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Conserved domains on  [gi|1443088345|ref|XP_015640992|]
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pentatricopeptide repeat-containing protein At5g06540 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03081 super family cl33631
pentatricopeptide (PPR) repeat-containing protein; Provisional
 214-638 5.28e-125

pentatricopeptide (PPR) repeat-containing protein; Provisional


The actual alignment was detected with superfamily member PLN03081:

Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 385.38  E-value: 5.28e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 214 GLVDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSALVACTGAGALGRGREIYRWVE 293
Cdd:PLN03081  273 GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLI 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 294 QSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARGLTTWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNV 373
Cdd:PLN03081  353 RTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAV 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 374 LTACAHAGEVSEGRRYLNHIVSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMPMDPDLAVLGALLGACKIHGDVDL 453
Cdd:PLN03081  433 LSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLEL 512

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 454 GEAIGWRVIDLDPDNSGRYVLLANLLAGAGRWDEVGKVRRLMDERNVSKEAGRSVIEVDGEACEFRCGNLRHPQAREIYA 533
Cdd:PLN03081  513 GRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQ 592

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 534 MAVDMVSRIRAEGYVPDTGEALHDVAEEDKEAALLCHSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFG 613
Cdd:PLN03081  593 KLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTK 672

                         410       420
                  ....*....|....*....|....*
gi 1443088345 614 REIVVRDRSRFHHFKDGMCSCKDYW 638
Cdd:PLN03081  673 REIVVRDASRFHHFKLGKCSCGDYW 697
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 199-226 4.19e-07

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: 46.57  E-value: 4.19e-07
                          10        20
                  ....*....|....*....|....*...
gi 1443088345 199 DVVSWTTMVGGLCRLGLVDDAREVFDAM 226
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 214-638 5.28e-125

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 385.38  E-value: 5.28e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 214 GLVDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSALVACTGAGALGRGREIYRWVE 293
Cdd:PLN03081  273 GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLI 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 294 QSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARGLTTWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNV 373
Cdd:PLN03081  353 RTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAV 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 374 LTACAHAGEVSEGRRYLNHIVSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMPMDPDLAVLGALLGACKIHGDVDL 453
Cdd:PLN03081  433 LSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLEL 512

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 454 GEAIGWRVIDLDPDNSGRYVLLANLLAGAGRWDEVGKVRRLMDERNVSKEAGRSVIEVDGEACEFRCGNLRHPQAREIYA 533
Cdd:PLN03081  513 GRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQ 592

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 534 MAVDMVSRIRAEGYVPDTGEALHDVAEEDKEAALLCHSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFG 613
Cdd:PLN03081  593 KLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTK 672

                         410       420
                  ....*....|....*....|....*
gi 1443088345 614 REIVVRDRSRFHHFKDGMCSCKDYW 638
Cdd:PLN03081  673 REIVVRDASRFHHFKLGKCSCGDYW 697
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 546-638 1.36e-46

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 159.12  E-value: 1.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 546 GYVPDTGEALHDVAEEDKEAALLCHSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFGREIVVRDRSRFH 625
Cdd:pfam14432   1 GYVPDLKFVLHDVDEEEKKQLLHGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIFGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1443088345 626 HFKDGMCSCKDYW 638
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 232-265 2.42e-07

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: 47.06  E-value: 2.42e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1443088345 232 VSWNSMISGYVKADRFLDALEVFDEMRALGVEGN 265
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 199-226 4.19e-07

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: 46.57  E-value: 4.19e-07
                          10        20
                  ....*....|....*....|....*...
gi 1443088345 199 DVVSWTTMVGGLCRLGLVDDAREVFDAM 226
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 380-487 6.72e-04

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.18  E-value: 6.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 380 AGEVSEGRRYLNHIVSRHGIEPkgEHYGCMVDLFGRAGQLDEAKKVIDE-MPMDPDLAVLGALLGACKIH-GDVDlgEAI 457
Cdd:COG4783    17 AGDYDEAEALLEKALELDPDNP--EAFALLGEILLQLGDLDEAIVLLHEaLELDPDEPEARLNLGLALLKaGDYD--EAL 92

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1443088345 458 GW--RVIDLDPDNSGRYVLLANLLAGAGRWDE 487
Cdd:COG4783    93 ALleKALKLDPEHPEAYLRLARAYRALGRPDE 124
 
Name Accession Description Interval E-value
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 214-638 5.28e-125

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 385.38  E-value: 5.28e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 214 GLVDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSALVACTGAGALGRGREIYRWVE 293
Cdd:PLN03081  273 GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLI 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 294 QSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARGLTTWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNV 373
Cdd:PLN03081  353 RTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAV 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 374 LTACAHAGEVSEGRRYLNHIVSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMPMDPDLAVLGALLGACKIHGDVDL 453
Cdd:PLN03081  433 LSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLEL 512

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 454 GEAIGWRVIDLDPDNSGRYVLLANLLAGAGRWDEVGKVRRLMDERNVSKEAGRSVIEVDGEACEFRCGNLRHPQAREIYA 533
Cdd:PLN03081  513 GRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQ 592

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 534 MAVDMVSRIRAEGYVPDTGEALHDVAEEDKEAALLCHSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFG 613
Cdd:PLN03081  593 KLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTK 672

                         410       420
                  ....*....|....*....|....*
gi 1443088345 614 REIVVRDRSRFHHFKDGMCSCKDYW 638
Cdd:PLN03081  673 REIVVRDASRFHHFKLGKCSCGDYW 697
PLN03077 PLN03077
Protein ECB2; Provisional
 216-636 6.08e-119

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 374.19  E-value: 6.08e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 216 VDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRaLGVEGNGFVATSALVACTGAGALGRGREIYRWVEQS 295
Cdd:PLN03077  440 IDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRT 518

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 296 GIEVDAKLATAVVDMYCKCGCVDEAWGVFDSlPARGLTTWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNVLT 375
Cdd:PLN03077  519 GIGFDGFLPNALLDLYVRCGRMNYAWNQFNS-HEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLC 597

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 376 ACAHAGEVSEGRRYLNHIVSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMPMDPDLAVLGALLGACKIHGDVDLGE 455
Cdd:PLN03077  598 ACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGE 677

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 456 AIGWRVIDLDPDNSGRYVLLANLLAGAGRWDEVGKVRRLMDERNVSKEAGRSVIEVDGEACEFRCGNLRHPQAREIYAMA 535
Cdd:PLN03077  678 LAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVL 757

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 536 VDMVSRIRAEGYVPDTGEALHDVaeEDKEAALLC-HSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFGR 614
Cdd:PLN03077  758 EGFYEKMKASGLAGSESSSMDEI--EVSKDDIFCgHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRR 835

                         410       420
                  ....*....|....*....|..
gi 1443088345 615 EIVVRDRSRFHHFKDGMCSCKD 636
Cdd:PLN03077  836 EISVRDTEQFHHFKDGECSCGD 857
DYW_deaminase pfam14432
DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases ...
 546-638 1.36e-46

DYW family of nucleic acid deaminases; This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.


Pssm-ID: 464172 [Multi-domain]  Cd Length: 93  Bit Score: 159.12  E-value: 1.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 546 GYVPDTGEALHDVAEEDKEAALLCHSEKLAIAFGLLRARPRETLRITKNLRVCRDCHEATKYVSRVFGREIVVRDRSRFH 625
Cdd:pfam14432   1 GYVPDLKFVLHDVDEEEKKQLLHGHSEKLALAYGLLTTPDGATIRITKNLRVCGDCHTAFKYISKIFGREIVVRDASRFH 80

                          90
                  ....*....|...
gi 1443088345 626 HFKDGMCSCKDYW 638
Cdd:pfam14432  81 HFKNGLCSCGDFW 93
PLN03077 PLN03077
Protein ECB2; Provisional
 206-500 1.00e-34

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 140.76  E-value: 1.00e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 206 MVGGLCRLGLVDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSALVACTGAGALGRG 285
Cdd:PLN03077  127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARG 206

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 286 REIYRWVEQSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARGLTTWNCMIGGFAVHGRCDDALELFHQMEAAGVAP 365
Cdd:PLN03077  207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDP 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 366 DDVTLLNVLTACAHAGEVSEGRRYLNHIVSRhGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMP--------------- 430
Cdd:PLN03077  287 DLMTITSVISACELLGDERLGREMHGYVVKT-GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMEtkdavswtamisgye 365

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 431 --------------MD-----PDLAVLGALLGACKIHGDVDLGeaigwrvIDLD--PDNSG--RYVLLANLL----AGAG 483
Cdd:PLN03077  366 knglpdkaletyalMEqdnvsPDEITIASVLSACACLGDLDVG-------VKLHelAERKGliSYVVVANALiemySKCK 438

                         330
                  ....*....|....*..
gi 1443088345 484 RWDEVGKVRRLMDERNV 500
Cdd:PLN03077  439 CIDKALEVFHNIPEKDV 455
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 448-510 1.15e-12

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: 62.95  E-value: 1.15e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443088345 448 HGDVDLGEAIGWRVIDLDPDNSGRYVLLANLLAGAGRWDEVGKVRRLMDERNVSKEAGRSVIE 510
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 286-457 4.45e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 66.05  E-value: 4.45e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  286 REIYRWVEQSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARG----LTTWNCMIGGFAVHGRCDDALELFHQMEAA 361
Cdd:PLN03218   457 LRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGveanVHTFGALIDGCARAGQVAKAFGAYGIMRSK 536

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  362 GVAPDDVTLLNVLTACAHAGEVSEGRRYLNHIVSR-HGIEPKGEHYGCMVDLFGRAGQLDEAKKV---IDEMPMDPDLAV 437
Cdd:PLN03218   537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAEtHPIDPDHITVGALMKACANAGQVDRAKEVyqmIHEYNIKGTPEV 616

                          170       180
                   ....*....|....*....|
gi 1443088345  438 LGALLGACKIHGDVDLGEAI 457
Cdd:PLN03218   617 YTIAVNSCSQKGDWDFALSI 636
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 317-452 1.05e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 64.90  E-value: 1.05e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  317 VDEAWGVFDSLPARGLTTwNCM-----IGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNVLTACAHAGEVSE-----G 386
Cdd:PLN03218   453 IDGALRVLRLVQEAGLKA-DCKlyttlISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKafgayG 531

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443088345  387 rrylnhIVSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEM-----PMDPDLAVLGALLGACKIHGDVD 452
Cdd:PLN03218   532 ------IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMkaethPIDPDHITVGALMKACANAGQVD 596
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 199-457 1.65e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 64.51  E-value: 1.65e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  199 DVVSWTTMVGGLCRLGLVDDAREVFDAMPAR------NLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSA 272
Cdd:PLN03218   541 DRVVFNALISACGQSGAVDRAFDVLAEMKAEthpidpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIA 620

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  273 LVACTGAGALGRGREIYRWVEQSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSLPARGL----TTWNCMIGGFAVHGRC 348
Cdd:PLN03218   621 VNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIklgtVSYSSLMGACSNAKNW 700

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  349 DDALELFHQMEAAGVAPdDVTLLNVL-TACAHAGEVSEGRRYLNHIvSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVID 427
Cdd:PLN03218   701 KKALELYEDIKSIKLRP-TVSTMNALiTALCEGNQLPKALEVLSEM-KRLGLCPNTITYSILLVASERKDDADVGLDLLS 778

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1443088345  428 EMPMD---PDLAVLGALLGACK--IHGDVDLGEAI 457
Cdd:PLN03218   779 QAKEDgikPNLVMCRCITGLCLrrFEKACALGEPV 813
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 188-454 1.49e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 61.43  E-value: 1.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  188 VLFRTSGGGAlDVVSWTTMVGGLCRLGLVDDAREVFDAMPAR----NLVSWNSMISG-------------Y-------VK 243
Cdd:PLN03218   461 RLVQEAGLKA-DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAgveaNVHTFGALIDGcaragqvakafgaYgimrsknVK 539

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  244 ADRFL---------------DALEVFDEMRAlgvEGNGF----VATSALV-ACTGAGALGRGREIYRWVEQSGIEVDAKL 303
Cdd:PLN03218   540 PDRVVfnalisacgqsgavdRAFDVLAEMKA---ETHPIdpdhITVGALMkACANAGQVDRAKEVYQMIHEYNIKGTPEV 616

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  304 ATAVVDMYCKCGCVDEAWGVFDSLPARGLTTWNCMIGGF---AVH-GRCDDALELFHQMEAAGVAPDDVTLLNVLTACAH 379
Cdd:PLN03218   617 YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALvdvAGHaGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSN 696

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443088345  380 AGEVSEGRRYLNHIVSRhGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMP---MDPDLAVLGALLGACKIHGDVDLG 454
Cdd:PLN03218   697 AKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQLPKALEVLSEMKrlgLCPNTITYSILLVASERKDDADVG 773
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 214-452 7.34e-09

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 59.12  E-value: 7.34e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  214 GLVDDAREVFDAMPARNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGNGFVATSALVACTGAGALGRGREIYRWVE 293
Cdd:PLN03218   420 RAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMV 499

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  294 QSGIEVDAKLATAVVDMYCKCGCVDEAWGVFDSL------PARglTTWNCMIGGFAVHGRCDDALELFHQM--EAAGVAP 365
Cdd:PLN03218   500 NAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMrsknvkPDR--VVFNALISACGQSGAVDRAFDVLAEMkaETHPIDP 577

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345  366 DDVTLLNVLTACAHAGEVSEGRRYLNHIvSRHGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEMPMD---PDLAVLGALL 442
Cdd:PLN03218   578 DHITVGALMKACANAGQVDRAKEVYQMI-HEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKgvkPDEVFFSALV 656

                          250
                   ....*....|
gi 1443088345  443 GACKIHGDVD 452
Cdd:PLN03218   657 DVAGHAGDLD 666
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 232-262 1.34e-08

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: 50.54  E-value: 1.34e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1443088345 232 VSWNSMISGYVKADRFLDALEVFDEMRALGV 262
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 ...
 334-379 2.93e-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: 50.05  E-value: 2.93e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1443088345 334 TWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNVLTACAH 379
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 199-243 3.60e-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: 50.05  E-value: 3.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1443088345 199 DVVSWTTMVGGLCRLGLVDDAREVFDAMPAR----NLVSWNSMISGYVK 243
Cdd:pfam13041   2 DVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 229-265 1.26e-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: 48.51  E-value: 1.26e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1443088345 229 RNLVSWNSMISGYVKADRFLDALEVFDEMRALGVEGN 265
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPN 37
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 232-265 2.42e-07

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: 47.06  E-value: 2.42e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1443088345 232 VSWNSMISGYVKADRFLDALEVFDEMRALGVEGN 265
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 334-367 3.77e-07

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: 46.68  E-value: 3.77e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1443088345 334 TWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDD 367
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 199-226 4.19e-07

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: 46.57  E-value: 4.19e-07
                          10        20
                  ....*....|....*....|....*...
gi 1443088345 199 DVVSWTTMVGGLCRLGLVDDAREVFDAM 226
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 334-363 9.75e-07

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: 45.53  E-value: 9.75e-07
                          10        20        30
                  ....*....|....*....|....*....|
gi 1443088345 334 TWNCMIGGFAVHGRCDDALELFHQMEAAGV 363
Cdd:pfam01535   2 TYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 201-231 2.00e-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: 2.00e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1443088345 201 VSWTTMVGGLCRLGLVDDAREVFDAMPARNL 231
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 230-258 5.12e-05

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: 40.41  E-value: 5.12e-05
                          10        20
                  ....*....|....*....|....*....
gi 1443088345 230 NLVSWNSMISGYVKADRFLDALEVFDEMR 258
Cdd:pfam12854   6 DVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 201-232 7.16e-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: 40.13  E-value: 7.16e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1443088345 201 VSWTTMVGGLCRLGLVDDAREVFDAMPARNLV 232
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 250-390 1.40e-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: 43.54  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 250 ALEVFDEMRALGVEGNGFVATSALVACTGAG---------ALGRGREIYRWVEQSGIEVDAKLATAVVDMYCKCGCVDEA 320
Cdd:pfam17177  30 ALALYDAAKAEGVRLAQYHYNVLLYLCSKAAdatdlkpqlAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAKGDGDLA 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1443088345 321 WGVFDSLPARGLT----TWNCMIGGFAVHGRCDDALELFHQMEAAGVAPDDVTLLNVLTACAHAGEVSEGRRYL 390
Cdd:pfam17177 110 FDLVKEMEAAGVSprlrSYSPALHAYCEAGDADKAYEVEEHMLAHGVELEEPELAALLKVSAKAGRADKVYAYL 183
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 305-343 3.96e-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: 38.50  E-value: 3.96e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1443088345 305 TAVVDMYCKCGCVDEAWGVFDSLPARGLT----TWNCMIGGFA 343
Cdd:pfam13041   7 NTLINGYCKKGKVEEAFKLFNEMKKRGVKpnvyTYTILINGLC 49
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 380-487 6.72e-04

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.18  E-value: 6.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 380 AGEVSEGRRYLNHIVSRHGIEPkgEHYGCMVDLFGRAGQLDEAKKVIDE-MPMDPDLAVLGALLGACKIH-GDVDlgEAI 457
Cdd:COG4783    17 AGDYDEAEALLEKALELDPDNP--EAFALLGEILLQLGDLDEAIVLLHEaLELDPDEPEARLNLGLALLKaGDYD--EAL 92

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1443088345 458 GW--RVIDLDPDNSGRYVLLANLLAGAGRWDE 487
Cdd:COG4783    93 ALleKALKLDPEHPEAYLRLARAYRALGRPDE 124
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 415-487 9.13e-04

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 39.79  E-value: 9.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443088345 415 RAGQLDEAKKVIDE-MPMDPDLAVLGALLGACKIH-GDVDlgEAIGW--RVIDLDPDNSGRYVLLANLLAGAGRWDE 487
Cdd:COG4783    16 LAGDYDEAEALLEKaLELDPDNPEAFALLGEILLQlGDLD--EAIVLlhEALELDPDEPEARLNLGLALLKAGDYDE 90
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 334-359 1.47e-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: 36.55  E-value: 1.47e-03
                          10        20
                  ....*....|....*....|....*.
gi 1443088345 334 TWNCMIGGFAVHGRCDDALELFHQME 359
Cdd:pfam12854   9 TYNTLINGLCRAGRVDEAFELLDEME 34
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 349-487 1.91e-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: 40.48  E-value: 1.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443088345 349 DDALELFhqMEAAGVAPDDVT-LLNVLTACAHAGEVSEGRRYLNHIVSrhgIEPKGEHYGC-MVDLFGRAGQLDEAKKVI 426
Cdd:COG2956    93 DRAEELL--EKLLELDPDDAEaLRLLAEIYEQEGDWEKAIEVLERLLK---LGPENAHAYCeLAELYLEQGDYDEAIEAL 167

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443088345 427 DE-MPMDPDLAVLGALLGACKI-HGDVDlgEAIGW--RVIDLDPDNSGRYVLLANLLAGAGRWDE 487
Cdd:COG2956   168 EKaLKLDPDCARALLLLAELYLeQGDYE--EAIAAleRALEQDPDYLPALPRLAELYEKLGDPEE 230
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 406-429 4.52e-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: 4.52e-03
                          10        20
                  ....*....|....*....|....
gi 1443088345 406 YGCMVDLFGRAGQLDEAKKVIDEM 429
Cdd:pfam01535   3 YNSLISGYCKNGKLEEALELFKEM 26
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 406-429 5.53e-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: 5.53e-03
                          10        20
                  ....*....|....*....|....
gi 1443088345 406 YGCMVDLFGRAGQLDEAKKVIDEM 429
Cdd:TIGR00756   3 YNTLIDGLCKAGRVEEALELFKEM 26
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 397-429 5.68e-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: 34.63  E-value: 5.68e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1443088345 397 HGIEPKGEHYGCMVDLFGRAGQLDEAKKVIDEM 429
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEM 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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