|
Name |
Accession |
Description |
Interval |
E-value |
| rRNA_proc-arch |
pfam13234 |
rRNA-processing arch domain; Mtr4 is the essential RNA helicase, and is an exosome-activating ... |
236-495 |
4.10e-109 |
|
rRNA-processing arch domain; Mtr4 is the essential RNA helicase, and is an exosome-activating cofactor. This arch domain is carried in Mtr4 and Ski2 (the cytosolic homolog of Mtr4). The arch domain is required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity.
Pssm-ID: 463813 Cd Length: 267 Bit Score: 331.17 E-value: 4.10e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 236 EYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEENVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVK 315
Cdd:pfam13234 1 EYMLKRSFSQFQNQASLPELEKKLKELEKELASIKIPDEEDIKEYYDLRQQLEKLNEDIREVILHPPYGLPFLQPGRLVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 316 VK-NEGDDFGWGVVVNFSKKSNvKPNSGELDPLYVVEVLLRCSKES-------LKNSATEAAKPAKPDEKGEMQVVPVLV 387
Cdd:pfam13234 81 VKdNGDQDFGWGVVVNFKKRKK-NGKAEPPQESYIVDVLLVLALVSspedldkFNDVNPEGFRPAPPGEKGEMEVVPVPL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 388 HLLSAISTVRLYIPKDLRPVDNRQSVLKSIQEVQRRFPDGVPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDP 467
Cdd:pfam13234 160 SDIEAISSVRLKLPKDLRPAEAREAVLKALQELKRRFPDGIPLLDPIEDMKIKDDEFKELLRKIEVLESRLESHPLHKSP 239
|
250 260
....*....|....*....|....*...
gi 1907094556 468 NLETVYTLCERKAQIALDIKSAKRELKK 495
Cdd:pfam13234 240 RLEELYALYHEKVELQEEIKELKKEISD 267
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
23-668 |
5.29e-82 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 275.28 E-value: 5.29e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 23 KGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFNNAidclsDEDKKLPQVEHVLPLL 102
Cdd:COG4581 224 LRPPSRHEVIEELDRGGLLPAIVFIFSRRGCDEAAQQLLSARLTTKEERAEIREAIDEF-----AEDFSVLFGKTLSRLL 298
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 103 KRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKDFRWISSGEYIQMSGRAGRRG 182
Cdd:COG4581 299 RRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSKFDGERHRPLTAREFHQIAGRAGRRG 378
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 183 MDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLR---VEEInpEYMLEKSFYQFQHYRAIPGVVEKV 259
Cdd:COG4581 379 IDTEGHVVVLAPEHDDPKKFARLASARPEPLRSSFRPSYNMVLNLLArpgLERA--RELLEDSFAQFQADRSVVGLARRA 456
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 260 KNSEEQYNKIVI---PNEENVVIYYKIRQQLAKLgkeieeyihkpkyclpflqpgrlvkvknegddfgwgvvvnfskksn 336
Cdd:COG4581 457 RELERALAGVVErlaCDLGDLQEYFALRQPLSPL---------------------------------------------- 490
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 337 vkpnsgeldplyvvevllrcskeslknsatEAAKPAKPDEkgEMQVVPVLVHLLSAISTVRLYIPKDLRpvDNRQSVLKS 416
Cdd:COG4581 491 ------------------------------EALERESPAY--ALDVVSVPEATLEDPRPVLLAQDRRAR--GEAAAAMKA 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 417 IQEVQRRfpdgvplldpiddmgiqdqglkkviqkVEAFEHRMYSHPLHNDPnLETVYTL----CERKAQIALDIKSAKRE 492
Cdd:COG4581 537 AIEYDER---------------------------MERLEEVLRPHPLHECP-LERAFELyretHPWVRDIELRPKSVARD 588
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 493 lkkartvlqMDELkcrKRVLRRLGFAtSSDVIEMKGRVACEISSAdelllTEMMFNGLFNDLSSEQATALLSCFVF---Q 569
Cdd:COG4581 589 ---------FDRF---CELLREYGYL-DDLTLTSEGLLLRYLYDA-----AEALRQGVPDDLDPEELAALISWLVEevrR 650
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 570 ENSSEMPKL-TEQLAGPLRQMQECAKRIAKVSAEAKLEideetylssfKPHLmDVVYTWATGATFAHICKMTDVFEGSII 648
Cdd:COG4581 651 VDSSEWERLpSPANRRAFVLVNALFRRLELLERRHGLP----------ELDP-GLAGAWASGADLAEVLDATDLDAGDFV 719
|
650 660
....*....|....*....|....
gi 1907094556 649 RCMRRL----EELLRQMCQAAKAI 668
Cdd:COG4581 720 RWVRQVidpdPELRRTARAAVDLI 743
|
|
| DSHCT |
pfam08148 |
DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box ... |
522-689 |
1.84e-71 |
|
DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Pssm-ID: 462374 Cd Length: 154 Bit Score: 228.87 E-value: 1.84e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 522 DVIEMKGRVACEISSADELLLTEMMFNGLFNDLSSEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAkVSA 601
Cdd:pfam08148 1 DVVTLKGRVACEIRSENELLLTELLFSGVFDDLDPEELAALLSAFVFEEKRREPYLPSPELAEALRLLEEIAHRIA-VSR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 602 EakleideetylssFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGI 681
Cdd:pfam08148 80 F-------------LDFGLMEVVYAWARGASFAEICKLTDLDEGDIVRLIRRLDELLRQIANAAKIIGDPELREKAEEAI 146
|
....*...
gi 1907094556 682 TKIKRDIV 689
Cdd:pfam08148 147 ELIKRDIV 154
|
|
| KOW_Mtr4 |
cd13154 |
KOW_Mtr4 is an inserted domain in Mtr4 globular domain; Mtr4 is a conserved helicase with a ... |
307-432 |
3.61e-71 |
|
KOW_Mtr4 is an inserted domain in Mtr4 globular domain; Mtr4 is a conserved helicase with a core DExH region that cooperates with the eukaryotic nuclear exosome in RNA processing and degradation. KOW_Mtr4 motif might be involved in presenting RNA substrates to the helicase core. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW motif is located at the extended insertion of Mtr4 protein.
Pssm-ID: 240518 Cd Length: 129 Bit Score: 227.07 E-value: 3.61e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 307 FLQPGRLVKVKNEGDDFGWGVVVNFSKKSNVKPNSGELDP--LYVVEVLLRCSKESLKNSA-TEAAKPAKPDEKGEMQVV 383
Cdd:cd13154 1 FLQPGRLVKVKVGDDDFGWGVVVNFQKRPNKKNGSENSPPqeSYVVDVLLNCSSGSSINNGsPSGIRPPGPGEKGEMEVV 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1907094556 384 PVLVHLLSAISTVRLYIPKDLRPVDNRQSVLKSIQEVQRRFPDGVPLLD 432
Cdd:cd13154 81 PVLLSLIQAISSIRLYLPKDLRSADARQSVGKSLQEVKRRFPDGLPLLD 129
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
2-194 |
2.59e-60 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 199.32 E-value: 2.59e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 2 QVLRDAGDLAKGDQKGRKggtKGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMtkldfntdeekkmveevfnna 81
Cdd:cd18795 8 YVLGFNGLGIKLRVDVMN---KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDL--------------------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 82 idclsdedkklpqvehvlpllkRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGK 161
Cdd:cd18795 64 ----------------------AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDGK 121
|
170 180 190
....*....|....*....|....*....|...
gi 1907094556 162 DFRWISSGEYIQMSGRAGRRGMDDRGIVILMVD 194
Cdd:cd18795 122 GYRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
20-228 |
1.49e-18 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 89.94 E-value: 1.49e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 20 GGTKGPSNVFKIVKMIMERNFQpVIIFSFSKKDCEAYAlqmtkldfntdeekKMVEEVFN--NAIDCLSDEDKKLPqvEH 97
Cdd:PRK01172 217 GYERSQVDINSLIKETVNDGGQ-VLVFVSSRKNAEDYA--------------EMLIQHFPefNDFKVSSENNNVYD--DS 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 98 VLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKDFRWISSGEYIQMSGR 177
Cdd:PRK01172 280 LNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNMEIKQMIGR 359
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1907094556 178 AGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLL 228
Cdd:PRK01172 360 AGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVRFNTL 410
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
94-182 |
3.91e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 73.79 E-value: 3.91e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 94 QVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMP-ARTVLFtnarkYDgkdfRWISSGEYI 172
Cdd:smart00490 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVII-----YD----LPWSPASYI 72
|
90
....*....|
gi 1907094556 173 QMSGRAGRRG 182
Cdd:smart00490 73 QRIGRAGRAG 82
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rRNA_proc-arch |
pfam13234 |
rRNA-processing arch domain; Mtr4 is the essential RNA helicase, and is an exosome-activating ... |
236-495 |
4.10e-109 |
|
rRNA-processing arch domain; Mtr4 is the essential RNA helicase, and is an exosome-activating cofactor. This arch domain is carried in Mtr4 and Ski2 (the cytosolic homolog of Mtr4). The arch domain is required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity.
Pssm-ID: 463813 Cd Length: 267 Bit Score: 331.17 E-value: 4.10e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 236 EYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYNKIVIPNEENVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVK 315
Cdd:pfam13234 1 EYMLKRSFSQFQNQASLPELEKKLKELEKELASIKIPDEEDIKEYYDLRQQLEKLNEDIREVILHPPYGLPFLQPGRLVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 316 VK-NEGDDFGWGVVVNFSKKSNvKPNSGELDPLYVVEVLLRCSKES-------LKNSATEAAKPAKPDEKGEMQVVPVLV 387
Cdd:pfam13234 81 VKdNGDQDFGWGVVVNFKKRKK-NGKAEPPQESYIVDVLLVLALVSspedldkFNDVNPEGFRPAPPGEKGEMEVVPVPL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 388 HLLSAISTVRLYIPKDLRPVDNRQSVLKSIQEVQRRFPDGVPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDP 467
Cdd:pfam13234 160 SDIEAISSVRLKLPKDLRPAEAREAVLKALQELKRRFPDGIPLLDPIEDMKIKDDEFKELLRKIEVLESRLESHPLHKSP 239
|
250 260
....*....|....*....|....*...
gi 1907094556 468 NLETVYTLCERKAQIALDIKSAKRELKK 495
Cdd:pfam13234 240 RLEELYALYHEKVELQEEIKELKKEISD 267
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
23-668 |
5.29e-82 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 275.28 E-value: 5.29e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 23 KGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFNNAidclsDEDKKLPQVEHVLPLL 102
Cdd:COG4581 224 LRPPSRHEVIEELDRGGLLPAIVFIFSRRGCDEAAQQLLSARLTTKEERAEIREAIDEF-----AEDFSVLFGKTLSRLL 298
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 103 KRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKDFRWISSGEYIQMSGRAGRRG 182
Cdd:COG4581 299 RRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSKFDGERHRPLTAREFHQIAGRAGRRG 378
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 183 MDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLR---VEEInpEYMLEKSFYQFQHYRAIPGVVEKV 259
Cdd:COG4581 379 IDTEGHVVVLAPEHDDPKKFARLASARPEPLRSSFRPSYNMVLNLLArpgLERA--RELLEDSFAQFQADRSVVGLARRA 456
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 260 KNSEEQYNKIVI---PNEENVVIYYKIRQQLAKLgkeieeyihkpkyclpflqpgrlvkvknegddfgwgvvvnfskksn 336
Cdd:COG4581 457 RELERALAGVVErlaCDLGDLQEYFALRQPLSPL---------------------------------------------- 490
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 337 vkpnsgeldplyvvevllrcskeslknsatEAAKPAKPDEkgEMQVVPVLVHLLSAISTVRLYIPKDLRpvDNRQSVLKS 416
Cdd:COG4581 491 ------------------------------EALERESPAY--ALDVVSVPEATLEDPRPVLLAQDRRAR--GEAAAAMKA 536
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 417 IQEVQRRfpdgvplldpiddmgiqdqglkkviqkVEAFEHRMYSHPLHNDPnLETVYTL----CERKAQIALDIKSAKRE 492
Cdd:COG4581 537 AIEYDER---------------------------MERLEEVLRPHPLHECP-LERAFELyretHPWVRDIELRPKSVARD 588
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 493 lkkartvlqMDELkcrKRVLRRLGFAtSSDVIEMKGRVACEISSAdelllTEMMFNGLFNDLSSEQATALLSCFVF---Q 569
Cdd:COG4581 589 ---------FDRF---CELLREYGYL-DDLTLTSEGLLLRYLYDA-----AEALRQGVPDDLDPEELAALISWLVEevrR 650
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 570 ENSSEMPKL-TEQLAGPLRQMQECAKRIAKVSAEAKLEideetylssfKPHLmDVVYTWATGATFAHICKMTDVFEGSII 648
Cdd:COG4581 651 VDSSEWERLpSPANRRAFVLVNALFRRLELLERRHGLP----------ELDP-GLAGAWASGADLAEVLDATDLDAGDFV 719
|
650 660
....*....|....*....|....
gi 1907094556 649 RCMRRL----EELLRQMCQAAKAI 668
Cdd:COG4581 720 RWVRQVidpdPELRRTARAAVDLI 743
|
|
| DSHCT |
pfam08148 |
DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box ... |
522-689 |
1.84e-71 |
|
DSHCT (NUC185) domain; This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Pssm-ID: 462374 Cd Length: 154 Bit Score: 228.87 E-value: 1.84e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 522 DVIEMKGRVACEISSADELLLTEMMFNGLFNDLSSEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAkVSA 601
Cdd:pfam08148 1 DVVTLKGRVACEIRSENELLLTELLFSGVFDDLDPEELAALLSAFVFEEKRREPYLPSPELAEALRLLEEIAHRIA-VSR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 602 EakleideetylssFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGI 681
Cdd:pfam08148 80 F-------------LDFGLMEVVYAWARGASFAEICKLTDLDEGDIVRLIRRLDELLRQIANAAKIIGDPELREKAEEAI 146
|
....*...
gi 1907094556 682 TKIKRDIV 689
Cdd:pfam08148 147 ELIKRDIV 154
|
|
| KOW_Mtr4 |
cd13154 |
KOW_Mtr4 is an inserted domain in Mtr4 globular domain; Mtr4 is a conserved helicase with a ... |
307-432 |
3.61e-71 |
|
KOW_Mtr4 is an inserted domain in Mtr4 globular domain; Mtr4 is a conserved helicase with a core DExH region that cooperates with the eukaryotic nuclear exosome in RNA processing and degradation. KOW_Mtr4 motif might be involved in presenting RNA substrates to the helicase core. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW motif is located at the extended insertion of Mtr4 protein.
Pssm-ID: 240518 Cd Length: 129 Bit Score: 227.07 E-value: 3.61e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 307 FLQPGRLVKVKNEGDDFGWGVVVNFSKKSNVKPNSGELDP--LYVVEVLLRCSKESLKNSA-TEAAKPAKPDEKGEMQVV 383
Cdd:cd13154 1 FLQPGRLVKVKVGDDDFGWGVVVNFQKRPNKKNGSENSPPqeSYVVDVLLNCSSGSSINNGsPSGIRPPGPGEKGEMEVV 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1907094556 384 PVLVHLLSAISTVRLYIPKDLRPVDNRQSVLKSIQEVQRRFPDGVPLLD 432
Cdd:cd13154 81 PVLLSLIQAISSIRLYLPKDLRSADARQSVGKSLQEVKRRFPDGLPLLD 129
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
2-194 |
2.59e-60 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 199.32 E-value: 2.59e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 2 QVLRDAGDLAKGDQKGRKggtKGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMtkldfntdeekkmveevfnna 81
Cdd:cd18795 8 YVLGFNGLGIKLRVDVMN---KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDL--------------------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 82 idclsdedkklpqvehvlpllkRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGK 161
Cdd:cd18795 64 ----------------------AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDGK 121
|
170 180 190
....*....|....*....|....*....|...
gi 1907094556 162 DFRWISSGEYIQMSGRAGRRGMDDRGIVILMVD 194
Cdd:cd18795 122 GYRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
20-298 |
3.46e-33 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 134.25 E-value: 3.46e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 20 GGTKGPSNVFKIVKMIMERNFQpVIIFSFSKKDCEAYALQMTKL--DFNTDEEKKMVEEVFNNAIDC--LSDEDKKLPQv 95
Cdd:COG1204 220 GSRRSKDPTLALALDLLEEGGQ-VLVFVSSRRDAESLAKKLADElkRRLTPEEREELEELAEELLEVseETHTNEKLAD- 297
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 96 ehvlpLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKDfrwISSGEYIQMS 175
Cdd:COG1204 298 -----CLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKRGGMVP---IPVLEFKQMA 369
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 176 GRAGRRGMDDRGIVILMVDEKMSPT-IGKQLLKGSADPLNSAFHLTYNMVLNLLRV---------EEINpEYmLEKSFYQ 245
Cdd:COG1204 370 GRAGRPGYDPYGEAILVAKSSDEADeLFERYILGEPEPIRSKLANESALRTHLLALiasgfansrEELL-DF-LENTFYA 447
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*
gi 1907094556 246 FQHYRA-IPGVVEKVKNSEEQYNKIvipNEENVviyykiRQQLAKLGKEI-EEYI 298
Cdd:COG1204 448 YQYDKGdLEEVVDDALEFLLENGFI---EEDGD------RLRATKLGKLVsRLYI 493
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
20-228 |
1.49e-18 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 89.94 E-value: 1.49e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 20 GGTKGPSNVFKIVKMIMERNFQpVIIFSFSKKDCEAYAlqmtkldfntdeekKMVEEVFN--NAIDCLSDEDKKLPqvEH 97
Cdd:PRK01172 217 GYERSQVDINSLIKETVNDGGQ-VLVFVSSRKNAEDYA--------------EMLIQHFPefNDFKVSSENNNVYD--DS 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 98 VLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKDFRWISSGEYIQMSGR 177
Cdd:PRK01172 280 LNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNMEIKQMIGR 359
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1907094556 178 AGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLL 228
Cdd:PRK01172 360 AGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVRFNTL 410
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
94-182 |
3.91e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 73.79 E-value: 3.91e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 94 QVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMP-ARTVLFtnarkYDgkdfRWISSGEYI 172
Cdd:smart00490 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVII-----YD----LPWSPASYI 72
|
90
....*....|
gi 1907094556 173 QMSGRAGRRG 182
Cdd:smart00490 73 QRIGRAGRAG 82
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
44-192 |
1.06e-15 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 81.16 E-value: 1.06e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 44 IIFSFSKKDCEAYALQMTkldfntDEEKKMVEEVFNNAIDCLSDEDKKLPQVEHVLPL---LKRGIGIHHGGLLPILKET 120
Cdd:PRK02362 247 LVFVSSRRNAEGFAKRAA------SALKKTLTAAERAELAELAEEIREVSDTETSKDLadcVAKGAAFHHAGLSREHREL 320
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907094556 121 IEILFSEGLIKALFATETFAMGINMPARTVLFTNARKYDGKD-FRWISSGEYIQMSGRAGRRGMDDRGIVILM 192
Cdd:PRK02362 321 VEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAgMQPIPVLEYHQMAGRAGRPGLDPYGEAVLL 393
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
44-247 |
2.93e-13 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 73.31 E-value: 2.93e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 44 IIFSFSKKDCEAYALQMTKL--DFNTDEEKKMVEEvfnnaidcLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETI 121
Cdd:PRK00254 242 LVFVNTRRSAEKEALELAKKikRFLTKPELRALKE--------LADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLI 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 122 EILFSEGLIKALFATETFAMGINMPARTVLFTNARKYdgKDFRW--ISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSP 199
Cdd:PRK00254 314 EDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRY--SNFGWedIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPS 391
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 1907094556 200 TIGKQLLKGSADPLNSAFHLTYNM---VLNLL------RVEEINPeyMLEKSFYQFQ 247
Cdd:PRK00254 392 KLMERYIFGKPEKLFSMLSNESAFrsqVLALItnfgvsNFKELVN--FLERTFYAHQ 446
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
110-214 |
9.94e-10 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 61.83 E-value: 9.94e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 110 HGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLF-TNARkydGKDfrWISSGEYIQMSGRAGRRGMDDRGI 188
Cdd:COG1202 455 HAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFdSLAM---GIE--WLSVQEFHQMLGRAGRPDYHDRGK 529
|
90 100 110
....*....|....*....|....*....|....*
gi 1907094556 189 VILMV------DEKMSPT---IGKQLLKGSADPLN 214
Cdd:COG1202 530 VYLLVepgksyHRSMEMTedeVAFKLLKGEMEDVA 564
|
|
| SF2_C_suv3 |
cd18805 |
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ... |
131-192 |
2.14e-08 |
|
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 is a DEAD-like helicase 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: 350192 [Multi-domain] Cd Length: 135 Bit Score: 53.33 E-value: 2.14e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907094556 131 KALFATETFAMGINMPARTVLFTNARKYDGKDFRWISSGEYIQMSGRAGRRGMD-DRGIVILM 192
Cdd:cd18805 72 DVLVASDAIGMGLNLNIRRVIFSSLSKFDGNEMRPLSPSEVKQIAGRAGRFGSHfPEGEVTTL 134
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
30-182 |
4.66e-08 |
|
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: 51.44 E-value: 4.66e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 30 KIVKMIMERNFQPVIIFSFSKKDCEAyalqmtkldfntdeekkmveevfnnaidclsdedkklpqvEHVLPLLKRGIGIH 109
Cdd:pfam00271 5 ALLELLKKERGGKVLIFSQTKKTLEA----------------------------------------ELLLEKEGIKVARL 44
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907094556 110 HGGLLPILKETIEILFSEGLIKALFATETFAMGINMP-ARTVLFtnarkYDGKDfrwiSSGEYIQMSGRAGRRG 182
Cdd:pfam00271 45 HGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPdVDLVIN-----YDLPW----NPASYIQRIGRAGRAG 109
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
118-191 |
6.29e-06 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The 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: 350172 [Multi-domain] Cd Length: 77 Bit Score: 44.62 E-value: 6.29e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907094556 118 KETIEILFSEglIKALFATETFAMGINMP-ARTVLFTNarkydgkdfRWISSGEYIQMSGRAGrRGMDDRGIVIL 191
Cdd:cd18785 13 IEHAEEIASS--LEILVATNVLGEGIDVPsLDTVIFFD---------PPSSAASYIQRVGRAG-RGGKDEGEVIL 75
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
61-183 |
1.05e-04 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 42.58 E-value: 1.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907094556 61 TKLDFNTDEEKKMVEEVFNNA--IDCLSDEDkklpqVEHVLPLLKRgIGIH----HGGLLPILKETIEILFSEGLIKALF 134
Cdd:cd18794 12 DKKDEKLDLLKRIKVEHLGGSgiIYCLSRKE-----CEQVAARLQS-KGISaaayHAGLEPSDRRDVQRKWLRDKIQVIV 85
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 1907094556 135 ATETFAMGINMP-ARTVLFTNARKydgkdfrwiSSGEYIQMSGRAGRRGM 183
Cdd:cd18794 86 ATVAFGMGIDKPdVRFVIHYSLPK---------SMESYYQESGRAGRDGL 126
|
|
| |
