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Conserved domains on  [gi|2085706843|gb|QZJ84559|]
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pentatricopeptide repeat-containing protein 97, partial [Acantholippia seriphioides]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 12127860)

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
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 107-153 5.10e-12

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: 58.91  E-value: 5.10e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2085706843 107 PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEG 153
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 super family cl33629
Protein ECB2; Provisional
 4-182 1.65e-07

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 51.77  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   4 NVATFGMLMQLYQ*GWVVEEAEYTFSHMRNLKIIcqsAYSSMITIYTRMGLHDKAEDIIRFLREDRVILNQENWLVVLNA 83
Cdd:PLN03077  322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAV---SWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSA 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  84 YCQQGKLSDA----ELALRAmresGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKefglEPDETTYRSLIEGWgRAGN 159
Cdd:PLN03077  399 CACLGDLDVGvklhELAERK----GLISYVVVANALIEMYSKCKCIDKALEVFHNIP----EKDVISWTSIIAGL-RLNN 469

                         170       180
                  ....*....|....*....|...
gi 2085706843 160 YKRANFYYAELKKLGFKPNSSNL 182
Cdd:PLN03077  470 RCFEALIFFRQMLLTLKPNSVTL 492
 
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 ...
 107-153 5.10e-12

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: 58.91  E-value: 5.10e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2085706843 107 PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEG 153
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 PLN03077
Protein ECB2; Provisional
 4-182 1.65e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 51.77  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   4 NVATFGMLMQLYQ*GWVVEEAEYTFSHMRNLKIIcqsAYSSMITIYTRMGLHDKAEDIIRFLREDRVILNQENWLVVLNA 83
Cdd:PLN03077  322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAV---SWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSA 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  84 YCQQGKLSDA----ELALRAmresGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKefglEPDETTYRSLIEGWgRAGN 159
Cdd:PLN03077  399 CACLGDLDVGvklhELAERK----GLISYVVVANALIEMYSKCKCIDKALEVFHNIP----EKDVISWTSIIAGL-RLNN 469

                         170       180
                  ....*....|....*....|...
gi 2085706843 160 YKRANFYYAELKKLGFKPNSSNL 182
Cdd:PLN03077  470 RCFEALIFFRQMLLTLKPNSVTL 492
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 79-121 3.97e-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: 3.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2085706843  79 VVLNAYCQQGKLSDAELALRAMRESGF*PNVVAYNTMITGYGK 121
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03077 PLN03077
Protein ECB2; Provisional
 108-178 2.68e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 44.84  E-value: 2.68e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085706843 108 NVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRANFYYAELK-KLGFKPN 178
Cdd:PLN03077  553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEeKYSITPN 624
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 110-144 5.03e-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: 39.36  E-value: 5.03e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2085706843 110 VAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDE 144
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 41-237 2.16e-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: 41.64  E-value: 2.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  41 AYSSMITIYTRMGLHDKAEDIIRFLREdrviLNQENWLVVLN---AYCQQGKLSDAELALRAMRESGF*pNVVAYNTMIT 117
Cdd:COG2956    44 AHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAEALLElaqDYLKAGLLDRAEELLEKLLELDPD-DAEALRLLAE 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843 118 GYGK*SNMAHAENLFQNLKEfgLEPDETTYRSLI-EGWGRAGNYKRANFYYAELkkLGFKPNSSNLYT-LIRLQAKHEDE 195
Cdd:COG2956   119 IYEQEGDWEKAIEVLERLLK--LGPENAHAYCELaELYLEQGDYDEAIEALEKA--LKLDPDCARALLlLAELYLEQGDY 194

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2085706843 196 EGAITTIDD*MMIGCEKSAILGIVLQAYEKANRLDKLSLVLE 237
Cdd:COG2956   195 EEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLR 236
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 77-109 1.98e-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: 35.12  E-value: 1.98e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2085706843  77 WLVVLNAYCQQGKLSDAELALRAMRESGF*PNV 109
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
 
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 ...
 107-153 5.10e-12

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: 58.91  E-value: 5.10e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2085706843 107 PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEG 153
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILING 47
PLN03077 PLN03077
Protein ECB2; Provisional
 4-182 1.65e-07

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 51.77  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   4 NVATFGMLMQLYQ*GWVVEEAEYTFSHMRNLKIIcqsAYSSMITIYTRMGLHDKAEDIIRFLREDRVILNQENWLVVLNA 83
Cdd:PLN03077  322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAV---SWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSA 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  84 YCQQGKLSDA----ELALRAmresGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKefglEPDETTYRSLIEGWgRAGN 159
Cdd:PLN03077  399 CACLGDLDVGvklhELAERK----GLISYVVVANALIEMYSKCKCIDKALEVFHNIP----EKDVISWTSIIAGL-RLNN 469

                         170       180
                  ....*....|....*....|...
gi 2085706843 160 YKRANFYYAELKKLGFKPNSSNL 182
Cdd:PLN03077  470 RCFEALIFFRQMLLTLKPNSVTL 492
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 79-121 3.97e-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: 3.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2085706843  79 VVLNAYCQQGKLSDAELALRAMRESGF*PNVVAYNTMITGYGK 121
Cdd:pfam13041   8 TLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 42-230 8.09e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 49.49  E-value: 8.09e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   42 YSSMITIYTRMGLHDKAEDIIRFLREDRVILNQENWLVVLNAYCQQGKLSDAELALRAMRESGF*PNVVAYNTMITGYGK 121
Cdd:PLN03218   582 VGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGH 661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  122 *SNMAHAENLFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRANFYYAELKKLGFKPNSSNLYTLIRLQAKHEDEEGAITT 201
Cdd:PLN03218   662 AGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEV 741

                          170       180       190
                   ....*....|....*....|....*....|
gi 2085706843  202 IDD*MMIG-CEKSAILGIVLQAYEKANRLD 230
Cdd:PLN03218   742 LSEMKRLGlCPNTITYSILLVASERKDDAD 771
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 11-178 4.90e-06

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 47.17  E-value: 4.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  11 LMQLYQ*GWVVEEAEYTFSHMRNLKIIcqsAYSSMITIYTRMGLHDKAEDIIRFLREDRVILNQENWLVVLNAYCQQGKL 90
Cdd:PLN03081  265 LIDMYSKCGDIEDARCVFDGMPEKTTV---AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALL 341

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  91 SDAELALRAMRESGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLepdeTTYRSLIEGWGRAGNYKRANFYYAEL 170
Cdd:PLN03081  342 EHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERM 417


                  ....*...
gi 2085706843 171 KKLGFKPN 178
Cdd:PLN03081  418 IAEGVAPN 425
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 131-178 1.22e-05

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: 41.96  E-value: 1.22e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2085706843 131 LFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRANFYYAELKKLGFKPN 178
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPT 49
PLN03077 PLN03077
Protein ECB2; Provisional
 108-178 2.68e-05

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 44.84  E-value: 2.68e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085706843 108 NVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRANFYYAELK-KLGFKPN 178
Cdd:PLN03077  553 DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEeKYSITPN 624
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 22-237 3.04e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 44.86  E-value: 3.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  22 EEAEYTFSHMRNLKI-ICQSAYSSMITIYTRMGLHDKAED----IIRFLREDRVILNQenwlVVLNAYCQQGKLSDAELA 96
Cdd:PLN03081  307 EEALCLYYEMRDSGVsIDQFTFSIMIRIFSRLALLEHAKQahagLIRTGFPLDIVANT----ALVDLYSKWGRMEDARNV 382

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  97 LRAMRESgf*pNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETT------------------------------ 146
Cdd:PLN03081  383 FDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTflavlsacrysglseqgweifqsmsenhri 458

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843 147 ------YRSLIEGWGRAGNYKRAnfyYAELKKLGFKPNSSNLYTLIRLQAKHEDEEGAITTIDD*MMIGCEKSAILGIVL 220
Cdd:PLN03081  459 kpramhYACMIELLGREGLLDEA---YAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLL 535

                         250
                  ....*....|....*..
gi 2085706843 221 QAYEKANRLDKLSLVLE 237
Cdd:PLN03081  536 NLYNSSGRQAEAAKVVE 552
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 85-186 4.68e-05

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 44.10  E-value: 4.68e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   85 CQQGKLSDAEL-ALRAMRESGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRA 163
Cdd:PLN03218   447 CASSQDIDGALrVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKA 526

                           90       100
                   ....*....|....*....|...
gi 2085706843  164 NFYYAELKKLGFKPNSSNLYTLI 186
Cdd:PLN03218   527 FGAYGIMRSKNVKPDRVVFNALI 549
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 110-144 5.03e-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: 39.36  E-value: 5.03e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2085706843 110 VAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDE 144
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 97-151 2.09e-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: 38.49  E-value: 2.09e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2085706843  97 LRAMRESGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLI 151
Cdd:pfam13812   3 LREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAIL 57
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 41-237 2.16e-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: 41.64  E-value: 2.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  41 AYSSMITIYTRMGLHDKAEDIIRFLREdrviLNQENWLVVLN---AYCQQGKLSDAELALRAMRESGF*pNVVAYNTMIT 117
Cdd:COG2956    44 AHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAEALLElaqDYLKAGLLDRAEELLEKLLELDPD-DAEALRLLAE 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843 118 GYGK*SNMAHAENLFQNLKEfgLEPDETTYRSLI-EGWGRAGNYKRANFYYAELkkLGFKPNSSNLYT-LIRLQAKHEDE 195
Cdd:COG2956   119 IYEQEGDWEKAIEVLERLLK--LGPENAHAYCELaELYLEQGDYDEAIEALEKA--LKLDPDCARALLlLAELYLEQGDY 194

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2085706843 196 EGAITTIDD*MMIGCEKSAILGIVLQAYEKANRLDKLSLVLE 237
Cdd:COG2956   195 EEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLR 236
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 104-132 3.52e-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: 36.94  E-value: 3.52e-04
                          10        20
                  ....*....|....*....|....*....
gi 2085706843 104 GF*PNVVAYNTMITGYGK*SNMAHAENLF 132
Cdd:pfam12854   2 GLKPDVVTYNTLINGLCRAGRVDEAFELL 30
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 100-171 1.14e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 39.86  E-value: 1.14e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085706843  100 MRESGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKEFGLEPDETTYRSLIEGWGRAGNYKRANFYYAELK 171
Cdd:PLN03218   498 MVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMK 569
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 110-140 1.60e-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: 35.13  E-value: 1.60e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2085706843 110 VAYNTMITGYGK*SNMAHAENLFQNLKEFGL 140
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 88-209 1.97e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 39.09  E-value: 1.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843   88 GKLSDAELALRAMRESGF*PNVVAYNTMITGYGK*SNMAHAenlFQNLKEFGLE-----PDETTYRSLIEGWGRAGNYKR 162
Cdd:PLN03218   521 GQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRA---FDVLAEMKAEthpidPDHITVGALMKACANAGQVDR 597

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2085706843  163 ANFYYAELKKLGFKpNSSNLYTL-IRLQAKHEDEEGAITTIDD*MMIG 209
Cdd:PLN03218   598 AKEVYQMIHEYNIK-GTPEVYTIaVNSCSQKGDWDFALSIYDDMKKKG 644
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 77-109 1.98e-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: 35.12  E-value: 1.98e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2085706843  77 WLVVLNAYCQQGKLSDAELALRAMRESGF*PNV 109
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03077 PLN03077
Protein ECB2; Provisional
 77-180 3.84e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 38.29  E-value: 3.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  77 WLVVLNAYCQQGKLSDAELALRAMRESGF*PNVVAYNTMITGYGK*SNMAHAENLFQNLKE-FGLEPDETTYRSLIEGWG 155
Cdd:PLN03077  557 WNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEkYSITPNLKHYACVVDLLG 636

                          90       100
                  ....*....|....*....|....*
gi 2085706843 156 RAGNYKRAnfyYAELKKLGFKPNSS 180
Cdd:PLN03077  637 RAGKLTEA---YNFINKMPITPDPA 658
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 80-121 5.71e-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: 34.26  E-value: 5.71e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2085706843  80 VLNAYCQQGKLSDAELALRAMRESGF*PNVVAYNTMITGYGK 121
Cdd:pfam13812  21 LLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 138-163 6.72e-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: 33.47  E-value: 6.72e-03
                          10        20
                  ....*....|....*....|....*.
gi 2085706843 138 FGLEPDETTYRSLIEGWGRAGNYKRA 163
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEA 26
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 13-206 8.00e-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: 36.63  E-value: 8.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  13 QLYQ*GWVVEEAEYTFSHMRNLKIICQSAYSSMITIYTRMGLHDKAEDIirFLREDRVILNQENWLVVL-NAYCQQGKLS 91
Cdd:COG2956    84 QDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEV--LERLLKLGPENAHAYCELaELYLEQGDYD 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085706843  92 DAELALRAMRESgf*PNVVAYNTMITG-YGK*SNMAHAENLFQNLKEfgLEPDET-TYRSLIEGWGRAGNYKRANFYYAE 169
Cdd:COG2956   162 EAIEALEKALKL--DPDCARALLLLAElYLEQGDYEEAIAALERALE--QDPDYLpALPRLAELYEKLGDPEEALELLRK 237

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2085706843 170 LKKLgfKPNSSNLYTLIRLQAKHEDEEGAITTIDD*M 206
Cdd:COG2956   238 ALEL--DPSDDLLLALADLLERKEGLEAALALLERQL 272
 
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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