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Conserved domains on  [gi|229577364|ref|NP_080095|]
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transcriptional protein SWT1 [Mus musculus]

Protein Classification

PIN_Swt1-like domain-containing protein( domain architecture ID 13036856)

PIN_Swt1-like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 398-537 2.30e-45

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: 159.64  E-value: 2.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFVKILKTTEIPGFDTLVLIIPWVVIQELDRMKAGKLLKHVQHKAVPAIHFINNSLKSQDRKLWGQSLQ 477
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDVEKLSLPVVIVIPWVVLQELDGLKKSKRKSSLGWLARRASTWLLEKLRSKHPRVRGQALS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 478 LASQKlYGLSDENNDDRVLKCCLQYQQLFPCSlVILCTDDRNLRTKGLISGVKSLSKEDL 537
Cdd:cd18727   81 ETLRA-SGDPGESNDDAILDCCLYFQEKYGAP-VVLLSNDKNLCNKALINGIPTISPEEG 138
 
Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 398-537 2.30e-45

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: 159.64  E-value: 2.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFVKILKTTEIPGFDTLVLIIPWVVIQELDRMKAGKLLKHVQHKAVPAIHFINNSLKSQDRKLWGQSLQ 477
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDVEKLSLPVVIVIPWVVLQELDGLKKSKRKSSLGWLARRASTWLLEKLRSKHPRVRGQALS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 478 LASQKlYGLSDENNDDRVLKCCLQYQQLFPCSlVILCTDDRNLRTKGLISGVKSLSKEDL 537
Cdd:cd18727   81 ETLRA-SGDPGESNDDAILDCCLYFQEKYGAP-VVLLSNDKNLCNKALINGIPTISPEEG 138
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 397-533 2.16e-29

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: 113.48  E-value: 2.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364  397 IVMDTNVLMNHLKFVKILKtteipgfDTLVLIIPWVVIQELDRMKAGKLLKH--VQHKAVPAIHFINNSLKSQDRKLWGQ 474
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFG-------EENDVVIPITVLEELDGLKKGSDESGreLARLARQANRWLDELLENNGGRLRGQ 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 229577364  475 SLqlaSQKLYGLSDENNDDRVLKCCLQYQQLFPCSLVILCTDDRNLRTKGLISGVKSLS 533
Cdd:pfam13638  74 TL---DERLPPDPFDKNDNRILAVALYLKEELPDRPVILVSKDINLRIKADALGIPAED 129
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 397-521 1.68e-07

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: 50.50  E-value: 1.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364   397 IVMDTNVLMNHLKFvKILkttEIPGFDTLVLIIPWVVIQELDRmKAGKLLKHVQHKAVPA-IHFInnslKSQDRKLWGQS 475
Cdd:smart00670   3 VVLDTNVLIDGLIR-DAL---EKLLEKKGEVYIPQTVLEELEY-LALRSLKKLEELALEGkIILK----VLKEERIEEEI 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 229577364   476 LQLASQKLYGLSdenNDDRVLKCCLQYQQlfpcslVILCTDDRNLR 521
Cdd:smart00670  74 LERLSLKLELLP---NDALILATAKELGN------VVLVTNDRDLR 110
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 398-540 2.11e-07

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: 54.32  E-value: 2.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFvkILKtteipgFDTLVLIIPWVVIQELDRMKAG----------------KLLKHVQ-HKAVP----- 455
Cdd:COG1875    8 VLDTNVLLHDPNA--IFR------FEEHDVVIPMVVLEELDKFKKGmselgrnarqasrlldELRAKGNlDEGVPlpngg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 456 AIHFINNSLKSQDRKlwgqslqlasqklyGLSDENNDDRVLKCCLQYQQLFPCSLVILCTDDRNLRTKGLISGVKSlskE 535
Cdd:COG1875   80 TLRVELNHKDSELPA--------------GLPLDKNDNRILAVALNLQEEYPGRPVILVSKDINLRIKADALGLEA---E 142


                 ....*
gi 229577364 536 DLDTE 540
Cdd:COG1875  143 DYRND 147
 
Name Accession Description Interval E-value
PIN_Swt1-like cd18727
VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins; ...
 398-537 2.30e-45

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: 159.64  E-value: 2.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFVKILKTTEIPGFDTLVLIIPWVVIQELDRMKAGKLLKHVQHKAVPAIHFINNSLKSQDRKLWGQSLQ 477
Cdd:cd18727    1 VLDTNVLISHLDLLKQLVEDVEKLSLPVVIVIPWVVLQELDGLKKSKRKSSLGWLARRASTWLLEKLRSKHPRVRGQALS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 478 LASQKlYGLSDENNDDRVLKCCLQYQQLFPCSlVILCTDDRNLRTKGLISGVKSLSKEDL 537
Cdd:cd18727   81 ETLRA-SGDPGESNDDAILDCCLYFQEKYGAP-VVLLSNDKNLCNKALINGIPTISPEEG 138
PIN_Smg5-6-like cd09880
VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related ...
 398-540 1.32e-29

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: 115.08  E-value: 1.32e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFVKILKTTEipgfdTLVLIIPWVVIQELDRMKAGKllKHVQHKAVPAIHFINNSLKSQDRKLWGQSLQ 477
Cdd:cd09880    1 VFDTNILLSHLDVLKLLVESG-----KWTVVIPLIVITELDGLKKNP--DPLGPKARSALRYIEACLKKHSRWLRVQTSK 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 229577364 478 LAS-----------QKLYGLSDENNDDRVLKCCLQYQQLF-----PCSLVILCTDDRNLRTKGLISGVKSLSKEDLDTE 540
Cdd:cd09880   74 GNYladltirseqlSDASELRRRNNDDRILECALWQQKHFvdredGDGKVVLVTNDRNLRLKARARGVEAVTVKELLKS 152
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 397-533 2.16e-29

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: 113.48  E-value: 2.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364  397 IVMDTNVLMNHLKFVKILKtteipgfDTLVLIIPWVVIQELDRMKAGKLLKH--VQHKAVPAIHFINNSLKSQDRKLWGQ 474
Cdd:pfam13638   1 YVLDTNVLLHDPDALFNFG-------EENDVVIPITVLEELDGLKKGSDESGreLARLARQANRWLDELLENNGGRLRGQ 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 229577364  475 SLqlaSQKLYGLSDENNDDRVLKCCLQYQQLFPCSLVILCTDDRNLRTKGLISGVKSLS 533
Cdd:pfam13638  74 TL---DERLPPDPFDKNDNRILAVALYLKEELPDRPVILVSKDINLRIKADALGIPAED 129
PIN_Smg6-like cd09885
VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar ...
 397-529 1.25e-14

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: 72.68  E-value: 1.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 397 IVMDTNVLMNHLK-FVKILKTteipgfDTLVLIIPWVVIQELDRMKAGKLLKH---------VQHKAVPAIHFI------ 460
Cdd:cd09885    8 LVPDTNCFIDHLElIEKLVES------RKFTVLVPLIVVNELDGLAKGSESDSyadeahaeeVQAKARKAVKFLeeqfea 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 461 -NNSLKSQDRKlwGQSLQL---ASQKLYGLSDENNDDRVLKCCLQYQQLFPCSL--------------VILCTDDRNLRT 522
Cdd:cd09885   82 rNPYVRALTSK--GTLLDTiafRSEDINDGDGGNNDDLILSCCLNLCKDKAVDFmpaskdqpirlyreVVLLTDDRNLRV 159


                 ....*..
gi 229577364 523 KGLISGV 529
Cdd:cd09885  160 KALSRNI 166
PIN_VapC_PhoHL-ATPase cd09883
VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains; ...
 398-540 2.30e-11

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: 62.56  E-value: 2.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFVKILKTTEIpgfdtlvlIIPWVVIQELDRMKagKLLKHVQHKAVPAIHFInNSLKSQDRKLWGQSLQ 477
Cdd:cd09883    5 VLDTNVLLHDPNAIFKFEDNDV--------VIPITVLEELDKLK--KRNDELGRNAREAIRNL-DELREKGSLAEGVPLE 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 229577364 478 L-----------ASQKLYGLSDENNDDRVLKCCLQYQQLFPCSlVILCTDDRNLRTKGLISGVKSlskEDLDTE 540
Cdd:cd09883   74 NggtlrvelnhkDLLPLPELDLDKNDNRILAVALKLKEEGDRP-VILVTKDINLRIKADALGIKA---EDYETD 143
PINc smart00670
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ...
 397-521 1.68e-07

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: 50.50  E-value: 1.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364   397 IVMDTNVLMNHLKFvKILkttEIPGFDTLVLIIPWVVIQELDRmKAGKLLKHVQHKAVPA-IHFInnslKSQDRKLWGQS 475
Cdd:smart00670   3 VVLDTNVLIDGLIR-DAL---EKLLEKKGEVYIPQTVLEELEY-LALRSLKKLEELALEGkIILK----VLKEERIEEEI 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 229577364   476 LQLASQKLYGLSdenNDDRVLKCCLQYQQlfpcslVILCTDDRNLR 521
Cdd:smart00670  74 LERLSLKLELLP---NDALILATAKELGN------VVLVTNDRDLR 110
YlaK COG1875
Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General ...
 398-540 2.11e-07

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: 54.32  E-value: 2.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 398 VMDTNVLMNHLKFvkILKtteipgFDTLVLIIPWVVIQELDRMKAG----------------KLLKHVQ-HKAVP----- 455
Cdd:COG1875    8 VLDTNVLLHDPNA--IFR------FEEHDVVIPMVVLEELDKFKKGmselgrnarqasrlldELRAKGNlDEGVPlpngg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 456 AIHFINNSLKSQDRKlwgqslqlasqklyGLSDENNDDRVLKCCLQYQQLFPCSLVILCTDDRNLRTKGLISGVKSlskE 535
Cdd:COG1875   80 TLRVELNHKDSELPA--------------GLPLDKNDNRILAVALNLQEEYPGRPVILVSKDINLRIKADALGLEA---E 142


                 ....*
gi 229577364 536 DLDTE 540
Cdd:COG1875  143 DYRND 147
Fcf1 COG1412
rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis];
397-533 8.39e-05

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


Pssm-ID: 441022 [Multi-domain]  Cd Length: 123  Bit Score: 42.89  E-value: 8.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229577364 397 IVMDTNVLMNHLKF-VKIlktteipgFDTL-------VLIIPWVVIQELDRmkagkllkhvqhkavpaihfINNSLKSQD 468
Cdd:COG1412    3 VLLDTNALMMPAQFgVDV--------FEELdrllgkyEFIVPEAVLEELEK--------------------LSRGAKGKE 54

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 229577364 469 RKLWGQSLQLASQ-KLYGLSDENNDDRVLKCCLQYQqlfpcslVILCTDDRNLRTKGLISGVKSLS 533
Cdd:COG1412   55 KRAARVALDLAERcEIVETEGGYADDAILELAKENG-------VIVATNDKELRRRLLEAGIPVIY 113
 
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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