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Conserved domains on  [gi|42572079|ref|NP_974130|]
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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 ...
323-605 1.40e-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: 58.22  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 323 NVAKEIL----ESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEEL 398
Cdd:COG5099 470 VIFNEILdqlvELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEEL 548
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 399 APRFKDLLE-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmH 477
Cdd:COG5099 549 RPYCLQLIKdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------H 594
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 478 VMGCLILQGIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGS 557
Cdd:COG5099 595 RYGSRVVQRCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFAS 671
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 42572079 558 FTVEKCFDACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 605
Cdd:COG5099 672 NVVEKCIKYASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
323-605 1.40e-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: 58.22  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 323 NVAKEIL----ESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEEL 398
Cdd:COG5099 470 VIFNEILdqlvELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEEL 548
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 399 APRFKDLLE-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmH 477
Cdd:COG5099 549 RPYCLQLIKdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------H 594
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 478 VMGCLILQGIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGS 557
Cdd:COG5099 595 RYGSRVVQRCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFAS 671
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 42572079 558 FTVEKCFDACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 605
Cdd:COG5099 672 NVVEKCIKYASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
323-581 5.73e-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: 5.73e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 323 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 401
Cdd:cd07920   6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 402 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 457
Cdd:cd07920  84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 458 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 536
Cdd:cd07920 160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 42572079 537 RRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLD 581
Cdd:cd07920 218 SRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILA 262
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
546-580 7.94e-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: 7.94e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42572079   546 HFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 580
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
323-605 1.40e-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: 58.22  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 323 NVAKEIL----ESMKDNSFSHLVEVILEVAPESLYNEMFNKVFKNsLFELSVDRCANFVIQALISHARDQEQMGIMWEEL 398
Cdd:COG5099 470 VIFNEILdqlvELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKH-LVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEEL 548
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 399 APRFKDLLE-QGKSGVVasliavsqrlqsheNKCCEAlvgavCSTNESRISILPrllFLDYyfgCRDKSTwewapgakmH 477
Cdd:COG5099 549 RPYCLQLIKdQNGNHVI--------------QKCIEK-----FNKEKNQFIFDS---INEN---LYDLST---------H 594
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 478 VMGCLILQGIFKFSSDHIQpyiTSLTSMKAEYITETAKDSSGARVIEAFLASDAATKQKRRLIIKLRGHFGELSLHTSGS 557
Cdd:COG5099 595 RYGSRVVQRCLENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFAS 671
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*....
gi 42572079 558 FTVEKCFDACNLT-LREAIASELLDVKVDLsktkqgPYLLRKLDIDGYA 605
Cdd:COG5099 672 NVVEKCIKYASDSfKRSRILNELTNRGIEK------PGFLMLILDDQYA 714
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
323-581 5.73e-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: 5.73e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 323 NVAKEILESM-KDNSFSHLVEVILEVAPESLYNEMFNKVfKNSLFELSVDRCANFVIQALISHArDQEQMGIMWEELAPR 401
Cdd:cd07920   6 DIKAGHIVEFaKDQHGSRFLQQKLEEATPEEKELIFDEI-LPHVVELMVDPFGNYVIQKLFEHG-TEEQRLQLLEKILGH 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 402 FKDL-----------------LEQGKSGVVASLIAVSQRLQSHEN------KCCEALVgavCSTNESRI-SILPRLLFLd 457
Cdd:cd07920  84 VVRLsldmygcrviqkllesiSEEQISLLVKELRGHVVELVKDQNgnhviqKCIEKFP---PEDLQFIIdAFKGNCVAL- 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 458 yyfgcrdkSTwewapgakmHVMGCLILQGIFKFSS-DHIQPYITSLTsmkaEYITETAKDSSGARVIEaFLASDAATKQK 536
Cdd:cd07920 160 --------ST---------HPYGCRVIQRCLEHCSeEQREPLLEEIL----EHALELVQDQFGNYVVQ-HVLELGDPDDT 217
                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*
gi 42572079 537 RRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLD 581
Cdd:cd07920 218 SRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERELIIDEILA 262
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
501-587 2.66e-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: 2.66e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 501 SLTSMKAEYITETAKDSSGARVIEAFLAsDAATKQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 580
Cdd:cd07920   3 TLQDIKAGHIVEFAKDQHGSRFLQQKLE-EATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81

                ....*..
gi 42572079 581 DVKVDLS 587
Cdd:cd07920  82 GHVVRLS 88
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
260-394 6.89e-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: 6.89e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 260 LSGLLSCSREDMKYLQVDQYSSLVLQTALRLMlkqDEQLLEIIPLILRCNstnkkvegfhietnvakeILESMKDNSFSH 339
Cdd:cd07920  73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESI---SEEQISLLVKELRGH------------------VVELVKDQNGNH 131
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 42572079 340 LVEVILEVAPESLYNEMFNkVFKNSLFELSVDRCANFVIQALISHARDQEQMGIM 394
Cdd:cd07920 132 VIQKCIEKFPPEDLQFIID-AFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLL 185
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
508-599 9.53e-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: 41.81  E-value: 9.53e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 508 EYITETAKDSSGARVIEAFLasDAAT-KQKRRLIIKLRGHFGELSLHTSGSFTVEKCFDACNLTLREAIASELLDVKVDL 586
Cdd:cd07920  46 PHVVELMVDPFGNYVIQKLF--EHGTeEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVEL 123
                        90
                ....*....|...
gi 42572079 587 SKTKQGPYLLRKL 599
Cdd:cd07920 124 VKDQNGNHVIQKC 136
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
546-580 7.94e-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: 7.94e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42572079   546 HFGELSLHTSGSFTVEKCFDACNLTLREAIASELL 580
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
476-592 8.40e-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: 8.40e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42572079 476 MHVMGCLILQGIFKFSSDhiqPYITSLTSMKAEYITETAKDSSGARVIEAFLASdAATKQKRRLIIKLRGHFGELSLHTS 555
Cdd:cd07920  53 VDPFGNYVIQKLFEHGTE---EQRLQLLEKILGHVVRLSLDMYGCRVIQKLLES-ISEEQISLLVKELRGHVVELVKDQN 128
                        90       100       110
                ....*....|....*....|....*....|....*..
gi 42572079 556 GSFTVEKCFDACNLTLREAIASELLDVKVDLSKTKQG 592
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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