NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1635381387|ref|NP_001357373|]
View 

nucleoporin NUP42 isoform 3 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 4-22 3.72e-06

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: 43.17  E-value: 3.72e-06
                          10
                  ....*....|....*....
gi 1635381387   4 CQFFLQGRCRFGDRCWNEH 22
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
PPE super family cl35037
PPE-repeat protein [Function unknown];
194-386 5.71e-06

PPE-repeat protein [Function unknown];


The actual alignment was detected with superfamily member COG5651:

Pssm-ID: 444372 [Multi-domain]  Cd Length: 385  Bit Score: 47.97  E-value: 5.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 194 SLNISTKLSDVKDGVNQAAPAFGFGSSQAATFMSPGFPVNNSSSDNAQNFSFKTNSGFAAASSGSPAGFGSSPAFGAAAS 273
Cdd:COG5651   174 ITNPGGLLGAQNAGSGNTSSNPGFANLGLTGLNQVGIGGLNSGSGPIGLNSGPGNTGFAGTGAAAGAAAAAAAAAAAAGA 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 274 TSSGISTSAPAFGFGKPEV----TSAASFSFKSPAASSFGSPGFSGLPASLATGPVRAPVAPAFGGGSSVAGFGSPGSHS 349
Cdd:COG5651   254 GASAALASLAATLLNASSLglaaTAASSAATNLGLAGSPLGLAGGGAGAAAATGLGLGAGGAAGAAGATGAGAALGAGAA 333

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1635381387 350 HTAFSKPSSDTFGNSSISTSLSASSSIIATDNVLFTP 386
Cdd:COG5651   334 AAAAGAAAGAGAAAAAAAGGAGGGGGGALGAGGGGGS 370
 
Name Accession Description Interval E-value
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 4-22 3.72e-06

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: 43.17  E-value: 3.72e-06
                          10
                  ....*....|....*....
gi 1635381387   4 CQFFLQGRCRFGDRCWNEH 22
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
PPE COG5651
PPE-repeat protein [Function unknown];
194-386 5.71e-06

PPE-repeat protein [Function unknown];


Pssm-ID: 444372 [Multi-domain]  Cd Length: 385  Bit Score: 47.97  E-value: 5.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 194 SLNISTKLSDVKDGVNQAAPAFGFGSSQAATFMSPGFPVNNSSSDNAQNFSFKTNSGFAAASSGSPAGFGSSPAFGAAAS 273
Cdd:COG5651   174 ITNPGGLLGAQNAGSGNTSSNPGFANLGLTGLNQVGIGGLNSGSGPIGLNSGPGNTGFAGTGAAAGAAAAAAAAAAAAGA 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 274 TSSGISTSAPAFGFGKPEV----TSAASFSFKSPAASSFGSPGFSGLPASLATGPVRAPVAPAFGGGSSVAGFGSPGSHS 349
Cdd:COG5651   254 GASAALASLAATLLNASSLglaaTAASSAATNLGLAGSPLGLAGGGAGAAAATGLGLGAGGAAGAAGATGAGAALGAGAA 333

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1635381387 350 HTAFSKPSSDTFGNSSISTSLSASSSIIATDNVLFTP 386
Cdd:COG5651   334 AAAAGAAAGAGAAAAAAAGGAGGGGGGALGAGGGGGS 370
ZnF_C3H1 smart00356
zinc finger;
1-23 8.73e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.23  E-value: 8.73e-06
                           10        20
                   ....*....|....*....|...
gi 1635381387    1 MAICQFFLQGRCRFGDRCWNEHP 23
Cdd:smart00356   4 TELCKFFKRGYCPRGDRCKFAHP 26
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 214-345 1.60e-04

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 43.70  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 214 AFGFGSSQAATFMSPGF---PVNNSSSDNAQNFSFKTNSGFAAASSGSPAG-FGSSPAFGAAASTSSGISTSAPAFGFGK 289
Cdd:cd23959    98 AFAMAPDESLGPFRAARvpnPFSASSSTQRETHKTAQVAPPKAEPQTAPVTpFGQLPMFGQHPPPAKPLPAAAAAQQSSA 177

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1635381387 290 PEVTSAASFSFKSPAASSFGSPGFSGLPASLATGPVRAPVAP-AFGGGSSVAGFGSP 345
Cdd:cd23959   178 SPGEVASPFASGTVSASPFATATDTAPSSGAPDGFPAEASAPsPFAAPASAASFPAA 234
PRK13875 PRK13875
conjugal transfer protein TrbL; Provisional
 252-347 2.64e-03

conjugal transfer protein TrbL; Provisional


Pssm-ID: 237537  Cd Length: 440  Bit Score: 39.89  E-value: 2.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 252 AAASSGSPAGFGSSPAFGAAASTSSGISTSAPAFGfgkpEVTSAASFSFKSPAASSFGSPGfSGLPASLATGpVRAPVAP 331
Cdd:PRK13875  308 AAARGGAAAAGGASSAYSAGAAGGSGAAGVAAGLG----GVARAGASAAASPLRRAASRAA-ESMKSSFRAG-ARSTGGG 381

                          90
                  ....*....|....*.
gi 1635381387 332 AFGGGSSVAGFGSPGS 347
Cdd:PRK13875  382 AGGAAAAAAAGAAAAG 397
 
Name Accession Description Interval E-value
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 4-22 3.72e-06

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: 43.17  E-value: 3.72e-06
                          10
                  ....*....|....*....
gi 1635381387   4 CQFFLQGRCRFGDRCWNEH 22
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
PPE COG5651
PPE-repeat protein [Function unknown];
194-386 5.71e-06

PPE-repeat protein [Function unknown];


Pssm-ID: 444372 [Multi-domain]  Cd Length: 385  Bit Score: 47.97  E-value: 5.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 194 SLNISTKLSDVKDGVNQAAPAFGFGSSQAATFMSPGFPVNNSSSDNAQNFSFKTNSGFAAASSGSPAGFGSSPAFGAAAS 273
Cdd:COG5651   174 ITNPGGLLGAQNAGSGNTSSNPGFANLGLTGLNQVGIGGLNSGSGPIGLNSGPGNTGFAGTGAAAGAAAAAAAAAAAAGA 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 274 TSSGISTSAPAFGFGKPEV----TSAASFSFKSPAASSFGSPGFSGLPASLATGPVRAPVAPAFGGGSSVAGFGSPGSHS 349
Cdd:COG5651   254 GASAALASLAATLLNASSLglaaTAASSAATNLGLAGSPLGLAGGGAGAAAATGLGLGAGGAAGAAGATGAGAALGAGAA 333

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1635381387 350 HTAFSKPSSDTFGNSSISTSLSASSSIIATDNVLFTP 386
Cdd:COG5651   334 AAAAGAAAGAGAAAAAAAGGAGGGGGGALGAGGGGGS 370
ZnF_C3H1 smart00356
zinc finger;
1-23 8.73e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.23  E-value: 8.73e-06
                           10        20
                   ....*....|....*....|...
gi 1635381387    1 MAICQFFLQGRCRFGDRCWNEHP 23
Cdd:smart00356   4 TELCKFFKRGYCPRGDRCKFAHP 26
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 3-23 1.43e-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: 38.72  E-value: 1.43e-04
                          10        20
                  ....*....|....*....|.
gi 1635381387   3 ICQFFLQGRCRFGDRCWNEHP 23
Cdd:pfam18044   2 LCRYFQKGGCRYGDNCRFSHD 22
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 214-345 1.60e-04

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 43.70  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 214 AFGFGSSQAATFMSPGF---PVNNSSSDNAQNFSFKTNSGFAAASSGSPAG-FGSSPAFGAAASTSSGISTSAPAFGFGK 289
Cdd:cd23959    98 AFAMAPDESLGPFRAARvpnPFSASSSTQRETHKTAQVAPPKAEPQTAPVTpFGQLPMFGQHPPPAKPLPAAAAAQQSSA 177

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1635381387 290 PEVTSAASFSFKSPAASSFGSPGFSGLPASLATGPVRAPVAP-AFGGGSSVAGFGSP 345
Cdd:cd23959   178 SPGEVASPFASGTVSASPFATATDTAPSSGAPDGFPAEASAPsPFAAPASAASFPAA 234
PRK13875 PRK13875
conjugal transfer protein TrbL; Provisional
 252-347 2.64e-03

conjugal transfer protein TrbL; Provisional


Pssm-ID: 237537  Cd Length: 440  Bit Score: 39.89  E-value: 2.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635381387 252 AAASSGSPAGFGSSPAFGAAASTSSGISTSAPAFGfgkpEVTSAASFSFKSPAASSFGSPGfSGLPASLATGpVRAPVAP 331
Cdd:PRK13875  308 AAARGGAAAAGGASSAYSAGAAGGSGAAGVAAGLG----GVARAGASAAASPLRRAASRAA-ESMKSSFRAG-ARSTGGG 381

                          90
                  ....*....|....*.
gi 1635381387 332 AFGGGSSVAGFGSPGS 347
Cdd:PRK13875  382 AGGAAAAAAAGAAAAG 397
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH