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Conserved domains on  [gi|17046383|gb|AAL34502|]
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SON DNA binding protein isoform F [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 2369-2419 9.79e-25

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member cd19870:

Pssm-ID: 444671  Cd Length: 75  Bit Score: 99.66  E-value: 9.79e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17046383 2369 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGALTRPNC 2419
Cdd:cd19870    1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2305-2349 5.95e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 5.95e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 17046383   2305 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2349
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
PspC_subgroup_2 super family cl41463
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 308-493 1.61e-10

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


The actual alignment was detected with superfamily member NF033839:

Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 66.33  E-value: 1.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   308 VSSETPTE-VYPEPSTSTT--MDFPESSAIEALRLPEQPVDVPSEIADSSMTRPQELPELPKTTA---LELQESSVASAM 381
Cdd:NF033839  279 LTQDTPKEpGNKKPSAPKPgmQPSPQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQP 358

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   382 ELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQE--LPGLPAP 459
Cdd:NF033839  359 EKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKP 438

                         170       180       190
                  ....*....|....*....|....*....|....
gi 17046383   460 SMGLEPPQEVPEPSVMAQELPGLPLVTAAVELPE 493
Cdd:NF033839  439 KPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPK 472
PHA03379 super family cl33730
EBNA-3A; Provisional
 340-673 2.68e-08

EBNA-3A; Provisional


The actual alignment was detected with superfamily member PHA03379:

Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 59.69  E-value: 2.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   340 PEQPVDVPSeiadssmtrpqelPELPKttalELQESSVASAMELPGPPATSMPElQGPPVTPVLELPGPSA----TPVPE 415
Cdd:PHA03379  416 PRPPVEKPR-------------PEVPQ----SLETATSHGSAQVPEPPPVHDLE-PGPLHDQHSMAPCPVAqlppGPLQD 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   416 L-PGPLSTPVPELPGPPATAVPELPGPSVTP-VPQLSQELPGLPAPSMGLEPPQE-VPEPSVmAQELPGLPLVT-AAVEL 491
Cdd:PHA03379  478 LePGDQLPGVVQDGRPACAPVPAPAGPIVRPwEASLSQVPGVAFAPVMPQPMPVEpVPVPTV-ALERPVCPAPPlIAMQG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   492 PEQPA--VTVAMELTEQPVTTTELEQPVGMTTVEHP--GHPE--VTTATGLLGQPEATMV-----LELPGQPVATTaleL 560
Cdd:PHA03379  557 PGETSgiVRVRERWRPAPWTPNPPRSPSQMSVRDRLarLRAEaqPYQASVEVQPPQLTQVspqqpMEYPLEPEQQM---F 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   561 PGQP--SVTGVPELPGLPS---ATRALELSgQPVATGAlelPGPLMAAGALEFS--GQSGAAGALELLGQPLATGVLE-- 631
Cdd:PHA03379  634 PGSPfsQVADVMRAGGVPAmqpQYFDLPLQ-QPISQGA---PLAPLRASMGPVPpvPATQPQYFDIPLTEPINQGASAah 709

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 17046383   632 -LPGQPGAPEL--PGQPVATVALEISVQSVVTTSELSTMTVSQSL 673
Cdd:PHA03379  710 fLPQQPMEGPLvpERWMFQGATLSQSVRPGVAQSQYFDLPLTQPI 754
rne super family cl35953
ribonuclease E; Reviewed
 1289-1481 8.66e-05

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 48.11  E-value: 8.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1289 PAMsAEPTVLASEPPVMSETAETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPESSAMAVLESSAVTVL 1368
Cdd:PRK10811  834 PEM-ASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVV 912

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1369 ESSTVTVLESSTVTvlepsvvtvpePPVVAEPDYVTIPVPVVSALEPSVPVLEPAVSVLQPS----MIVSEPSVSVQEST 1444
Cdd:PRK10811  913 ETTHPEVIAAPVTE-----------QPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAA 981

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 17046383  1445 VTVSEPAVTVSEQTQVIPTEVAIESTPMILESSIMSS 1481
Cdd:PRK10811  982 PVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATA 1018
rne super family cl35953
ribonuclease E; Reviewed
 1195-1381 1.17e-04

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 47.73  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1195 WPTEVPsLPSEESVSQPEPPVSQSEISEPSAVPTDYSVSASDPSVLVSEAAVTVPEPPPEpessiTLTPVESAVVAEEHE 1274
Cdd:PRK10811  819 YPTQSP-MPLTVACASPEMASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAA-----AVEPVVSAPVVEAVA 892

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1275 VVPERPVtcmVSETPAMSAEPTVLASEPPVMSETA-ETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPE 1353
Cdd:PRK10811  893 EVVEEPV---VVAEPQPEEVVVVETTHPEVIAAPVtEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVV 969

                         170       180
                  ....*....|....*....|....*...
gi 17046383  1354 SSAMAVLESSAVTVLESSTVTVLESSTV 1381
Cdd:PRK10811  970 VAEPEVVAQPAAPVVAEVAAEVETVTAV 997
 
Name Accession Description Interval E-value
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 2369-2419 9.79e-25

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 99.66  E-value: 9.79e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17046383 2369 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGALTRPNC 2419
Cdd:cd19870    1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2305-2349 5.95e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 5.95e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 17046383   2305 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2349
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 2303-2349 2.34e-15

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 71.81  E-value: 2.34e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 17046383    2303 PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2349
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 308-493 1.61e-10

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 66.33  E-value: 1.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   308 VSSETPTE-VYPEPSTSTT--MDFPESSAIEALRLPEQPVDVPSEIADSSMTRPQELPELPKTTA---LELQESSVASAM 381
Cdd:NF033839  279 LTQDTPKEpGNKKPSAPKPgmQPSPQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQP 358

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   382 ELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQE--LPGLPAP 459
Cdd:NF033839  359 EKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKP 438

                         170       180       190
                  ....*....|....*....|....*....|....
gi 17046383   460 SMGLEPPQEVPEPSVMAQELPGLPLVTAAVELPE 493
Cdd:NF033839  439 KPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPK 472
PHA03247 PHA03247
large tegument protein UL36; Provisional
 170-474 8.52e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 61.49  E-value: 8.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   170 PTRAFGPSETNESPAVVLEPPVVSMEVSEPHIleTLKPATK-TAELSVVSTSVISEQSEQSVAVMPEPSMTKILdsfAAA 248
Cdd:PHA03247 2704 PPPTPEPAPHALVSATPLPPGPAAARQASPAL--PAAPAPPaVPAGPATPGGPARPARPPTTAGPPAPAPPAAP---AAG 2778

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   249 PVPTTTLVLKSSEPVVTMSVeyqmksvlksveSTSPEPSKIMLVEPPVAKVLEPSETLVVSSETPTEVYPEPSTSTTMDF 328
Cdd:PHA03247 2779 PPRRLTRPAVASLSESRESL------------PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   329 PESSAIEALRLPEQPVD--VPSEIADSSMTRPQElPELPKTTALELQESSVASAMELPGPPATSMPELQGPPVTPVLELP 406
Cdd:PHA03247 2847 PPSLPLGGSVAPGGDVRrrPPSRSPAAKPAAPAR-PPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPP 2925

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17046383   407 GPSATPVPELPGPLSTPVPELPGP-----PATAVPE------LPGPSVTPVPQLSQELPGLPAPSMGLEPPQEVPEPSV 474
Cdd:PHA03247 2926 PPQPQPPPPPPPRPQPPLAPTTDPagagePSGAVPQpwlgalVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRV 3004
PHA03379 PHA03379
EBNA-3A; Provisional
 340-673 2.68e-08

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 59.69  E-value: 2.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   340 PEQPVDVPSeiadssmtrpqelPELPKttalELQESSVASAMELPGPPATSMPElQGPPVTPVLELPGPSA----TPVPE 415
Cdd:PHA03379  416 PRPPVEKPR-------------PEVPQ----SLETATSHGSAQVPEPPPVHDLE-PGPLHDQHSMAPCPVAqlppGPLQD 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   416 L-PGPLSTPVPELPGPPATAVPELPGPSVTP-VPQLSQELPGLPAPSMGLEPPQE-VPEPSVmAQELPGLPLVT-AAVEL 491
Cdd:PHA03379  478 LePGDQLPGVVQDGRPACAPVPAPAGPIVRPwEASLSQVPGVAFAPVMPQPMPVEpVPVPTV-ALERPVCPAPPlIAMQG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   492 PEQPA--VTVAMELTEQPVTTTELEQPVGMTTVEHP--GHPE--VTTATGLLGQPEATMV-----LELPGQPVATTaleL 560
Cdd:PHA03379  557 PGETSgiVRVRERWRPAPWTPNPPRSPSQMSVRDRLarLRAEaqPYQASVEVQPPQLTQVspqqpMEYPLEPEQQM---F 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   561 PGQP--SVTGVPELPGLPS---ATRALELSgQPVATGAlelPGPLMAAGALEFS--GQSGAAGALELLGQPLATGVLE-- 631
Cdd:PHA03379  634 PGSPfsQVADVMRAGGVPAmqpQYFDLPLQ-QPISQGA---PLAPLRASMGPVPpvPATQPQYFDIPLTEPINQGASAah 709

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 17046383   632 -LPGQPGAPEL--PGQPVATVALEISVQSVVTTSELSTMTVSQSL 673
Cdd:PHA03379  710 fLPQQPMEGPLvpERWMFQGATLSQSVRPGVAQSQYFDLPLTQPI 754
DSRM smart00358
Double-stranded RNA binding motif;
2372-2408 2.75e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.57  E-value: 2.75e-07
                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 17046383    2372 PVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTV 36
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 2372-2412 8.48e-07

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 48.88  E-value: 8.48e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 17046383   2372 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNG 2412
Cdd:pfam14709    3 AVSHLEELCQKNKWGSPVYELHSTAGPDGKQLFTYKVVIPG 43
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 258-459 1.32e-06

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 53.62  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   258 KSSEPVVTMSVEYQMKSVLKSVESTSPEPSKIMLVEPPVAKVLEPSETlvvsseTPTEVYPEPSTSTTMDFPESSAIEAL 337
Cdd:NF033839  291 KPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEK------PKPEVKPQLETPKPEVKPQPEKPKPE 364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   338 RLPEQPVDVPSEIADSSMTRPQELPELPKTT-----ALELQESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATP 412
Cdd:NF033839  365 VKPQPEKPKPEVKPQPETPKPEVKPQPEKPKpevkpQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKP 444

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 17046383   413 VPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAP 459
Cdd:NF033839  445 QPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPDNSKPQA 491
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 205-534 1.44e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.69  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    205 LKPATKTAELSVVSTSVISEQSEQSVAVMPEPSMTKILDSFAAAPVPTTTLVLKSSEPVVT-MSVEYQMKSVLKSVESTS 283
Cdd:pfam05109  396 LGTAPKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTnLTAPASTGPTVSTADVTS 475

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    284 PEPSKIMLVEPPVAKVLEP-------------SETLVVSSETPTEVYPEPSTSTTMDFPESSAIEALRlPEQPVDVPSEI 350
Cdd:pfam05109  476 PTPAGTTSGASPVTPSPSPrdngteskapdmtSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTS-PTSAVTTPTPN 554

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    351 ADSSMtrPQELPELPKTTALELQESSVASAMELPGPPATSmpelqgppvtPVLELPGPSA-TPVPELPGPLSTPVPELPg 429
Cdd:pfam05109  555 ATSPT--PAVTTPTPNATIPTLGKTSPTSAVTTPTPNATS----------PTVGETSPQAnTTNHTLGGTSSTPVVTSP- 621

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    430 ppatavpelPGPSVTPVPQLSQELPGLPAPSMGLEPPQ--EVPEPSVMAQELPGLPLVTAAVELPEQ------PAVTVAM 501
Cdd:pfam05109  622 ---------PKNATSAVTTGQHNITSSSTSSMSLRPSSisETLSPSTSDNSTSHMPLLTSAHPTGGEnitqvtPASTSTH 692

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 17046383    502 ELTE-----QPVTTTELEQPVGMTTVEHPGHPEVTTAT 534
Cdd:pfam05109  693 HVSTsspapRPGTTSQASGPGNSSTSTKPGEVNVTKGT 730
rne PRK10811
ribonuclease E; Reviewed
 1289-1481 8.66e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 48.11  E-value: 8.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1289 PAMsAEPTVLASEPPVMSETAETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPESSAMAVLESSAVTVL 1368
Cdd:PRK10811  834 PEM-ASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVV 912

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1369 ESSTVTVLESSTVTvlepsvvtvpePPVVAEPDYVTIPVPVVSALEPSVPVLEPAVSVLQPS----MIVSEPSVSVQEST 1444
Cdd:PRK10811  913 ETTHPEVIAAPVTE-----------QPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAA 981

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 17046383  1445 VTVSEPAVTVSEQTQVIPTEVAIESTPMILESSIMSS 1481
Cdd:PRK10811  982 PVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATA 1018
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 312-477 9.54e-05

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 47.76  E-value: 9.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    312 TPTEVYPEPSTSTTMdfPESSAIEALRLPEQPVDVPSEIADSSMTRPQELPELPkttalelqESSVASAMELPG--PPAT 389
Cdd:TIGR01645  283 TPPDALLQPATVSAI--PAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPATP--------SSSLPTDIGNKAvvSSAK 352

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    390 SMPELQG--PPVTPVLELPGPSATPVPELPGPLstPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMGLEPPQ 467
Cdd:TIGR01645  353 KEAEEVPplPQAAPAVVKPGPMEIPTPVPPPGL--AIPSLVAPPGLVAPTEINPSFLASPRKKMKREKLPVTFGALDDTL 430

                          170
                   ....*....|
gi 17046383    468 EVPEPSVMAQ 477
Cdd:TIGR01645  431 AWKEPSKEDQ 440
rne PRK10811
ribonuclease E; Reviewed
 1195-1381 1.17e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 47.73  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1195 WPTEVPsLPSEESVSQPEPPVSQSEISEPSAVPTDYSVSASDPSVLVSEAAVTVPEPPPEpessiTLTPVESAVVAEEHE 1274
Cdd:PRK10811  819 YPTQSP-MPLTVACASPEMASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAA-----AVEPVVSAPVVEAVA 892

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1275 VVPERPVtcmVSETPAMSAEPTVLASEPPVMSETA-ETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPE 1353
Cdd:PRK10811  893 EVVEEPV---VVAEPQPEEVVVVETTHPEVIAAPVtEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVV 969

                         170       180
                  ....*....|....*....|....*...
gi 17046383  1354 SSAMAVLESSAVTVLESSTVTVLESSTV 1381
Cdd:PRK10811  970 VAEPEVVAQPAAPVVAEVAAEVETVTAV 997
SAV_2336_NTERM NF041121
SAV_2336 family N-terminal domain; This HMM describes an N-terminal domain shared by SAV_2336 ...
 405-503 2.36e-03

SAV_2336 family N-terminal domain; This HMM describes an N-terminal domain shared by SAV_2336 (BAC70047.1) whose C-terminal region suggests restriction enzyme activity (PMID: 18456708), and with other proteins with unrelated C-terminal regions. A member protein was also identified in a kanamycin biosynthetic gene cluster (PMID:16766657), while N-terminal regions of two other member proteins were named Trypco1 in a bioinformatic study (PMID:32101166) of predicted bacterial conflict systems.


Pssm-ID: 469044 [Multi-domain]  Cd Length: 473  Bit Score: 43.07  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   405 LPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQlsqelpglPAPSMGLEPPQEVPEPSVMAQELPGLPL 484
Cdd:NF041121   15 MGRAAAPPSPEGPAPTAASQPATPPPPAAPPSPPGDPPEPPAPE--------PAPLPAPYPGSLAPPPPPPPGPAGAAPG 86

                          90
                  ....*....|....*....
gi 17046383   485 VTAAVELPEQPAVTVAMEL 503
Cdd:NF041121   87 AALPVRVPAPPALPNPLEL 105
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2362-2409 4.81e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.85  E-value: 4.81e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 17046383 2362 AAMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVL 2409
Cdd:COG0571  149 EIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVL 196
 
Name Accession Description Interval E-value
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 2369-2419 9.79e-25

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 99.66  E-value: 9.79e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17046383 2369 GKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGALTRPNC 2419
Cdd:cd19870    1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSV 51
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 2305-2349 5.95e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 76.39  E-value: 5.95e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 17046383   2305 TGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2349
Cdd:pfam01585    1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 2303-2349 2.34e-15

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 71.81  E-value: 2.34e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 17046383    2303 PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAV 2349
Cdd:smart00443    1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 308-493 1.61e-10

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 66.33  E-value: 1.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   308 VSSETPTE-VYPEPSTSTT--MDFPESSAIEALRLPEQPVDVPSEIADSSMTRPQELPELPKTTA---LELQESSVASAM 381
Cdd:NF033839  279 LTQDTPKEpGNKKPSAPKPgmQPSPQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEKPKPEVkpqLETPKPEVKPQP 358

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   382 ELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQE--LPGLPAP 459
Cdd:NF033839  359 EKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPevKPQPEKP 438

                         170       180       190
                  ....*....|....*....|....*....|....
gi 17046383   460 SMGLEPPQEVPEPSVMAQELPGLPLVTAAVELPE 493
Cdd:NF033839  439 KPEVKPQPEKPKPEVKPQPETPKPEVKPQPEKPK 472
PHA03247 PHA03247
large tegument protein UL36; Provisional
 170-474 8.52e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 61.49  E-value: 8.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   170 PTRAFGPSETNESPAVVLEPPVVSMEVSEPHIleTLKPATK-TAELSVVSTSVISEQSEQSVAVMPEPSMTKILdsfAAA 248
Cdd:PHA03247 2704 PPPTPEPAPHALVSATPLPPGPAAARQASPAL--PAAPAPPaVPAGPATPGGPARPARPPTTAGPPAPAPPAAP---AAG 2778

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   249 PVPTTTLVLKSSEPVVTMSVeyqmksvlksveSTSPEPSKIMLVEPPVAKVLEPSETLVVSSETPTEVYPEPSTSTTMDF 328
Cdd:PHA03247 2779 PPRRLTRPAVASLSESRESL------------PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   329 PESSAIEALRLPEQPVD--VPSEIADSSMTRPQElPELPKTTALELQESSVASAMELPGPPATSMPELQGPPVTPVLELP 406
Cdd:PHA03247 2847 PPSLPLGGSVAPGGDVRrrPPSRSPAAKPAAPAR-PPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPP 2925

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17046383   407 GPSATPVPELPGPLSTPVPELPGP-----PATAVPE------LPGPSVTPVPQLSQELPGLPAPSMGLEPPQEVPEPSV 474
Cdd:PHA03247 2926 PPQPQPPPPPPPRPQPPLAPTTDPagagePSGAVPQpwlgalVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRV 3004
PHA03379 PHA03379
EBNA-3A; Provisional
 340-673 2.68e-08

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 59.69  E-value: 2.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   340 PEQPVDVPSeiadssmtrpqelPELPKttalELQESSVASAMELPGPPATSMPElQGPPVTPVLELPGPSA----TPVPE 415
Cdd:PHA03379  416 PRPPVEKPR-------------PEVPQ----SLETATSHGSAQVPEPPPVHDLE-PGPLHDQHSMAPCPVAqlppGPLQD 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   416 L-PGPLSTPVPELPGPPATAVPELPGPSVTP-VPQLSQELPGLPAPSMGLEPPQE-VPEPSVmAQELPGLPLVT-AAVEL 491
Cdd:PHA03379  478 LePGDQLPGVVQDGRPACAPVPAPAGPIVRPwEASLSQVPGVAFAPVMPQPMPVEpVPVPTV-ALERPVCPAPPlIAMQG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   492 PEQPA--VTVAMELTEQPVTTTELEQPVGMTTVEHP--GHPE--VTTATGLLGQPEATMV-----LELPGQPVATTaleL 560
Cdd:PHA03379  557 PGETSgiVRVRERWRPAPWTPNPPRSPSQMSVRDRLarLRAEaqPYQASVEVQPPQLTQVspqqpMEYPLEPEQQM---F 633

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   561 PGQP--SVTGVPELPGLPS---ATRALELSgQPVATGAlelPGPLMAAGALEFS--GQSGAAGALELLGQPLATGVLE-- 631
Cdd:PHA03379  634 PGSPfsQVADVMRAGGVPAmqpQYFDLPLQ-QPISQGA---PLAPLRASMGPVPpvPATQPQYFDIPLTEPINQGASAah 709

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 17046383   632 -LPGQPGAPEL--PGQPVATVALEISVQSVVTTSELSTMTVSQSL 673
Cdd:PHA03379  710 fLPQQPMEGPLvpERWMFQGATLSQSVRPGVAQSQYFDLPLTQPI 754
PHA03247 PHA03247
large tegument protein UL36; Provisional
 340-648 1.78e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 57.26  E-value: 1.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   340 PEQPVDVPSEIADSSM--TRPQELPELPKTTALEL------QESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSAT 411
Cdd:PHA03247 2553 PPLPPAAPPAAPDRSVppPRPAPRPSEPAVTSRARrpdappQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPS 2632

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   412 PVP-ELPGPLSTPVPELPGPPATAVPelpgPSVTPVPQLSQE--LPGLPAPSMGLEPPQEVPE-PSVMAQELPGLPlvta 487
Cdd:PHA03247 2633 PAAnEPDPHPPPTVPPPERPRDDPAP----GRVSRPRRARRLgrAAQASSPPQRPRRRAARPTvGSLTSLADPPPP---- 2704

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   488 avELPEQPAVTVAMELTEQPVTTTELEQPVGMTTVEhPGHPEVTTATGLLGQPEATMVLELPGQPVATTAlelPGQPSVT 567
Cdd:PHA03247 2705 --PPTPEPAPHALVSATPLPPGPAAARQASPALPAA-PAPPAVPAGPATPGGPARPARPPTTAGPPAPAP---PAAPAAG 2778

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   568 GVPELPGLPSATRALELSGQPVATGALELPGPLMAAGALEFSGQSGAAGAlellgqPLATGVlelpgQPGAPELPGQPVA 647
Cdd:PHA03247 2779 PPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPL------PPPTSA-----QPTAPPPPPGPPP 2847


                  .
gi 17046383   648 T 648
Cdd:PHA03247 2848 P 2848
DSRM smart00358
Double-stranded RNA binding motif;
2372-2408 2.75e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.57  E-value: 2.75e-07
                            10        20        30
                    ....*....|....*....|....*....|....*..
gi 17046383    2372 PVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:smart00358    1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTV 36
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 2370-2412 6.86e-07

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 48.64  E-value: 6.86e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 17046383 2370 KHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNG 2412
Cdd:cd10845    1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNG 43
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 2372-2412 8.48e-07

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 48.88  E-value: 8.48e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 17046383   2372 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNG 2412
Cdd:pfam14709    3 AVSHLEELCQKNKWGSPVYELHSTAGPDGKQLFTYKVVIPG 43
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 258-459 1.32e-06

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 53.62  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   258 KSSEPVVTMSVEYQMKSVLKSVESTSPEPSKIMLVEPPVAKVLEPSETlvvsseTPTEVYPEPSTSTTMDFPESSAIEAL 337
Cdd:NF033839  291 KPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKPKPEVKPQPEK------PKPEVKPQLETPKPEVKPQPEKPKPE 364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   338 RLPEQPVDVPSEIADSSMTRPQELPELPKTT-----ALELQESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATP 412
Cdd:NF033839  365 VKPQPEKPKPEVKPQPETPKPEVKPQPEKPKpevkpQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKPQPEKPKPEVKP 444

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 17046383   413 VPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAP 459
Cdd:NF033839  445 QPEKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQPEKPKPDNSKPQA 491
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 97-579 1.49e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 54.00  E-value: 1.49e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383     97 TDPTDEIPTKKSKKHKKHKNKKKKKKKEKEKKYKRQPEESE----SKTKSHDDGNIDLESDSFLKfDSEPSAVALELPTR 172
Cdd:pfam03154   55 NDSKAESMKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPErataKKSKTQEISRPNSPSEGEGE-SSDGRSVNDEGSSD 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    173 AFGPSETNESPAVVLEPP----VVSMEVSEPHILETLKPATKTAELSVVSTSVISEQSEQSVAVMPEPSMTkildSFAAA 248
Cdd:pfam03154  134 PKDIDQDNRSTSPSIPSPqdneSDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAP----SVPPQ 209

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    249 PVPTTTLVLKSSEPVVTMSVEYQMKSVLKSVESTSPEPSKIMLVEPPVAKVLEPSETLVVSSETPTEVYPEPSTSTTMDF 328
Cdd:pfam03154  210 GSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHM 289

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    329 PESsaiealrLPEQPVDVPSEIADS------SMTRPQELPELPKTTALELQESSVASAMELPGPPA-TSMPELQGPPVTP 401
Cdd:pfam03154  290 QHP-------VPPQPFPLTPQSSQSqvppgpSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPApLSMPHIKPPPTTP 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    402 VLELPGPSATPVP---ELPGPLSTPvPELPGPPA----TAVPELPGPSVTPVP-QL---SQELPGLPAPSMGLEPPQEVP 470
Cdd:pfam03154  363 IPQLPNPQSHKHPphlSGPSPFQMN-SNLPPPPAlkplSSLSTHHPPSAHPPPlQLmpqSQQLPPPPAQPPVLTQSQSLP 441

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    471 EPSVMAQELPGLPLVTAAVELPEQPAVTVAMELTEQPvTTTELEQPVGMTTVEHPGHPEVTTATGLLGQPEATmvleLPG 550
Cdd:pfam03154  442 PPAASHPPTSGLHQVPSQSPFPQHPFVPGGPPPITPP-SGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCP----LPP 516

                          490       500
                   ....*....|....*....|....*....
gi 17046383    551 QPVATTALELPGQPSVTGVPELPGLPSAT 579
Cdd:pfam03154  517 VQIKEEALDEAEEPESPPPPPRSPSPEPT 545
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 2371-2404 2.15e-06

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 46.99  E-value: 2.15e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 17046383 2371 HPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHF 2404
Cdd:cd19863    1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEF 34
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
 2301-2346 2.96e-06

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 46.50  E-value: 2.96e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 17046383   2301 AAPVtGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGL 2346
Cdd:pfam12656   11 KVPV-EEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGL 55
PHA03378 PHA03378
EBNA-3B; Provisional
 181-480 3.19e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 52.76  E-value: 3.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   181 ESPAVVLEPPVVSMEVSEPhILETLKPATKTAELSVVSTSViseqseqsvavmpEPSMTKILDSFAAAPVPTTTLVLKSS 260
Cdd:PHA03378  486 VTPVILHQPPAQGVQAHGS-MLDLLEKDDEDMEQRVMATLL-------------PPSPPQPRAGRRAPCVYTEDLDIESD 551

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   261 EPVVTMSVEYQMKSV-----LKSVESTSPEPSKIMLVEPPVAKVLEPSETLVVSSETPTEVYPEPSTSTTMDFPESSAIE 335
Cdd:PHA03378  552 EPASTEPVHDQLLPApglgpLQIQPLTSPTTSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETSAPRQWPMPLRPI 631

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   336 ALRL---------------PEQPVDVPSEIADSSMTRPQELPELPKTT--ALELQESSVASAMELPGPPATSMPELQGPP 398
Cdd:PHA03378  632 PMRPlrmqpitfnvlvfptPHQPPQVEITPYKPTWTQIGHIPYQPSPTgaNTMLPIQWAPGTMQPPPRAPTPMRPPAAPP 711

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   399 V------TPVLELPGPSATP-VPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSqelPGLPAPSmglEPPQEVPE 471
Cdd:PHA03378  712 GraqrpaAATGRARPPAAAPgRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAA---PGAPTPQ---PPPQAPPA 785


                  ....*....
gi 17046383   472 PSVMAQELP 480
Cdd:PHA03378  786 PQQRPRGAP 794
PHA03247 PHA03247
large tegument protein UL36; Provisional
 318-525 5.32e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.25  E-value: 5.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   318 PEPSTSTTMDFPESSAIEALRLPEQPVDVPSEIADSSMTRPQEL----PELPKTTALElqessvASAMELPGPPATSMP- 392
Cdd:PHA03247 2779 PPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAAspagPLPPPTSAQP------TAPPPPPGPPPPSLPl 2852

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   393 ----------ELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMG 462
Cdd:PHA03247 2853 ggsvapggdvRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPP 2932

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17046383   463 LEPPQEVPEPSVMAQELPGLPLVTAAVELPEQPA-----VTVAMELTEQPVTTTELEQPVGMTTVEHP 525
Cdd:PHA03247 2933 PPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGAlvpgrVAVPRFRVPQPAPSREAPASSTPPLTGHS 3000
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 2378-2408 5.72e-06

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380698  Cd Length: 70  Bit Score: 46.21  E-value: 5.72e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 17046383 2378 EICNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:cd19869    2 EICLKRRWPMPVYRCVEEEGPAHAKRFTYMV 32
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 387-558 1.21e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 50.63  E-value: 1.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   387 PATSMPELQGPPVtPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMGLEPP 466
Cdd:PRK07994  361 PAAPLPEPEVPPQ-SAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAK 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   467 QEVPEPSVMAQELPGL-----PLVTAAVELPEQPAVTVAMELTEQPVTTTELEQPVGMT----TVEHPGHPEVTTATGLL 537
Cdd:PRK07994  440 KSEPAAASRARPVNSAlerlaSVRPAPSALEKAPAKKEAYRWKATNPVEVKKEPVATPKalkkALEHEKTPELAAKLAAE 519

                         170       180
                  ....*....|....*....|....*.
gi 17046383   538 GQPE---ATMV--LELPGqPVATTAL 558
Cdd:PRK07994  520 AIERdpwAALVsqLGLPG-LVEQLAL 544
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 205-534 1.44e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.69  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    205 LKPATKTAELSVVSTSVISEQSEQSVAVMPEPSMTKILDSFAAAPVPTTTLVLKSSEPVVT-MSVEYQMKSVLKSVESTS 283
Cdd:pfam05109  396 LGTAPKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTnLTAPASTGPTVSTADVTS 475

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    284 PEPSKIMLVEPPVAKVLEP-------------SETLVVSSETPTEVYPEPSTSTTMDFPESSAIEALRlPEQPVDVPSEI 350
Cdd:pfam05109  476 PTPAGTTSGASPVTPSPSPrdngteskapdmtSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTS-PTSAVTTPTPN 554

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    351 ADSSMtrPQELPELPKTTALELQESSVASAMELPGPPATSmpelqgppvtPVLELPGPSA-TPVPELPGPLSTPVPELPg 429
Cdd:pfam05109  555 ATSPT--PAVTTPTPNATIPTLGKTSPTSAVTTPTPNATS----------PTVGETSPQAnTTNHTLGGTSSTPVVTSP- 621

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    430 ppatavpelPGPSVTPVPQLSQELPGLPAPSMGLEPPQ--EVPEPSVMAQELPGLPLVTAAVELPEQ------PAVTVAM 501
Cdd:pfam05109  622 ---------PKNATSAVTTGQHNITSSSTSSMSLRPSSisETLSPSTSDNSTSHMPLLTSAHPTGGEnitqvtPASTSTH 692

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 17046383    502 ELTE-----QPVTTTELEQPVGMTTVEHPGHPEVTTAT 534
Cdd:pfam05109  693 HVSTsspapRPGTTSQASGPGNSSTSTKPGEVNVTKGT 730
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 388-572 7.56e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   388 ATSMPELQGPPVTPVLELPgpsatPVPELPGPLSTPVPELPGPPAtavPELPGPSVTPVPQLSQELPGLPAPSMGLEPPQ 467
Cdd:PRK10263  326 ATTATQSWAAPVEPVTQTP-----PVASVDVPPAQPTVAWQPVPG---PQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPL 397

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   468 EVPEPSVMAQELPGLPLVTAAVELPEQPAVTVAMELTEQPVTTTELEQPVGMTTVEHPGHPEVTTatgllgQPEATMVLE 547
Cdd:PRK10263  398 QQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTY------QTEQTYQQP 471

                         170       180
                  ....*....|....*....|....*
gi 17046383   548 LPGQPVATTALELPGQPSVTGVPEL 572
Cdd:PRK10263  472 AAQEPLYQQPQPVEQQPVVEPEPVV 496
rne PRK10811
ribonuclease E; Reviewed
 1289-1481 8.66e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 48.11  E-value: 8.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1289 PAMsAEPTVLASEPPVMSETAETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPESSAMAVLESSAVTVL 1368
Cdd:PRK10811  834 PEM-ASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVV 912

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1369 ESSTVTVLESSTVTvlepsvvtvpePPVVAEPDYVTIPVPVVSALEPSVPVLEPAVSVLQPS----MIVSEPSVSVQEST 1444
Cdd:PRK10811  913 ETTHPEVIAAPVTE-----------QPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAetaeVVVAEPEVVAQPAA 981

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 17046383  1445 VTVSEPAVTVSEQTQVIPTEVAIESTPMILESSIMSS 1481
Cdd:PRK10811  982 PVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATA 1018
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 312-477 9.54e-05

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 47.76  E-value: 9.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    312 TPTEVYPEPSTSTTMdfPESSAIEALRLPEQPVDVPSEIADSSMTRPQELPELPkttalelqESSVASAMELPG--PPAT 389
Cdd:TIGR01645  283 TPPDALLQPATVSAI--PAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPATP--------SSSLPTDIGNKAvvSSAK 352

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    390 SMPELQG--PPVTPVLELPGPSATPVPELPGPLstPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMGLEPPQ 467
Cdd:TIGR01645  353 KEAEEVPplPQAAPAVVKPGPMEIPTPVPPPGL--AIPSLVAPPGLVAPTEINPSFLASPRKKMKREKLPVTFGALDDTL 430

                          170
                   ....*....|
gi 17046383    468 EVPEPSVMAQ 477
Cdd:TIGR01645  431 AWKEPSKEDQ 440
rne PRK10811
ribonuclease E; Reviewed
 1195-1381 1.17e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 47.73  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1195 WPTEVPsLPSEESVSQPEPPVSQSEISEPSAVPTDYSVSASDPSVLVSEAAVTVPEPPPEpessiTLTPVESAVVAEEHE 1274
Cdd:PRK10811  819 YPTQSP-MPLTVACASPEMASGKVWIRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAA-----AVEPVVSAPVVEAVA 892

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1275 VVPERPVtcmVSETPAMSAEPTVLASEPPVMSETA-ETFDSMRASGHVASEVSTSLLVPAVTTPVLAESILEPPAMAAPE 1353
Cdd:PRK10811  893 EVVEEPV---VVAEPQPEEVVVVETTHPEVIAAPVtEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVV 969

                         170       180
                  ....*....|....*....|....*...
gi 17046383  1354 SSAMAVLESSAVTVLESSTVTVLESSTV 1381
Cdd:PRK10811  970 VAEPEVVAQPAAPVVAEVAAEVETVTAV 997
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 319-677 1.40e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 47.47  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   319 EPSTSTTMDFPESSAIEALRLPeQPVDVPSEIADSSMTRPQEL---PELPKTTALELQESSVASAMELP-GPPATSMPEL 394
Cdd:PHA03307    1 SDNAPDLYDLIEAAAEGGEFFP-RPPATPGDAADDLLSGSQGQlvsDSAELAAVTVVAGAAACDRFEPPtGPPPGPGTEA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   395 QGPPVTPVLELPGPSATPVPELPGPLSTP--VPELPGPPATAVPELPGPSvtPVPQLSQELPglPAPSMGLEPPQEVPEP 472
Cdd:PHA03307   80 PANESRSTPTWSLSTLAPASPAREGSPTPpgPSSPDPPPPTPPPASPPPS--PAPDLSEMLR--PVGSPGPPPAASPPAA 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   473 SVMAQELPglplvtAAVELPEQPAVTVAM-ELTEQPVTTTELEQPVGMTTVEHPGHPEVttatglLGQPEATMVLELPGQ 551
Cdd:PHA03307  156 GASPAAVA------SDAASSRQAALPLSSpEETARAPSSPPAEPPPSTPPAAASPRPPR------RSSPISASASSPAPA 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   552 PVATTALELPGQPSVTGVPELPGLPSATRALELSGQPvatGALELPGPLMAA-----GALEFSGQSGAAGALELLGQPla 626
Cdd:PHA03307  224 PGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRP---APITLPTRIWEAsgwngPSSRPGPASSSSSPRERSPSP-- 298

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17046383   627 tgvleLPGQPGAPELPGQPVAtVALEISVQSVVTTSELSTMTVSQSLEVPS 677
Cdd:PHA03307  299 -----SPSSPGSGPAPSSPRA-SSSSSSSRESSSSSTSSSSESSRGAAVSP 343
DUF3729 pfam12526
Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins ...
 369-452 2.31e-04

Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important.


Pssm-ID: 372164 [Multi-domain]  Cd Length: 115  Bit Score: 42.76  E-value: 2.31e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383    369 ALELQESSVASAMELPGPPATSMPelqgPPVTPVLELPGPSATPVPELPGPlsTPVPELPGPPATAVPELPGPSVTPVPQ 448
Cdd:pfam12526   31 PPESAHPDPPPPVGDPRPPVVDTP----PPVSAVWVLPPPSEPAAPEPDLV--PPVTGPAGPPSPLAPPAPAQKPPLPPP 104


                   ....
gi 17046383    449 LSQE 452
Cdd:pfam12526  105 RPQR 108
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 2370-2408 2.85e-04

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 41.09  E-value: 2.85e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 17046383 2370 KHPVSALMEICNKRRWqPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:cd19862    1 KTPISVLQELCAKRGI-TPKYELISSEGAVHEPTFTFRV 38
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
332-520 3.08e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 46.02  E-value: 3.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   332 SAIEALRLPEQPVDVPSEIADSSMTRPQELPELPKTTALELQESSVASAMELPGP---PATSMPELQGPPVTPVLElPGP 408
Cdd:PRK12323  376 TAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPealAAARQASARGPGGAPAPA-PAP 454

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   409 SATPVPELPGPLSTPVPelPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMGLEPPQEVPEPSVMAQELPGLPLVTAA 488
Cdd:PRK12323  455 AAAPAAAARPAAAGPRP--VAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATA 532

                         170       180       190
                  ....*....|....*....|....*....|..
gi 17046383   489 VELPEQPAVTVAMELTEQPVTTTELEQPVGMT 520
Cdd:PRK12323  533 DPDDAFETLAPAPAAAPAPRAAAATEPVVAPR 564
PHA03247 PHA03247
large tegument protein UL36; Provisional
 382-706 5.74e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 5.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   382 ELPGPPATSMPEL-----QGPPVTPVL--------ELPGPSA-TPVPELPGPLSTPVPELPGPPATAVPELPGPSVT--- 444
Cdd:PHA03247 2507 DAPPAPSRLAPAIlpdepVGEPVHPRMltwirgleELASDDAgDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTsra 2586

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   445 -----PVPQLSQELPG------------LPAPSMGLEPPQEVPEPSVMAQELPGLPlvTAAVELPEQPAVTVAMELTEQP 507
Cdd:PHA03247 2587 rrpdaPPQSARPRAPVddrgdprgpappSPLPPDTHAPDPPPPSPSPAANEPDPHP--PPTVPPPERPRDDPAPGRVSRP 2664

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   508 VTTTELEQPVGMT-TVEHPGHPEVTTATGLL---GQPEATMVLELPGQPVATTALELPGQPSVTGvPELPGLPSATRALE 583
Cdd:PHA03247 2665 RRARRLGRAAQASsPPQRPRRRAARPTVGSLtslADPPPPPPTPEPAPHALVSATPLPPGPAAAR-QASPALPAAPAPPA 2743

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   584 LSGQPVATGALELPG-PLMAAGAlefsgQSGAAGALELLGQPLATGVleLPGQPGAPELPGQPVATVALEISVQSVVTTS 662
Cdd:PHA03247 2744 VPAGPATPGGPARPArPPTTAGP-----PAPAPPAAPAAGPPRRLTR--PAVASLSESRESLPSPWDPADPPAAVLAPAA 2816

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 17046383   663 ELSTMTVSQSLEVPSTTALESYNTVAQE-LPTTLVGETSVTVGVD 706
Cdd:PHA03247 2817 ALPPAASPAGPLPPPTSAQPTAPPPPPGpPPPSLPLGGSVAPGGD 2861
dnaA PRK14086
chromosomal replication initiator protein DnaA;
369-578 6.66e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.82  E-value: 6.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   369 ALELQESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQ 448
Cdd:PRK14086   85 AITVDPSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADD 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   449 LSQELP--GLPAPSMGLEPPQEVPEPSvmaQELPGLPLVTAAVELPEQPAVTVAMELTEQPVTTTELEQPvgmttveHPG 526
Cdd:PRK14086  165 YGWQQQrlGFPPRAPYASPASYAPEQE---RDREPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPEP-------PPG 234

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 17046383   527 -HPEVTTATGLLGQPEATMVLELPGQPVAttaleLPGQPSVTGVpelPGLPSA 578
Cdd:PRK14086  235 aGHVHRGGPGPPERDDAPVVPIRPSAPGP-----LAAQPAPAPG---PGEPTA 279
rne PRK10811
ribonuclease E; Reviewed
 1271-1444 1.03e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 44.65  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1271 EEHEVVPERPVTcMVSETPAMSAEPTVLASEPPVMSETAETFDSMRASGHVASE--VSTSLLVPAVTTPVLAESILEPPA 1348
Cdd:PRK10811  851 QDVQVEEQREAE-EVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEpqPEEVVVVETTHPEVIAAPVTEQPQ 929

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1349 MAAPESSAMAvlessAVTVLESSTVTVLESSTVTVLEPSVVTVPEPpvvAEPDYVTIPVPVVSALEPSVPVLEPAVSVLQ 1428
Cdd:PRK10811  930 VITESDVAVA-----QEVAEHAEPVVEPQDETADIEEAAETAEVVV---AEPEVVAQPAAPVVAEVAAEVETVTAVEPEV 1001

                         170
                  ....*....|....*.
gi 17046383  1429 PSMIVSEPSVSVQEST 1444
Cdd:PRK10811 1002 APAQVPEATVEHNHAT 1017
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 378-513 1.21e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 43.93  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   378 ASAMELPGPPATSmpelqgPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQELPGLP 457
Cdd:PRK14951  367 AAAAEAAAPAEKK------TPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAA 440

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 17046383   458 APSmglEPPQEVPEPSVMAQELPGLPLVTAAVELPEQPAVTVAMELTEQPVTTTEL 513
Cdd:PRK14951  441 APA---AVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEE 493
PHA03247 PHA03247
large tegument protein UL36; Provisional
 386-509 1.48e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.16  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   386 PPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATA--VPELPGPSVTPVPQLSQELPGLPAPSMGL 463
Cdd:PHA03247  379 SLPTRKRRSARHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAppPPATPLPSAEPGSDDGPAPPPERQPPAPA 458

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 17046383   464 EPPQEVPEPSVMAQELPGLplvtAAVELPEQPAVTVAMELTEQPVT 509
Cdd:PHA03247  459 TEPAPDDPDDATRKALDAL----RERRPPEPPGADLAELLGRHPDT 500
DSRM_A1CF cd19900
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar ...
 2370-2408 1.80e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar proteins; A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. It contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380729  Cd Length: 81  Bit Score: 39.38  E-value: 1.80e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 17046383 2370 KHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:cd19900    1 KSPPQILEEICQKNNWGQPVYQLHSTIGPDQRQLFLYKV 39
SAV_2336_NTERM NF041121
SAV_2336 family N-terminal domain; This HMM describes an N-terminal domain shared by SAV_2336 ...
 405-503 2.36e-03

SAV_2336 family N-terminal domain; This HMM describes an N-terminal domain shared by SAV_2336 (BAC70047.1) whose C-terminal region suggests restriction enzyme activity (PMID: 18456708), and with other proteins with unrelated C-terminal regions. A member protein was also identified in a kanamycin biosynthetic gene cluster (PMID:16766657), while N-terminal regions of two other member proteins were named Trypco1 in a bioinformatic study (PMID:32101166) of predicted bacterial conflict systems.


Pssm-ID: 469044 [Multi-domain]  Cd Length: 473  Bit Score: 43.07  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   405 LPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQlsqelpglPAPSMGLEPPQEVPEPSVMAQELPGLPL 484
Cdd:NF041121   15 MGRAAAPPSPEGPAPTAASQPATPPPPAAPPSPPGDPPEPPAPE--------PAPLPAPYPGSLAPPPPPPPGPAGAAPG 86

                          90
                  ....*....|....*....
gi 17046383   485 VTAAVELPEQPAVTVAMEL 503
Cdd:NF041121   87 AALPVRVPAPPALPNPLEL 105
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 365-483 2.55e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 43.13  E-value: 2.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   365 PKTTALELQESSVASAMELPG-------PPATSMPELQGPPVTPvlelpGPSATPVPELPGPLSTPVPELPGPPATAVPE 437
Cdd:PRK14959  381 PSGSAAEGPASGGAATIPTPGtqgpqgtAPAAGMTPSSAAPATP-----APSAAPSPRVPWDDAPPAPPRSGIPPRPAPR 455

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 17046383   438 LPGPSvtpvpqlsqELPGLPAP-SMGLEPPQEVPEPSVMAQELPGLP 483
Cdd:PRK14959  456 MPEAS---------PVPGAPDSvASASDAPPTLGDPSDTAEHTPSGP 493
rne PRK10811
ribonuclease E; Reviewed
 356-531 2.80e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 43.10  E-value: 2.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   356 TRPQELPELPKTTALELQESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAV 435
Cdd:PRK10811  848 VRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQ 927

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   436 PELPGPSVTPVPQLSQELPglpapsmglEPPQEVPEPSVMAQElpglPLVTAAVELPEQPAVTVAMELTEQPVTTTELEQ 515
Cdd:PRK10811  928 PQVITESDVAVAQEVAEHA---------EPVVEPQDETADIEE----AAETAEVVVAEPEVVAQPAAPVVAEVAAEVETV 994

                         170
                  ....*....|....*.
gi 17046383   516 PVGMTTVEHPGHPEVT 531
Cdd:PRK10811  995 TAVEPEVAPAQVPEAT 1010
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 2371-2408 3.04e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 38.43  E-value: 3.04e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 17046383 2371 HPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:cd19872    1 NPVQILEEICQKNGWGEPVYQLLSTSSNNEVQLFIYKV 38
rne PRK10811
ribonuclease E; Reviewed
 1262-1472 3.63e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 42.72  E-value: 3.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1262 TPVESAVVAEEHEVVPERPVTCMVSETPAMSAEPTVLASEPPVMSETAETfdsmrasghvASEVSTSLLVPAVTTPVLAE 1341
Cdd:PRK10811  853 VQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVA----------EPQPEEVVVVETTHPEVIAA 922

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383  1342 SILEPPAMAAPESSAMAvlessAVTVLESSTVTvlesstvtvlepsvvtvpeppvvaEPDYVTIPVPVVSALEPsVPVLE 1421
Cdd:PRK10811  923 PVTEQPQVITESDVAVA-----QEVAEHAEPVV------------------------EPQDETADIEEAAETAE-VVVAE 972

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17046383  1422 PAVSVLQPSMIVSEPSVSVQESTVtvsEPAVTVSEQTQVIPTEVAIESTPM 1472
Cdd:PRK10811  973 PEVVAQPAAPVVAEVAAEVETVTA---VEPEVAPAQVPEATVEHNHATAPM 1020
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 2370-2408 4.46e-03

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 37.90  E-value: 4.46e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 17046383 2370 KHPVSALMEiCNKRRWQPPEFLLVHDSGPDHRKHFLFRV 2408
Cdd:cd19914    1 KNPISVLME-HSQKSGNMCEFQLLSQEGPPHDPKFTYCV 38
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
2362-2409 4.81e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.85  E-value: 4.81e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 17046383 2362 AAMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVL 2409
Cdd:COG0571  149 EIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVL 196
PHA03369 PHA03369
capsid maturational protease; Provisional
 353-691 5.19e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 41.91  E-value: 5.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   353 SSMTRPQELPELPKTTALELQESSVASAMELP--GPPAT-SMPELQGPPVTP---VLELPGPSAT----PVPELPGPLST 422
Cdd:PHA03369  336 STINGLKAHNEILKTASLTAPSRVLAAAAKVAviAAPQThTGPADRQRPQRPdgiPYSVPARSPMtaypPVPQFCGDPGL 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   423 PVPELPGPPATAVPELPGPSVTPVPqlsqelpglpapsmgleppqevPEPSVMAQELPGLPLVTAAVELPEQPAVTVAME 502
Cdd:PHA03369  416 VSPYNPQSPGTSYGPEPVGPVPPQP----------------------TNPYVMPISMANMVYPGHPQEHGHERKRKRGGE 473

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   503 LTEQpvtTTELEQPVGMTTVEHPGHPEVTTATGLLGQPEATMVLELPGQPVATTALELPGQPSVT-GVPELPGLPSATRA 581
Cdd:PHA03369  474 LKEE---LIETLKLVKKLKEEQESLAKELEATAHKSEIKKIAESEFKNAGAKTAAANIEPNCSADaAAPATKRARPETKT 550

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   582 LELSGQPVATGALELPGPlMAAGALEFSGQSGAAGALELLGQPLATGVLEL----PGQPGAPELPGQPVATVALeiSVQS 657
Cdd:PHA03369  551 ELEAVVRFPYQIRNMESP-AFVHSFTSTTLAAAAGQGSDTAEALAGAIETLltqaSAQPAGLSLPAPAVPVNAS--TPAS 627

                         330       340       350
                  ....*....|....*....|....*....|....
gi 17046383   658 VVTTSELSTMTVsqslEVPSTTALESYNTVAQEL 691
Cdd:PHA03369  628 TPPPLAPQEPPQ----PGTSAPSLETSLPQQKPV 657
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 280-472 5.61e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 41.84  E-value: 5.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   280 ESTSPEPSKIMLVEPPVAKVLE--PSETLVVSS-----------ETPTEVYPEPSTSTTmdfPESSAIEALRLPEQPVDV 346
Cdd:PLN03209  337 DGPKPVPTKPVTPEAPSPPIEEepPQPKAVVPRplspytayedlKPPTSPIPTPPSSSP---ASSKSVDAVAKPAEPDVV 413

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   347 PSEIADSSMTRPQELPELPKTTA----------LELQESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATPVPEL 416
Cdd:PLN03209  414 PSPGSASNVPEVEPAQVEAKKTRplspyaryedLKPPTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAPPPAN 493

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 17046383   417 PGPLST-PVPELPGPPATAVPELPGPSVTPVPQLSQELPGLPAPSMGLEPPQEVPEP 472
Cdd:PLN03209  494 MRPLSPyAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQP 550
PRK14960 PRK14960
DNA polymerase III subunit gamma/tau;
347-597 5.80e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237868 [Multi-domain]  Cd Length: 702  Bit Score: 41.96  E-value: 5.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   347 PSEIADSSMTRPQELPELPKTTALElQESSVASAMELPGPPATSMPELQGPPVTPVLElPGPSATPVPElpgplstPVPE 426
Cdd:PRK14960  363 PNEILVSEPVQQNGQAEVGLNSQAQ-TAQEITPVSAVQPVEVISQPAMVEPEPEPEPE-PEPEPEPEPE-------PEPE 433

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   427 lpgppatavpelPGPSVTPVPQLSQELPGLPAPS---MGLEppQEVPEPSVMAQELPGLPlvtaaveLPEQPAVTVamel 503
Cdd:PRK14960  434 ------------PEPEPEPEPQPNQDLMVFDPNHhelIGLE--SAVVQETVSVLEEDFIP-------VPEQKLVQV---- 488

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   504 teQPVTTTELEQPVGMTTVEHPGHPEVTTATGLLGQPeaTMVLELPGQPV--ATTALELPGQPSVTGVPElpglPSATRA 581
Cdd:PRK14960  489 --QAETQVKQIEPEPASTAEPIGLFEASSAEFSLAQD--TSAYDLVSEPVieQQSLVQAEIVETVAVVKE----PNATDN 560

                         250
                  ....*....|....*.
gi 17046383   582 LELSGQPVatgaLELP 597
Cdd:PRK14960  561 SQLMPQDI----LKLP 572
PHA03379 PHA03379
EBNA-3A; Provisional
 161-474 5.82e-03

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 41.97  E-value: 5.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   161 EPSAVALELPTRAFGPSETNESPAVVLEPPVVSMEVSEP--HILETLKPAtktaeLSVVSTSVISEQSEQSVAVMPEPSM 238
Cdd:PHA03379  463 APCPVAQLPPGPLQDLEPGDQLPGVVQDGRPACAPVPAPagPIVRPWEAS-----LSQVPGVAFAPVMPQPMPVEPVPVP 537

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   239 TKILDSfAAAPVPTTTLVLKSSEPvvTMSVEYQMKSVLKSVESTSPEPSKIMLVEPPVAKV------------LEPSETL 306
Cdd:PHA03379  538 TVALER-PVCPAPPLIAMQGPGET--SGIVRVRERWRPAPWTPNPPRSPSQMSVRDRLARLraeaqpyqasveVQPPQLT 614

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   307 VVSSETPTEVYPEPSTSTTMDFPESSAIEALRLPEQPVDVPSEIaDSSMTRPQE--------------LPELPKTTALEL 372
Cdd:PHA03379  615 QVSPQQPMEYPLEPEQQMFPGSPFSQVADVMRAGGVPAMQPQYF-DLPLQQPISqgaplaplrasmgpVPPVPATQPQYF 693

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   373 Q-------ESSVASAMELPGPPATS--MPELQGPPVTPVLELPGPSATPVPELPGPLSTPV-------PELPGPPATA-- 434
Cdd:PHA03379  694 DipltepiNQGASAAHFLPQQPMEGplVPERWMFQGATLSQSVRPGVAQSQYFDLPLTQPInhgapaaHFLHQPPMEGpw 773

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 17046383   435 VPE---LPGPSVTP-VPQLSQELPGLPAPSMGLEPPQEVPEPSV 474
Cdd:PHA03379  774 VPEqwmFQGAPPSQgTDVVQHQLDALGYVLHVLNHPGVPVSPAV 817
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 2370-2412 7.56e-03

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 37.27  E-value: 7.56e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 17046383 2370 KHPVSALMEICNKRRwQPPEFLLVHDSGPDHRKHFLFRVLRNG 2412
Cdd:cd19902    1 KNPVSALMEYAQSRG-VTAEIEVLSQSGPPHNPRFKAAVFVGG 42
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 374-516 8.11e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.51  E-value: 8.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   374 ESSVASAMELPGPPATSMPELQGPPVTPVLELPGPSATPVPELPGPLSTPVPELPGPPATAVPELPGPSVTPVPQLSQEL 453
Cdd:PRK07764  638 EASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDP 717

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17046383   454 PGLPA-PSMGLEPPQEVPEPSVMAQELPGLPLVTAAVEL---PEQPAVTVAMELTEQPVTTTELEQP 516
Cdd:PRK07764  718 AAQPPqAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAqppPPPAPAPAAAPAAAPPPSPPSEEEE 784
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 347-474 8.83e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 41.24  E-value: 8.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17046383   347 PSEIADSSMTRPQELPELPKTTALELQESSVASAMELPGPPATSMPELQgPPVTPVLELPGPSATPVPELPGPLSTPVPE 426
Cdd:PRK14951  348 PDEYAALTMVLLRLLAFKPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQ-AAAAPAPAAAPAAAASAPAAPPAAAPPAPV 426

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 17046383   427 LPgPPATAVPELPGPSVTPVPQlSQELPGLPAPSMGLEPPQEVPEPSV 474
Cdd:PRK14951  427 AA-PAAAAPAAAPAAAPAAVAL-APAPPAQAAPETVAIPVRVAPEPAV 472
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 2372-2404 9.45e-03

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380681  Cd Length: 67  Bit Score: 37.01  E-value: 9.45e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 17046383 2372 PVSALMEICNKRRWQPPEFLLVHDSGPDHRKHF 2404
Cdd:cd10844    2 PVGALQELVVQKGWRLPEYTVTQESGPAHRKEF 34
 
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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