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Conserved domains on  [gi|157818805|ref|NP_001099671|]
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DNA cross-link repair 1A protein [Rattus norvegicus]

Protein Classification

DNA cross-link repair protein( domain architecture ID 11039898)

DNA cross-link repair protein similar to Mus musculus DNA cross-link repair 1A protein that may be required for DNA interstrand cross-link repair, and also required for checkpoint mediated cell cycle arrest in early prophase in response to mitotic spindle poisons

CATH:  3.40.50.12650|3.60.15.10
Gene Ontology:  GO:0003684|GO:0046872|GO:0006281|GO:0035312|GO:0036297
PubMed:  12177301|20528238|11471246|11513844|17597585

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 675-830 1.42e-99

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


The actual alignment was detected with superfamily member cd16298:

Pssm-ID: 451500 [Multi-domain]  Cd Length: 157  Bit Score: 309.83  E-value: 1.42e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818805  755 YIHQLPMDTECIVDGVKVVLLDANHCPGATMILFQLPNGAVTLHTGDFRADPSMERS-LLASRKVHTLFLDTTYCSP 830
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDANHCPGAVMILFRLPSGTLVLHTGDFRADPSMERYpELIGQKIHTLYLDTTYCSP 157
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 900-1005 1.62e-47

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


:

Pssm-ID: 429512  Cd Length: 108  Bit Score: 164.76  E-value: 1.62e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805   900 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 978
Cdd:pfam07522    1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                           90       100
                   ....*....|....*....|....*..
gi 157818805   979 EHSSYLEMKRFVQWLKPQKIIPTVNVG 1005
Cdd:pfam07522   81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
 
Name Accession Description Interval E-value
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 675-830 1.42e-99

5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) which is a 5'-exonuclease and functions in interstrand cross-links (ICL) repair. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293856 [Multi-domain]  Cd Length: 157  Bit Score: 309.83  E-value: 1.42e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818805  755 YIHQLPMDTECIVDGVKVVLLDANHCPGATMILFQLPNGAVTLHTGDFRADPSMERS-LLASRKVHTLFLDTTYCSP 830
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDANHCPGAVMILFRLPSGTLVLHTGDFRADPSMERYpELIGQKIHTLYLDTTYCSP 157
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 900-1005 1.62e-47

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 164.76  E-value: 1.62e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805   900 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 978
Cdd:pfam07522    1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                           90       100
                   ....*....|....*....|....*..
gi 157818805   979 EHSSYLEMKRFVQWLKPQKIIPTVNVG 1005
Cdd:pfam07522   81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 715-844 1.45e-10

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 62.99  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHYAGLsKDFTR-------PIYCSEITGSLLKKKLRVQEQY------IHQLPMDTECIVDGVKVVLLDANH-C 780
Cdd:COG1235    73 LLTHEHADHIAGL-DDLRPrygpnpiPVYATPGTLEALERRFPYLFAPypgkleFHEIEPGEPFEIGGLTVTPFPVPHdA 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818805  781 PGATMILFQLPNGAVTLhTGDFRADPSMERSLLasRKVHTLFLDTTYCSPEYTFPSQQEAIQFA 844
Cdd:COG1235   152 GDPVGYRIEDGGKKLAY-ATDTGYIPEEVLELL--RGADLLILDATYDDPEPGHLSNEEALELL 212
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 715-829 9.84e-07

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 50.24  E-value: 9.84e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805    715 FLTHFHSDHYAG---LSKDFTRPIYCSEITGSLLKKKLRVQEQYIHQLPM--DTECIVDGVKVVL----LDANHCPGATM 785
Cdd:smart00849   40 ILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELLKDLLALLGELGAEAEPapPDRTLKDGDELDLgggeLEVIHTPGHTP 119

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 157818805    786 --ILFQLPNGAVtLHTGDFR------------ADPSMERSLLASRKVHTLFLDTTYCS 829
Cdd:smart00849  120 gsIVLYLPEGKI-LFTGDLLfaggdgrtlvdgGDAAASDALESLLKLLKLLPKLVVPG 176
 
Name Accession Description Interval E-value
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 675-830 1.42e-99

5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) which is a 5'-exonuclease and functions in interstrand cross-links (ICL) repair. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293856 [Multi-domain]  Cd Length: 157  Bit Score: 309.83  E-value: 1.42e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818805  755 YIHQLPMDTECIVDGVKVVLLDANHCPGATMILFQLPNGAVTLHTGDFRADPSMERS-LLASRKVHTLFLDTTYCSP 830
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDANHCPGAVMILFRLPSGTLVLHTGDFRADPSMERYpELIGQKIHTLYLDTTYCSP 157
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 684-830 3.62e-86

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293831  Cd Length: 160  Bit Score: 274.03  E-value: 3.62e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  684 RRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTR-PIYCSEITGSLLKKKLRVQEQYIHQLPMD 762
Cdd:cd16273    10 KKPCPFYKIIPGTSFVVDAFKYGKIPGISAYFLSHFHSDHYGGLTKSWSHgPIYCSEITANLVKLKLKVDEEYIVVLPMN 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157818805  763 TEC-IVDGVKVVLLDANHCPGATMILFQLPNGAVTLHTGDFRADPSM--ERSLLASRKVHTLFLDTTYCSP 830
Cdd:cd16273    90 TPVeIDGDVSVTLLDANHCPGAVMFLFELPDGRRILHTGDFRANPEMleHPLLLGKRRIDTVYLDTTYCNP 160
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 900-1005 1.62e-47

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 164.76  E-value: 1.62e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805   900 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 978
Cdd:pfam07522    1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                           90       100
                   ....*....|....*....|....*..
gi 157818805   979 EHSSYLEMKRFVQWLKPQKIIPTVNVG 1005
Cdd:pfam07522   81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
 699-830 8.10e-19

artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Inactivation of Artemis causes severe combined immunodeficiency (SCID). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293855  Cd Length: 171  Bit Score: 84.87  E-value: 8.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  699 TVDAFQYGEIEGcTAYFLTHFHSDHYAGLSKDFTRP---------IYCSEITGSLL--KKKLRVQEQYIHQLPMDTEC-- 765
Cdd:cd16297    15 SIDRFDRENLRA-RAYFLSHCHKDHMKGLRAPGLKRrlkaslkvkLYCSPVTKELLltNPKYAFWENHIVSLEIDTPTqi 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  766 -IVD-------GVKVVLLDANHCPGATMILFQLPNGAVtLHTGDFR----ADPSMErsLLAS----RKVHTLFLDTTYCS 829
Cdd:cd16297    94 sLVDeatgekeDVVVTLLPAGHCPGSVMFLFQGNNGTV-LYTGDFRlavgEAARME--LLHSgdrvKDIQSVYLDTTFCD 170


                  .
gi 157818805  830 P 830
Cdd:cd16297   171 P 171
RNaseJ_MBL-fold cd07714
RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a ...
 715-875 4.29e-11

RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a prokaryotic ribonuclease which plays a key part in RNA processing and in RNA degradation. It can act as an endonuclease which is specific for single-stranded regions of RNA irrespective of their sequence or location, and as a processive 5' exonuclease which only acts on substrates having a single phosphate or a hydroxyl at the 5' end. Many bacterial species have only one RNase J, but some, such as Bacillus subtilis, have two. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293800 [Multi-domain]  Cd Length: 248  Bit Score: 64.35  E-value: 4.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHYAGLS---KDFTRPIYCSEITGSLLKKKLR----VQEQYIHQLPMDTECIVDGVKVVLLDANHC-PGATMI 786
Cdd:cd07714    60 FITHGHEDHIGALPyllPELNVPIYATPLTLALIKKKLEefklIKKVKLNEIKPGERIKLGDFEVEFFRVTHSiPDSVGL 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  787 LFQLPNGAVtLHTGDFRADPS--------MER-SLLASRKVHTLFLDTTYCSPeytFPSQQEaIQFAINtafeavTLNPR 857
Cdd:cd07714   140 AIKTPEGTI-VHTGDFKFDQTpvdgkptdLEKlAELGKEGVLLLLSDSVHVSG---HASQED-LKLMIN------LLKPK 208

                         170       180       190
                  ....*....|....*....|....*....|..
gi 157818805  858 ALI-VCGTY-------------CIGKEKVFLA 875
Cdd:cd07714   209 YFIpVHGEYrhlvahaklaeelGIPEENIFLL 240
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 715-844 1.45e-10

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 62.99  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHYAGLsKDFTR-------PIYCSEITGSLLKKKLRVQEQY------IHQLPMDTECIVDGVKVVLLDANH-C 780
Cdd:COG1235    73 LLTHEHADHIAGL-DDLRPrygpnpiPVYATPGTLEALERRFPYLFAPypgkleFHEIEPGEPFEIGGLTVTPFPVPHdA 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818805  781 PGATMILFQLPNGAVTLhTGDFRADPSMERSLLasRKVHTLFLDTTYCSPEYTFPSQQEAIQFA 844
Cdd:COG1235   152 GDPVGYRIEDGGKKLAY-ATDTGYIPEEVLELL--RGADLLILDATYDDPEPGHLSNEEALELL 212
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 715-869 3.15e-10

RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 63.28  E-value: 3.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHyAGL-----SKDFTRPIYCS----EITGSLLKKKLRVQEQYIHQLPMDTE-----CI-------------V 767
Cdd:COG1236    55 VLTHAHLDH-SGAlpllvKEGFRGPIYATpataDLARILLGDSAKIQEEEAEAEPLYTEedaerALelfqtvdygepfeI 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  768 DGVKVVLLDANHCPGATMILFQLpNGAVTLHTGDF--RADPSMeRSLLASRKVHTLFLDTTYCSPEYtfPSQQEAIQfAI 845
Cdd:COG1236   134 GGVRVTFHPAGHILGSAQVELEV-GGKRIVFSGDYgrEDDPLL-APPEPVPPADVLITESTYGDRLH--PPREEVEA-EL 208

                         170       180
                  ....*....|....*....|....
gi 157818805  846 NTAFEAVTLNPRALIVcGTYCIGK 869
Cdd:COG1236   209 AEWVRETLARGGTVLI-PAFALGR 231
RnjA COG0595
mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];
713-807 1.03e-09

mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440360 [Multi-domain]  Cd Length: 553  Bit Score: 62.39  E-value: 1.03e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  713 AYFLTHFHSDHYAGLS---KDFTRPIYCSEITGSLLKKKLR----VQEQYIHQLPMDTECIVDGVKVVLLDANH-CPGAT 784
Cdd:COG0595    66 GIVLTHGHEDHIGALPyllKELNVPVYGTPLTLALLEAKLKehglLKKVKLHVVKPGDRIKFGPFKVEFFRVTHsIPDSL 145

                          90       100
                  ....*....|....*....|...
gi 157818805  785 MILFQLPNGAVtLHTGDFRADPS 807
Cdd:COG0595   146 GLAIRTPAGTI-VHTGDFKFDQT 167
metallo-hydrolase-like_MBL-fold cd07732
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 693-804 3.34e-08

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain; Includes functionally uncharacterized Enterococcus faecalis EF2904. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry.


Pssm-ID: 293818 [Multi-domain]  Cd Length: 202  Bit Score: 54.93  E-value: 3.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  693 IPGTGFTVDAFQYGEIEG---CTAYFLTHFHSDHYAGLSK-DFTRPIYCSEITGSLLKKKLRV---QEQYIHQL----PM 761
Cdd:cd07732    55 IVGLYRDPLLLGGLRSEEdpsVDAVLLSHAHLDHYGLLNYlRPDIPVYMGEATKRILKALLPFfgeGDPVPRNIrvfeSG 134

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 157818805  762 DTECIVD-GVKVVLLDanH-CPGATMILFQLPNGAVtLHTGDFRA 804
Cdd:cd07732   135 KSFTIGDfTVTPYLVD--HsAPGAYAFLIEAPGKRI-FYTGDFRF 176
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 715-829 9.84e-07

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 50.24  E-value: 9.84e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805    715 FLTHFHSDHYAG---LSKDFTRPIYCSEITGSLLKKKLRVQEQYIHQLPM--DTECIVDGVKVVL----LDANHCPGATM 785
Cdd:smart00849   40 ILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELLKDLLALLGELGAEAEPapPDRTLKDGDELDLgggeLEVIHTPGHTP 119

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 157818805    786 --ILFQLPNGAVtLHTGDFR------------ADPSMERSLLASRKVHTLFLDTTYCS 829
Cdd:smart00849  120 gsIVLYLPEGKI-LFTGDLLfaggdgrtlvdgGDAAASDALESLLKLLKLLPKLVVPG 176
metallo-hydrolase-like_MBL-fold cd06262
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 694-826 7.86e-06

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


Pssm-ID: 293792 [Multi-domain]  Cd Length: 188  Bit Score: 47.67  E-value: 7.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  694 PGTGFTVDAFQYGEIEG--CTAYFLTHFHSDHYAGLS--KDFTR-PIYCSEITGSLLK---KKLRVQEQYIHQLPMDTEC 765
Cdd:cd06262    27 PGAGALEKILEAIEELGlkIKAILLTHGHFDHIGGLAelKEAPGaPVYIHEADAELLEdpeLNLAFFGGGPLPPPEPDIL 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  766 IVDGVKVVLLDAN--------HCPGATMILFQ----------LPNGAV---TLHTGDFRAdpsMERSLLasRKVHTLFLD 824
Cdd:cd06262   107 LEDGDTIELGGLElevihtpgHTPGSVCFYIEeegvlftgdtLFAGSIgrtDLPGGDPEQ---LIESIK--KLLLLLPDD 181


                  ..
gi 157818805  825 TT 826
Cdd:cd06262   182 TV 183
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
712-827 2.68e-05

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 46.73  E-value: 2.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  712 TAYFLTHFHSDHYAGL--------SKDFTRP--IYCSEITGSLLKKKLRVQEQY------IHQLPMDTECIVDGVKVVLL 775
Cdd:COG1234    54 DAIFITHLHGDHIAGLpgllstrsLAGREKPltIYGPPGTKEFLEALLKASGTDldfpleFHEIEPGEVFEIGGFTVTAF 133

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 157818805  776 DANHCPGATMILFQLPNGAVTLhTGDFRADPSMERsllASRKVHTLFLDTTY 827
Cdd:COG1234   134 PLDHPVPAYGYRFEEPGRSLVY-SGDTRPCEALVE---LAKGADLLIHEATF 181
GloB COG0491
Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General ...
 715-801 3.56e-04

Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General function prediction only];


Pssm-ID: 440257 [Multi-domain]  Cd Length: 215  Bit Score: 43.14  E-value: 3.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHYAG---LSKDFTRPIYCSEITGSLLKKKLRvQEQYIHQLPMDTECIVDGVKVVLLDAN----HCPGAT--M 785
Cdd:COG0491    56 LLTHLHPDHVGGlaaLAEAFGAPVYAHAAEAEALEAPAA-GALFGREPVPPDRTLEDGDTLELGGPGleviHTPGHTpgH 134

                          90
                  ....*....|....*.
gi 157818805  786 ILFQLPNGAVtLHTGD 801
Cdd:COG0491   135 VSFYVPDEKV-LFTGD 149
metallo-hydrolase-like_MBL-fold cd16279
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo; ...
 715-785 4.21e-04

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. Some members of this subgroup are named as octanoyltransferase (also known as lipoate-protein ligase B).


Pssm-ID: 293837 [Multi-domain]  Cd Length: 193  Bit Score: 42.46  E-value: 4.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  715 FLTHFHSDHYAGLS--KDFTR------PIYCSEITGSLLKKKLRVQEQY----------IHQLPMDTECIVDGVKVVLLD 776
Cdd:cd16279    71 LLTHAHADHIHGLDdlRPFNRlqqrpiPVYASEETLDDLKRRFPYFFAAtggggvpkldLHIIEPDEPFTIGGLEITPLP 150


                  ....*....
gi 157818805  777 ANHCPGATM 785
Cdd:cd16279   151 VLHGKLPSL 159
UlaG COG2220
L-ascorbate lactonase UlaG, metallo-beta-lactamase superfamily [Carbohydrate transport and ...
 694-823 2.68e-03

L-ascorbate lactonase UlaG, metallo-beta-lactamase superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 441822 [Multi-domain]  Cd Length: 224  Bit Score: 40.67  E-value: 2.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  694 PGTGFTVDAFQYGEIEGCTAYFLTHFHSDHY-----AGLSKDFTrPIYCSEITGSLLKKKLRVQeqyIHQLPMDTECIVD 768
Cdd:COG2220    32 RASPVNPLPLDPEDLPKIDAVLVTHDHYDHLddatlRALKRTGA-TVVAPLGVAAWLRAWGFPR---VTELDWGESVELG 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818805  769 GVKVVLLDANHCPG--------ATMILFQLPNGAVtLHTGDFRADPSMERsLLASRKVHTLFL 823
Cdd:COG2220   108 GLTVTAVPARHSSGrpdrngglWVGFVIETDGKTI-YHAGDTGYFPEMKE-IGERFPIDVALL 168
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 700-802 2.75e-03

cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain; CPSF3 (also known as cleavage and polyadenylation specificity factor 73 kDa subunit/CPSF-73) functions as a 3' endonuclease in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and in 3' end processing of metazoan histone pre-mRNAs. This subgroup also contains the yeast homolog of CPSF-73, Ysh1/Brr5 which has roles in mRNA and snoRNA synthesis. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain, and a RMMBL domain (RNA-metabolizing metallo-beta-lactamase). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293850  Cd Length: 194  Bit Score: 40.26  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818805  700 VDAFQYGEIEGCtayFLTHFHSDHYAGL-----SKDFTRPIYCSEITGS----LLKKKLRVQEQYIHQLP---------M 761
Cdd:cd16292    45 FDEIDLSEIDLL---LITHFHLDHCGALpyflqKTNFKGRVFMTHPTKAiykwLLSDYVRVSNISSDEMLytetdleasM 121

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 157818805  762 D-TECI-------VDGVKVVLLDANHCPGATMILFQLPnGAVTLHTGDF 802
Cdd:cd16292   122 DkIETIdfhqeveVNGIKFTAYNAGHVLGAAMFMVEIA-GVRVLYTGDY 169
 
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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