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Conserved domains on  [gi|530410166|ref|XP_005256626|]
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telomerase-binding protein EST1A isoform X1 [Homo sapiens]

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 ...
 1210-1385 1.25e-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: 1.25e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1210 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1288
Cdd:cd09885     1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1289 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1367
Cdd:cd09885    81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                         170
                  ....*....|....*...
gi 530410166 1368 ALTRNVPVRDIPAFLTWA 1385
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 ...
 720-1072 8.42e-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: 8.42e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   720 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 799
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   800 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 879
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   880 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 956
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   957 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1036
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 530410166  1037 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1072
Cdd:pfam10373  241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 607-712 5.91e-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: 5.91e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   607 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 678
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 530410166   679 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 712
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 116-307 2.54e-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: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  116 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 193
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  194 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 272
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 530410166  273 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 307
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 ...
 1210-1385 1.25e-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: 1.25e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1210 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1288
Cdd:cd09885     1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1289 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1367
Cdd:cd09885    81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                         170
                  ....*....|....*...
gi 530410166 1368 ALTRNVPVRDIPAFLTWA 1385
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 ...
 720-1072 8.42e-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: 8.42e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   720 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 799
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   800 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 879
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   880 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 956
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   957 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1036
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 530410166  1037 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1072
Cdd:pfam10373  241 LLSSTLLNssFDVEKRPKRDYL---LEEDVELKGFSPL 275
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 1217-1377 4.49e-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: 4.49e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  1217 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 1296
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  1297 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 1376
Cdd:pfam13638   73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                   .
gi 530410166  1377 D 1377
Cdd:pfam13638  129 D 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1217-1366 1.15e-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: 65.52  E-value: 1.15e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   1217 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 1295
Cdd:smart00670    3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530410166   1296 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 1366
Cdd:smart00670   73 -------ILERLSLKLELLP-----NDALILATAKELGN--------------------VVLVTNDRDLRR 111
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 607-712 5.91e-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: 5.91e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   607 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 678
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 530410166   679 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 712
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
1218-1375 4.27e-06

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 47.13  E-value: 4.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 1290
Cdd:COG1412     4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1291 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDFmpaskeepirllrEVVLLTDDRNLRVKALT 1370
Cdd:COG1412    68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                  ....*
gi 530410166 1371 RNVPV 1375
Cdd:COG1412   107 AGIPV 111
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 116-307 2.54e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.20  E-value: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  116 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 193
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  194 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 272
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 530410166  273 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 307
Cdd:PRK12678  252 GDDG--EGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 716-787 8.24e-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: 38.79  E-value: 8.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530410166  716 NYGKARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAE 787
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 ...
 1210-1385 1.25e-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: 1.25e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1210 LEIRPLFLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGG-YARVVQEKARKSIEFLEQRFE 1288
Cdd:cd09885     1 IEVRPRYLVPDTNCFIDHLELIEKLVESRKFTVLVPLIVVNELDGLAKGSESDSYADEaHAEEVQAKARKAVKFLEEQFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1289 SRDSCLRALTSRGNELESIAFRSEDITGQLG-NNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVK 1367
Cdd:cd09885    81 ARNPYVRALTSKGTLLDTIAFRSEDINDGDGgNNDDLILSCCLNLCKDKAVDFMPASKDQPIRLYREVVLLTDDRNLRVK 160

                         170
                  ....*....|....*...
gi 530410166 1368 ALTRNVPVRDIPAFLTWA 1385
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 ...
 720-1072 8.42e-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: 8.42e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   720 ARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAEQMEKKQheefdl 799
Cdd:pfam10373    1 ALRYYLLAILLLPSNGEPYNQLGVIALYVGNHLDAVYYFLRSLLSRNPFPTAKNNLELLFDKIRSKLEQGELKL------ 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   800 spdqwrkgkkstfrhvgddttrleiwihpshprssqgtesGKDSEQEnglgsLSPSDLNKRFILSFLHAHGKLFTRIGME 879
Cdd:pfam10373   75 ----------------------------------------SPESLQE-----GTPGDLLERLISLFLYLHGKLYTPTDFS 109

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   880 TFPAVAEKVLKEFQVLLQHSPSP---IGSTRMLQLMTINMFAVHNSQLKdcfSEECRSVIQEQAAALGLAmFSLLVRRCT 956
Cdd:pfam10373  110 EFPELEDEVLKKLEILLKESLLSrylKSRSLLLKMLLINIFAFENAKDK---SSPEETKQFLLRLALRFF-FTLFGLLLE 185

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   957 CLLKESAKAQLSspedqddqddikvssfvPDLKELLPSVKVWSDWMLGYPDTWNppptsldlPSHVAVDVWSTLADFCNI 1036
Cdd:pfam10373  186 EVNTLEALKSFT-----------------PVATRYLPALRVYLCWLKSNPSVLE--------FEDKDEKLVDSLSDLWNE 240

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 530410166  1037 LTAVNQSE--VPLYKDPDDDLTlliLEEDRLLSGFVPL 1072
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 ...
 1218-1384 9.59e-49

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: 9.59e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKGQETdhraggyarvVQEKARKSIEFLEQRFESRDSCLRAL 1297
Cdd:cd09880     1 VFDTNILLSHLDVLKLLVESGKWTVVIPLIVITELDGLKKNPDP----------LGPKARSALRYIEACLKKHSRWLRVQ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1298 TSRGNELESIAFRSE----DITGQLGNNDDLILSCCLHYCKDKAKDFMPASKeepirllreVVLLTDDRNLRVKALTRNV 1373
Cdd:cd09880    71 TSKGNYLADLTIRSEqlsdASELRRRNNDDRILECALWQQKHFVDREDGDGK---------VVLVTNDRNLRLKARARGV 141

                         170
                  ....*....|.
gi 530410166 1374 PVRDIPAFLTW 1384
Cdd:cd09880   142 EAVTVKELLKS 152
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 1218-1384 3.16e-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: 3.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGFIDHLASLARLLE-----SRKYILVVPLIVINELDGLAKGQETDHraggyarvVQEKARKSIEFLEQRFESRDS 1292
Cdd:cd18727     1 VLDTNVLISHLDLLKQLVEdveklSLPVVIVIPWVVLQELDGLKKSKRKSS--------LGWLARRASTWLLEKLRSKHP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1293 CLRALTsrgnelesiafRSEDITGQ---LGNNDDLILSCCLHYCKdkakdfmpaskeepiRLLREVVLLTDDRNLRVKAL 1369
Cdd:cd18727    73 RVRGQA-----------LSETLRASgdpGESNDDAILDCCLYFQE---------------KYGAPVVLLSNDKNLCNKAL 126

                         170
                  ....*....|....*
gi 530410166 1370 TRNVPVRDIPAFLTW 1384
Cdd:cd18727   127 INGIPTISPEEGMTA 141
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 1217-1377 4.49e-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: 4.49e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  1217 LVPDTNGFIDHLASLARLLEsrKYILVVPLIVINELDGLAKGQETDHRaggyarVVQEKARKSIEFLEQRFESRDSCLRA 1296
Cdd:pfam13638    1 YVLDTNVLLHDPDALFNFGE--ENDVVIPITVLEELDGLKKGSDESGR------ELARLARQANRWLDELLENNGGRLRG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  1297 LTSRGNELESIAFRseditgqlgnNDDLILSCCLHYckdkakdfmpaSKEEPIRllrEVVLLTDDRNLRVKALTRNVPVR 1376
Cdd:pfam13638   73 QTLDERLPPDPFDK----------NDNRILAVALYL-----------KEELPDR---PVILVSKDINLRIKADALGIPAE 128


                   .
gi 530410166  1377 D 1377
Cdd:pfam13638  129 D 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 1217-1366 1.15e-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: 65.52  E-value: 1.15e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   1217 LVPDTNGFIDHLAS-LARLLESRKYILVVPLIVINELDGLAKgqetdHRAGGYARVVQEKARKSIEFLEQRFESRdsclr 1295
Cdd:smart00670    3 VVLDTNVLIDGLIRdALEKLLEKKGEVYIPQTVLEELEYLAL-----RSLKKLEELALEGKIILKVLKEERIEEE----- 72

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530410166   1296 altsrgnELESIAFRSEDITgqlgnNDDLILSCCLHYCKdkakdfmpaskeepirllreVVLLTDDRNLRV 1366
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; ...
 1218-1377 1.71e-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: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGFI-DHLAslarLLESRKYILVVPLIVINELDGLAKGQETDHRaggyarvvqeKARKSIEFLEQRFESRDSCLRA 1296
Cdd:cd09883     5 VLDTNVLLhDPNA----IFKFEDNDVVIPITVLEELDKLKKRNDELGR----------NAREAIRNLDELREKGSLAEGV 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1297 LTSRGNELE-SIAFRSEDITGQL--GNNDDLILSCCLHYCKDKAKDfmpaskeepirllreVVLLTDDRNLRVKALTRNV 1373
Cdd:cd09883    71 PLENGGTLRvELNHKDLLPLPELdlDKNDNRILAVALKLKEEGDRP---------------VILVTKDINLRIKADALGI 135


                  ....
gi 530410166 1374 PVRD 1377
Cdd:cd09883   136 KAED 139
EST1 pfam10374
Telomerase activating protein Est1; Est1 is a protein which recruits or activates telomerase ...
 607-712 5.91e-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: 5.91e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166   607 NVDQILWKNAFYQVIEKFRQLVK--DPNVENP------EQIRNRLLELLDEGSDFFDSLLQKLQvtykfKLEDymdglai 678
Cdd:pfam10374    1 KVLDLLWRKTHYPIIKWFRKWRKrlDGNSKKKkypvefRKLNSKLRKFLKSAQKFYYGLIQRLV-----SREA------- 68

                           90       100       110
                   ....*....|....*....|....*....|....
gi 530410166   679 rSKPLRKTVKYALisaQRCMICQGDIARYREQAS 712
Cdd:pfam10374   69 -SSSLTALALLSC---HRCLIYLGDLHRYRELLE 98
PIN_Smg5-like cd09884
VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar ...
 1216-1303 1.14e-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: 1.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1216 FLVPDTNGFIDHLASLARLLESRKYILVVPLIVINELDGLAKgqetdhraggyarvVQEKARKSIEFLEQRFESRDSCLR 1295
Cdd:cd09884     2 YLVPDTSALCDHLHLIKQLVQSGKFIVIIPLAVIDGLDELKK--------------ESAGAREAIRWLEAEFKKGNRYIR 67


                  ....*...
gi 530410166 1296 ALtsRGNE 1303
Cdd:cd09884    68 AQ--KPNE 73
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 1218-1376 2.34e-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: 48.43  E-value: 2.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGFIDHLAS------LARLLESR--KYILVVPLIVINELDGLAKGQETDHRAggyarvvqEKARKSIEFLEQRFES 1289
Cdd:cd09854     1 VLDTNVLIALLSSepeseaAKELLALLlgDSELVIPPLVLAELLRLLARERGARRA--------LEILELLRALEVVEEE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1290 RDSclraltsrgnELESIAFRSEDITGQLGNNDDLILSCCLHYckdkakdfmpaskeepirllREVVLLTDDRNLRvKAL 1369
Cdd:cd09854    73 PAL----------AEIALEVLALGLERGLDFGDALILALAKEL--------------------GGAVLVTNDRDFR-RLA 121


                  ....*..
gi 530410166 1370 TRNVPVR 1376
Cdd:cd09854   122 KLGLKVI 128
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
1218-1375 4.27e-06

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 47.13  E-value: 4.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQetdhrAGGYARvvqeKARKSIEFLEQrfesr 1290
Cdd:COG1412     4 LLDTNALmmpaqfgVDVFEELDRLL--GKYEFIVPEAVLEELEKLSRGA-----KGKEKR----AARVALDLAER----- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1291 dsclraltsrgnelesiaFRSEDITGqlGNNDDLILSCclhyckdkAKDFmpaskeepirllrEVVLLTDDRNLRVKALT 1370
Cdd:COG1412    68 ------------------CEIVETEG--GYADDAILEL--------AKEN-------------GVIVATNDKELRRRLLE 106


                  ....*
gi 530410166 1371 RNVPV 1375
Cdd:COG1412   107 AGIPV 111
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 1242-1368 4.08e-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: 4.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1242 LVVPLIVINELDGLAKGQ-ETdhragGYArvvqekARKSIEFLEQrfesrdsclraLTSRGN-----ELES---IAFRSE 1312
Cdd:COG1875    29 VVIPMVVLEELDKFKKGMsEL-----GRN------ARQASRLLDE-----------LRAKGNldegvPLPNggtLRVELN 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530410166 1313 DITGQL------GNNDDLILSCCLHYCKDKAKdfmpaskeepirllREVVLLTDDRNLRVKA 1368
Cdd:COG1875    87 HKDSELpaglplDKNDNRILAVALNLQEEYPG--------------RPVILVSKDINLRIKA 134
PIN_VapC_AF0591-like cd09879
VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal ...
 1218-1375 2.86e-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: 42.06  E-value: 2.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1218 VPDTNGF-------IDHLASLARLLesRKYILVVPLIVINELDGLAKGQETDHRAggYARVvqekARKSIEfleqRFESR 1290
Cdd:cd09879     2 ILDTNFLmypfqfgVDIFEELERLL--GKYEIVVPSAVIEELERLAKKGKGKDKR--AARL----ALKLAE----RCKVV 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166 1291 DsclraltsrgnelesiafrSEDITGqlgnnDDLIlsccLHYCKDKakdfmpaskeepirllrEVVLLTDDRNLRVKALT 1370
Cdd:cd09879    70 E-------------------SEGEPA-----DDAI----LELAKEL-----------------GAIVATNDRELRKRLRE 104


                  ....*
gi 530410166 1371 RNVPV 1375
Cdd:cd09879   105 KGIPV 109
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 116-307 2.54e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.20  E-value: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  116 QPGRRLQTVSKESASRVEEEEVLNQVEQLRVEEDECRGNVAKEEVANKPDRAEIEKSPGGGRVGA--AKGEKGKRMGKGE 193
Cdd:PRK12678   92 QPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEAraDAAERTEEEERDE 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530410166  194 GVRETHDDPARGRPGSAKRYSRSDKRRNRYRTRSTSSAGSNNSAEGAGLTDNGCRR-RRQDRTKERPRLKKQVSVSSTDS 272
Cdd:PRK12678  172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRgRRRRRDRRDARGDDNREDRGDRD 251

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 530410166  273 LDEDriDEPDGLGPRRSSERKRHLERNWSGRGEGE 307
Cdd:PRK12678  252 GDDG--EGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 716-787 8.24e-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: 38.79  E-value: 8.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530410166  716 NYGKARSWYLKAQHIAPKNGRPYNQLALLAVYTRRKLDAVYYYMRSLAASNPILTAKESLMSLFEETKRKAE 787
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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