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Conserved domains on  [gi|1270003696|ref|XP_022748496.1|]
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pumilio homolog 1-like isoform X2 [Durio zibethinus]

Protein Classification

pumilio/puf RNA binding domain-containing protein( domain architecture ID 10278242)

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 ...
 636-956 8.90e-175

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: 510.98  E-value: 8.90e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 636 FELSEIA-GHVVEFSADQYGSRFIQQKLETATTEEKNMVFHEIMPRMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLT 714
Cdd:cd07920     2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 715 GHVLTLSLQMYGCRVIQKAIEVVELDQKTKMVKELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIVSTFYDQVVTLST 794
Cdd:cd07920    82 GHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALST 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 795 HPYGCRVIQRVLEHCHEAKtQHIMMDEIFRSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIRKLTGQIVQMSQQKFASNV 874
Cdd:cd07920   162 HPYGCRVIQRCLEHCSEEQ-REPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 875 IEKCLTFGTPAERQNLVNEMLGLTDENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVA 954
Cdd:cd07920   241 VEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                  ..
gi 1270003696 955 RV 956
Cdd:cd07920   321 KL 322
NABP super family cl06847
Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid ...
 251-639 6.74e-138

Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterized and contains two putative phosphorylation sites and a possible dimerization / leucine zipper domain.


The actual alignment was detected with superfamily member pfam07990:

Pssm-ID: 400378  Cd Length: 387  Bit Score: 418.41  E-value: 6.74e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 251 RAPSPRIPPICGQSSSIEKRSVTGSNTFNAVgsnssngfSTSVGESAELVAALSGLNLSTNGVVDEENHSQCWAHHGIDD 330
Cdd:pfam07990   1 RSPSPCLPPVGVRVSSSDKKNIVGSNSFNGV--------SSGMTESADIVAALSGLNLSGNGLLDEENHLRSQLQQEFDD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 331 NHNpfnhSLINLQGDQKHIKQNSYLNKLEPEHFHLHstaqsgkGPYLNTSKGSGVGMDLMKSSLMADGPIELRK----SA 406
Cdd:pfam07990  73 QQN----FLFNMQGGQNQSLQQQLLDKSDSANLNNS-------PSYSDLPKSNGNLSNLNASKLSSDGQVELPKqtvsSN 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 407 NSYPKGPLTHTVNGL-GSPPNHQNLDNMNSTLPKYGLTGYSINPSSPPMLGNQLGSGTLPPLFENAAALSAMGGtglesr 485
Cdd:pfam07990 142 NSYSKGPSSSTLSGGgGSPSLYQNADSPNIDFSNYGLSGYSSNPGLPSMMNNHLGLSSGPAGNSDGQNLNRLGN------ 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 486 alEGGNGLHAQQLDPLYLQYL-RSNELAGAQVAAINDAMIDREYSGNSYMDLIGLQKAYIGSL---QKS----------- 550
Cdd:pfam07990 216 --QVGSGLQSPFMDPMYLQYLqRTSDYAAHQAASLNDPSMGRNYMGSSYMDLLGLQKAYLGALlaqQKSqygvpllgksg 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 551 -----YYGNLALGLGMSYPGGPLVGPLFPNSPVGSGSPVRHNDRNLRFASGLRNVSGGVMRAWHSEAAGNLDDGLASALL 625
Cdd:pfam07990 294 glnhgYYGNPAFGLGMPYPGSPLASPVLPSSPVGSGSPVRQGERNMRFPSGMRNSTGGVMGSWHSDNGGNMEEGFASSLL 373

                         410
                  ....*....|....
gi 1270003696 626 DEFKSNKTKCFELS 639
Cdd:pfam07990 374 EEFKSNKTRSFELS 387
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 636-956 8.90e-175

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: 510.98  E-value: 8.90e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 636 FELSEIA-GHVVEFSADQYGSRFIQQKLETATTEEKNMVFHEIMPRMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLT 714
Cdd:cd07920     2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 715 GHVLTLSLQMYGCRVIQKAIEVVELDQKTKMVKELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIVSTFYDQVVTLST 794
Cdd:cd07920    82 GHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALST 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 795 HPYGCRVIQRVLEHCHEAKtQHIMMDEIFRSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIRKLTGQIVQMSQQKFASNV 874
Cdd:cd07920   162 HPYGCRVIQRCLEHCSEEQ-REPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 875 IEKCLTFGTPAERQNLVNEMLGLTDENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVA 954
Cdd:cd07920   241 VEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                  ..
gi 1270003696 955 RV 956
Cdd:cd07920   321 KL 322
NABP pfam07990
Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid ...
 251-639 6.74e-138

Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterized and contains two putative phosphorylation sites and a possible dimerization / leucine zipper domain.


Pssm-ID: 400378  Cd Length: 387  Bit Score: 418.41  E-value: 6.74e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 251 RAPSPRIPPICGQSSSIEKRSVTGSNTFNAVgsnssngfSTSVGESAELVAALSGLNLSTNGVVDEENHSQCWAHHGIDD 330
Cdd:pfam07990   1 RSPSPCLPPVGVRVSSSDKKNIVGSNSFNGV--------SSGMTESADIVAALSGLNLSGNGLLDEENHLRSQLQQEFDD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 331 NHNpfnhSLINLQGDQKHIKQNSYLNKLEPEHFHLHstaqsgkGPYLNTSKGSGVGMDLMKSSLMADGPIELRK----SA 406
Cdd:pfam07990  73 QQN----FLFNMQGGQNQSLQQQLLDKSDSANLNNS-------PSYSDLPKSNGNLSNLNASKLSSDGQVELPKqtvsSN 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 407 NSYPKGPLTHTVNGL-GSPPNHQNLDNMNSTLPKYGLTGYSINPSSPPMLGNQLGSGTLPPLFENAAALSAMGGtglesr 485
Cdd:pfam07990 142 NSYSKGPSSSTLSGGgGSPSLYQNADSPNIDFSNYGLSGYSSNPGLPSMMNNHLGLSSGPAGNSDGQNLNRLGN------ 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 486 alEGGNGLHAQQLDPLYLQYL-RSNELAGAQVAAINDAMIDREYSGNSYMDLIGLQKAYIGSL---QKS----------- 550
Cdd:pfam07990 216 --QVGSGLQSPFMDPMYLQYLqRTSDYAAHQAASLNDPSMGRNYMGSSYMDLLGLQKAYLGALlaqQKSqygvpllgksg 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 551 -----YYGNLALGLGMSYPGGPLVGPLFPNSPVGSGSPVRHNDRNLRFASGLRNVSGGVMRAWHSEAAGNLDDGLASALL 625
Cdd:pfam07990 294 glnhgYYGNPAFGLGMPYPGSPLASPVLPSSPVGSGSPVRQGERNMRFPSGMRNSTGGVMGSWHSDNGGNMEEGFASSLL 373

                         410
                  ....*....|....
gi 1270003696 626 DEFKSNKTKCFELS 639
Cdd:pfam07990 374 EEFKSNKTRSFELS 387
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 568-968 2.68e-87

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 296.66  E-value: 2.68e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 568 LVGPLFPNSPVGSGSPVRHNDRNLRFASGLRNVSGGVMRawhseaaGNLDDGLASalLDEFKSNKTKCFELSEIAGHVVE 647
Cdd:COG5099   374 KKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKT-------SSNLTNLNS--LLKEKLSNSSSVSATDILGPSII 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 648 FS-ADQYGSRFIQQKLETATTEEKNMVFHEIMPRMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLTGHVLTLSLQMYG 726
Cdd:COG5099   445 VScKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 727 CRVIQKAIEVV-ELDQKTKMVKELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIVSTFYDQVVTLSTHPYGCRVIQRV 805
Cdd:COG5099   525 TRVLQKAIDIVsTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 806 LEHCHEaKTQHIMMDEIFRSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIRK-LTGQIVQMSQQKFASNVIEKCLTFGTP 884
Cdd:COG5099   605 LENCNS-EDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKlLSKRVVELSTHKFASNVVEKCIKYASD 683

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 885 AE-RQNLVNEMLGLT-DENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEKLVAA 962
Cdd:COG5099   684 SFkRSRILNELTNRGiEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSS 763


                  ....*.
gi 1270003696 963 GERRIS 968
Cdd:COG5099   764 SQSSIS 769
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 788-822 2.57e-10

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: 56.15  E-value: 2.57e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1270003696 788 QVVTLSTHPYGCRVIQRVLEHCHEAKTQHImMDEI 822
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQI-LDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 904-934 3.11e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.43  E-value: 3.11e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1270003696  904 LQVMMKDQFANYVVQKVLETCDDQQLELILN 934
Cdd:smart00025   6 LLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 636-956 8.90e-175

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: 510.98  E-value: 8.90e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 636 FELSEIA-GHVVEFSADQYGSRFIQQKLETATTEEKNMVFHEIMPRMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLT 714
Cdd:cd07920     2 LTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 715 GHVLTLSLQMYGCRVIQKAIEVVELDQKTKMVKELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIVSTFYDQVVTLST 794
Cdd:cd07920    82 GHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALST 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 795 HPYGCRVIQRVLEHCHEAKtQHIMMDEIFRSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIRKLTGQIVQMSQQKFASNV 874
Cdd:cd07920   162 HPYGCRVIQRCLEHCSEEQ-REPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 875 IEKCLTFGTPAERQNLVNEMLGLTDENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVA 954
Cdd:cd07920   241 VEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                  ..
gi 1270003696 955 RV 956
Cdd:cd07920   321 KL 322
NABP pfam07990
Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid ...
 251-639 6.74e-138

Nucleic acid binding protein NABP; Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterized and contains two putative phosphorylation sites and a possible dimerization / leucine zipper domain.


Pssm-ID: 400378  Cd Length: 387  Bit Score: 418.41  E-value: 6.74e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 251 RAPSPRIPPICGQSSSIEKRSVTGSNTFNAVgsnssngfSTSVGESAELVAALSGLNLSTNGVVDEENHSQCWAHHGIDD 330
Cdd:pfam07990   1 RSPSPCLPPVGVRVSSSDKKNIVGSNSFNGV--------SSGMTESADIVAALSGLNLSGNGLLDEENHLRSQLQQEFDD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 331 NHNpfnhSLINLQGDQKHIKQNSYLNKLEPEHFHLHstaqsgkGPYLNTSKGSGVGMDLMKSSLMADGPIELRK----SA 406
Cdd:pfam07990  73 QQN----FLFNMQGGQNQSLQQQLLDKSDSANLNNS-------PSYSDLPKSNGNLSNLNASKLSSDGQVELPKqtvsSN 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 407 NSYPKGPLTHTVNGL-GSPPNHQNLDNMNSTLPKYGLTGYSINPSSPPMLGNQLGSGTLPPLFENAAALSAMGGtglesr 485
Cdd:pfam07990 142 NSYSKGPSSSTLSGGgGSPSLYQNADSPNIDFSNYGLSGYSSNPGLPSMMNNHLGLSSGPAGNSDGQNLNRLGN------ 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 486 alEGGNGLHAQQLDPLYLQYL-RSNELAGAQVAAINDAMIDREYSGNSYMDLIGLQKAYIGSL---QKS----------- 550
Cdd:pfam07990 216 --QVGSGLQSPFMDPMYLQYLqRTSDYAAHQAASLNDPSMGRNYMGSSYMDLLGLQKAYLGALlaqQKSqygvpllgksg 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 551 -----YYGNLALGLGMSYPGGPLVGPLFPNSPVGSGSPVRHNDRNLRFASGLRNVSGGVMRAWHSEAAGNLDDGLASALL 625
Cdd:pfam07990 294 glnhgYYGNPAFGLGMPYPGSPLASPVLPSSPVGSGSPVRQGERNMRFPSGMRNSTGGVMGSWHSDNGGNMEEGFASSLL 373

                         410
                  ....*....|....
gi 1270003696 626 DEFKSNKTKCFELS 639
Cdd:pfam07990 374 EEFKSNKTRSFELS 387
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 568-968 2.68e-87

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 296.66  E-value: 2.68e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 568 LVGPLFPNSPVGSGSPVRHNDRNLRFASGLRNVSGGVMRawhseaaGNLDDGLASalLDEFKSNKTKCFELSEIAGHVVE 647
Cdd:COG5099   374 KKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKT-------SSNLTNLNS--LLKEKLSNSSSVSATDILGPSII 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 648 FS-ADQYGSRFIQQKLETATTEEKNMVFHEIMPRMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLTGHVLTLSLQMYG 726
Cdd:COG5099   445 VScKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 727 CRVIQKAIEVV-ELDQKTKMVKELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIVSTFYDQVVTLSTHPYGCRVIQRV 805
Cdd:COG5099   525 TRVLQKAIDIVsTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 806 LEHCHEaKTQHIMMDEIFRSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIRK-LTGQIVQMSQQKFASNVIEKCLTFGTP 884
Cdd:COG5099   605 LENCNS-EDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKlLSKRVVELSTHKFASNVVEKCIKYASD 683

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270003696 885 AE-RQNLVNEMLGLT-DENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEKLVAA 962
Cdd:COG5099   684 SFkRSRILNELTNRGiEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSS 763


                  ....*.
gi 1270003696 963 GERRIS 968
Cdd:COG5099   764 SQSSIS 769
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 788-822 2.57e-10

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: 56.15  E-value: 2.57e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1270003696 788 QVVTLSTHPYGCRVIQRVLEHCHEAKTQHImMDEI 822
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQI-LDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 644-678 3.87e-10

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: 55.38  E-value: 3.87e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1270003696 644 HVVEFSADQYGSRFIQQKLETATTEEKNMVFHEIM 678
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 716-749 3.52e-08

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: 49.99  E-value: 3.52e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1270003696 716 HVLTLSLQMYGCRVIQKAIEVVELDQKTKMVKEL 749
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 826-859 8.09e-08

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: 48.84  E-value: 8.09e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1270003696 826 VCMLAQDQYGNYVVQHVLEHGKPHERSAIIRKLT 859
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 861-895 2.78e-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: 47.30  E-value: 2.78e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1270003696 861 QIVQMSQQKFASNVIEKCLTFGTPAERQNLVNEML 895
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 904-934 3.11e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.43  E-value: 3.11e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1270003696  904 LQVMMKDQFANYVVQKVLETCDDQQLELILN 934
Cdd:smart00025   6 LLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 679-709 8.21e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.27  E-value: 8.21e-07
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1270003696  679 PRMLSLMTDVFGNYVIQKFFEHGSASQIREL 709
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 713-747 1.30e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.50  E-value: 1.30e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1270003696  713 LTGHVLTLSLQMYGCRVIQKAIEVVELDQKTKMVK 747
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 748-782 1.42e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.50  E-value: 1.42e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1270003696  748 ELDGHVMRCVRDQNGNHVIQKCIECVPEDAIQFIV 782
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 680-714 1.82e-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: 1.82e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1270003696 680 RMLSLMTDVFGNYVIQKFFEHGSASQIRELADQLT 714
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 907-936 2.75e-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: 44.60  E-value: 2.75e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 1270003696 907 MMKDQFANYVVQKVLETCDDQQLELILNRI 936
Cdd:pfam00806   5 LATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 857-892 3.27e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 44.35  E-value: 3.27e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1270003696  857 KLTGQIVQMSQQKFASNVIEKCLTFGTPAERQNLVN 892
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 829-856 1.05e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 1.05e-05
                           10        20
                   ....*....|....*....|....*...
gi 1270003696  829 LAQDQYGNYVVQHVLEHGKPHERSAIIR 856
Cdd:smart00025   9 LSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 787-812 1.07e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 1.07e-05
                           10        20
                   ....*....|....*....|....*.
gi 1270003696  787 DQVVTLSTHPYGCRVIQRVLEHCHEA 812
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASES 29
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 752-783 9.61e-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: 40.36  E-value: 9.61e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1270003696 752 HVMRCVRDQNGNHVIQKCIECVPEDAIQFIVS 783
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 640-675 1.94e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 39.34  E-value: 1.94e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1270003696  640 EIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFH 675
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
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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