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Conserved domains on  [gi|429892591|gb|AGA18840|]
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spindle E, partial [Drosophila melanogaster]

Protein Classification

DEAD-like_helicase_N and TUDOR domain-containing protein( domain architecture ID 13388263)

DEAD-like_helicase_N and TUDOR domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 4-101 5.92e-46

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


:

Pssm-ID: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 162.70  E-value: 5.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591    4 KVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCR 83
Cdd:cd18791    74 KLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAE 153

                          90
                  ....*....|....*...
gi 429892591   84 QRAGRVGRLRSGRVYRMV 101
Cdd:cd18791   154 QRAGRAGRTRPGKCYRLY 171
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
14-305 3.47e-37

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG1643:

Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 151.00  E-value: 3.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   14 MTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRAGRVGRLR 93
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLA 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   94 SGRVYRMVNKHFYQReMPEFGIPEMLRLPLQNSVLKAKVLNMGSPVEiLALaLSPP---NLSDIHNtilLLKEVGALylt 170
Cdd:COG1643   337 PGICYRLWSEEDFAR-RPAFTDPEILRADLASLILELAAWGLGDPED-LPF-LDPPparAIADARA---LLQELGAL--- 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  171 vdgiyDPlDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGlfaheg*******sfwmhyIFSDGS 250
Cdd:COG1643   408 -----DA-DGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERD-------------------PRRGAA 462

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 429892591  251 GSDLvaiwrvyLTYLNIVENGHDQesairwaKRFHVSLRSLKEIHLLVQELRVRC 305
Cdd:COG1643   463 GSDL-------LARLNLWRRLREQ-------QREFLSYLRLREWRDLARQLRRLL 503
TUDOR pfam00567
Tudor domain;
500-624 1.35e-21

Tudor domain;


:

Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 90.88  E-value: 1.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   500 KTISGSITCIVNCGKFFFQPQS----FEECIRNMSEIFNAPQQlrnyVTNASAIAKGMMVLAKRDSYFQRATVirpeNQS 575
Cdd:pfam00567    1 STIDVVVSHIESPSTFYIQPKSdskkLEKLTEELQEYYASKPP----ESLPPAVGDGCVAAFSEDGKWYRAKI----TES 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 429892591   576 NRQPMFYVRFIDYGNCTLLPMQLMRLMPRELTEqygdLPPRVFECRLAM 624
Cdd:pfam00567   73 LDDGLVEVLFIDYGNTETVPLSDLRPLPPELES----LPPQAIKCQLAG 117
 
Name Accession Description Interval E-value
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 4-101 5.92e-46

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 162.70  E-value: 5.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591    4 KVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCR 83
Cdd:cd18791    74 KLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAE 153

                          90
                  ....*....|....*...
gi 429892591   84 QRAGRVGRLRSGRVYRMV 101
Cdd:cd18791   154 QRAGRAGRTRPGKCYRLY 171
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
14-305 3.47e-37

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 151.00  E-value: 3.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   14 MTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRAGRVGRLR 93
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLA 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   94 SGRVYRMVNKHFYQReMPEFGIPEMLRLPLQNSVLKAKVLNMGSPVEiLALaLSPP---NLSDIHNtilLLKEVGALylt 170
Cdd:COG1643   337 PGICYRLWSEEDFAR-RPAFTDPEILRADLASLILELAAWGLGDPED-LPF-LDPPparAIADARA---LLQELGAL--- 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  171 vdgiyDPlDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGlfaheg*******sfwmhyIFSDGS 250
Cdd:COG1643   408 -----DA-DGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERD-------------------PRRGAA 462

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 429892591  251 GSDLvaiwrvyLTYLNIVENGHDQesairwaKRFHVSLRSLKEIHLLVQELRVRC 305
Cdd:COG1643   463 GSDL-------LARLNLWRRLREQ-------QREFLSYLRLREWRDLARQLRRLL 503
TUDOR pfam00567
Tudor domain;
500-624 1.35e-21

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 90.88  E-value: 1.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   500 KTISGSITCIVNCGKFFFQPQS----FEECIRNMSEIFNAPQQlrnyVTNASAIAKGMMVLAKRDSYFQRATVirpeNQS 575
Cdd:pfam00567    1 STIDVVVSHIESPSTFYIQPKSdskkLEKLTEELQEYYASKPP----ESLPPAVGDGCVAAFSEDGKWYRAKI----TES 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 429892591   576 NRQPMFYVRFIDYGNCTLLPMQLMRLMPRELTEqygdLPPRVFECRLAM 624
Cdd:pfam00567   73 LDDGLVEVLFIDYGNTETVPLSDLRPLPPELES----LPPQAIKCQLAG 117
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 7-222 1.79e-21

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 101.29  E-value: 1.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591    7 IVRCFSLMTPENQRDVFNPPppGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRA 86
Cdd:PRK11131  316 ILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRK 393

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   87 GRVGRLRSGRVYRMVNKH-FYQRemPEFGIPEMLRLPLQNSVLKAKVLNMGspvEILALA-LSPPNLSDIHNTILLLKEV 164
Cdd:PRK11131  394 GRCGRVSEGICIRLYSEDdFLSR--PEFTDPEILRTNLASVILQMTALGLG---DIAAFPfVEAPDKRNIQDGVRLLEEL 468

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591  165 GALYLTVDGiydpLDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLS 222
Cdd:PRK11131  469 GAITTDEQA----SAYKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALS 522
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 14-120 1.25e-12

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 72.26  E-value: 1.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   14 MTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRAGRVGRLR 93
Cdd:PRK11664  249 LSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLE 328

                          90       100
                  ....*....|....*....|....*..
gi 429892591   94 SGRVYRMVNKHFYQReMPEFGIPEMLR 120
Cdd:PRK11664  329 PGICLHLYSKEQAER-AAAQSEPEILH 354
HELICc smart00490
helicase superfamily c-terminal domain;
2-91 2.84e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 2.84e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591      2 NIKVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLakvkvtdtassfsslrltWASKAN 81
Cdd:smart00490    9 ELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL------------------PWSPAS 70

                            90
                    ....*....|
gi 429892591     82 CRQRAGRVGR 91
Cdd:smart00490   71 YIQRIGRAGR 80
Tudor_vreteno-like_rpt1 cd20444
first Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins; ...
 549-606 5.20e-10

first Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins; Vreteno is a gonad-specific protein essential for germline development to repress transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process in both germline and somatic gonadal tissues by mediating the repression of transposable elements during meiosis. Vreteno contains two Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410515  Cd Length: 55  Bit Score: 55.77  E-value: 5.20e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591  549 IAKGMMVLAKRDSYFQRATVIRPENqsnRQPMFYVRFIDYGNCTLLPMQLMRLMPREL 606
Cdd:cd20444     1 PTPGQMVIAKFDGNHYRAIVLRVLN---PDLKILVRFVDFGNVEVMKLENLYECPEYL 55
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 158-231 1.71e-09

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 56.09  E-value: 1.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 429892591   158 ILLLKEVGALyltvdgiyDPlDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGLFAHEG 231
Cdd:pfam04408    2 LELLYYLGAL--------DE-DGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPN 66
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 179-256 2.21e-09

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 54.97  E-value: 2.21e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591    179 DGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGLFAHEG*******sfwMHYIFSDGsGSDLVA 256
Cdd:smart00847    8 DGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKREDADA----ARRRFADP-ESDHLT 80
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 2-91 2.41e-09

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 55.68  E-value: 2.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591     2 NIKVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLakvkvtdtassfsslrltWASKAN 81
Cdd:pfam00271   36 KEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDL------------------PWNPAS 97

                           90
                   ....*....|
gi 429892591    82 CRQRAGRVGR 91
Cdd:pfam00271   98 YIQRIGRAGR 107
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 547-606 2.52e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.20  E-value: 2.52e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 429892591    547 SAIAKGMMVLAK-RDSYFQRATVIRPENQSnrqpMFYVRFIDYGNCTLLPMQLMRLMPREL 606
Cdd:smart00333    1 PTFKVGDKVAARwEDGEWYRARIVKVDGEQ----LYEVFFIDYGNEEVVPPSDLRQLPEEL 57
 
Name Accession Description Interval E-value
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 4-101 5.92e-46

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 162.70  E-value: 5.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591    4 KVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCR 83
Cdd:cd18791    74 KLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAE 153

                          90
                  ....*....|....*...
gi 429892591   84 QRAGRVGRLRSGRVYRMV 101
Cdd:cd18791   154 QRAGRAGRTRPGKCYRLY 171
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
14-305 3.47e-37

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 151.00  E-value: 3.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   14 MTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRAGRVGRLR 93
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLA 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   94 SGRVYRMVNKHFYQReMPEFGIPEMLRLPLQNSVLKAKVLNMGSPVEiLALaLSPP---NLSDIHNtilLLKEVGALylt 170
Cdd:COG1643   337 PGICYRLWSEEDFAR-RPAFTDPEILRADLASLILELAAWGLGDPED-LPF-LDPPparAIADARA---LLQELGAL--- 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  171 vdgiyDPlDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGlfaheg*******sfwmhyIFSDGS 250
Cdd:COG1643   408 -----DA-DGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERD-------------------PRRGAA 462

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 429892591  251 GSDLvaiwrvyLTYLNIVENGHDQesairwaKRFHVSLRSLKEIHLLVQELRVRC 305
Cdd:COG1643   463 GSDL-------LARLNLWRRLREQ-------QREFLSYLRLREWRDLARQLRRLL 503
TUDOR pfam00567
Tudor domain;
500-624 1.35e-21

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 90.88  E-value: 1.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   500 KTISGSITCIVNCGKFFFQPQS----FEECIRNMSEIFNAPQQlrnyVTNASAIAKGMMVLAKRDSYFQRATVirpeNQS 575
Cdd:pfam00567    1 STIDVVVSHIESPSTFYIQPKSdskkLEKLTEELQEYYASKPP----ESLPPAVGDGCVAAFSEDGKWYRAKI----TES 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 429892591   576 NRQPMFYVRFIDYGNCTLLPMQLMRLMPRELTEqygdLPPRVFECRLAM 624
Cdd:pfam00567   73 LDDGLVEVLFIDYGNTETVPLSDLRPLPPELES----LPPQAIKCQLAG 117
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 7-222 1.79e-21

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 101.29  E-value: 1.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591    7 IVRCFSLMTPENQRDVFNPPppGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRA 86
Cdd:PRK11131  316 ILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRK 393

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   87 GRVGRLRSGRVYRMVNKH-FYQRemPEFGIPEMLRLPLQNSVLKAKVLNMGspvEILALA-LSPPNLSDIHNTILLLKEV 164
Cdd:PRK11131  394 GRCGRVSEGICIRLYSEDdFLSR--PEFTDPEILRTNLASVILQMTALGLG---DIAAFPfVEAPDKRNIQDGVRLLEEL 468

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591  165 GALYLTVDGiydpLDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLS 222
Cdd:PRK11131  469 GAITTDEQA----SAYKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALS 522
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 14-120 1.25e-12

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 72.26  E-value: 1.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   14 MTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLAKVKVTDTASSFSSLRLTWASKANCRQRAGRVGRLR 93
Cdd:PRK11664  249 LSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLE 328

                          90       100
                  ....*....|....*....|....*..
gi 429892591   94 SGRVYRMVNKHFYQReMPEFGIPEMLR 120
Cdd:PRK11664  329 PGICLHLYSKEQAER-AAAQSEPEILH 354
HELICc smart00490
helicase superfamily c-terminal domain;
2-91 2.84e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 2.84e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591      2 NIKVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLakvkvtdtassfsslrltWASKAN 81
Cdd:smart00490    9 ELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL------------------PWSPAS 70

                            90
                    ....*....|
gi 429892591     82 CRQRAGRVGR 91
Cdd:smart00490   71 YIQRIGRAGR 80
Tudor_vreteno-like_rpt1 cd20444
first Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins; ...
 549-606 5.20e-10

first Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins; Vreteno is a gonad-specific protein essential for germline development to repress transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process in both germline and somatic gonadal tissues by mediating the repression of transposable elements during meiosis. Vreteno contains two Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410515  Cd Length: 55  Bit Score: 55.77  E-value: 5.20e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591  549 IAKGMMVLAKRDSYFQRATVIRPENqsnRQPMFYVRFIDYGNCTLLPMQLMRLMPREL 606
Cdd:cd20444     1 PTPGQMVIAKFDGNHYRAIVLRVLN---PDLKILVRFVDFGNVEVMKLENLYECPEYL 55
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 158-231 1.71e-09

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 56.09  E-value: 1.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 429892591   158 ILLLKEVGALyltvdgiyDPlDGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGLFAHEG 231
Cdd:pfam04408    2 LELLYYLGAL--------DE-DGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPN 66
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 179-256 2.21e-09

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 54.97  E-value: 2.21e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 429892591    179 DGDLTYWGTIMSRLPLDTRQSRLIILGYIFNMLEEAIIIAAGLSTPGLFAHEG*******sfwMHYIFSDGsGSDLVA 256
Cdd:smart00847    8 DGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKREDADA----ARRRFADP-ESDHLT 80
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 2-91 2.41e-09

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 55.68  E-value: 2.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591     2 NIKVSIVRCFSLMTPENQRDVFNPPPPGFRKIILTTNIAESSITVPDVSYVIDFCLakvkvtdtassfsslrltWASKAN 81
Cdd:pfam00271   36 KEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDL------------------PWNPAS 97

                           90
                   ....*....|
gi 429892591    82 CRQRAGRVGR 91
Cdd:pfam00271   98 YIQRIGRAGR 107
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 547-606 2.52e-09

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 54.20  E-value: 2.52e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 429892591    547 SAIAKGMMVLAK-RDSYFQRATVIRPENQSnrqpMFYVRFIDYGNCTLLPMQLMRLMPREL 606
Cdd:smart00333    1 PTFKVGDKVAARwEDGEWYRARIVKVDGEQ----LYEVFFIDYGNEEVVPPSDLRQLPEEL 57
Tudor_TDRD1_rpt1 cd20408
first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 504-639 5.05e-06

first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410479  Cd Length: 130  Bit Score: 46.98  E-value: 5.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  504 GSITCIVNCGKFFFQPQSfEECIRNMSEIfnaPQQLRNYVTNASAIA-----KGMMVLAK--RDSYFQRATVirpENQSN 576
Cdd:cd20408     1 GTVTEFKNPGEFYIQIYT-LEVLESLVKL---TSQLKKTYASVNNHKeyipeVGEVCVAKysEDQNWYRALV---QTVDV 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 429892591  577 RQPMFYVRFIDYGNCTLLPMQlmRLMPreLTEQYGDLPPRVFECRLAMVQPSsvvsgNNRWST 639
Cdd:cd20408    74 QQKKAGVFYIDYGNEETVPLN--RIQP--LKKDIELFPPCAIKCCLANVKPP-----SGSWSE 127
Tudor_TDRD6_rpt6 cd20425
sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 506-608 5.31e-05

sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410496  Cd Length: 115  Bit Score: 43.60  E-value: 5.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  506 ITCIVNCGKFFFQPQSFEECIRNMSEIFNAPQQLRNYVtNASAIAKGMMVLA--KRDSYFQRATVirPENQSNRqpMFYV 583
Cdd:cd20425     6 VSHVNSPSDFYVQLAQDEDELSMISEKLNASKANDEEV-ECESLQLGDLICAeyPEDGLWYRAVV--KEKIPNN--LVSV 80

                          90       100
                  ....*....|....*....|....*.
gi 429892591  584 RFIDYGNCTLL-PMQLMRLmPRELTE 608
Cdd:cd20425    81 QFIDYGNTSVVqPSKIHRL-PKELLS 105
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 33-220 7.53e-05

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 46.89  E-value: 7.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591   33 IILTTNIAESSITVPDVSYVIDfcLAKVKVtdtaSSFSSLRLTWASKANCRQRAGRVGRLRSG---RVYRMVNKHFYQRE 109
Cdd:PHA02653  449 IIISTPYLESSVTIRNATHVYD--TGRVYV----PEPFGGKEMFISKSMRTQRKGRVGRVSPGtyvYFYDLDLLKPIKRI 522

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  110 MPEFgipemlrlpLQNSVLKAKVLNMGSPVEILalaLSPPNLSDIHNTILLLKEVGAlyltvdgiydpldgDLTYWGTIM 189
Cdd:PHA02653  523 DSEF---------LHNYILYAKYFNLTLPEDLF---VIPSNLDRLRKTEEYIDSFNI--------------SIEKWYEIL 576

                         170       180       190
                  ....*....|....*....|....*....|.
gi 429892591  190 SRlpldtrqsrliilgYIFNMLEEAIIIAAG 220
Cdd:PHA02653  577 SN--------------YYVNMLEYAKIYVKG 593
Tudor_AtTudor1-like cd20443
Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor ...
 537-627 1.48e-04

Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor 2 (AtTudor2), and similar proteins; The family includes AtTudor1 (also called Tudor-SN protein 1) and AtTudor2 (also called Tudor-SN protein 2 or 100 kDa coactivator-like protein). They are cytoprotective ribonucleases (RNases) required for resistance to abiotic stresses, acting as positive regulators of mRNA decapping during stress. Members of this family contain one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410514 [Multi-domain]  Cd Length: 117  Bit Score: 42.45  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  537 QQLRNYVTNASAI-------AKGMMVLAK--RDSYFQRATVIRPENQ--SNRQPMFYVRFIDYGNCTLLPMQLMRLMPRE 605
Cdd:cd20443    19 QQLEGLSLKDKANppggfnpKKGELVLAQfsADNSWNRAMVVNAPRQgtQSPKDEYEVFYIDYGNQETVPLSALRPLDPS 98

                          90       100
                  ....*....|....*....|..
gi 429892591  606 LTEqygdLPPRVFECRLAMVQP 627
Cdd:cd20443    99 VSS----APGLAQLCSLAHIKV 116
Tudor_TDRD4_rpt5 cd20418
fifth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 552-641 1.75e-04

fifth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410489  Cd Length: 105  Bit Score: 42.01  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  552 GMMVLAK-RDSYFQRATVIRPENQSnrQPMFYVRFIDYGNCTLLPMQLMRLMPRELTeQYgdlPPRVFECRLAMVQPSSV 630
Cdd:cd20418     7 EMPCLAEySDGKWYRAKLLSILEFN--PVKILVRHVDYGSTAALPTSRLRQIPAELM-QY---PCQAIKVKLAGFKPPLN 80

                          90
                  ....*....|....*..
gi 429892591  631 VSGNNR------WSTAA 641
Cdd:cd20418    81 DSETERipycpeWSMKA 97
Tudor_TDRD15_rpt2 cd20437
second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 506-623 2.02e-03

second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410508  Cd Length: 120  Bit Score: 39.32  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  506 ITCIVNCGKFFFQPQSFEECIRNMSEIFNAPQQLRNYVTNASAIAKGMMVLAKR-DSYFQRATVIR--PENQSNrqpmfy 582
Cdd:cd20437     9 ITAAVSPSKFYCQLLSWEPELSKLTTQMTLHYESVSKELNPSCENFGLLCAAKGkDGQWHRGFLQQllPPSQVK------ 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 429892591  583 VRFIDYGNCTLLPMQLMRLMPRELTeqygDLPPRVFECRLA 623
Cdd:cd20437    83 VWFIDYGNSEAVSSHSVLKLPPDFF----SLPLMSFPCSLS 119
Tudor_TDRD15_rpt6 cd20441
sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 511-590 2.29e-03

sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410512  Cd Length: 108  Bit Score: 38.57  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429892591  511 NCGKFFFQPQSFEECIRNMSEIFNApQQLRNYVTNASAIAKGMMVLAK--RDSYFQRATVIRPENQSNrqpmFYVRFIDY 588
Cdd:cd20441     1 SPSRFFIQLSEDEKVILQLAEELNE-TSEKSRENAAVKLKVGDLVAAEydEDLALYRAVITAVLPGKS----FKVEFIDY 75


                  ..
gi 429892591  589 GN 590
Cdd:cd20441    76 GN 77
 
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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