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Conserved domains on  [gi|673040669|ref|XP_008874295|]
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hypothetical protein H310_09878 [Aphanomyces invadans]

Protein Classification

Pumilio-family RNA binding repeat-containing protein; pumilio/Puf RNA-binding domain-containing protein; Pumilio-family RNA binding repeat-containing protein; pumilio/Puf RNA-binding domain-containing protein; pumilio/puf RNA binding domain-containing protein( domain architecture ID 10647031)

Pumilio-family RNA binding repeat-containing protein harbors PUF repeats, which mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio; it may function as a translational repressor in early embryonic development by binding to sequences in the 3' UTR of target mRNAs; pumilio/Puf RNA-binding domain-containing protein family member, identified by the presence of eight tandem copies of an imperfectly repeated, 36 amino acid sequence motif, the PUM repeat, and containing evolutionarily conserved sequences that are amino- and carboxy-terminal to the repeated region of the protein. The eight repeats, together with the terminal conserved sequences, form a sequence-specific RNA binding domain.; Pumilio-family RNA binding repeat-containing protein harbors PUF repeats, which mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio; it may function as a translational repressor in early embryonic development by binding to sequences in the 3' UTR of target mRNAs; pumilio/Puf RNA-binding domain-containing protein family member, identified by the presence of eight tandem copies of an imperfectly repeated, 36 amino acid sequence motif, the PUM repeat, and containing evolutionarily conserved sequences that are amino- and carboxy-terminal to the repeated region of the protein. The eight repeats, together with the terminal conserved sequences, form a sequence-specific RNA binding domain.; pumilio/puf RNA-binding domain-containing protein family members are identified by the presence of eight tandem copies of an imperfectly repeated, 36 amino acid sequence motif, the PUM repeat, and contain evolutionarily conserved sequences that are amino- and carboxy-terminal to the repeated region of the protein. The eight repeats, together with the terminal conserved sequences, form a sequence-specific RNA binding domain.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 354-682 1.02e-114

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: 348.81  E-value: 1.02e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 354 LSLDDLR-GRVFAMSKDQNGCRLLQEQLDNSvdqvhhprtATDLCDVIYTESLPHLVDMMVDPFGNYLFQKLLECGTESQ 432
Cdd:cd07920    2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEA---------TPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 433 RFAIVQQVAHHLVAAALNLHGTRSVQKVVEICSsssmPQLVELIVDALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFV 512
Cdd:cd07920   73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESIS----EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFI 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 513 FDAVSAECTVVGTHRHGCCVLQRCVDAANPAQRREVIAQVEKHAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVGHV 592
Cdd:cd07920  149 IDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNI 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 593 LELSIQKFSSNVIEKCLELAPDYLCQTFVREIIASP----RMHRMLQDQYANYVVQRALSVASDENCLDLVTAMRPHLTS 668
Cdd:cd07920  229 VQLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPS 308

                        330
                 ....*....|....
gi 673040669 669 MKNTQGGRRIQARI 682
Cdd:cd07920  309 LRKSPYGKHILAKL 322
ZnF_C3H1 smart00356
zinc finger;
289-309 1.54e-05

zinc finger;


:

Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.23  E-value: 1.54e-05
                           10        20
                   ....*....|....*....|.
gi 673040669   289 KPCKFFAQGHCRMGNKCKFAH 309
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 354-682 1.02e-114

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: 348.81  E-value: 1.02e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 354 LSLDDLR-GRVFAMSKDQNGCRLLQEQLDNSvdqvhhprtATDLCDVIYTESLPHLVDMMVDPFGNYLFQKLLECGTESQ 432
Cdd:cd07920    2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEA---------TPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 433 RFAIVQQVAHHLVAAALNLHGTRSVQKVVEICSsssmPQLVELIVDALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFV 512
Cdd:cd07920   73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESIS----EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFI 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 513 FDAVSAECTVVGTHRHGCCVLQRCVDAANPAQRREVIAQVEKHAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVGHV 592
Cdd:cd07920  149 IDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNI 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 593 LELSIQKFSSNVIEKCLELAPDYLCQTFVREIIASP----RMHRMLQDQYANYVVQRALSVASDENCLDLVTAMRPHLTS 668
Cdd:cd07920  229 VQLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPS 308

                        330
                 ....*....|....
gi 673040669 669 MKNTQGGRRIQARI 682
Cdd:cd07920  309 LRKSPYGKHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 367-686 4.39e-69

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 241.57  E-value: 4.39e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 367 SKDQNGCRLLQEQLDNSvdqvhhprtATDLCDVIYTESLPHLVDMMVDPFGNYLFQKLLECGTESQRFAIVQQVAHHLVA 446
Cdd:COG5099  447 CKDQHGSRFLQKLLDSN---------SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVS 517

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 447 AALNLHGTRSVQKVVEICSSssmPQLVELIVDALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFVFDAVSAECTVVGTH 526
Cdd:COG5099  518 LSVHKYGTRVLQKAIDIVST---DIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTH 594

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 527 RHGCCVLQRCVDAANPAQRREVIAQVEKHAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVG-HVLELSIQKFSSNVI 605
Cdd:COG5099  595 RYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSkRVVELSTHKFASNVV 674

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 606 EKCLELAPDylcqTFVREII----ASPRMHR------MLQDQYANYVVQRALSVASDENCLDLVTAMRPHLTSMKNTQGG 675
Cdd:COG5099  675 EKCIKYASD----SFKRSRIlnelTNRGIEKpgflmlILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYG 750

                        330
                 ....*....|.
gi 673040669 676 RRIqARILKRF 686
Cdd:COG5099  751 QHI-LALLEKV 760
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 403-438 3.58e-08

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 3.58e-08
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 673040669   403 ESLPHLVDMMVDPFGNYLFQKLLECGTESQRFAIVQ 438
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 525-552 4.36e-07

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: 46.52  E-value: 4.36e-07
                          10        20
                  ....*....|....*....|....*...
gi 673040669  525 THRHGCCVLQRCVDAANPAQRREVIAQV 552
Cdd:pfam00806   7 TDQYGCRVIQKCLEHATEEQREQILDEI 34
ZnF_C3H1 smart00356
zinc finger;
289-309 1.54e-05

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.23  E-value: 1.54e-05
                           10        20
                   ....*....|....*....|.
gi 673040669   289 KPCKFFAQGHCRMGNKCKFAH 309
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 291-309 8.77e-05

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 39.71  E-value: 8.77e-05
                          10
                  ....*....|....*....
gi 673040669  291 CKFFAQGHCRMGNKCKFAH 309
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 354-682 1.02e-114

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: 348.81  E-value: 1.02e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 354 LSLDDLR-GRVFAMSKDQNGCRLLQEQLDNSvdqvhhprtATDLCDVIYTESLPHLVDMMVDPFGNYLFQKLLECGTESQ 432
Cdd:cd07920    2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEA---------TPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 433 RFAIVQQVAHHLVAAALNLHGTRSVQKVVEICSsssmPQLVELIVDALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFV 512
Cdd:cd07920   73 RLQLLEKILGHVVRLSLDMYGCRVIQKLLESIS----EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFI 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 513 FDAVSAECTVVGTHRHGCCVLQRCVDAANPAQRREVIAQVEKHAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVGHV 592
Cdd:cd07920  149 IDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNI 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 593 LELSIQKFSSNVIEKCLELAPDYLCQTFVREIIASP----RMHRMLQDQYANYVVQRALSVASDENCLDLVTAMRPHLTS 668
Cdd:cd07920  229 VQLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPS 308

                        330
                 ....*....|....
gi 673040669 669 MKNTQGGRRIQARI 682
Cdd:cd07920  309 LRKSPYGKHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 367-686 4.39e-69

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 241.57  E-value: 4.39e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 367 SKDQNGCRLLQEQLDNSvdqvhhprtATDLCDVIYTESLPHLVDMMVDPFGNYLFQKLLECGTESQRFAIVQQVAHHLVA 446
Cdd:COG5099  447 CKDQHGSRFLQKLLDSN---------SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVS 517

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 447 AALNLHGTRSVQKVVEICSSssmPQLVELIVDALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFVFDAVSAECTVVGTH 526
Cdd:COG5099  518 LSVHKYGTRVLQKAIDIVST---DIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTH 594

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 527 RHGCCVLQRCVDAANPAQRREVIAQVEKHAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVG-HVLELSIQKFSSNVI 605
Cdd:COG5099  595 RYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSkRVVELSTHKFASNVV 674

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 606 EKCLELAPDylcqTFVREII----ASPRMHR------MLQDQYANYVVQRALSVASDENCLDLVTAMRPHLTSMKNTQGG 675
Cdd:COG5099  675 EKCIKYASD----SFKRSRIlnelTNRGIEKpgflmlILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYG 750

                        330
                 ....*....|.
gi 673040669 676 RRIqARILKRF 686
Cdd:COG5099  751 QHI-LALLEKV 760
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 403-438 3.58e-08

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 3.58e-08
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 673040669   403 ESLPHLVDMMVDPFGNYLFQKLLECGTESQRFAIVQ 438
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 525-552 4.36e-07

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: 46.52  E-value: 4.36e-07
                          10        20
                  ....*....|....*....|....*...
gi 673040669  525 THRHGCCVLQRCVDAANPAQRREVIAQV 552
Cdd:pfam00806   7 TDQYGCRVIQKCLEHATEEQREQILDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 407-441 1.47e-06

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: 44.98  E-value: 1.47e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 673040669  407 HLVDMMVDPFGNYLFQKLLECGTESQRFAIVQQVA 441
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
ZnF_C3H1 smart00356
zinc finger;
289-309 1.54e-05

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.23  E-value: 1.54e-05
                           10        20
                   ....*....|....*....|.
gi 673040669   289 KPCKFFAQGHCRMGNKCKFAH 309
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 591-625 1.79e-05

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: 41.90  E-value: 1.79e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 673040669  591 HVLELSIQKFSSNVIEKCLELAPDYLCQTFVREII 625
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 479-514 4.77e-05

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 40.88  E-value: 4.77e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 673040669   479 ALKDDAVRLCIDSNGNHVIQRALQYMPATYNQFVFD 514
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 552-581 6.86e-05

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 40.50  E-value: 6.86e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 673040669   552 VEKHAMKLMQDPYGNYVVQYVLDACSTADV 581
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQR 31
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 291-309 8.77e-05

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 39.71  E-value: 8.77e-05
                          10
                  ....*....|....*....
gi 673040669  291 CKFFAQGHCRMGNKCKFAH 309
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 528-691 2.64e-04

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 44.35  E-value: 2.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 528 HGCCVLQRCVDAaNPAQRREVIAQVEK-HAMKLMQDPYGNYVVQYVLDACSTADVVGVMTKCVGHVLELSIQKFSSNVIE 606
Cdd:COG5099  451 HGSRFLQKLLDS-NSSPEIEVIFNEILdQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQ 529

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673040669 607 KCLELAPdylcqtfvreiiasprmhrmlqdqyanyvvqralsvaSDENCLDLVTAMRPHLTSMKNTQGGRR-IQARILK- 684
Cdd:COG5099  530 KAIDIVS-------------------------------------TDIQISLLVEELRPYCLQLIKDQNGNHvIQKCIEKf 572


                 ....*..
gi 673040669 685 RFPHLDV 691
Cdd:COG5099  573 NKEKNQF 579
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 289-309 3.39e-04

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 38.34  E-value: 3.39e-04
                          10        20
                  ....*....|....*....|.
gi 673040669  289 KPCKFFAQGHCRMGNKCKFAH 309
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
290-309 1.51e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 36.40  E-value: 1.51e-03
                          10        20
                  ....*....|....*....|.
gi 673040669  290 PCKFFAQ-GHCRMGNKCKFAH 309
Cdd:pfam00642   5 LCRFFLRtGYCKYGDRCKFAH 25
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 627-659 1.81e-03

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 36.26  E-value: 1.81e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 673040669   627 SPRMHRMLQDQYANYVVQRALSVASDENCLDLV 659
Cdd:smart00025   3 KGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 590-622 1.89e-03

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 36.26  E-value: 1.89e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 673040669   590 GHVLELSIQKFSSNVIEKCLELAPDYLCQTFVR 622
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 555-580 3.35e-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: 35.74  E-value: 3.35e-03
                          10        20
                  ....*....|....*....|....*.
gi 673040669  555 HAMKLMQDPYGNYVVQYVLDACSTAD 580
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQ 26
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 525-549 8.85e-03

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 34.33  E-value: 8.85e-03
                           10        20
                   ....*....|....*....|....*
gi 673040669   525 THRHGCCVLQRCVDAANPAQRREVI 549
Cdd:smart00025  11 KDQYGNRVVQKLLEHASESQREQII 35
 
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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