NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|30802081|gb|AAH51278|]
View 

APOB protein [Homo sapiens]

Protein Classification

Vitellogenin_N and DUF1943 domain-containing protein (domain architecture ID 12016796)

Vitellogenin_N and DUF1943 domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
Vitellogenin_N pfam01347
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
43-594 1.10e-133

Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.


:

Pssm-ID: 279663  Cd Length: 582  Bit Score: 413.98  E-value: 1.10e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    43 FKHLRKYTYNYEAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCILKEVYGFNPEgKALLKKTKNSEEFAAA 122
Cdd:pfam01347   1 FQPGKTYTYKYEGRTLSGLPEVGLQYSGLKISAKVEISAKSDNTLVLKLSNPELAEYNGQLPK-DPFLPAEKLTYELAPQ 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   123 MSRyELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLF---LDTVYGNCSTHFTVKTRKGNVATE 199
Cdd:pfam01347  80 LSK-PFKFEYSNGRVGELYVPKDVPTWSLNIKRGILSQLQVDLKGKEKTQGVYklqETTVTGDCETLYTVSEDKEGDLII 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   200 ISTERDLGQCDRFKPIRTGIsPLALIKGMTRPLSTLISSSQSCQYTLDAKRKH--VAEAICKEQHLFLPFSYKNKYGMVa 277
Cdd:pfam01347 159 VTKTKNFNNCQERVSYRYGL-AYAEWCPGCNQMGKFLSRSSVSTYILKGKLKGflIQSAETTEKVLVSPFLENSQKAEV- 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   278 QVTQTLKLEDTPKINSRFFGEG--TKKMGLAFESTK---------------STSPPKQAEAVLKTLQELKKLTISEQNIQ 340
Cdd:pfam01347 237 ESRQNLTLEEVEKTPGLIPPPAnpRHRGSLVYEYETeqaslsqellqspssLSSVPNAVELIKEILKHLVQNPSNMVKED 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   341 RANLFNKLVTELRGLSDEAVTSLLPQLIEVSS-----PITLQALVQCGQPQCSTHILQWLKRVHANPLLIDVVTYLVALI 415
Cdd:pfam01347 317 ALAKFLILVRLLRTASEEQLEQIWRQLYAGKPkyrrwPAFLDAVAQAGTPPALKFIKQWIKSKKITGLEAAQVLAVLPHT 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   416 PEPSAQQLREIFNMARDQRSR-------ATLYALSHAVNNYHKTNPTGTQELLDIANYLMEQIQDDCT-GDEDYTYLILR 487
Cdd:pfam01347 397 RYPTEEYMKALFELAESPEVKnqpylntSALLAYGSLVNKYCVNNPSCPREFEEYLPPLAQKLKEAVEkGDSEKIQLYLK 476
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   488 VIGNMGQtmeqltPELKSSILKCV-QSTKPSLMIQKAAIQALRKMEPKDKD--QEVLLQTFLDDASPGDKRLAAYLMLMR 564
Cdd:pfam01347 477 ALGNAGH------PESLKVLEKYLeGAEELSTFVRVAAVQALRNLAKKCPRkvQEVLLQIYLNTAEPPEVRMAAVLVLME 550
                         570       580       590
                  ....*....|....*....|....*....|.
gi 30802081   565 S-PSQADINKIVQILPWEQNEQVKNFVASHI 594
Cdd:pfam01347 551 TnPSAALLQRIAESTNKEPNLQVASFVYSHI 581
DUF1943 super family cl11721
Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of ...
629-814 5.87e-36

Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined.


The actual alignment was detected with superfamily member pfam09172:

Pssm-ID: 312626  Cd Length: 293  Bit Score: 139.32  E-value: 5.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   629 KFSRNYQLYKSVSLpslDPASAKIEGNLIFDPNNYLPKESMLKTTLTAFGFaSADLIEIGLEGKGFEPTLEALFGKQGFF 708
Cdd:pfam09172   1 KYSRNYELSYFSDE---LNLGAALEFNLIFSPDSYLPRSAMLNLTLYLFGW-SVNLLEVGFRVEGLEPLLEKLFGPKGFF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   709 PDSvnkalywvngqvpdgVSKVLVDHFGYTKDDKHEQDmvngimlSVEKLIKDLKSK----EVPEARAYLRILGEELGFA 784
Cdd:pfam09172  77 PDK---------------LSEKLKESSGLRRKRRASKG-------KLEKIAKLLKIWkeepEQPEASLYLKLFGNELAFL 134
                         170       180       190
                  ....*....|....*....|....*....|
gi 30802081   785 SLHDLQLLGKLLLMDRPDSLTIPAAQARKD 814
Cdd:pfam09172 135 SFDDQTQELLELILDFLREGPLNLKKLLKK 164
 
Name Accession Description Interval E-value
Vitellogenin_N pfam01347
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
43-594 1.10e-133

Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.


Pssm-ID: 279663  Cd Length: 582  Bit Score: 413.98  E-value: 1.10e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    43 FKHLRKYTYNYEAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCILKEVYGFNPEgKALLKKTKNSEEFAAA 122
Cdd:pfam01347   1 FQPGKTYTYKYEGRTLSGLPEVGLQYSGLKISAKVEISAKSDNTLVLKLSNPELAEYNGQLPK-DPFLPAEKLTYELAPQ 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   123 MSRyELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLF---LDTVYGNCSTHFTVKTRKGNVATE 199
Cdd:pfam01347  80 LSK-PFKFEYSNGRVGELYVPKDVPTWSLNIKRGILSQLQVDLKGKEKTQGVYklqETTVTGDCETLYTVSEDKEGDLII 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   200 ISTERDLGQCDRFKPIRTGIsPLALIKGMTRPLSTLISSSQSCQYTLDAKRKH--VAEAICKEQHLFLPFSYKNKYGMVa 277
Cdd:pfam01347 159 VTKTKNFNNCQERVSYRYGL-AYAEWCPGCNQMGKFLSRSSVSTYILKGKLKGflIQSAETTEKVLVSPFLENSQKAEV- 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   278 QVTQTLKLEDTPKINSRFFGEG--TKKMGLAFESTK---------------STSPPKQAEAVLKTLQELKKLTISEQNIQ 340
Cdd:pfam01347 237 ESRQNLTLEEVEKTPGLIPPPAnpRHRGSLVYEYETeqaslsqellqspssLSSVPNAVELIKEILKHLVQNPSNMVKED 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   341 RANLFNKLVTELRGLSDEAVTSLLPQLIEVSS-----PITLQALVQCGQPQCSTHILQWLKRVHANPLLIDVVTYLVALI 415
Cdd:pfam01347 317 ALAKFLILVRLLRTASEEQLEQIWRQLYAGKPkyrrwPAFLDAVAQAGTPPALKFIKQWIKSKKITGLEAAQVLAVLPHT 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   416 PEPSAQQLREIFNMARDQRSR-------ATLYALSHAVNNYHKTNPTGTQELLDIANYLMEQIQDDCT-GDEDYTYLILR 487
Cdd:pfam01347 397 RYPTEEYMKALFELAESPEVKnqpylntSALLAYGSLVNKYCVNNPSCPREFEEYLPPLAQKLKEAVEkGDSEKIQLYLK 476
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   488 VIGNMGQtmeqltPELKSSILKCV-QSTKPSLMIQKAAIQALRKMEPKDKD--QEVLLQTFLDDASPGDKRLAAYLMLMR 564
Cdd:pfam01347 477 ALGNAGH------PESLKVLEKYLeGAEELSTFVRVAAVQALRNLAKKCPRkvQEVLLQIYLNTAEPPEVRMAAVLVLME 550
                         570       580       590
                  ....*....|....*....|....*....|.
gi 30802081   565 S-PSQADINKIVQILPWEQNEQVKNFVASHI 594
Cdd:pfam01347 551 TnPSAALLQRIAESTNKEPNLQVASFVYSHI 581
LPD_N smart00638
Lipoprotein N-terminal Domain;
43-594 9.43e-121

Lipoprotein N-terminal Domain;


Pssm-ID: 214755  Cd Length: 574  Bit Score: 380.15  E-value: 9.43e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081     43 FKHLRKYTYNYEAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCILKEVYGFNPegKALLKKTKNSEEFAAA 122
Cdd:smart00638   1 FQPGKTYVYKYEGRTLSGLPEVGSQYSGLKIRAKVEIQAVSPNTLVLKLSDPKLAEYNGIWP--KEPFEPKLKLKELLLE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    123 MSRYELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLFLDTVYGNCSTHFTVKTRKGNVAT-EIS 201
Cdd:smart00638  79 QLPFPIRFEYNGGVVGEICVPEDDPTWSLNIKKGILSLLQVDLKKSQNVYKLQETDVTGDCETLYTVSELPKAELQiQVT 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    202 TERDLGQCDRFKPIRTGISPLALIKGMTRPLSTLISSSQSCQYTLDAK--RKHVAEAICKEQHLFLPFSYKNKYGMVAQV 279
Cdd:smart00638 159 KTKNLNNCQQREAYHFGLAAYAEKCPECTNRMGNLKSTSSVNYIIKNGklGVLIIEAVVTEEKVVVSPNIYNGQKAIVES 238
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    280 TQTLKLEDTPKIN-SRFFGEGTKKMGLAFEST--------KSTSPPKQAEAVLKTLQELKKLTISEQNIQRANLFNKLVT 350
Cdd:smart00638 239 RQKLTLKSVKKTPsSPPPGEPRNRGSLVYEFEstnqqlpiRLLKAPSNEVQIVEVLKHLVQDIASDVQEPAAAKFLRLVR 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    351 ELRGLSDEAVTSLLPQLIEVSS---PITLQALVQCGQPQCSTHILQWLK-RVHANPLLIDVVTYLVALIPEPSAQQLREI 426
Cdd:smart00638 319 LLRTLSEEQLEQLWRQLYEKKKkarRIFLDAVAQAGTPPALKFIKQWIKnKKITPLEAAQLLAVLPHTARYPTEEILKAL 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    427 FNMARDQRSRATLYALSHAVNNYHKTNPTGTQELL--------DIANYLMEQIQDD-CTGDEDYTYLILRVIGNMGQTME 497
Cdd:smart00638 399 FELAESPEVQKQPYLRESALLAYGSLVRRYCVNTPscpdfvleELLKYLHELLQQAvSKGDEEEIQLYLKALGNAGHPSS 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    498 QLTPELKSsilkcVQSTKPSLMIQKAAIQALRKMEPKD--KDQEVLLQTFLDDASPGDKRLAAYLMLMRS-PSQADINKI 574
Cdd:smart00638 479 IKVLEPYL-----EGAEPLSTFIRLAAILALRNLAKRDprKVQEVLLPIYLNRAEPPEVRMAAVLVLMETkPSVALLQRI 553
                          570       580
                   ....*....|....*....|
gi 30802081    575 VQILPWEQNEQVKNFVASHI 594
Cdd:smart00638 554 AELLNKEPNLQVASFVYSHI 573
DUF1943 pfam09172
Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of ...
629-814 5.87e-36

Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined.


Pssm-ID: 312626  Cd Length: 293  Bit Score: 139.32  E-value: 5.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   629 KFSRNYQLYKSVSLpslDPASAKIEGNLIFDPNNYLPKESMLKTTLTAFGFaSADLIEIGLEGKGFEPTLEALFGKQGFF 708
Cdd:pfam09172   1 KYSRNYELSYFSDE---LNLGAALEFNLIFSPDSYLPRSAMLNLTLYLFGW-SVNLLEVGFRVEGLEPLLEKLFGPKGFF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   709 PDSvnkalywvngqvpdgVSKVLVDHFGYTKDDKHEQDmvngimlSVEKLIKDLKSK----EVPEARAYLRILGEELGFA 784
Cdd:pfam09172  77 PDK---------------LSEKLKESSGLRRKRRASKG-------KLEKIAKLLKIWkeepEQPEASLYLKLFGNELAFL 134
                         170       180       190
                  ....*....|....*....|....*....|
gi 30802081   785 SLHDLQLLGKLLLMDRPDSLTIPAAQARKD 814
Cdd:pfam09172 135 SFDDQTQELLELILDFLREGPLNLKKLLKK 164
RsmE COG1385
16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis];
594-709 7.03e-03

16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis];


Pssm-ID: 224303  Cd Length: 246  Bit Score: 38.79  E-value: 7.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081 594 IANILNSEELDIQDLKKLVKEALKESQ---LPTVMDFRKFSRnyqlyksvSLPSLDPASAKIegnLIFDPNNylpKESML 670
Cdd:COG1385 116 VVKLDGKKAAKLERWQKIAIEAAEQSGrnvVPEIKPPESLKE--------LLKEIDDEDALK---LIYEEKA---KEGLL 181
                        90       100       110
                ....*....|....*....|....*....|....*....
gi 30802081 671 KTTLTAFGFASADLIEIGLEGkGFEPTLEALFGKQGFFP 709
Cdd:COG1385 182 ALPLLEALPEGKVLLIIGPEG-GFSEDEIELLREAGFTP 219
 
Name Accession Description Interval E-value
Vitellogenin_N pfam01347
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
43-594 1.10e-133

Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.


Pssm-ID: 279663  Cd Length: 582  Bit Score: 413.98  E-value: 1.10e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    43 FKHLRKYTYNYEAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCILKEVYGFNPEgKALLKKTKNSEEFAAA 122
Cdd:pfam01347   1 FQPGKTYTYKYEGRTLSGLPEVGLQYSGLKISAKVEISAKSDNTLVLKLSNPELAEYNGQLPK-DPFLPAEKLTYELAPQ 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   123 MSRyELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLF---LDTVYGNCSTHFTVKTRKGNVATE 199
Cdd:pfam01347  80 LSK-PFKFEYSNGRVGELYVPKDVPTWSLNIKRGILSQLQVDLKGKEKTQGVYklqETTVTGDCETLYTVSEDKEGDLII 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   200 ISTERDLGQCDRFKPIRTGIsPLALIKGMTRPLSTLISSSQSCQYTLDAKRKH--VAEAICKEQHLFLPFSYKNKYGMVa 277
Cdd:pfam01347 159 VTKTKNFNNCQERVSYRYGL-AYAEWCPGCNQMGKFLSRSSVSTYILKGKLKGflIQSAETTEKVLVSPFLENSQKAEV- 236
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   278 QVTQTLKLEDTPKINSRFFGEG--TKKMGLAFESTK---------------STSPPKQAEAVLKTLQELKKLTISEQNIQ 340
Cdd:pfam01347 237 ESRQNLTLEEVEKTPGLIPPPAnpRHRGSLVYEYETeqaslsqellqspssLSSVPNAVELIKEILKHLVQNPSNMVKED 316
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   341 RANLFNKLVTELRGLSDEAVTSLLPQLIEVSS-----PITLQALVQCGQPQCSTHILQWLKRVHANPLLIDVVTYLVALI 415
Cdd:pfam01347 317 ALAKFLILVRLLRTASEEQLEQIWRQLYAGKPkyrrwPAFLDAVAQAGTPPALKFIKQWIKSKKITGLEAAQVLAVLPHT 396
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   416 PEPSAQQLREIFNMARDQRSR-------ATLYALSHAVNNYHKTNPTGTQELLDIANYLMEQIQDDCT-GDEDYTYLILR 487
Cdd:pfam01347 397 RYPTEEYMKALFELAESPEVKnqpylntSALLAYGSLVNKYCVNNPSCPREFEEYLPPLAQKLKEAVEkGDSEKIQLYLK 476
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   488 VIGNMGQtmeqltPELKSSILKCV-QSTKPSLMIQKAAIQALRKMEPKDKD--QEVLLQTFLDDASPGDKRLAAYLMLMR 564
Cdd:pfam01347 477 ALGNAGH------PESLKVLEKYLeGAEELSTFVRVAAVQALRNLAKKCPRkvQEVLLQIYLNTAEPPEVRMAAVLVLME 550
                         570       580       590
                  ....*....|....*....|....*....|.
gi 30802081   565 S-PSQADINKIVQILPWEQNEQVKNFVASHI 594
Cdd:pfam01347 551 TnPSAALLQRIAESTNKEPNLQVASFVYSHI 581
LPD_N smart00638
Lipoprotein N-terminal Domain;
43-594 9.43e-121

Lipoprotein N-terminal Domain;


Pssm-ID: 214755  Cd Length: 574  Bit Score: 380.15  E-value: 9.43e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081     43 FKHLRKYTYNYEAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCILKEVYGFNPegKALLKKTKNSEEFAAA 122
Cdd:smart00638   1 FQPGKTYVYKYEGRTLSGLPEVGSQYSGLKIRAKVEIQAVSPNTLVLKLSDPKLAEYNGIWP--KEPFEPKLKLKELLLE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    123 MSRYELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLFLDTVYGNCSTHFTVKTRKGNVAT-EIS 201
Cdd:smart00638  79 QLPFPIRFEYNGGVVGEICVPEDDPTWSLNIKKGILSLLQVDLKKSQNVYKLQETDVTGDCETLYTVSELPKAELQiQVT 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    202 TERDLGQCDRFKPIRTGISPLALIKGMTRPLSTLISSSQSCQYTLDAK--RKHVAEAICKEQHLFLPFSYKNKYGMVAQV 279
Cdd:smart00638 159 KTKNLNNCQQREAYHFGLAAYAEKCPECTNRMGNLKSTSSVNYIIKNGklGVLIIEAVVTEEKVVVSPNIYNGQKAIVES 238
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    280 TQTLKLEDTPKIN-SRFFGEGTKKMGLAFEST--------KSTSPPKQAEAVLKTLQELKKLTISEQNIQRANLFNKLVT 350
Cdd:smart00638 239 RQKLTLKSVKKTPsSPPPGEPRNRGSLVYEFEstnqqlpiRLLKAPSNEVQIVEVLKHLVQDIASDVQEPAAAKFLRLVR 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    351 ELRGLSDEAVTSLLPQLIEVSS---PITLQALVQCGQPQCSTHILQWLK-RVHANPLLIDVVTYLVALIPEPSAQQLREI 426
Cdd:smart00638 319 LLRTLSEEQLEQLWRQLYEKKKkarRIFLDAVAQAGTPPALKFIKQWIKnKKITPLEAAQLLAVLPHTARYPTEEILKAL 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    427 FNMARDQRSRATLYALSHAVNNYHKTNPTGTQELL--------DIANYLMEQIQDD-CTGDEDYTYLILRVIGNMGQTME 497
Cdd:smart00638 399 FELAESPEVQKQPYLRESALLAYGSLVRRYCVNTPscpdfvleELLKYLHELLQQAvSKGDEEEIQLYLKALGNAGHPSS 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081    498 QLTPELKSsilkcVQSTKPSLMIQKAAIQALRKMEPKD--KDQEVLLQTFLDDASPGDKRLAAYLMLMRS-PSQADINKI 574
Cdd:smart00638 479 IKVLEPYL-----EGAEPLSTFIRLAAILALRNLAKRDprKVQEVLLPIYLNRAEPPEVRMAAVLVLMETkPSVALLQRI 553
                          570       580
                   ....*....|....*....|
gi 30802081    575 VQILPWEQNEQVKNFVASHI 594
Cdd:smart00638 554 AELLNKEPNLQVASFVYSHI 573
DUF1943 pfam09172
Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of ...
629-814 5.87e-36

Domain of unknown function (DUF1943); Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined.


Pssm-ID: 312626  Cd Length: 293  Bit Score: 139.32  E-value: 5.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   629 KFSRNYQLYKSVSLpslDPASAKIEGNLIFDPNNYLPKESMLKTTLTAFGFaSADLIEIGLEGKGFEPTLEALFGKQGFF 708
Cdd:pfam09172   1 KYSRNYELSYFSDE---LNLGAALEFNLIFSPDSYLPRSAMLNLTLYLFGW-SVNLLEVGFRVEGLEPLLEKLFGPKGFF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081   709 PDSvnkalywvngqvpdgVSKVLVDHFGYTKDDKHEQDmvngimlSVEKLIKDLKSK----EVPEARAYLRILGEELGFA 784
Cdd:pfam09172  77 PDK---------------LSEKLKESSGLRRKRRASKG-------KLEKIAKLLKIWkeepEQPEASLYLKLFGNELAFL 134
                         170       180       190
                  ....*....|....*....|....*....|
gi 30802081   785 SLHDLQLLGKLLLMDRPDSLTIPAAQARKD 814
Cdd:pfam09172 135 SFDDQTQELLELILDFLREGPLNLKKLLKK 164
RsmE COG1385
16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis];
594-709 7.03e-03

16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis];


Pssm-ID: 224303  Cd Length: 246  Bit Score: 38.79  E-value: 7.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30802081 594 IANILNSEELDIQDLKKLVKEALKESQ---LPTVMDFRKFSRnyqlyksvSLPSLDPASAKIegnLIFDPNNylpKESML 670
Cdd:COG1385 116 VVKLDGKKAAKLERWQKIAIEAAEQSGrnvVPEIKPPESLKE--------LLKEIDDEDALK---LIYEEKA---KEGLL 181
                        90       100       110
                ....*....|....*....|....*....|....*....
gi 30802081 671 KTTLTAFGFASADLIEIGLEGkGFEPTLEALFGKQGFFP 709
Cdd:COG1385 182 ALPLLEALPEGKVLLIIGPEG-GFSEDEIELLREAGFTP 219
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH