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Conserved domains on  [gi|1102546650|gb|APC57482|]
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Rep (plasmid) [Enterococcus faecium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rep_trans super family cl47209
Replication initiation factor; Plasmid replication is initiated by the replication initiation ...
 136-219 6.81e-08

Replication initiation factor; Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family, including myelin transcription factor 2 and cerebrin-50.


The actual alignment was detected with superfamily member pfam02486:

Pssm-ID: 426796  Cd Length: 201  Bit Score: 51.95  E-value: 6.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102546650 136 FTRLDLAFDFEDDLSDYYAMTDKA-------VKKTVFYGRNGKPE---------TKYFGVRDSDRFIRIYNKKQERKDNA 199
Cdd:pfam02486   3 ITRIDLAIDDFDGELDIEELKKKYrnglcisRFRRFKYYGSGELVdgedvgtgkTLYIGSRKSEKYLRIYEKGYEQGDKE 82

                          90       100
                  ....*....|....*....|.
gi 1102546650 200 DVEVVSehLW-RVEVELKRDM 219
Cdd:pfam02486  83 GIPVES--PWvRYELRLRNER 101
 
Name Accession Description Interval E-value
Rep_trans pfam02486
Replication initiation factor; Plasmid replication is initiated by the replication initiation ...
 136-219 6.81e-08

Replication initiation factor; Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family, including myelin transcription factor 2 and cerebrin-50.


Pssm-ID: 426796  Cd Length: 201  Bit Score: 51.95  E-value: 6.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102546650 136 FTRLDLAFDFEDDLSDYYAMTDKA-------VKKTVFYGRNGKPE---------TKYFGVRDSDRFIRIYNKKQERKDNA 199
Cdd:pfam02486   3 ITRIDLAIDDFDGELDIEELKKKYrnglcisRFRRFKYYGSGELVdgedvgtgkTLYIGSRKSEKYLRIYEKGYEQGDKE 82

                          90       100
                  ....*....|....*....|.
gi 1102546650 200 DVEVVSehLW-RVEVELKRDM 219
Cdd:pfam02486  83 GIPVES--PWvRYELRLRNER 101
NicK COG2946
DNA relaxase NicK [Replication, recombination and repair];
136-216 1.79e-06

DNA relaxase NicK [Replication, recombination and repair];


Pssm-ID: 442189 [Multi-domain]  Cd Length: 302  Bit Score: 48.46  E-value: 1.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102546650 136 FTRLDLAFDFEDDLSDYYAMTDKaVKKTVFYGRNGKP----------------ETKYFGVRDSDRFIRIYNKKQERKDNA 199
Cdd:COG2946   107 ITRIDLAIDDFDGELSIEQAVSK-YKKGLFISRGRRPkyelvgtdwengkgkgRTLYIGSRESGKYWRIYEKGKELGDKE 185

                          90
                  ....*....|....*..
gi 1102546650 200 DVEVvsehlwRVEVELK 216
Cdd:COG2946   186 SSWV------RFELRLK 196
 
Name Accession Description Interval E-value
Rep_trans pfam02486
Replication initiation factor; Plasmid replication is initiated by the replication initiation ...
 136-219 6.81e-08

Replication initiation factor; Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family, including myelin transcription factor 2 and cerebrin-50.


Pssm-ID: 426796  Cd Length: 201  Bit Score: 51.95  E-value: 6.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102546650 136 FTRLDLAFDFEDDLSDYYAMTDKA-------VKKTVFYGRNGKPE---------TKYFGVRDSDRFIRIYNKKQERKDNA 199
Cdd:pfam02486   3 ITRIDLAIDDFDGELDIEELKKKYrnglcisRFRRFKYYGSGELVdgedvgtgkTLYIGSRKSEKYLRIYEKGYEQGDKE 82

                          90       100
                  ....*....|....*....|.
gi 1102546650 200 DVEVVSehLW-RVEVELKRDM 219
Cdd:pfam02486  83 GIPVES--PWvRYELRLRNER 101
NicK COG2946
DNA relaxase NicK [Replication, recombination and repair];
136-216 1.79e-06

DNA relaxase NicK [Replication, recombination and repair];


Pssm-ID: 442189 [Multi-domain]  Cd Length: 302  Bit Score: 48.46  E-value: 1.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102546650 136 FTRLDLAFDFEDDLSDYYAMTDKaVKKTVFYGRNGKP----------------ETKYFGVRDSDRFIRIYNKKQERKDNA 199
Cdd:COG2946   107 ITRIDLAIDDFDGELSIEQAVSK-YKKGLFISRGRRPkyelvgtdwengkgkgRTLYIGSRESGKYWRIYEKGKELGDKE 185

                          90
                  ....*....|....*..
gi 1102546650 200 DVEVvsehlwRVEVELK 216
Cdd:COG2946   186 SSWV------RFELRLK 196
 
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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