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Conserved domains on  [gi|1575772092|ref|WP_130066602|]
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toprim domain-containing protein [Aliivibrio finisterrensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 9-105 4.93e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


:

Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 56.21  E-value: 4.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESPKIAALLQHnlFKLGVITSVMATSGHLYdytfhnnNIVQQPINKTIIE-DLRALNGQPIIIATDPDPQGDLIAEH 87
Cdd:pfam01751   3 IIVEGPSDAIALEK--ALGGGFQAVVAVLGHLL-------SLEKGPKKKALKAlKELALKAKEVILATDPDREGEAIALK 73

                          90       100
                  ....*....|....*....|
gi 1575772092  88 IKNLTP--DSEHGRCIFNDI 105
Cdd:pfam01751  74 LLELKEllENAGGRVEFSEL 93
PTZ00407 super family cl31766
DNA topoisomerase IA; Provisional
 37-244 1.24e-04

DNA topoisomerase IA; Provisional


The actual alignment was detected with superfamily member PTZ00407:

Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 44.55  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092  37 SGHLYDYTFHNNNIVQQPINKTI---IEDlRALNGQPIIIATDPDPQGDLIAEH----IKNLTP--DSEHGRCIFNDISE 107
Cdd:PTZ00407   92 NGTLAEYTLEWELLPGRRIQETLeryIEE-KADNVTEIILATDPDREGELIAVHalqtIKRLYPklKVPFSRAYMHSITE 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 108 IGITLTLNRYNKGEFDFNQNQA-------------LKAALIKVTNLHMR------------------KMSSKSNRNNylT 156
Cdd:PTZ00407  171 DGIRKAMRERHVEACDYDLANAaetrhamdrifgfLGSSVVRAANSQMRsigrvqtpalilineredKIKAFLESNK--S 248

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 157 TTGISLAKQFDAV--GRINQVQQRGFNVEG----------VQHVCNvptQWHDANAAT-------KVNPTIT-------- 209
Cdd:PTZ00407  249 TFEVQAMCQFPSPhgTTFSQVVTITPDRKGgashwateaeARRCLE---QWKLNNCTGfsvplepKPQPSVVpppqpftm 325

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1575772092 210 RDLIT--DRALSGRKLTVAEELQDAFINGRISYTRTD 244
Cdd:PTZ00407  326 ATAIAkaNRQLKYSSEMVSGCLQDLFQLGHITYPRTD 362
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 9-105 4.93e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 56.21  E-value: 4.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESPKIAALLQHnlFKLGVITSVMATSGHLYdytfhnnNIVQQPINKTIIE-DLRALNGQPIIIATDPDPQGDLIAEH 87
Cdd:pfam01751   3 IIVEGPSDAIALEK--ALGGGFQAVVAVLGHLL-------SLEKGPKKKALKAlKELALKAKEVILATDPDREGEAIALK 73

                          90       100
                  ....*....|....*....|
gi 1575772092  88 IKNLTP--DSEHGRCIFNDI 105
Cdd:pfam01751  74 LLELKEllENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
9-91 2.01e-07

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.03  E-value: 2.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092    9 IIVESPKIAALLQHNLFKLGVITsvmATSGHLYdytfhnnnivqqpiNKTIIEDLRAL-NGQPIIIATDPDPQGDLIAEH 87
Cdd:smart00493   4 IIVEGPADAIALEKAGGKRGNVV---ALGGHLL--------------SKEQIKLLKKLaKKAEVILATDPDREGEAIAWE 66


                   ....
gi 1575772092   88 IKNL 91
Cdd:smart00493  67 LAEL 70
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 9-91 2.71e-07

TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 49.53  E-value: 2.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESP----KIAALL-----QHNLFKLGVITSVMATSGHLYDYTFH-----------------NNNIVQQPINKTIIED 62
Cdd:cd01028     4 IIAEKPskakTIAKILgkgskKKGFYGEGGGYVVTASVGHLLELPFPeeyvdwdkdwplelfpfEPKYVVIPDKKKQLKA 83

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1575772092  63 LRAL--NGQPIIIATDPDPQGDLIAEHIKNL 91
Cdd:cd01028    84 LKKLakKADEIVLATDPDREGELIAWEILEV 114
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
9-111 4.50e-05

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 45.86  E-value: 4.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESP----KIAALLQhNLFKlgvitsVMATSGHLYDYTFHNNNI-VQ-------QPINKT--IIEDLRAL--NGQPII 72
Cdd:COG0550     4 VIVESPakakTIAKYLG-KDYV------VTASVGHLRDLPKPELDVdVEndfepkyEVIPGKkkQVKELKKLakKADEVI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1575772092  73 IATDPDPQGDLIAEHIKN-LTPDSEHGRCIFNDISEIGIT 111
Cdd:COG0550    77 LATDPDREGEAIAWHLLElLGDKKPVKRVVFNEITKKAIK 116
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 37-244 1.24e-04

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 44.55  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092  37 SGHLYDYTFHNNNIVQQPINKTI---IEDlRALNGQPIIIATDPDPQGDLIAEH----IKNLTP--DSEHGRCIFNDISE 107
Cdd:PTZ00407   92 NGTLAEYTLEWELLPGRRIQETLeryIEE-KADNVTEIILATDPDREGELIAVHalqtIKRLYPklKVPFSRAYMHSITE 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 108 IGITLTLNRYNKGEFDFNQNQA-------------LKAALIKVTNLHMR------------------KMSSKSNRNNylT 156
Cdd:PTZ00407  171 DGIRKAMRERHVEACDYDLANAaetrhamdrifgfLGSSVVRAANSQMRsigrvqtpalilineredKIKAFLESNK--S 248

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 157 TTGISLAKQFDAV--GRINQVQQRGFNVEG----------VQHVCNvptQWHDANAAT-------KVNPTIT-------- 209
Cdd:PTZ00407  249 TFEVQAMCQFPSPhgTTFSQVVTITPDRKGgashwateaeARRCLE---QWKLNNCTGfsvplepKPQPSVVpppqpftm 325

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1575772092 210 RDLIT--DRALSGRKLTVAEELQDAFINGRISYTRTD 244
Cdd:PTZ00407  326 ATAIAkaNRQLKYSSEMVSGCLQDLFQLGHITYPRTD 362
PRK07219 PRK07219
DNA topoisomerase I; Validated
 28-125 6.73e-03

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 38.83  E-value: 6.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092  28 GVITSVMATSGHLYDYTFHNN---------------NIVQQPINKTIIEDLRALNGQP--IIIATDPDPQGDLI---AEH 87
Cdd:PRK07219   41 GEKWIVIGLSGHIVTVDFPEEygdwrdvdpaelidaDPVKKITKQNYINALKKLAKDAdeIIIATDYDREGELIgkeAYH 120

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1575772092  88 IKNLTPDSEHGRCIFNDISEIGITLTLNryNKGEFDFN 125
Cdd:PRK07219  121 ILREVCQVPVKRARFSSLTKKEIRKAFE--NPDEIDFN 156
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 9-105 4.93e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 56.21  E-value: 4.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESPKIAALLQHnlFKLGVITSVMATSGHLYdytfhnnNIVQQPINKTIIE-DLRALNGQPIIIATDPDPQGDLIAEH 87
Cdd:pfam01751   3 IIVEGPSDAIALEK--ALGGGFQAVVAVLGHLL-------SLEKGPKKKALKAlKELALKAKEVILATDPDREGEAIALK 73

                          90       100
                  ....*....|....*....|
gi 1575772092  88 IKNLTP--DSEHGRCIFNDI 105
Cdd:pfam01751  74 LLELKEllENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
9-91 2.01e-07

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.03  E-value: 2.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092    9 IIVESPKIAALLQHNLFKLGVITsvmATSGHLYdytfhnnnivqqpiNKTIIEDLRAL-NGQPIIIATDPDPQGDLIAEH 87
Cdd:smart00493   4 IIVEGPADAIALEKAGGKRGNVV---ALGGHLL--------------SKEQIKLLKKLaKKAEVILATDPDREGEAIAWE 66


                   ....
gi 1575772092   88 IKNL 91
Cdd:smart00493  67 LAEL 70
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 9-91 2.71e-07

TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 49.53  E-value: 2.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESP----KIAALL-----QHNLFKLGVITSVMATSGHLYDYTFH-----------------NNNIVQQPINKTIIED 62
Cdd:cd01028     4 IIAEKPskakTIAKILgkgskKKGFYGEGGGYVVTASVGHLLELPFPeeyvdwdkdwplelfpfEPKYVVIPDKKKQLKA 83

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1575772092  63 LRAL--NGQPIIIATDPDPQGDLIAEHIKNL 91
Cdd:cd01028    84 LKKLakKADEIVLATDPDREGELIAWEILEV 114
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 9-91 3.08e-07

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 47.81  E-value: 3.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESPKIAALLQHNLFKLGVITSVMatsGHlydytfhnnnivqqPINKTIIEDLRALNGQ-PIIIATDPDPQGDLIAEH 87
Cdd:cd00188     4 IIVEGPSDALALAQAGGYGGAVVALG---GH--------------ALNKTRELLKRLLGEAkEVIIATDADREGEAIALR 66


                  ....
gi 1575772092  88 IKNL 91
Cdd:cd00188    67 LLEL 70
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 9-107 7.03e-06

TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173783 [Multi-domain]  Cd Length: 123  Bit Score: 45.24  E-value: 7.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESPKIAALLQHNLFKLGVitsVMATSGHLYDYTFHN-----NNIVQQPI------NKTIIEDLRAL--NGQPIIIAT 75
Cdd:cd03363     4 VIVESPAKAKTIKKYLGKEYE---VLASVGHIRDLPKKGlgvdgEDDGFEPKyvvipgKKKVVKELKKLakKADEIYLAT 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1575772092  76 DPDPQGDLIAEHIKN-LTPDSEHGRCIFNDISE 107
Cdd:cd03363    81 DPDREGEAIAWHLAEvLKLKKNVKRVVFNEITK 113
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
9-111 4.50e-05

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 45.86  E-value: 4.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092   9 IIVESP----KIAALLQhNLFKlgvitsVMATSGHLYDYTFHNNNI-VQ-------QPINKT--IIEDLRAL--NGQPII 72
Cdd:COG0550     4 VIVESPakakTIAKYLG-KDYV------VTASVGHLRDLPKPELDVdVEndfepkyEVIPGKkkQVKELKKLakKADEVI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1575772092  73 IATDPDPQGDLIAEHIKN-LTPDSEHGRCIFNDISEIGIT 111
Cdd:COG0550    77 LATDPDREGEAIAWHLLElLGDKKPVKRVVFNEITKKAIK 116
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 37-244 1.24e-04

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 44.55  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092  37 SGHLYDYTFHNNNIVQQPINKTI---IEDlRALNGQPIIIATDPDPQGDLIAEH----IKNLTP--DSEHGRCIFNDISE 107
Cdd:PTZ00407   92 NGTLAEYTLEWELLPGRRIQETLeryIEE-KADNVTEIILATDPDREGELIAVHalqtIKRLYPklKVPFSRAYMHSITE 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 108 IGITLTLNRYNKGEFDFNQNQA-------------LKAALIKVTNLHMR------------------KMSSKSNRNNylT 156
Cdd:PTZ00407  171 DGIRKAMRERHVEACDYDLANAaetrhamdrifgfLGSSVVRAANSQMRsigrvqtpalilineredKIKAFLESNK--S 248

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092 157 TTGISLAKQFDAV--GRINQVQQRGFNVEG----------VQHVCNvptQWHDANAAT-------KVNPTIT-------- 209
Cdd:PTZ00407  249 TFEVQAMCQFPSPhgTTFSQVVTITPDRKGgashwateaeARRCLE---QWKLNNCTGfsvplepKPQPSVVpppqpftm 325

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1575772092 210 RDLIT--DRALSGRKLTVAEELQDAFINGRISYTRTD 244
Cdd:PTZ00407  326 ATAIAkaNRQLKYSSEMVSGCLQDLFQLGHITYPRTD 362
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 54-97 1.17e-03

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 39.62  E-value: 1.17e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1575772092  54 PINKTIIEDLR-ALNGQPIIIATDPDPQGDLIAEHIKNLTPDSEH 97
Cdd:COG1658    37 AISEETLELIKvAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81
PRK07219 PRK07219
DNA topoisomerase I; Validated
 28-125 6.73e-03

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 38.83  E-value: 6.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1575772092  28 GVITSVMATSGHLYDYTFHNN---------------NIVQQPINKTIIEDLRALNGQP--IIIATDPDPQGDLI---AEH 87
Cdd:PRK07219   41 GEKWIVIGLSGHIVTVDFPEEygdwrdvdpaelidaDPVKKITKQNYINALKKLAKDAdeIIIATDYDREGELIgkeAYH 120

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1575772092  88 IKNLTPDSEHGRCIFNDISEIGITLTLNryNKGEFDFN 125
Cdd:PRK07219  121 ILREVCQVPVKRARFSSLTKKEIRKAFE--NPDEIDFN 156
 
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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