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Conserved domains on  [gi|969849158|ref|WP_058610021|]
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DNA-binding protein [Enterobacter cancerogenus]

Protein Classification

DNA-binding protein( domain architecture ID 10569863)

DNA-binding protein such as Paenibacillus popilliae plasmid KfrA proteins and Pseudomonas aeruginosa plasmid cointegrate resolution protein T (TnpT)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KfrA_N pfam11740
Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to ...
 26-125 3.44e-12

Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.


:

Pssm-ID: 432038 [Multi-domain]  Cd Length: 117  Bit Score: 60.77  E-value: 3.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158   26 NPTNEQVRQHLGGGSLSHISPVMRAFRARQREQAAEQTTPLPPELAQLLTGQLGLLWQAAVKQAEAGALAAREQADDDIA 105
Cdd:pfam11740  18 RPTVDAVRERLGTGSPTTIHRHLKEWRAERAAASAVPAAALPEALQDAAQELLARLWQAALEEAEERLAAARAELQAERA 97

                          90       100
                  ....*....|....*....|
gi 969849158  106 RADQERDEALAKVAALESEL 125
Cdd:pfam11740  98 ALEAERAEAEQRAEALEAEL 117
Smc super family cl34174
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 83-183 1.96e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


The actual alignment was detected with superfamily member COG1196:

Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.76  E-value: 1.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  83 QAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESELAVLREVVAERDRLLQEVRELRAEVLPLREQVARLTAT 162
Cdd:COG1196  245 EAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEE 324

                         90       100
                 ....*....|....*....|.
gi 969849158 163 GEHLAAQLKETKAELKGAREE 183
Cdd:COG1196  325 LAELEEELEELEEELEELEEE 345
 
Name Accession Description Interval E-value
KfrA_N pfam11740
Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to ...
 26-125 3.44e-12

Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.


Pssm-ID: 432038 [Multi-domain]  Cd Length: 117  Bit Score: 60.77  E-value: 3.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158   26 NPTNEQVRQHLGGGSLSHISPVMRAFRARQREQAAEQTTPLPPELAQLLTGQLGLLWQAAVKQAEAGALAAREQADDDIA 105
Cdd:pfam11740  18 RPTVDAVRERLGTGSPTTIHRHLKEWRAERAAASAVPAAALPEALQDAAQELLARLWQAALEEAEERLAAARAELQAERA 97

                          90       100
                  ....*....|....*....|
gi 969849158  106 RADQERDEALAKVAALESEL 125
Cdd:pfam11740  98 ALEAERAEAEQRAEALEAEL 117
MARTX_Nterm NF012221
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model ...
 83-165 2.14e-05

MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains.


Pssm-ID: 467957 [Multi-domain]  Cd Length: 1848  Bit Score: 44.44  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158   83 QAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESEL------AVLREVVAERDRLLQEVRELRAEVLPLREQV 156
Cdd:NF012221 1550 HAKQDDAAQNALADKERAEADRQRLEQEKQQQLAAISGSQSQLestdqnALETNGQAQRDAILEESRAVTKELTTLAQGL 1629


                  ....*....
gi 969849158  157 ARLTATGEH 165
Cdd:NF012221 1630 DALDSQATY 1638
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 83-183 1.96e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.76  E-value: 1.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  83 QAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESELAVLREVVAERDRLLQEVRELRAEVLPLREQVARLTAT 162
Cdd:COG1196  245 EAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEE 324

                         90       100
                 ....*....|....*....|.
gi 969849158 163 GEHLAAQLKETKAELKGAREE 183
Cdd:COG1196  325 LAELEEELEELEEELEELEEE 345
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 48-183 2.15e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.38  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  48 MRAFRARQREQAAEQTtplppelAQLLTGQLGLLWQAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESELAV 127
Cdd:COG1196  234 LRELEAELEELEAELE-------ELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIAR 306

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 969849158 128 LREvvaERDRLLQEVRELRAEVLPLREQVARLTATGEHLAAQLKETKAELKGAREE 183
Cdd:COG1196  307 LEE---RRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAE 359
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
94-183 8.58e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 36.58  E-value: 8.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  94 LAAREQADDDIARADQERDEALAKVAALESELAVLREVVAERDRLLQEVRELRAEVLPLREQVARLTATGEHLAAQLKET 173
Cdd:PRK03918 185 IKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIREL 264

                         90
                 ....*....|
gi 969849158 174 KAELKGAREE 183
Cdd:PRK03918 265 EERIEELKKE 274
 
Name Accession Description Interval E-value
KfrA_N pfam11740
Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to ...
 26-125 3.44e-12

Plasmid replication region DNA-binding N-term; The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.


Pssm-ID: 432038 [Multi-domain]  Cd Length: 117  Bit Score: 60.77  E-value: 3.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158   26 NPTNEQVRQHLGGGSLSHISPVMRAFRARQREQAAEQTTPLPPELAQLLTGQLGLLWQAAVKQAEAGALAAREQADDDIA 105
Cdd:pfam11740  18 RPTVDAVRERLGTGSPTTIHRHLKEWRAERAAASAVPAAALPEALQDAAQELLARLWQAALEEAEERLAAARAELQAERA 97

                          90       100
                  ....*....|....*....|
gi 969849158  106 RADQERDEALAKVAALESEL 125
Cdd:pfam11740  98 ALEAERAEAEQRAEALEAEL 117
MARTX_Nterm NF012221
MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model ...
 83-165 2.14e-05

MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region; This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains.


Pssm-ID: 467957 [Multi-domain]  Cd Length: 1848  Bit Score: 44.44  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158   83 QAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESEL------AVLREVVAERDRLLQEVRELRAEVLPLREQV 156
Cdd:NF012221 1550 HAKQDDAAQNALADKERAEADRQRLEQEKQQQLAAISGSQSQLestdqnALETNGQAQRDAILEESRAVTKELTTLAQGL 1629


                  ....*....
gi 969849158  157 ARLTATGEH 165
Cdd:NF012221 1630 DALDSQATY 1638
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 83-183 1.96e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.76  E-value: 1.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  83 QAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESELAVLREVVAERDRLLQEVRELRAEVLPLREQVARLTAT 162
Cdd:COG1196  245 EAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEE 324

                         90       100
                 ....*....|....*....|.
gi 969849158 163 GEHLAAQLKETKAELKGAREE 183
Cdd:COG1196  325 LAELEEELEELEEELEELEEE 345
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 48-183 2.15e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.38  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  48 MRAFRARQREQAAEQTtplppelAQLLTGQLGLLWQAAVKQAEAGALAAREQADDDIARADQERDEALAKVAALESELAV 127
Cdd:COG1196  234 LRELEAELEELEAELE-------ELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIAR 306

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 969849158 128 LREvvaERDRLLQEVRELRAEVLPLREQVARLTATGEHLAAQLKETKAELKGAREE 183
Cdd:COG1196  307 LEE---RRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAE 359
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
94-183 8.58e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 36.58  E-value: 8.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 969849158  94 LAAREQADDDIARADQERDEALAKVAALESELAVLREVVAERDRLLQEVRELRAEVLPLREQVARLTATGEHLAAQLKET 173
Cdd:PRK03918 185 IKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIREL 264

                         90
                 ....*....|
gi 969849158 174 KAELKGAREE 183
Cdd:PRK03918 265 EERIEELKKE 274
 
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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