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Conserved domains on  [gi|754407684|ref|XP_011273519|]
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uncharacterized protein BN7_4199 [Wickerhamomyces ciferrii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MSC pfam09402
Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which ...
 625-978 2.33e-117

Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organization. The C terminal nucleoplasmic region forms a DNA binding winged helix and binds to Smad. This C-terminal tail is also found in S. cerevisiae and is thought to consist of three conserved helices followed by two downstream strands.


:

Pssm-ID: 430586  Cd Length: 333  Bit Score: 362.76  E-value: 2.33e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  625 FFTILIISSLWYREQRILIGYCGLEINdktfPNTDNEILIKIDEFLDQNLKPTCLEAPENSIALPYLQIKCKPDYIVYQP 704
Cdd:pfam09402   1 LIVLLILFGLWYREEKIAVGYCGTGSP----TNSIDEEREQVPAWLLESLKPQCTPCPEHAICYPGLELTCEPDYVLKPH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  705 WYKIHGLLPFSDYCIKDTKKELIIKEVVSKSLELLRIKNANVQCGDCTNDE---IVGITNDELYEFFFNSKSNSITDEEF 781
Cdd:pfam09402  77 PLSLGGLLPLPPTCVPDTEKARKVKEVADKALELLREKNAKVECGEGKDDLgalESGISEEELKDILSEKKSPSLSDEEF 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  782 NELWVNVLKDLQNEPEITLRYTDIVDSNSTQDNlstnevedetddiqqttersiIFRSNSKLKLSIKCKFQKEIYDNFEK 861
Cdd:pfam09402 157 EELWAAALGELKKRPEIVWRQDSVGNSDGESTR---------------------LLRSTSLAYLPLKCRLRRSVRDTLAR 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  862 NKKILISFLTISILILIGYNKIKSIQKRNLKIKEISDIILIKLQKQSKNSQLDSTGLTKRFLSNIQLRDELLINYHN-KE 940
Cdd:pfam09402 216 YRLILLGLLLLLLAILYLRSRYRRRRAEKARVEELVQEVLERLKNQKALHAEDPSLYPDPYLSSVQLRDDILRDEHSlKR 295

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 754407684  941 KFKIWELILNNLEKNSNIRILTKEIHGEIVKVLEWIGD 978
Cdd:pfam09402 296 RNRLWKRVVKVVEGNSNVRTSLREVHGEIMRVWEWIGP 333
LEM_like super family cl06998
LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also ...
 9-38 2.35e-03

LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain.


The actual alignment was detected with superfamily member cd12935:

Pssm-ID: 415001  Cd Length: 36  Bit Score: 36.60  E-value: 2.35e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 754407684   9 PDLRRILHFNNIEFPNSFKKKDLVNKWNEE 38
Cdd:cd12935    7 AELRSILTEHGVEYPSNAKKAELVKLFNKH 36
 
Name Accession Description Interval E-value
MSC pfam09402
Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which ...
 625-978 2.33e-117

Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organization. The C terminal nucleoplasmic region forms a DNA binding winged helix and binds to Smad. This C-terminal tail is also found in S. cerevisiae and is thought to consist of three conserved helices followed by two downstream strands.


Pssm-ID: 430586  Cd Length: 333  Bit Score: 362.76  E-value: 2.33e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  625 FFTILIISSLWYREQRILIGYCGLEINdktfPNTDNEILIKIDEFLDQNLKPTCLEAPENSIALPYLQIKCKPDYIVYQP 704
Cdd:pfam09402   1 LIVLLILFGLWYREEKIAVGYCGTGSP----TNSIDEEREQVPAWLLESLKPQCTPCPEHAICYPGLELTCEPDYVLKPH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  705 WYKIHGLLPFSDYCIKDTKKELIIKEVVSKSLELLRIKNANVQCGDCTNDE---IVGITNDELYEFFFNSKSNSITDEEF 781
Cdd:pfam09402  77 PLSLGGLLPLPPTCVPDTEKARKVKEVADKALELLREKNAKVECGEGKDDLgalESGISEEELKDILSEKKSPSLSDEEF 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  782 NELWVNVLKDLQNEPEITLRYTDIVDSNSTQDNlstnevedetddiqqttersiIFRSNSKLKLSIKCKFQKEIYDNFEK 861
Cdd:pfam09402 157 EELWAAALGELKKRPEIVWRQDSVGNSDGESTR---------------------LLRSTSLAYLPLKCRLRRSVRDTLAR 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  862 NKKILISFLTISILILIGYNKIKSIQKRNLKIKEISDIILIKLQKQSKNSQLDSTGLTKRFLSNIQLRDELLINYHN-KE 940
Cdd:pfam09402 216 YRLILLGLLLLLLAILYLRSRYRRRRAEKARVEELVQEVLERLKNQKALHAEDPSLYPDPYLSSVQLRDDILRDEHSlKR 295

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 754407684  941 KFKIWELILNNLEKNSNIRILTKEIHGEIVKVLEWIGD 978
Cdd:pfam09402 296 RNRLWKRVVKVVEGNSNVRTSLREVHGEIMRVWEWIGP 333
LEM_like cd12935
LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also ...
 9-38 2.35e-03

LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain.


Pssm-ID: 240596  Cd Length: 36  Bit Score: 36.60  E-value: 2.35e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 754407684   9 PDLRRILHFNNIEFPNSFKKKDLVNKWNEE 38
Cdd:cd12935    7 AELRSILTEHGVEYPSNAKKAELVKLFNKH 36
HeH pfam12949
HeH/LEM domain; This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) ...
 9-33 2.58e-03

HeH/LEM domain; This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) structures. It was demonstrated that the DNA-binding activity of the HEH/LEM domain assists the association of proteins with the centromeric region. This domain is closely related to pfam03020 and pfam02037.


Pssm-ID: 403988  Cd Length: 35  Bit Score: 36.23  E-value: 2.58e-03
                          10        20
                  ....*....|....*....|....*
gi 754407684    9 PDLRRILHFNNIEFPNSFKKKDLVN 33
Cdd:pfam12949   7 AQLRRILVEHGIEYPSNAKKADLVR 31
 
Name Accession Description Interval E-value
MSC pfam09402
Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which ...
 625-978 2.33e-117

Man1-Src1p-C-terminal domain; MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organization. The C terminal nucleoplasmic region forms a DNA binding winged helix and binds to Smad. This C-terminal tail is also found in S. cerevisiae and is thought to consist of three conserved helices followed by two downstream strands.


Pssm-ID: 430586  Cd Length: 333  Bit Score: 362.76  E-value: 2.33e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  625 FFTILIISSLWYREQRILIGYCGLEINdktfPNTDNEILIKIDEFLDQNLKPTCLEAPENSIALPYLQIKCKPDYIVYQP 704
Cdd:pfam09402   1 LIVLLILFGLWYREEKIAVGYCGTGSP----TNSIDEEREQVPAWLLESLKPQCTPCPEHAICYPGLELTCEPDYVLKPH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  705 WYKIHGLLPFSDYCIKDTKKELIIKEVVSKSLELLRIKNANVQCGDCTNDE---IVGITNDELYEFFFNSKSNSITDEEF 781
Cdd:pfam09402  77 PLSLGGLLPLPPTCVPDTEKARKVKEVADKALELLREKNAKVECGEGKDDLgalESGISEEELKDILSEKKSPSLSDEEF 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  782 NELWVNVLKDLQNEPEITLRYTDIVDSNSTQDNlstnevedetddiqqttersiIFRSNSKLKLSIKCKFQKEIYDNFEK 861
Cdd:pfam09402 157 EELWAAALGELKKRPEIVWRQDSVGNSDGESTR---------------------LLRSTSLAYLPLKCRLRRSVRDTLAR 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754407684  862 NKKILISFLTISILILIGYNKIKSIQKRNLKIKEISDIILIKLQKQSKNSQLDSTGLTKRFLSNIQLRDELLINYHN-KE 940
Cdd:pfam09402 216 YRLILLGLLLLLLAILYLRSRYRRRRAEKARVEELVQEVLERLKNQKALHAEDPSLYPDPYLSSVQLRDDILRDEHSlKR 295

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 754407684  941 KFKIWELILNNLEKNSNIRILTKEIHGEIVKVLEWIGD 978
Cdd:pfam09402 296 RNRLWKRVVKVVEGNSNVRTSLREVHGEIMRVWEWIGP 333
LEM_like cd12935
LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also ...
 9-38 2.35e-03

LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain.


Pssm-ID: 240596  Cd Length: 36  Bit Score: 36.60  E-value: 2.35e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 754407684   9 PDLRRILHFNNIEFPNSFKKKDLVNKWNEE 38
Cdd:cd12935    7 AELRSILTEHGVEYPSNAKKAELVKLFNKH 36
HeH pfam12949
HeH/LEM domain; This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) ...
 9-33 2.58e-03

HeH/LEM domain; This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) structures. It was demonstrated that the DNA-binding activity of the HEH/LEM domain assists the association of proteins with the centromeric region. This domain is closely related to pfam03020 and pfam02037.


Pssm-ID: 403988  Cd Length: 35  Bit Score: 36.23  E-value: 2.58e-03
                          10        20
                  ....*....|....*....|....*
gi 754407684    9 PDLRRILHFNNIEFPNSFKKKDLVN 33
Cdd:pfam12949   7 AQLRRILVEHGIEYPSNAKKADLVR 31
 
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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