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Conserved domains on  [gi|91771922|sp|Q86US8|]
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RecName: Full=Telomerase-binding protein EST1A; AltName: Full=Ever shorter telomeres 1A; Short=hEST1A; AltName: Full=Nonsense mediated mRNA decay factor SMG6; AltName: Full=Smg-6 homolog; AltName: Full=hSmg5/7a

Protein Classification

EST1_DNA_bind and PIN_Smg6-like domain-containing protein( domain architecture ID 13487037)

protein containing domains EST1, EST1_DNA_bind, and PIN_Smg6-like

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 1241-1416 1.36e-95

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


:

Pssm-ID: 350233  Cd Length: 178  Bit Score: 304.57  E-value: 1.36e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1241 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1319
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1320 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1398
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 91771922 1399 ALTRNVPVRDIPAFLTWA 1416
Cdd:cd09885  161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 751-1103 8.64e-51

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


:

Pssm-ID: 431239  Cd Length: 279  Bit Score: 181.07  E-value: 8.64e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    751 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 830
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    831 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 910
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    911 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 987
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    988 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1067
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 91771922   1068 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1103
Cdd:pfam10373  241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 638-743 5.59e-11

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


:

Pssm-ID: 463062  Cd Length: 98  Bit Score: 60.40  E-value: 5.59e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    638 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 709
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 91771922    710 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 743
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 147-338 2.81e-03

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.20  E-value: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   147 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 224
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   225 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 303
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 91771922   304 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 338
Cdd:PRK12678  252 GDDG--EGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
 
Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 1241-1416 1.36e-95

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


Pssm-ID: 350233  Cd Length: 178  Bit Score: 304.57  E-value: 1.36e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1241 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1319
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1320 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1398
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 91771922 1399 ALTRNVPVRDIPAFLTWA 1416
Cdd:cd09885  161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 751-1103 8.64e-51

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


Pssm-ID: 431239  Cd Length: 279  Bit Score: 181.07  E-value: 8.64e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    751 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 830
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    831 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 910
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    911 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 987
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    988 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1067
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 91771922   1068 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1103
Cdd:pfam10373  241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 1248-1408 4.34e-24

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 433369  Cd Length: 131  Bit Score: 98.84  E-value: 4.34e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   1248 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 1327
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   1328 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 1407
Cdd:pfam13638   73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                   .
gi 91771922   1408 D 1408
Cdd:pfam13638  129 D 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1248-1397 1.13e-12

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 65.91  E-value: 1.13e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    1248 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 1326
Cdd:smart00670    3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91771922    1327 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 1397
Cdd:smart00670   73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 638-743 5.59e-11

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


Pssm-ID: 463062  Cd Length: 98  Bit Score: 60.40  E-value: 5.59e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    638 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 709
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 91771922    710 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 743
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
1249-1406 4.90e-06

rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 47.13  E-value: 4.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 1321
Cdd:COG1412    4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1322 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDFmpaskeepirllrEVVLLTDDRNLRVKALT 1401
Cdd:COG1412   68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                 ....*
gi 91771922 1402 RNVPV 1406
Cdd:COG1412  107 AGIPV 111
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 147-338 2.81e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.20  E-value: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   147 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 224
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   225 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 303
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 91771922   304 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 338
Cdd:PRK12678  252 GDDG--EGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 747-818 9.53e-03

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


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.40  E-value: 9.53e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 91771922  747 NYGKARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAE 818
Cdd:COG5010   69 DFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDE 140
 
Name Accession Description Interval E-value
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 1241-1416 1.36e-95

VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1.


Pssm-ID: 350233  Cd Length: 178  Bit Score: 304.57  E-value: 1.36e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1241 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1319
Cdd:cd09885    1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1320 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1398
Cdd:cd09885   81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                        170
                 ....*....|....*...
gi 91771922 1399 ALTRNVPVRDIPAFLTWA 1416
Cdd:cd09885  161 ALSRNIPVRDLPSFLKWA 178
EST1_DNA_bind pfam10373
Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the ...
 751-1103 8.64e-51

Est1 DNA/RNA binding domain; Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1.


Pssm-ID: 431239  Cd Length: 279  Bit Score: 181.07  E-value: 8.64e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    751 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 830
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    831 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 910
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    911 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 987
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    988 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1067
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 91771922   1068 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1103
Cdd:pfam10373  241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 1249-1415 1.01e-48

VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related proteins; PIN (PilT N terminus) domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and homologs are included in this family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain.


Pssm-ID: 350228  Cd Length: 152  Bit Score: 170.17  E-value: 1.01e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETdhraggyarvVQEKARKSIEFLEQRFESRDSCLRAL 1328
Cdd:cd09880    1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDP----------LGPKARSALRYIEACLKKHSRWLRVQ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1329 TSRGNELESIAFRSE----DITGQLGNNDDLILSCCLHYCKDKAKDFMPASKeepirllreVVLLTDDRNLRVKALTRNV 1404
Cdd:cd09880   71 TSKGNYLADLTIRSEqlsdASELRRRNNDDRILECALWQQKHFVDREDGDGK---------VVLVTNDRNLRLKARARGV 141

                        170
                 ....*....|.
gi 91771922 1405 PVRDIPAFLTW 1415
Cdd:cd09880  142 EAVTVKELLKS 152
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 1249-1415 3.02e-27

VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; Saccharomyces cerevisiae mRNA-processing endoribonuclease Swt1p plays an important role in quality control of nuclear mRNPs in eukaryotes. Human transcriptional protein SWT1 (RNA endoribonuclease homolog, also known as HsSwt1, C1orf26, and chromosome 1 open reading frame 26) is an RNA endonuclease that participates in quality control of nuclear mRNPs and can associate with the nuclear pore complex (NPC). This subfamily belongs to the Smg5 and Smg6-like PIN domain family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo.


Pssm-ID: 350294  Cd Length: 141  Bit Score: 108.41  E-value: 3.02e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGFIDHLASLARLLE-----SRKYILVVPLIVINELDGLAKGQETDHraggyarvVQEKARKSIEFLEQRFESRDS 1323
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEdveklSLPVVIVIPWVVLQELDGLKKSKRKSS--------LGWLARRASTWLLEKLRSKHP 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1324 CLRALTsrgnelesiafRSEDITGQ---LGNNDDLILSCCLHYCKdkakdfmpaskeepiRLLREVVLLTDDRNLRVKAL 1400
Cdd:cd18727   73 RVRGQA-----------LSETLRASgdpGESNDDAILDCCLYFQE---------------KYGAPVVLLSNDKNLCNKAL 126

                        170
                 ....*....|....*
gi 91771922 1401 TRNVPVRDIPAFLTW 1415
Cdd:cd18727  127 INGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 1248-1408 4.34e-24

PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).


Pssm-ID: 433369  Cd Length: 131  Bit Score: 98.84  E-value: 4.34e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   1248 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 1327
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   1328 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 1407
Cdd:pfam13638   73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                   .
gi 91771922   1408 D 1408
Cdd:pfam13638  129 D 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1248-1397 1.13e-12

Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.


Pssm-ID: 214771 [Multi-domain]  Cd Length: 111  Bit Score: 65.91  E-value: 1.13e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    1248 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 1326
Cdd:smart00670    3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 91771922    1327 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 1397
Cdd:smart00670   73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 1249-1408 1.74e-12

VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; PIN (PilT N terminus) domain of Smg6-like bacterial proteins with C-terminal PhoH-like ATPase domains and other similar homologs are included in this family. Eukaryotic Smg5 and Smg6 nucleases are essential factors in nonsense-mediated mRNA decay (NMD), a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues). Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain and are predicted to be ATPases which are induced by phosphate starvation.


Pssm-ID: 350231  Cd Length: 146  Bit Score: 66.41  E-value: 1.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGFI-DHLAslarLLESRKYILVVPLIVINELDGLAKGQETDHRaggyarvvqeKARKSIEFLEQRFESRDSCLRA 1327
Cdd:cd09883    5 VLDTNVLLhDPNA----IFKFEDNDVVIPITVLEELDKLKKRNDELGR----------NAREAIRNLDELREKGSLAEGV 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1328 LTSRGNELE-SIAFRSEDITGQL--GNNDDLILSCCLHYCKDKAKDfmpaskeepirllreVVLLTDDRNLRVKALTRNV 1404
Cdd:cd09883   71 PLENGGTLRvELNHKDLLPLPELdlDKNDNRILAVALKLKEEGDRP---------------VILVTKDINLRIKADALGI 135


                 ....
gi 91771922 1405 PVRD 1408
Cdd:cd09883  136 KAED 139
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 638-743 5.59e-11

Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat.


Pssm-ID: 463062  Cd Length: 98  Bit Score: 60.40  E-value: 5.59e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922    638 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 709
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 91771922    710 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 743
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 1247-1334 1.11e-10

VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs; Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo.


Pssm-ID: 350232  Cd Length: 160  Bit Score: 61.52  E-value: 1.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1247 FLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKgqetdhraggyarvVQEKARKSIEFLEQRFESRDSCLR 1326
Cdd:cd09884    2 YLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKK--------------ESAGAREAIRWLEAEFKKGNRYIR 67


                 ....*...
gi 91771922 1327 ALtsRGNE 1334
Cdd:cd09884   68 AQ--KPNE 73
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 1249-1407 2.85e-06

VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs; PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350205  Cd Length: 129  Bit Score: 48.04  E-value: 2.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGFIDHLAS------LARLLESR--KYILVVPLIVINELDGLAKGQETDHRAggyarvvqEKARKSIEFLEQRFES 1320
Cdd:cd09854    1 VLDTNVLIALLSSepeseaAKELLALLlgDSELVIPPLVLAELLRLLARERGARRA--------LEILELLRALEVVEEE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1321 RDSclraltsrgnELESIAFRSEDITGQLGNNDDLILSCCLHYckdkakdfmpaskeepirllREVVLLTDDRNLRvKAL 1400
Cdd:cd09854   73 PAL----------AEIALEVLALGLERGLDFGDALILALAKEL--------------------GGAVLVTNDRDFR-RLA 121


                 ....*..
gi 91771922 1401 TRNVPVR 1407
Cdd:cd09854  122 KLGLKVI 128
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
1249-1406 4.90e-06

rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 47.13  E-value: 4.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 1321
Cdd:COG1412    4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1322 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDFmpaskeepirllrEVVLLTDDRNLRVKALT 1401
Cdd:COG1412   68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                 ....*
gi 91771922 1402 RNVPV 1406
Cdd:COG1412  107 AGIPV 111
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 1273-1399 4.41e-05

Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General function prediction only];


Pssm-ID: 441479 [Multi-domain]  Cd Length: 441  Bit Score: 47.78  E-value: 4.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1273 LVVPLIVINELDGLAKGQ-ETdhragGYArvvqekARKSIEFLEQrfesrdsclraLTSRGN-----ELES---IAFRSE 1343
Cdd:COG1875   29 VVIPMVVLEELDKFKKGMsEL-----GRN------ARQASRLLDE-----------LRAKGNldegvPLPNggtLRVELN 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 91771922 1344 DITGQL------GNNDDLILSCCLHYCKDKAKdfmpaskeepirllREVVLLTDDRNLRVKA 1399
Cdd:COG1875   87 HKDSELpaglplDKNDNRILAVALNLQEEYPG--------------RPVILVSKDINLRIKA 134
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 1249-1406 3.23e-04

VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs; PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved putative metal-binding, active site residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains and included distant subgroups, this subgroup includes some sequences belonging to one of these, PIN_14.


Pssm-ID: 350227 [Multi-domain]  Cd Length: 118  Bit Score: 41.68  E-value: 3.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1249 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQETDHRAggYARVvqekARKSIEfleqRFESR 1321
Cdd:cd09879    2 ILDTNFLmypfqfgVDIFEELERLL--GKYEIVVPSAVIEELERLAKKGKGKDKR--AARL----ALKLAE----RCKVV 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922 1322 DsclraltsrgnelesiafrSEDITGqlgnnDDLIlsccLHYCKDKakdfmpaskeepirllrEVVLLTDDRNLRVKALT 1401
Cdd:cd09879   70 E-------------------SEGEPA-----DDAI----LELAKEL-----------------GAIVATNDRELRKRLRE 104


                 ....*
gi 91771922 1402 RNVPV 1406
Cdd:cd09879  105 KGIPV 109
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 147-338 2.81e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.20  E-value: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   147 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 224
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 91771922   225 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 303
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 91771922   304 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 338
Cdd:PRK12678  252 GDDG--EGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 747-818 9.53e-03

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


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.40  E-value: 9.53e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 91771922  747 NYGKARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAE 818
Cdd:COG5010   69 DFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDE 140
 
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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