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Conserved domains on  [gi|83753496|pdb|1VQP|Y]
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Chain Y, 50S ribosomal protein L32E

Protein Classification

PRK12766 family protein( domain architecture ID 11486180)

PRK12766 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12766 PRK12766
50S ribosomal protein L32e; Provisional
 14-241 1.41e-130

50S ribosomal protein L32e; Provisional


:

Pssm-ID: 183731 [Multi-domain]  Cd Length: 232  Bit Score: 368.02  E-value: 1.41e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        14 YTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLEVESETEAEVEEEGGEEAPDE- 92
Cdd:PRK12766   2 PEELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEVSEETEAEVEDEGGEEEEEEd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        93 -DVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRS 171
Cdd:PRK12766  82 aDVETELRPRGLTEKTPELSDEEARLLTQRRREGKPQFNRQDYHKKKRTPTSWRRPRGGLSKQRRGIKGKGDTVEAGFRT 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y       172 PTAVRGKHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEVEVSE 241
Cdd:PRK12766 162 PTAVRGKHPSGFEEVRVHNTDDLEGVDGDTEAVRIASKVGARKRERIEEVAEEQGIRVLNPTYVEVEVED 231
 
Name Accession Description Interval E-value
PRK12766 PRK12766
50S ribosomal protein L32e; Provisional
 14-241 1.41e-130

50S ribosomal protein L32e; Provisional


Pssm-ID: 183731 [Multi-domain]  Cd Length: 232  Bit Score: 368.02  E-value: 1.41e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        14 YTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLEVESETEAEVEEEGGEEAPDE- 92
Cdd:PRK12766   2 PEELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEVSEETEAEVEDEGGEEEEEEd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        93 -DVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRS 171
Cdd:PRK12766  82 aDVETELRPRGLTEKTPELSDEEARLLTQRRREGKPQFNRQDYHKKKRTPTSWRRPRGGLSKQRRGIKGKGDTVEAGFRT 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y       172 PTAVRGKHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEVEVSE 241
Cdd:PRK12766 162 PTAVRGKHPSGFEEVRVHNTDDLEGVDGDTEAVRIASKVGARKRERIEEVAEEQGIRVLNPTYVEVEVED 231
Rpl32e COG1717
Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 107-236 8.45e-74

Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]; Ribosomal protein L32E is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441323  Cd Length: 132  Bit Score: 220.50  E-value: 8.45e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y      107 TPDLSDEDARLLTQR--HRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFE 184
Cdd:COG1717   1 TPELSEETKRLLKLRkkQKRKKPEFKRQDWWKYKRLGDSWRKPRGIDNKQRLQLKGKPPLVKVGYRSPKAVRGLHPSGFE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
1VQP_Y      185 EVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVE 236
Cdd:COG1717  81 EVLVHNVKDLEGLDPETQAVRIASTVGLRKREEIEEKAKELGIKVLNPTVVE 132
Ribosomal_L32e pfam01655
Ribosomal protein L32; This family includes ribosomal protein L32 from eukaryotes and ...
 126-231 1.40e-49

Ribosomal protein L32; This family includes ribosomal protein L32 from eukaryotes and archaebacteria.


Pssm-ID: 460283  Cd Length: 108  Bit Score: 157.99  E-value: 1.40e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        126 KPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVD--GDTEA 203
Cdd:pfam01655   1 TKKFKRHQSDRYKRLKESWRKPRGIDNKVRRRFKGQPPMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLLmcNKSYA 80

                          90       100
                  ....*....|....*....|....*...
1VQP_Y        204 VRIASKVGARKRERIEEEAEDAGIRVLN 231
Cdd:pfam01655  81 AEIAHTVGSKKRKEIVERAAELGIKVLN 108
Ribosomal_L32_L32e cd00513
Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed ...
 127-231 1.15e-48

Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.


Pssm-ID: 238284  Cd Length: 107  Bit Score: 155.38  E-value: 1.15e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y      127 PQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVDG--DTEAV 204
Cdd:cd00513   1 KKFKRHQSDRYKRLGDSWRKPRGIDNKVRRRFKGKPAMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLDMhnRTYAA 80

                        90       100
                ....*....|....*....|....*..
1VQP_Y      205 RIASKVGARKRERIEEEAEDAGIRVLN 231
Cdd:cd00513  81 RIAHTVGARKRKEIVERAKELGIKVLN 107
 
Name Accession Description Interval E-value
PRK12766 PRK12766
50S ribosomal protein L32e; Provisional
 14-241 1.41e-130

50S ribosomal protein L32e; Provisional


Pssm-ID: 183731 [Multi-domain]  Cd Length: 232  Bit Score: 368.02  E-value: 1.41e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        14 YTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLEVESETEAEVEEEGGEEAPDE- 92
Cdd:PRK12766   2 PEELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEVSEETEAEVEDEGGEEEEEEd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        93 -DVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRS 171
Cdd:PRK12766  82 aDVETELRPRGLTEKTPELSDEEARLLTQRRREGKPQFNRQDYHKKKRTPTSWRRPRGGLSKQRRGIKGKGDTVEAGFRT 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y       172 PTAVRGKHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEVEVSE 241
Cdd:PRK12766 162 PTAVRGKHPSGFEEVRVHNTDDLEGVDGDTEAVRIASKVGARKRERIEEVAEEQGIRVLNPTYVEVEVED 231
Rpl32e COG1717
Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 107-236 8.45e-74

Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]; Ribosomal protein L32E is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441323  Cd Length: 132  Bit Score: 220.50  E-value: 8.45e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y      107 TPDLSDEDARLLTQR--HRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFE 184
Cdd:COG1717   1 TPELSEETKRLLKLRkkQKRKKPEFKRQDWWKYKRLGDSWRKPRGIDNKQRLQLKGKPPLVKVGYRSPKAVRGLHPSGFE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
1VQP_Y      185 EVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVE 236
Cdd:COG1717  81 EVLVHNVKDLEGLDPETQAVRIASTVGLRKREEIEEKAKELGIKVLNPTVVE 132
rpl32e PRK08562
50S ribosomal protein L32e; Validated
 112-233 1.57e-53

50S ribosomal protein L32e; Validated


Pssm-ID: 236288  Cd Length: 125  Bit Score: 168.56  E-value: 1.57e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y       112 DEDARLLTQR--HRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVH 189
Cdd:PRK08562   1 SERKRLLKLRlkLKRKKPEFKRQDWHRYKRLGDKWRRPRGLDSKMRLKLKGKPAIVEVGYRSPKAVRGLHPSGYEEVLVH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
1VQP_Y       190 NVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPT 233
Cdd:PRK08562  81 NVKELEKLDPETQAARIASTVGKRKRLEILKKARELGIKVLNPG 124
Ribosomal_L32e pfam01655
Ribosomal protein L32; This family includes ribosomal protein L32 from eukaryotes and ...
 126-231 1.40e-49

Ribosomal protein L32; This family includes ribosomal protein L32 from eukaryotes and archaebacteria.


Pssm-ID: 460283  Cd Length: 108  Bit Score: 157.99  E-value: 1.40e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y        126 KPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVD--GDTEA 203
Cdd:pfam01655   1 TKKFKRHQSDRYKRLKESWRKPRGIDNKVRRRFKGQPPMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLLmcNKSYA 80

                          90       100
                  ....*....|....*....|....*...
1VQP_Y        204 VRIASKVGARKRERIEEEAEDAGIRVLN 231
Cdd:pfam01655  81 AEIAHTVGSKKRKEIVERAAELGIKVLN 108
Ribosomal_L32_L32e cd00513
Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed ...
 127-231 1.15e-48

Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.


Pssm-ID: 238284  Cd Length: 107  Bit Score: 155.38  E-value: 1.15e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y      127 PQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVDG--DTEAV 204
Cdd:cd00513   1 KKFKRHQSDRYKRLGDSWRKPRGIDNKVRRRFKGKPAMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLDMhnRTYAA 80

                        90       100
                ....*....|....*....|....*..
1VQP_Y      205 RIASKVGARKRERIEEEAEDAGIRVLN 231
Cdd:cd00513  81 RIAHTVGARKRKEIVERAKELGIKVLN 107
PTZ00159 PTZ00159
60S ribosomal protein L32; Provisional
 129-233 1.07e-20

60S ribosomal protein L32; Provisional


Pssm-ID: 240297  Cd Length: 133  Bit Score: 84.28  E-value: 1.07e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1VQP_Y       129 FNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGV--DGDTEAVRI 206
Cdd:PTZ00159  18 FTRFQSERFPRVKPSWRKPRGIDNRVRRRFKGTRLMPKIGYGSDKKTRYLLPSGFYKFPVRNVKDLEMLlmHNRKYAAEI 97

                         90       100
                 ....*....|....*....|....*..
1VQP_Y       207 ASKVGARKRERIEEEAEDAGIRVLNPT 233
Cdd:PTZ00159  98 AHNVSARKRKAIVERAKELNVRVLNGN 124
HHH_5 pfam14520
Helix-hairpin-helix domain;
16-65 1.62e-11

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 57.88  E-value: 1.62e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
1VQP_Y         16 ELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIK 65
Cdd:pfam14520   3 ELLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRII 52
radA PRK04301
DNA repair and recombination protein RadA; Validated
 16-70 3.08e-09

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 56.04  E-value: 3.08e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
1VQP_Y        16 ELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARI------KADVGG 70
Cdd:PRK04301   7 DLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIieaareAADIGG 67
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
20-65 1.38e-04

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 41.70  E-value: 1.38e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
1VQP_Y       20 ISGVGPSKAESLREAgFESVEDVRGADQSALADVSGIGNALAARIK 65
Cdd:COG1948 160 LPGIGPKLARRLLEH-FGSVEAVFNASEEELMKVEGIGEKTAERIR 204
DNA_pol_lambd_f pfam10391
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
 16-43 2.48e-04

Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.


Pssm-ID: 463069 [Multi-domain]  Cd Length: 51  Bit Score: 37.82  E-value: 2.48e-04
                          10        20
                  ....*....|....*....|....*...
1VQP_Y         16 ELTDISGVGPSKAESLREAGFESVEDVR 43
Cdd:pfam10391   2 LFTGIYGVGPTTARKWYAQGYRTLDDLR 29
PRK13766 PRK13766
Hef nuclease; Provisional
 20-65 4.94e-04

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 41.01  E-value: 4.94e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
1VQP_Y        20 ISGVGPSKAESLREAgFESVEDVRGADQSALADVSGIGNALAARIK 65
Cdd:PRK13766 720 LPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKRIR 764
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 16-45 5.85e-04

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 40.26  E-value: 5.85e-04
                        10        20        30
                ....*....|....*....|....*....|
1VQP_Y       16 ELTDISGVGPSKAESLREAGFESVEDVRGA 45
Cdd:cd00141  86 LLLRVPGVGPKTARKLYELGIRTLEDLRKA 115
PRK02362 PRK02362
ATP-dependent DNA helicase;
16-64 1.49e-03

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 39.56  E-value: 1.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
1VQP_Y        16 ELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVsgIGNALAARI 64
Cdd:PRK02362 653 DLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENI 699
uvrC PRK14668
excinuclease ABC subunit C; Provisional
 15-66 3.47e-03

excinuclease ABC subunit C; Provisional


Pssm-ID: 184785 [Multi-domain]  Cd Length: 577  Bit Score: 38.21  E-value: 3.47e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
1VQP_Y        15 TELTDISGVGPSKAESLREAgFESVEDVRGADQSALADVSGIGNALAARIKA 66
Cdd:PRK14668 525 TVLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEKTAETIRE 575
 
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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