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Conserved domains on  [gi|167045373|gb|ABZ10029|]
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putative ribosomal S3Ae family protein [uncultured marine microorganism HF4000_APKG10F13]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPS3A COG1890
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 1-210 9.60e-65

Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins


:

Pssm-ID: 441494  Cd Length: 208  Bit Score: 200.85  E-value: 9.60e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   1 MA-KPQRKTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFT 79
Cdd:COG1890    1 MArKRARRVKDKWKEKKWYTVYAPEFFGEVEIGETPADDPEKLIGRVVETTLGDLTGDFSKQNIKLYFKINDVEGDKAYT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373  80 AFDGHRLTSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKR 159
Cdd:COG1890   81 EFIGHELTRDYLRSLVRRGSSKIDAIVDVTTKDGYKVRVKPVAFTTKRANTSQKHAIRKIMRDIVEEKAKELTFDEFVQE 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 167045373 160 IYSGELARELAKELRIIYLTRRVEIAKIELLSpavlmdvPPSEEELERILA 210
Cdd:COG1890  161 IVFGKLSSDIYKEAKKIYPLRRVEIRKSKLLA-------RPEEEAPEEEVA 204
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 225-255 2.94e-10

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


:

Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 53.94  E-value: 2.94e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 167045373  225 YESLTVPELKELLKAQGLPVSGRKADLIERL 255
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERL 31
 
Name Accession Description Interval E-value
RPS3A COG1890
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 1-210 9.60e-65

Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441494  Cd Length: 208  Bit Score: 200.85  E-value: 9.60e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   1 MA-KPQRKTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFT 79
Cdd:COG1890    1 MArKRARRVKDKWKEKKWYTVYAPEFFGEVEIGETPADDPEKLIGRVVETTLGDLTGDFSKQNIKLYFKINDVEGDKAYT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373  80 AFDGHRLTSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKR 159
Cdd:COG1890   81 EFIGHELTRDYLRSLVRRGSSKIDAIVDVTTKDGYKVRVKPVAFTTKRANTSQKHAIRKIMRDIVEEKAKELTFDEFVQE 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 167045373 160 IYSGELARELAKELRIIYLTRRVEIAKIELLSpavlmdvPPSEEELERILA 210
Cdd:COG1890  161 IVFGKLSSDIYKEAKKIYPLRRVEIRKSKLLA-------RPEEEAPEEEVA 204
Ribosomal_S3Ae pfam01015
Ribosomal S3Ae family;
3-191 1.69e-60

Ribosomal S3Ae family;


Pssm-ID: 425987  Cd Length: 191  Bit Score: 189.62  E-value: 1.69e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373    3 KPQRKTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFTAFD 82
Cdd:pfam01015   1 GKKKKVVDKWKKKEWYDVKAPSMFGGREIGKTPADDPEKLKGRVVEVTLADLTGDFSKENRKLKFKIDDVQGDNALTNFH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   83 GHRLTSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKRIYS 162
Cdd:pfam01015  81 GHELTRDYLRSLVRRWSSLIEAIVDVKTKDGYKLRVFVIAFTKRRAKSSQKRAIRKKMFEIITEEASELDLKEFVKKLIP 160

                         170       180
                  ....*....|....*....|....*....
gi 167045373  163 GELARELAKELRIIYLTRRVEIAKIELLS 191
Cdd:pfam01015 161 GKIGKEIEKACKKIYPLRRVEIRKVKVLK 189
PRK04057 PRK04057
30S ribosomal protein S3Ae; Validated
 7-208 5.49e-60

30S ribosomal protein S3Ae; Validated


Pssm-ID: 235216  Cd Length: 203  Bit Score: 188.55  E-value: 5.49e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   7 KTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFTAFDGHRL 86
Cdd:PRK04057   1 RVKDKWKEKKWYTVYAPEFFGGVEIGETPADDPEKLIGRVVETTLGDLTGDFSKQNVKLYFKIDNVEGDKAYTRFIGHEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373  87 TSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKRIYSGELA 166
Cdd:PRK04057  81 TRDYLRSLVRRRTSKIDAIVDVTTKDGYKVRVKPVALTTKRARTSQKHAIRKIMEEIIEEKASELTFEEFVQEIVFGKLA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 167045373 167 RELAKELRIIYLTRRVEIAKIELLSpavlmdvPPSEEELERI 208
Cdd:PRK04057 161 SEIYKEAKKIYPLRRVEIRKSKVLA-------RPEEVEAEEE 195
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 225-255 2.94e-10

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 53.94  E-value: 2.94e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 167045373  225 YESLTVPELKELLKAQGLPVSGRKADLIERL 255
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERL 31
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
225-255 4.94e-08

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 47.87  E-value: 4.94e-08
                           10        20        30
                   ....*....|....*....|....*....|.
gi 167045373   225 YESLTVPELKELLKAQGLPVSGRKADLIERL 255
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRL 31
LEM_like cd12935
LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also ...
 227-253 8.11e-04

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: 36.21  E-value: 8.11e-04
                         10        20
                 ....*....|....*....|....*....
gi 167045373 227 SLTVPELKELLKAQG--LPVSGRKADLIE 253
Cdd:cd12935    3 SLTVAELRSILTEHGveYPSNAKKAELVK 31
PLN03124 PLN03124
poly [ADP-ribose] polymerase; Provisional
 224-262 1.12e-03

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215591 [Multi-domain]  Cd Length: 643  Bit Score: 40.21  E-value: 1.12e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 167045373 224 DYESLTVPELKELLKAQGLPVSGRKADLIERLSSAGSNE 262
Cdd:PLN03124  78 EVKGMTVRELREAASERGLATTGRKKDLLERLCAALESD 116
 
Name Accession Description Interval E-value
RPS3A COG1890
Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 1-210 9.60e-65

Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]; Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441494  Cd Length: 208  Bit Score: 200.85  E-value: 9.60e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   1 MA-KPQRKTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFT 79
Cdd:COG1890    1 MArKRARRVKDKWKEKKWYTVYAPEFFGEVEIGETPADDPEKLIGRVVETTLGDLTGDFSKQNIKLYFKINDVEGDKAYT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373  80 AFDGHRLTSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKR 159
Cdd:COG1890   81 EFIGHELTRDYLRSLVRRGSSKIDAIVDVTTKDGYKVRVKPVAFTTKRANTSQKHAIRKIMRDIVEEKAKELTFDEFVQE 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 167045373 160 IYSGELARELAKELRIIYLTRRVEIAKIELLSpavlmdvPPSEEELERILA 210
Cdd:COG1890  161 IVFGKLSSDIYKEAKKIYPLRRVEIRKSKLLA-------RPEEEAPEEEVA 204
Ribosomal_S3Ae pfam01015
Ribosomal S3Ae family;
3-191 1.69e-60

Ribosomal S3Ae family;


Pssm-ID: 425987  Cd Length: 191  Bit Score: 189.62  E-value: 1.69e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373    3 KPQRKTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFTAFD 82
Cdd:pfam01015   1 GKKKKVVDKWKKKEWYDVKAPSMFGGREIGKTPADDPEKLKGRVVEVTLADLTGDFSKENRKLKFKIDDVQGDNALTNFH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   83 GHRLTSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKRIYS 162
Cdd:pfam01015  81 GHELTRDYLRSLVRRWSSLIEAIVDVKTKDGYKLRVFVIAFTKRRAKSSQKRAIRKKMFEIITEEASELDLKEFVKKLIP 160

                         170       180
                  ....*....|....*....|....*....
gi 167045373  163 GELARELAKELRIIYLTRRVEIAKIELLS 191
Cdd:pfam01015 161 GKIGKEIEKACKKIYPLRRVEIRKVKVLK 189
PRK04057 PRK04057
30S ribosomal protein S3Ae; Validated
 7-208 5.49e-60

30S ribosomal protein S3Ae; Validated


Pssm-ID: 235216  Cd Length: 203  Bit Score: 188.55  E-value: 5.49e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373   7 KTKDRWKGKAWYSLHAPAMFNYAVMAWTPADSPEAVTGRVAEISLDRLSGDFAQKNYIVRFRVGEVRGPNAFTAFDGHRL 86
Cdd:PRK04057   1 RVKDKWKEKKWYTVYAPEFFGGVEIGETPADDPEKLIGRVVETTLGDLTGDFSKQNVKLYFKIDNVEGDKAYTRFIGHEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167045373  87 TSDYKRALTRRRNTRVDCNFILTTADDVRLRLKPMLVVDNRIRGSQEKLLRARTTALVSETLSGLSLAEGLKRIYSGELA 166
Cdd:PRK04057  81 TRDYLRSLVRRRTSKIDAIVDVTTKDGYKVRVKPVALTTKRARTSQKHAIRKIMEEIIEEKASELTFEEFVQEIVFGKLA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 167045373 167 RELAKELRIIYLTRRVEIAKIELLSpavlmdvPPSEEELERI 208
Cdd:PRK04057 161 SEIYKEAKKIYPLRRVEIRKSKVLA-------RPEEVEAEEE 195
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 225-255 2.94e-10

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 53.94  E-value: 2.94e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 167045373  225 YESLTVPELKELLKAQGLPVSGRKADLIERL 255
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERL 31
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
225-255 4.94e-08

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 47.87  E-value: 4.94e-08
                           10        20        30
                   ....*....|....*....|....*....|.
gi 167045373   225 YESLTVPELKELLKAQGLPVSGRKADLIERL 255
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRL 31
LEM_like cd12935
LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins; LAP2, also ...
 227-253 8.11e-04

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: 36.21  E-value: 8.11e-04
                         10        20
                 ....*....|....*....|....*....
gi 167045373 227 SLTVPELKELLKAQG--LPVSGRKADLIE 253
Cdd:cd12935    3 SLTVAELRSILTEHGveYPSNAKKAELVK 31
PLN03124 PLN03124
poly [ADP-ribose] polymerase; Provisional
 224-262 1.12e-03

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215591 [Multi-domain]  Cd Length: 643  Bit Score: 40.21  E-value: 1.12e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 167045373 224 DYESLTVPELKELLKAQGLPVSGRKADLIERLSSAGSNE 262
Cdd:PLN03124  78 EVKGMTVRELREAASERGLATTGRKKDLLERLCAALESD 116
FANC_SAP pfam18081
Fanconi anemia-associated nuclease SAP domain; This domain is found in ...
 228-258 5.93e-03

Fanconi anemia-associated nuclease SAP domain; This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for processing DNA inter-strand cross-links (ICLs). The domain, known as the SAP domain, helps to augment the overall protein DNA interaction by interacting with the 3' and 5' ends of the template strand. Support of the pre-nick segment binding is crucial as multiple mutations in this domain resulted in hypersensitivity to a cross-linking agent in the SAP domain of Caenorhabditis elegans' FAN1. The helix-hairpin-helix of the SAP recognize three consecutive phosphate groups (C19, A20 and A21) at the 3' end of the template via the basic residues K116, K135 and K117.


Pssm-ID: 465639  Cd Length: 51  Bit Score: 34.17  E-value: 5.93e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 167045373  228 LTVPELKELLKAQGLPVSGRKADLIERLSSA 258
Cdd:pfam18081  11 LTKPELAAAFALQLSPASARKAELLEALRAQ 41
 
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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