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Conserved domains on  [gi|75268148|sp|Q9C552|]
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RecName: Full=Pumilio homolog 23; Short=APUM-23; Short=AtPUM23

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 75268148 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099 478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099 557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099 603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679
                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 75268148 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 75268148 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099 478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099 557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099 603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679
                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 75268148 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 75268148 345 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 423
Cdd:cd07920   6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 424 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 479
Cdd:cd07920  84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 480 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 558
Cdd:cd07920 160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 75268148 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 75268148   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 75268148 349 EILESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEELAPRFKDLL 428
Cdd:COG5099 478 QLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLI 556
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 429 E-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmHVMGCLILQ 507
Cdd:COG5099 557 KdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------HRYGSRVVQ 602
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 508 GIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFD 587
Cdd:COG5099 603 RCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIK 679
                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 75268148 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 75268148 345 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 423
Cdd:cd07920   6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 424 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 479
Cdd:cd07920  84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75268148 480 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 558
Cdd:cd07920 160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 75268148 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 75268148 523 SLTSMKAEYITETAKDSSGARVIEAFLAsDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 602
Cdd:cd07920   3 TLQDIKAGHIVEFAKDQHGSRFLQQKLE-EATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81

                ....*..
gi 75268148 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 75268148 282 LSGLLSCSREDMKYLQVDQYSSLVLQTALRLMlkqDEQLLEIIPLILRCNstnkkvegfhietnvakeILESMKDNSFSH 361
Cdd:cd07920  73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESI---SEEQISLLVKELRGH------------------VVELVKDQNGNH 131
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 75268148 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 75268148 530 EYITETAKDSSGARVIEAFLasDAAT-KQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLDVKVDL 608
Cdd:cd07920  46 PHVVELMVDPFGNYVIQKLF--EHGTeEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVEL 123
                        90
                ....*....|...
gi 75268148 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 75268148   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 75268148 498 MHVMGCLILQGIFKFSSDhiqPYITSLTSMKAEYITETAKDSSGARVIEAFLASdAATKQKRRLIIKLRGHFGELSLHTS 577
Cdd:cd07920  53 VDPFGNYVIQKLFEHGTE---EQRLQLLEKILGHVVRLSLDMYGCRVIQKLLES-ISEEQISLLVKELRGHVVELVKDQN 128
                        90       100       110
                ....*....|....*....|....*....|....*..
gi 75268148 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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