNAMARVLGREDCIDRFWKVVDEMRSHGYEM 323
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 462-494 5.55e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 35.01  E-value: 5.55e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2047905266 462 GCNPDNKTWASLIEGLCAAGDLAMASDCIHKMV 494
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 541-572 6.84e-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: 34.74  E-value: 6.84e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2047905266 541 TYKALINKLLQRGEFKEALKLLGMMRNHEFPP 572
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
 
Name Accession Description Interval E-value
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 443-609 9.90e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 45.64  E-value: 9.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  443 SRTGKSDEANDFMNGLEASGCNPDNKTWASLIEGLCAAGDLAMASDCIHKMVEKgDVSSAGYALDLIINAYCQKRRETDA 522
Cdd:PLN03218   483 AKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALISACGQSGAVDRA 561

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266  523 SHLLSDL-VDGKQLKPWHSTYKALINKLLQRGEFKEALKLLGMMRNHEFPPFIEPF---ISYVSKSGTSDDAIGFLKAMT 598
Cdd:PLN03218   562 FDVLAEMkAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYtiaVNSCSQKGDWDFALSIYDDMK 641

                          170
                   ....*....|.
gi 2047905266  599 SKRFPSTSVFL 609
Cdd:PLN03218   642 KKGVKPDEVFF 652
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 479-656 1.87e-03

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 40.87  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266 479 AAGDLAMASDCIHKMVEKGDvsSAGYALDLIINAYCQKRRETDASHLLSDLVDGKQLKPWHSTYKALInkLLQRGEFKEA 558
Cdd:COG2956    88 KAGLLDRAEELLEKLLELDP--DDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAEL--YLEQGDYDEA 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2047905266 559 LKLLGMMRNHEfPPFIEPFISYV---SKSGTSDDAIGFLKAMTSKRFPSTSVFLHLFEAFFQAGRHGDAQDFLSKCPSDI 635
Cdd:COG2956   164 IEALEKALKLD-PDCARALLLLAelyLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD 242

                         170       180
                  ....*....|....*....|....
gi 2047905266 636 RNHADVLNL---FYSMKPVEAAAS 656
Cdd:COG2956   243 PSDDLLLALadlLERKEGLEAALA 266
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 292-323 2.88e-03

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


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 35.51  E-value: 2.88e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2047905266 292 TYNAMARVLGREDCIDRFWKVVDEMRSHGYEM 323
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 462-494 5.55e-03

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


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 35.01  E-value: 5.55e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2047905266 462 GCNPDNKTWASLIEGLCAAGDLAMASDCIHKMV 494
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 442-478 6.04e-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: 6.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2047905266 442 LSRTGKSDEANDFMNGLEASGCNPDNKTWASLIEGLC 478
Cdd:pfam13041  13 YCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLC 49
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 541-572 6.84e-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: 34.74  E-value: 6.84e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2047905266 541 TYKALINKLLQRGEFKEALKLLGMMRNHEFPP 572
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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