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Conserved domains on  [gi|1063696310|ref|NP_001321803|]
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pumilio 23 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5099 super family cl34901
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 349-627 1.81e-08

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG5099:

Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 57.83  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099   478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099   557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099   603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1063696310 588 ACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 627
Cdd:COG5099   680 YASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 349-627 1.81e-08

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 57.83  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099   478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099   557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099   603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1063696310 588 ACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 627
Cdd:COG5099   680 YASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 345-603 5.60e-08

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 55.29  E-value: 5.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 345 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 423
Cdd:cd07920     6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 424 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 479
Cdd:cd07920    84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 480 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 558
Cdd:cd07920   160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1063696310 559 RRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLD 603
Cdd:cd07920   218 SRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILA 262
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 568-602 7.86e-03

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 34.58  E-value: 7.86e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063696310 568 HFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 602
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 349-627 1.81e-08

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 57.83  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099   478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099   557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099   603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1063696310 588 ACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 627
Cdd:COG5099   680 YASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 345-603 5.60e-08

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 55.29  E-value: 5.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 345 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 423
Cdd:cd07920     6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 424 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 479
Cdd:cd07920    84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 480 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 558
Cdd:cd07920   160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1063696310 559 RRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLD 603
Cdd:cd07920   218 SRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILA 262
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 523-609 2.72e-05

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 46.82  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 523 SLTSMKAEYITETAKDSSGARVIEAFLAsDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 602
Cdd:cd07920     3 TLQDIKAGHIVEFAKDQHGSRFLQQKLE-EATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81


                  ....*..
gi 1063696310 603 DVKVDLS 609
Cdd:cd07920    82 GHVVRLS 88
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 282-416 7.21e-04

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 42.58  E-value: 7.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 282 LSGLLSCSREDMKYLQVDQYSSLVLQTALRLMlkqDEQLLEIIPLILRCNstnkkvegfhietnvakeILESMKDNSFSH 361
Cdd:cd07920    73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESI---SEEQISLLVKELRGH------------------VVELVKDQNGNH 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063696310 362 LVEVILEVAPESLYNEMFNkVFKNSLFELSVDRCANFVIQALISHARDQEQMGIM 416
Cdd:cd07920   132 VIQKCIEKFPPEDLQFIID-AFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLL 185
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 530-621 9.72e-04

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 42.19  E-value: 9.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 530 EYITETAKDSSGARVIEAFLasDAAT-KQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLDVKVDL 608
Cdd:cd07920    46 PHVVELMVDPFGNYVIQKLF--EHGTeEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVEL 123

                          90
                  ....*....|...
gi 1063696310 609 SKTKQGPYLLRKL 621
Cdd:cd07920   124 VKDQNGNHVIQKC 136
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 568-602 7.86e-03

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 34.58  E-value: 7.86e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063696310 568 HFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 602
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 498-614 8.94e-03

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 39.11  E-value: 8.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063696310 498 MHVMGCLILQGIFKFSSDhiqPYITSLTSMKAEYITETAKDSSGARVIEAFLASdAATKQKRRLIIKLRGHFGELSLHTS 577
Cdd:cd07920    53 VDPFGNYVIQKLFEHGTE---EQRLQLLEKILGHVVRLSLDMYGCRVIQKLLES-ISEEQISLLVKELRGHVVELVKDQN 128

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1063696310 578 GSFTVEKCFDACNLTLREAIASELLDVKVDLSKTKQG 614
Cdd:cd07920   129 GNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYG 165
 
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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