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Conserved domains on  [gi|15226879|ref|NP_181048|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 1000585)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03077 super family cl33629
Protein ECB2; Provisional
 52-610 7.85e-113

Protein ECB2; Provisional


The actual alignment was detected with superfamily member PLN03077:

Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 358.01  E-value: 7.85e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   52 LIGELCKVGKIAEARKLFDGLPERDVVTWTHVITGYIKLGDMREARELFDR---VDSRKNVVTW---------------- 112
Cdd:PLN03077 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRmlwAGVRPDVYTFpcvlrtcggipdlarg 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  113 -------------------TAMVSGYLRSKQLSIAEMLFQEMPERNVVSWNTMIDGYAQSGRIDKALELFDEMPER---- 169
Cdd:PLN03077 207 revhahvvrfgfeldvdvvNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELsvdp 286

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  170 -----------------------------------NIVSWNSMVKALVQRGRIDEAMNLFERMPRRDVVSWTAMVDGLAK 214
Cdd:PLN03077 287 dlmtitsvisacellgderlgremhgyvvktgfavDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  215 NGKVDEARRLFDCMPERNI----ISWNAMITGYAQNNRIDEADQLFQVMPERDFASW----NTMITGFIRNREMNKACGL 286
Cdd:PLN03077 367 NGLPDKALETYALMEQDNVspdeITIASVLSACACLGDLDVGVKLHELAERKGLISYvvvaNALIEMYSKCKCIDKALEV 446

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  287 FDRMPEKNVISWTTMITGYVENKENEEALNVFSKMLrdGSVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVHQKNE 366
Cdd:PLN03077 447 FHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDG 524

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  367 IVTSALLNMYSKSGELIAARKMFDnglVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSH 446
Cdd:PLN03077 525 FLPNALLDLYVRCGRMNYAWNQFN---SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSR 601

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  447 AGLVEKGMEFFKDLVRDESLPLREEHYTCLVDLCGRAGRLKDVTNFINCDDARLSRSFYGAILSACNVHNEVSIAKEVVK 526
Cdd:PLN03077 602 SGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQ 681

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  527 KVLETGSDDAGTYVLMSNIYAANGKREEAAEMRMKMKEKGLKKQPGCSWVKVGKQNHLFVVGDKSHPQFEALDSILSDLR 606
Cdd:PLN03077 682 HIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFY 761


                 ....
gi 15226879  607 NKMR 610
Cdd:PLN03077 762 EKMK 765
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 52-610 7.85e-113

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 358.01  E-value: 7.85e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   52 LIGELCKVGKIAEARKLFDGLPERDVVTWTHVITGYIKLGDMREARELFDR---VDSRKNVVTW---------------- 112
Cdd:PLN03077 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRmlwAGVRPDVYTFpcvlrtcggipdlarg 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  113 -------------------TAMVSGYLRSKQLSIAEMLFQEMPERNVVSWNTMIDGYAQSGRIDKALELFDEMPER---- 169
Cdd:PLN03077 207 revhahvvrfgfeldvdvvNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELsvdp 286

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  170 -----------------------------------NIVSWNSMVKALVQRGRIDEAMNLFERMPRRDVVSWTAMVDGLAK 214
Cdd:PLN03077 287 dlmtitsvisacellgderlgremhgyvvktgfavDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  215 NGKVDEARRLFDCMPERNI----ISWNAMITGYAQNNRIDEADQLFQVMPERDFASW----NTMITGFIRNREMNKACGL 286
Cdd:PLN03077 367 NGLPDKALETYALMEQDNVspdeITIASVLSACACLGDLDVGVKLHELAERKGLISYvvvaNALIEMYSKCKCIDKALEV 446

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  287 FDRMPEKNVISWTTMITGYVENKENEEALNVFSKMLrdGSVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVHQKNE 366
Cdd:PLN03077 447 FHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDG 524

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  367 IVTSALLNMYSKSGELIAARKMFDnglVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSH 446
Cdd:PLN03077 525 FLPNALLDLYVRCGRMNYAWNQFN---SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSR 601

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  447 AGLVEKGMEFFKDLVRDESLPLREEHYTCLVDLCGRAGRLKDVTNFINCDDARLSRSFYGAILSACNVHNEVSIAKEVVK 526
Cdd:PLN03077 602 SGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQ 681

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  527 KVLETGSDDAGTYVLMSNIYAANGKREEAAEMRMKMKEKGLKKQPGCSWVKVGKQNHLFVVGDKSHPQFEALDSILSDLR 606
Cdd:PLN03077 682 HIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFY 761


                 ....
gi 15226879  607 NKMR 610
Cdd:PLN03077 762 EKMK 765
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 515-577 2.38e-14

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: 67.95  E-value: 2.38e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15226879   515 HNEVSIAKEVVKKVLETGSDDAGTYVLMSNIYAANGKREEAAEMRMKMKEKGLKKQPGCSWVK 577
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
87-226 2.38e-10

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 61.18  E-value: 2.38e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQ---EMPERNVVSWNTMIDGYAQSGRIDKALE 161
Cdd:COG0457  18 YRRLGRYEEAIEDYEKAleLDPDDAEALYNLGLAYLRLGRYEEALADYEqalELDPDDAEALNNLGLALQALGRYEEALE 97

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15226879 162 LFD---EMPERNIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGLAKNGKVDEARRLFD 226
Cdd:COG0457  98 DYDkalELDPDDAEALYNLGLALLELGRYDEAIEAYERaleLDPDDADALYNLGIALEKLGRYEEALELLE 168
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 141-172 9.31e-08

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: 48.22  E-value: 9.31e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226879   141 VSWNTMIDGYAQSGRIDKALELFDEMPERNIV 172
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
 
Name Accession Description Interval E-value
PLN03077 PLN03077
Protein ECB2; Provisional
 52-610 7.85e-113

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 358.01  E-value: 7.85e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   52 LIGELCKVGKIAEARKLFDGLPERDVVTWTHVITGYIKLGDMREARELFDR---VDSRKNVVTW---------------- 112
Cdd:PLN03077 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRmlwAGVRPDVYTFpcvlrtcggipdlarg 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  113 -------------------TAMVSGYLRSKQLSIAEMLFQEMPERNVVSWNTMIDGYAQSGRIDKALELFDEMPER---- 169
Cdd:PLN03077 207 revhahvvrfgfeldvdvvNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELsvdp 286

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  170 -----------------------------------NIVSWNSMVKALVQRGRIDEAMNLFERMPRRDVVSWTAMVDGLAK 214
Cdd:PLN03077 287 dlmtitsvisacellgderlgremhgyvvktgfavDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK 366

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  215 NGKVDEARRLFDCMPERNI----ISWNAMITGYAQNNRIDEADQLFQVMPERDFASW----NTMITGFIRNREMNKACGL 286
Cdd:PLN03077 367 NGLPDKALETYALMEQDNVspdeITIASVLSACACLGDLDVGVKLHELAERKGLISYvvvaNALIEMYSKCKCIDKALEV 446

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  287 FDRMPEKNVISWTTMITGYVENKENEEALNVFSKMLrdGSVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVHQKNE 366
Cdd:PLN03077 447 FHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDG 524

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  367 IVTSALLNMYSKSGELIAARKMFDnglVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSH 446
Cdd:PLN03077 525 FLPNALLDLYVRCGRMNYAWNQFN---SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSR 601

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  447 AGLVEKGMEFFKDLVRDESLPLREEHYTCLVDLCGRAGRLKDVTNFINCDDARLSRSFYGAILSACNVHNEVSIAKEVVK 526
Cdd:PLN03077 602 SGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQ 681

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  527 KVLETGSDDAGTYVLMSNIYAANGKREEAAEMRMKMKEKGLKKQPGCSWVKVGKQNHLFVVGDKSHPQFEALDSILSDLR 606
Cdd:PLN03077 682 HIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFY 761


                 ....
gi 15226879  607 NKMR 610
Cdd:PLN03077 762 EKMK 765
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 91-623 1.51e-87

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 287.15  E-value: 1.51e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   91 GDMREARELFDRVDSRK----NVVTWTAMVSGYLRSKQLSIAEMLFQEMP----ERNVVSWNTMIDGYAQSGRIDKALEL 162
Cdd:PLN03081 101 GRHREALELFEILEAGCpftlPASTYDALVEACIALKSIRCVKAVYWHVEssgfEPDQYMMNRVLLMHVKCGMLIDARRL 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  163 FDEMPERNIVSWNSMVKALVQRGRIDEAMNLFERM--------PRRDVVswtaMVDGLAKNGKVDEARRLFDC-----MP 229
Cdd:PLN03081 181 FDEMPERNLASWGTIIGGLVDAGNYREAFALFREMwedgsdaePRTFVV----MLRASAGLGSARAGQQLHCCvlktgVV 256

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  230 ERNIISWnAMITGYAQNNRIDEADQLFqvmperdfaswntmitgfirnremnkacglfDRMPEKNVISWTTMITGYVENK 309
Cdd:PLN03081 257 GDTFVSC-ALIDMYSKCGDIEDARCVF-------------------------------DGMPEKTTVAWNSMLAGYALHG 304

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  310 ENEEALNVFSKMlRDGSVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVHQKNEIVTSALLNMYSKSGELIAARKMF 389
Cdd:PLN03081 305 YSEEALCLYYEM-RDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVF 383

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  390 DNglVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSHAGLVEKGMEFFKDLVRDESLPLR 469
Cdd:PLN03081 384 DR--MPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPR 461

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  470 EEHYTCLVDLCGRAGRLKDVTNFINCDDARLSRSFYGAILSACNVHNEVSIAKEVVKKVLETGSDDAGTYVLMSNIYAAN 549
Cdd:PLN03081 462 AMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSS 541

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  550 GKREEAAEMRMKMKEKGLKKQPGCSWVKVGKQNHLFVVGDKSHPQ----FEALDSILSDLRNK--MRKNKNVTSDAEEAE 623
Cdd:PLN03081 542 GRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQsreiYQKLDELMKEISEYgyVAEENELLPDVDEDE 621
PLN03077 PLN03077
Protein ECB2; Provisional
 211-444 1.50e-28

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 121.50  E-value: 1.50e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  211 GLAKNGKVDEARRLFDCMPERNII----SWNAMITGYAQNNRIDEADQLFQV----MPERDFASWNTMITGFIRNREMNK 282
Cdd:PLN03077  60 ALCSHGQLEQALKLLESMQELRVPvdedAYVALFRLCEWKRAVEEGSRVCSRalssHPSLGVRLGNAMLSMFVRFGELVH 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  283 ACGLFDRMPEKNVISWTTMITGYVENKENEEALNVFSKMLRDGsVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVH 362
Cdd:PLN03077 140 AWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAG-VRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGF 218

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  363 QKNEIVTSALLNMYSKSGELIAARKMFDNglVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLF 442
Cdd:PLN03077 219 ELDVDVVNALITMYVKCGDVVSARLVFDR--MPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVIS 296


                 ..
gi 15226879  443 AC 444
Cdd:PLN03077 297 AC 298
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 147-460 1.11e-17

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 87.24  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   147 IDGYA---QSGRIDKALELFDEMPERNIVSWN-----SMVKALVQRGRIDEAMNLFERMPRRDVVSWTAMVDGLAKNGKV 218
Cdd:PLN03218  374 IDAYNrllRDGRIKDCIDLLEDMEKRGLLDMDkiyhaKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDI 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   219 DEARRLFDCMPERNIIS----WNAMITGYAQNNRIDeadQLFQVMPERDFA-------SWNTMITGFIRNREMNKACGLF 287
Cdd:PLN03218  454 DGALRVLRLVQEAGLKAdcklYTTLISTCAKSGKVD---AMFEVFHEMVNAgveanvhTFGALIDGCARAGQVAKAFGAY 530

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   288 DRMPEKNV----ISWTTMITGYVENKENEEALNVFSKMLRDGS-VKPNVGTYVSILSACSDlAGLVE-GQQIHQLISKSV 361
Cdd:PLN03218  531 GIMRSKNVkpdrVVFNALISACGQSGAVDRAFDVLAEMKAETHpIDPDHITVGALMKACAN-AGQVDrAKEVYQMIHEYN 609

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   362 HQKNEIVTSALLNMYSKSGELIAARKMFDNGLV--CQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLN 439
Cdd:PLN03218  610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKkgVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSS 689

                         330       340
                  ....*....|....*....|.
gi 15226879   440 LLFACSHAGLVEKGMEFFKDL 460
Cdd:PLN03218  690 LMGACSNAKNWKKALELYEDI 710
E_motif pfam20431
E motif; This entry represents the E motif found in plant pentatricopeptide repeat (PPR) ...
 515-577 2.38e-14

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: 67.95  E-value: 2.38e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15226879   515 HNEVSIAKEVVKKVLETGSDDAGTYVLMSNIYAANGKREEAAEMRMKMKEKGLKKQPGCSWVK 577
Cdd:pfam20431   1 YSNVELAEKAANILLELEKTNDGNYTLLSNIYAYAGRWKDVERIRKLMKSSGIKKRPGCSWIE 63
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 167-530 6.52e-13

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 72.22  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   167 PERNIVSWNSMVKALVQRGRIDEAMNLFERMPRRDV-----VSWTAMVDGLAKNGKVDEARRLFDCMPERNIISWNAMIT 241
Cdd:PLN03218  366 GKRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLldmdkIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMS 445

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   242 GYAQNNRIDEAdqlFQVMperdfaswntmitGFIRNREMNKACGLFdrmpeknviswTTMITGYVENKENEEALNVFSKM 321
Cdd:PLN03218  446 VCASSQDIDGA---LRVL-------------RLVQEAGLKADCKLY-----------TTLISTCAKSGKVDAMFEVFHEM 498

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   322 LRDGsVKPNVGTYVSILSACSDlAGlvegqQIHQ-------LISKSVhQKNEIVTSALLNMYSKSGeliAARKMFD---- 390
Cdd:PLN03218  499 VNAG-VEANVHTFGALIDGCAR-AG-----QVAKafgaygiMRSKNV-KPDRVVFNALISACGQSG---AVDRAFDvlae 567

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   391 ---NGLVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSHAGLVEKGMEFFKDLVRDESLP 467
Cdd:PLN03218  568 mkaETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKP 647

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15226879   468 lREEHYTCLVDLCGRAGRLKDVTNFIncDDAR-----LSRSFYGAILSACnvhnevSIAKEvVKKVLE 530
Cdd:PLN03218  648 -DEVFFSALVDVAGHAGDLDKAFEIL--QDARkqgikLGTVSYSSLMGAC------SNAKN-WKKALE 705
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 138-181 7.25e-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: 60.45  E-value: 7.25e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15226879   138 RNVVSWNTMIDGYAQSGRIDKALELFDEMPERNI----VSWNSMVKAL 181
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVkpnvYTYTILINGL 48
PLN03077 PLN03077
Protein ECB2; Provisional
 312-462 2.55e-11

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 66.80  E-value: 2.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  312 EEALNVFSKMlRDGSVKPNVGTYVSILSACSDLAGLVEGQQIHQLISKSVHQKNEIVTSALLNMYSKSGELIAARKMFdn 391
Cdd:PLN03077  68 EQALKLLESM-QELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVF-- 144

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15226879  392 GLVCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSHAGLVEKGMEFFKDLVR 462
Cdd:PLN03077 145 GKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVR 215
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 397-446 2.56e-11

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: 2.56e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226879   397 RDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSAVTYLNLLFACSH 446
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 76-341 4.24e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 66.05  E-value: 4.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879    76 DVVTWTHVITGYIKLGDMREARELFDRVDS---RKNVVTWTAMVSGYLRSKQLSIAEMLFQEMPERNV----VSWNTMID 148
Cdd:PLN03218  471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNagvEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALIS 550

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   149 GYAQSGRIDKALELFDEM--------PERniVSWNSMVKALVQRGRIDEAMNLFERMPRRDVVS----WTAMVDGLAKNG 216
Cdd:PLN03218  551 ACGQSGAVDRAFDVLAEMkaethpidPDH--ITVGALMKACANAGQVDRAKEVYQMIHEYNIKGtpevYTIAVNSCSQKG 628

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   217 KVDEARRLFDCMPERNI----ISWNAMI--TGYAQnnRIDEADQLFQVMPERDF----ASWNTMITGFIRNREMNKACGL 286
Cdd:PLN03218  629 DWDFALSIYDDMKKKGVkpdeVFFSALVdvAGHAG--DLDKAFEILQDARKQGIklgtVSYSSLMGACSNAKNWKKALEL 706

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15226879   287 FDR------MPekNVISWTTMITGYVENKENEEALNVFSKMLRDGsVKPNVGTYVSILSAC 341
Cdd:PLN03218  707 YEDiksiklRP--TVSTMNALITALCEGNQLPKALEVLSEMKRLG-LCPNTITYSILLVAS 764
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
87-226 2.38e-10

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 61.18  E-value: 2.38e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQ---EMPERNVVSWNTMIDGYAQSGRIDKALE 161
Cdd:COG0457  18 YRRLGRYEEAIEDYEKAleLDPDDAEALYNLGLAYLRLGRYEEALADYEqalELDPDDAEALNNLGLALQALGRYEEALE 97

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15226879 162 LFD---EMPERNIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGLAKNGKVDEARRLFD 226
Cdd:COG0457  98 DYDkalELDPDDAEALYNLGLALLELGRYDEAIEAYERaleLDPDDADALYNLGIALEKLGRYEEALELLE 168
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 293-343 3.38e-10

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: 55.45  E-value: 3.38e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15226879   293 KNVISWTTMITGYVENKENEEALNVFSKMLRDGsVKPNVGTYVSILSACSD 343
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRG-VKPNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 169-214 6.02e-10

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: 55.06  E-value: 6.02e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226879   169 RNIVSWNSMVKALVQRGRIDEAMNLFERMPRR----DVVSWTAMVDGLAK 214
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 112-482 6.10e-10

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 62.59  E-value: 6.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   112 WTAMVSGYLRSKQLSIAEMLFQEMP----ERNVVSWNTMIDGYAQSGRIDKALELFDEMPERNI----VSWNSMVKALVQ 183
Cdd:PLN03218  475 YTTLISTCAKSGKVDAMFEVFHEMVnagvEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVkpdrVVFNALISACGQ 554

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   184 RGRIDEAMNLFERMPRR------DVVSWTAMVDGLAKNGKVDEARRLFDCMPERNIISWNAMITgYAQNNRIDEADQLFq 257
Cdd:PLN03218  555 SGAVDRAFDVLAEMKAEthpidpDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYT-IAVNSCSQKGDWDF- 632

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   258 vmperdfaswntmitgfirnremnkACGLFDRMPEKNVISWTTMITGYVE----NKENEEALNVFSKMLRDGsVKPNVGT 333
Cdd:PLN03218  633 -------------------------ALSIYDDMKKKGVKPDEVFFSALVDvaghAGDLDKAFEILQDARKQG-IKLGTVS 686

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879   334 YVSILSACSDLAGLVEGQQIHQlisksvhqknEIVTSALLNMYSKSGELIAArkmfdnglVCQRDLISwnsmiavyahhg 413
Cdd:PLN03218  687 YSSLMGACSNAKNWKKALELYE----------DIKSIKLRPTVSTMNALITA--------LCEGNQLP------------ 736

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15226879   414 hgkEAIEMYNQMRKHGFKPSAVTYLNLLFACSHAGLVEKGMEFFKDLvRDESLPLREEHYTCLVDLCGR 482
Cdd:PLN03218  737 ---KALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQA-KEDGIKPNLVMCRCITGLCLR 801
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 107-152 2.83e-09

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: 53.14  E-value: 2.83e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226879   107 KNVVTWTAMVSGYLRSKQLSIAEMLFQEMPER----NVVSWNTMIDGYAQ 152
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGLCK 50
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 141-171 5.57e-09

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: 51.70  E-value: 5.57e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   141 VSWNTMIDGYAQSGRIDKALELFDEMPERNI 171
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 137-166 6.24e-09

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: 51.58  E-value: 6.24e-09
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226879   137 ERNVVSWNTMIDGYAQSGRIDKALELFDEM 166
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 200-245 1.66e-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: 50.82  E-value: 1.66e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226879   200 RDVVSWTAMVDGLAKNGKVDEARRLFDCMPERNI----ISWNAMITGYAQ 245
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVkpnvYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 231-274 4.79e-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: 49.67  E-value: 4.79e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15226879   231 RNIISWNAMITGYAQNNRIDEADQLFQVMPER----DFASWNTMITGF 274
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 60-257 5.72e-08

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: 54.35  E-value: 5.72e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  60 GKIAEARKLFDGLPERDVVTW-THVITG--YIKLGDMREARELFDRVDSR--KNVVTWTAMVSGYLRSKQLSIAEMLFQ- 133
Cdd:COG2956  22 GQPDKAIDLLEEALELDPETVeAHLALGnlYRRRGEYDRAIRIHQKLLERdpDRAEALLELAQDYLKAGLLDRAEELLEk 101

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 134 --EMPERNVVSWNTMIDGYAQSGRIDKALELFDEMPER---NIVSWNSMVKALVQRGRIDEAMNLFERMPRRD---VVSW 205
Cdd:COG2956 102 llELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLgpeNAHAYCELAELYLEQGDYDEAIEALEKALKLDpdcARAL 181

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15226879 206 TAMVDGLAKNGKVDEARRLFDCMPERN---IISWNAMITGYAQNNRIDEADQLFQ 257
Cdd:COG2956 182 LLLAELYLEQGDYEEAIAALERALEQDpdyLPALPRLAELYEKLGDPEEALELLR 236
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 141-172 9.31e-08

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: 48.22  E-value: 9.31e-08
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226879   141 VSWNTMIDGYAQSGRIDKALELFDEMPERNIV 172
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 75-121 1.57e-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: 48.13  E-value: 1.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15226879    75 RDVVTWTHVITGYIKLGDMREARELFDRVDSRK---NVVTWTAMVSGYLR 121
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGvkpNVYTYTILINGLCK 50
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 266-305 1.96e-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: 47.74  E-value: 1.96e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15226879   266 SWNTMITGFIRNREMNKACGLFDRMPEK----NVISWTTMITGY 305
Cdd:pfam13041   5 TYNTLINGYCKKGKVEEAFKLFNEMKKRgvkpNVYTYTILINGL 48
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
60-196 2.70e-07

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 52.32  E-value: 2.70e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  60 GKIAEARKLFD---GLPERDVVTWTHVITGYIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQ- 133
Cdd:COG0457  22 GRYEEAIEDYEkalELDPDDAEALYNLGLAYLRLGRYEEALADYEQAleLDPDDAEALNNLGLALQALGRYEEALEDYDk 101

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15226879 134 --EMPERNVVSWNTMIDGYAQSGRIDKALELFD---EMPERNIVSWNSMVKALVQRGRIDEAMNLFER 196
Cdd:COG0457 102 alELDPDDAEALYNLGLALLELGRYDEAIEAYEralELDPDDADALYNLGIALEKLGRYEEALELLEK 169
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 150-257 9.43e-07

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: 48.65  E-value: 9.43e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 150 YAQSGRIDKALELFDEMPER---NIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGLAKNGKVDEARR 223
Cdd:COG4783  14 LLLAGDYDEAEALLEKALELdpdNPEAFALLGEILLQLGDLDEAIVLLHEaleLDPDEPEARLNLGLALLKAGDYDEALA 93

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15226879 224 LFD----CMPErNIISWNAMITGYAQNNRIDEADQLFQ 257
Cdd:COG4783  94 LLEkalkLDPE-HPEAYLRLARAYRALGRPDEAIAALE 130
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 400-434 1.25e-06

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: 45.14  E-value: 1.25e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15226879   400 ISWNSMIAVYAHHGHGKEAIEMYNQMRKHGFKPSA 434
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
139-257 1.92e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 49.62  E-value: 1.92e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 139 NVVSWNTMIDGYAQSGRIDKALELFD---EMPERNIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGL 212
Cdd:COG0457   7 DAEAYNNLGLAYRRLGRYEEAIEDYEkalELDPDDAEALYNLGLAYLRLGRYEEALADYEQaleLDPDDAEALNNLGLAL 86

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 15226879 213 AKNGKVDEARRLFDC---MPERNIISWNAMITGYAQNNRIDEADQLFQ 257
Cdd:COG0457  87 QALGRYEEALEDYDKaleLDPDDAEALYNLGLALLELGRYDEAIEAYE 134
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 150-388 2.11e-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: 49.73  E-value: 2.11e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 150 YAQSGRIDKALELFDEM----PErNIVSWNSMVKALVQRGRIDEAMNLFERMPRRDVVSWTAMVdGLA----KNGKVDEA 221
Cdd:COG2956  18 YLLNGQPDKAIDLLEEAleldPE-TVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDRAEALL-ELAqdylKAGLLDRA 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 222 RRLFDC---MPERNIISWNAMITGYAQNNRIDEA----DQLFQVMPERDFAsWNTMITGFIRNREMNKACGLFDRMPE-- 292
Cdd:COG2956  96 EELLEKlleLDPDDAEALRLLAEIYEQEGDWEKAievlERLLKLGPENAHA-YCELAELYLEQGDYDEAIEALEKALKld 174

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 293 -KNVISWTTMITGYVENKENEEALNVFSKMLRDgsvKPNVGTYVSILSACSDLAGLVEgQQIHQLISKSVHQKNEIVTSA 371
Cdd:COG2956 175 pDCARALLLLAELYLEQGDYEEAIAALERALEQ---DPDYLPALPRLAELYEKLGDPE-EALELLRKALELDPSDDLLLA 250

                       250
                ....*....|....*..
gi 15226879 372 LLNMYSKSGELIAARKM 388
Cdd:COG2956 251 LADLLERKEGLEAALAL 267
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 201-228 2.33e-06

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: 44.26  E-value: 2.33e-06
                          10        20
                  ....*....|....*....|....*...
gi 15226879   201 DVVSWTAMVDGLAKNGKVDEARRLFDCM 228
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 ...
 203-233 2.60e-06

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: 43.99  E-value: 2.60e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   203 VSWTAMVDGLAKNGKVDEARRLFDCMPERNI 233
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
150-226 6.39e-06

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 44.78  E-value: 6.39e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 150 YAQSGRIDKALELFDE----MPErNIVSWNSMVKALVQRGRIDEAMNLFE--RMPRRDVVSWTAMVDGLAKNGKVDEARR 223
Cdd:COG3063   2 YLKLGDLEEAEEYYEKalelDPD-NADALNNLGLLLLEQGRYDEAIALEKalKLDPNNAEALLNLAELLLELGDYDEALA 80


                ...
gi 15226879 224 LFD 226
Cdd:COG3063  81 YLE 83
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 400-430 6.74e-06

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: 42.84  E-value: 6.74e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   400 ISWNSMIAVYAHHGHGKEAIEMYNQMRKHGF 430
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 119-225 8.19e-06

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: 45.95  E-value: 8.19e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 119 YLRSKQLSIAEMLFQEMPER---NVVSWNTMIDGYAQSGRIDKALELFDEM----PErNIVSWNSMVKALVQRGRIDEAM 191
Cdd:COG4783  14 LLLAGDYDEAEALLEKALELdpdNPEAFALLGEILLQLGDLDEAIVLLHEAleldPD-EPEARLNLGLALLKAGDYDEAL 92

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15226879 192 NLFER---MPRRDVVSWTAMVDGLAKNGKVDEARRLF 225
Cdd:COG4783  93 ALLEKalkLDPEHPEAYLRLARAYRALGRPDEAIAAL 129
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 172-202 9.41e-06

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: 42.45  E-value: 9.41e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   172 VSWNSMVKALVQRGRIDEAMNLFERMPRRDV 202
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 87-201 2.80e-05

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: 44.41  E-value: 2.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQEM----PErNVVSWNTMIDGYAQSGRIDKAL 160
Cdd:COG4783  14 LLLAGDYDEAEALLEKAleLDPDNPEAFALLGEILLQLGDLDEAIVLLHEAleldPD-EPEARLNLGLALLKAGDYDEAL 92

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 15226879 161 ELFD---EMPERNIVSWNSMVKALVQRGRIDEAMNLFERMPRRD 201
Cdd:COG4783  93 ALLEkalKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 150-226 2.88e-05

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 44.57  E-value: 2.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 150 YAQSGRIDKALELFDEMPE---RNIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGLAKNGKVDEARR 223
Cdd:COG5010  64 YNKLGDFEESLALLEQALQldpNNPELYYNLALLYSRSGDKDEAKEYYEKalaLSPDNPNAYSNLAALLLSLGQDDEAKA 143


                ...
gi 15226879 224 LFD 226
Cdd:COG5010 144 ALQ 146
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 172-203 4.02e-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: 40.90  E-value: 4.02e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226879   172 VSWNSMVKALVQRGRIDEAMNLFERMPRRDVV 203
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 87-201 5.01e-05

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: 45.49  E-value: 5.01e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQEMPERN---VVSWNTMIDGYAQSGRIDKALE 161
Cdd:COG2956 154 YLEQGDYDEAIEALEKAlkLDPDCARALLLLAELYLEQGDYEEAIAALERALEQDpdyLPALPRLAELYEKLGDPEEALE 233

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15226879 162 LFDEMPERN--IVSWNSMVKALVQRGRIDEAMNLFERMPRRD 201
Cdd:COG2956 234 LLRKALELDpsDDLLLALADLLERKEGLEAALALLERQLRRH 275
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 234-264 5.78e-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: 40.14  E-value: 5.78e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   234 ISWNAMITGYAQNNRIDEADQLFQVMPERDF 264
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 292-343 6.70e-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: 41.19  E-value: 6.70e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15226879   292 EKNVISWTTMITGYVENKENEEALNVFSKMLRDGsVKPNVGTYVSILSACSD 343
Cdd:pfam13812  12 QLNVNTYTHLLHAYANVGNLKLALEIFERMKKKG-IKPTLDTYNAILGVIGG 62
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 168-197 1.38e-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: 39.25  E-value: 1.38e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226879   168 ERNIVSWNSMVKALVQRGRIDEAMNLFERM 197
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDEM 33
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 296-325 1.91e-04

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: 38.99  E-value: 1.91e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226879   296 ISWTTMITGYVENKENEEALNVFSKMLRDG 325
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKG 30
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 266-295 1.99e-04

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: 38.99  E-value: 1.99e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226879   266 SWNTMITGFIRNREMNKACGLFDRMPEKNV 295
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 ...
 110-140 3.22e-04

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: 38.22  E-value: 3.22e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   110 VTWTAMVSGYLRSKQLSIAEMLFQEMPERNV 140
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 234-264 4.13e-04

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: 37.82  E-value: 4.13e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   234 ISWNAMITGYAQNNRIDEADQLFQVMPERDF 264
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 266-295 6.36e-04

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: 37.43  E-value: 6.36e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 15226879   266 SWNTMITGFIRNREMNKACGLFDRMPEKNV 295
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGI 31
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 305-557 6.41e-04

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 42.02  E-value: 6.41e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 305 YVENKENEEALNVFSKMLRdgsVKPNvgtYVSILSAcsdLAGLVEGQ-------QIHQ-LISKSvhQKNEIVTSALLNMY 376
Cdd:COG2956  18 YLLNGQPDKAIDLLEEALE---LDPE---TVEAHLA---LGNLYRRRgeydraiRIHQkLLERD--PDRAEALLELAQDY 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 377 SKSGELIAARKMFDNGL-VCQRDLISWNSMIAVYAHHGHGKEAIEMYNQMRKHGfKPSAVTYLNLLFACSHAGLVEKGME 455
Cdd:COG2956  87 LKAGLLDRAEELLEKLLeLDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG-PENAHAYCELAELYLEQGDYDEAIE 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 456 FFKDLVRDESlplreehytclvdlcgragrlkdvtnfiNCDDARLSRsfyGAILSACNVHNEvsiAKEVVKKVLETGSDD 535
Cdd:COG2956 166 ALEKALKLDP----------------------------DCARALLLL---AELYLEQGDYEE---AIAALERALEQDPDY 211

                       250       260
                ....*....|....*....|..
gi 15226879 536 AGTYVLMSNIYAANGKREEAAE 557
Cdd:COG2956 212 LPALPRLAELYEKLGDPEEALE 233
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 203-233 1.21e-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: 36.66  E-value: 1.21e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15226879   203 VSWTAMVDGLAKNGKVDEARRLFDCMPERNI 233
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGI 31
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 225-259 1.44e-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: 1.44e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15226879   225 FDCMPerNIISWNAMITGYAQNNRIDEADQLFQVM 259
Cdd:pfam12854   1 KGLKP--DVVTYNTLINGLCRAGRVDEAFELLDEM 33
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
94-255 1.49e-03

Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 40.64  E-value: 1.49e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  94 REARELFDRVDSRKNVVTWTAMVSGYLRSKQLSIAEMLFQE-----MPERNVVSWNtMIDGYAQSGRIDKALELFDEMPE 168
Cdd:COG4700  74 RELRELEKALEFADTVQNRVRLADALLELGRYDEAIELYEEaltgiFADDPHILLG-LAQALFELGRYAEALETLEKLIA 152

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 169 RNIVSWNSMV-----KALVQRGRIDEAMNLFERMPRR----DVVSWTAMVdgLAKNGKVDEARRLFDCMpernIISWNAM 239
Cdd:COG4700 153 KNPDFKSSDAhllyaRALEALGDLEAAEAELEALARRysgpEARYRYAKF--LARQGRTAEAKELLEEI----LDEAKHM 226

                       170
                ....*....|....*...
gi 15226879 240 ITGYAQNNR--IDEADQL 255
Cdd:COG4700 227 PKHYRRLNRewIREAKKL 244
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
374-557 1.71e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 40.38  E-value: 1.71e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 374 NMYSKSGELIAARKMFDNGLVCQRDL-ISWNSMIAVYAHHGHGKEAIEMYNQMRKhgFKP-SAVTYLNLLFACSHAGLVE 451
Cdd:COG0457  16 LAYRRLGRYEEAIEDYEKALELDPDDaEALYNLGLAYLRLGRYEEALADYEQALE--LDPdDAEALNNLGLALQALGRYE 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 452 KGMEFFkdlvrDESLPLREEHYTCLVDL---CGRAGRLKDvtnfincddarlsrsfygailsacnvhnevsiAKEVVKKV 528
Cdd:COG0457  94 EALEDY-----DKALELDPDDAEALYNLglaLLELGRYDE--------------------------------AIEAYERA 136

                       170       180
                ....*....|....*....|....*....
gi 15226879 529 LETGSDDAGTYVLMSNIYAANGKREEAAE 557
Cdd:COG0457 137 LELDPDDADALYNLGIALEKLGRYEEALE 165
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 78-102 2.02e-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: 35.90  E-value: 2.02e-03
                          10        20
                  ....*....|....*....|....*
gi 15226879    78 VTWTHVITGYIKLGDMREARELFDR 102
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKE 25
TPR_19 pfam14559
Tetratricopeptide repeat;
153-201 2.41e-03

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 36.79  E-value: 2.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15226879   153 SGRIDKALELFDEMPER---NIVSWNSMVKALVQRGRIDEAMNLFERMPRRD 201
Cdd:pfam14559   1 EGDYAEALELLEQALAEdpdNAEARLGLAEALLALGRLDEAEALLAALPAAD 52
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 119-201 2.67e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.79  E-value: 2.67e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 119 YLRSKQLSIAEMLFQEMPE---RNVVSWNTMIDGYAQSGRIDKALELFD---EMPERNIVSWNSMVKALVQRGRIDEAMN 192
Cdd:COG5010  64 YNKLGDFEESLALLEQALQldpNNPELYYNLALLYSRSGDKDEAKEYYEkalALSPDNPNAYSNLAALLLSLGQDDEAKA 143


                ....*....
gi 15226879 193 LFERMPRRD 201
Cdd:COG5010 144 ALQRALGTS 152
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 110-141 2.90e-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: 2.90e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 15226879   110 VTWTAMVSGYLRSKQLSIAEMLFQEMPERNVV 141
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
87-166 3.60e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 37.07  E-value: 3.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRVDSR--KNVVTWTAMVSGYLRSKQLSIAEMLFQ--EMPERNVVSWNTMIDGYAQSGRIDKALEL 162
Cdd:COG3063   2 YLKLGDLEEAEEYYEKALELdpDNADALNNLGLLLLEQGRYDEAIALEKalKLDPNNAEALLNLAELLLELGDYDEALAY 81


                ....
gi 15226879 163 FDEM 166
Cdd:COG3063  82 LERA 85
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 87-166 3.92e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 38.06  E-value: 3.92e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879  87 YIKLGDMREARELFDRV--DSRKNVVTWTAMVSGYLRSKQLSIAEMLFQEM----PErNVVSWNTMIDGYAQSGRIDKAL 160
Cdd:COG4235  27 YLRLGRYDEALAAYEKAlrLDPDNADALLDLAEALLAAGDTEEAEELLERAlaldPD-NPEALYLLGLAAFQQGDYAEAI 105


                ....*.
gi 15226879 161 ELFDEM 166
Cdd:COG4235 106 AAWQKL 111
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 131-184 4.21e-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: 36.18  E-value: 4.21e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15226879   131 LFQEMPER----NVVSWNTMIDGYAQSGRIDKALELFDEMPER----NIVSWNSMVKALVQR 184
Cdd:pfam13812   2 ILREMVRDgiqlNVNTYTHLLHAYANVGNLKLALEIFERMKKKgikpTLDTYNAILGVIGGR 63
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
170-320 4.28e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 39.22  E-value: 4.28e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 170 NIVSWNSMVKALVQRGRIDEAMNLFER---MPRRDVVSWTAMVDGLAKNGKVDEARRLFDC---MPERNIISWNAMITGY 243
Cdd:COG0457   7 DAEAYNNLGLAYRRLGRYEEAIEDYEKaleLDPDDAEALYNLGLAYLRLGRYEEALADYEQaleLDPDDAEALNNLGLAL 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 244 AQNNRIDEADQLFQ----VMPErDFASWNTMITGFIRNREMNKACGLFDR---MPEKNVISWTTMITGYVENKENEEALN 316
Cdd:COG0457  87 QALGRYEEALEDYDkaleLDPD-DAEALYNLGLALLELGRYDEAIEAYERaleLDPDDADALYNLGIALEKLGRYEEALE 165


                ....
gi 15226879 317 VFSK 320
Cdd:COG0457 166 LLEK 169
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 74-102 4.54e-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: 4.54e-03
                          10        20
                  ....*....|....*....|....*....
gi 15226879    74 ERDVVTWTHVITGYIKLGDMREARELFDR 102
Cdd:pfam12854   4 KPDVVTYNTLINGLCRAGRVDEAFELLDE 32
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 296-331 6.62e-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: 6.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 15226879   296 ISWTTMITGYVENKENEEALNVFSKMLRDGsVKPNV 331
Cdd:TIGR00756   1 VTYNTLIDGLCKAGRVEEALELFKEMKERG-IEPDV 35
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
119-197 7.93e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 36.30  E-value: 7.93e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226879 119 YLRSKQLSIAEMLFQE----MPErNVVSWNTMIDGYAQSGRIDKALELFD--EMPERNIVSWNSMVKALVQRGRIDEAMN 192
Cdd:COG3063   2 YLKLGDLEEAEEYYEKalelDPD-NADALNNLGLLLLEQGRYDEAIALEKalKLDPNNAEALLNLAELLLELGDYDEALA 80


                ....*
gi 15226879 193 LFERM 197
Cdd:COG3063  81 YLERA 85
 
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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