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Conserved domains on  [gi|2508193483|gb|WHP38535|]
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gyrB, partial [Enterobacter sp.]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
gyrB super family cl36442
DNA gyrase subunit B; Provisional
 1-144 5.36e-98

DNA gyrase subunit B; Provisional


The actual alignment was detected with superfamily member PRK14939:

Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 297.39  E-value: 5.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PRK14939  254 EVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKF 333

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:PRK14939  334 SSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKG 397
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-144 5.36e-98

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 297.39  E-value: 5.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PRK14939  254 EVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKF 333

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:PRK14939  334 SSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKG 397
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-144 2.70e-72

DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273421 [Multi-domain]  Cd Length: 654  Bit Score: 228.01  E-value: 2.70e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:TIGR01059 249 EVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQF 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:TIGR01059 329 EGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKS 392
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 1-125 6.69e-69

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 205.49  E-value: 6.69e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:cd00822    34 EVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQF 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:cd00822   114 EGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-144 6.94e-64

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 205.26  E-value: 6.94e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:COG0187   254 EVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQF 333

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:COG0187   334 EGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKS 397
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 1-125 1.32e-58

DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.


Pssm-ID: 425522 [Multi-domain]  Cd Length: 173  Bit Score: 179.35  E-value: 1.32e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:pfam00204  35 EVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQF 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:pfam00204 115 EGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-125 2.10e-45

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 155.41  E-value: 2.10e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483    1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVsaTGDDAREGLIAVVSVKVPDPKF 80
Cdd:smart00433 220 EVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQF 297

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2508193483   81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:smart00433 298 EGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLL 342
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-144 5.36e-98

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 297.39  E-value: 5.36e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PRK14939  254 EVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKF 333

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:PRK14939  334 SSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKG 397
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-144 2.70e-72

DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273421 [Multi-domain]  Cd Length: 654  Bit Score: 228.01  E-value: 2.70e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:TIGR01059 249 EVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQF 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:TIGR01059 329 EGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKS 392
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 1-125 6.69e-69

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 205.49  E-value: 6.69e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:cd00822    34 EVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQF 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:cd00822   114 EGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-144 6.94e-64

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 205.26  E-value: 6.94e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:COG0187   254 EVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQF 333

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:COG0187   334 EGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKS 397
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-144 2.06e-62

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 201.48  E-value: 2.06e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PRK05644  256 EVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQF 335

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARKAREMTRRKG 144
Cdd:PRK05644  336 EGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 1-125 1.32e-58

DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.


Pssm-ID: 425522 [Multi-domain]  Cd Length: 173  Bit Score: 179.35  E-value: 1.32e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:pfam00204  35 EVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQF 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:pfam00204 115 EGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-125 2.10e-45

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 155.41  E-value: 2.10e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483    1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVsaTGDDAREGLIAVVSVKVPDPKF 80
Cdd:smart00433 220 EVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQF 297

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2508193483   81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:smart00433 298 EGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLL 342
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-125 7.17e-45

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 154.49  E-value: 7.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKvSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PRK05559  255 EWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQF 333

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2508193483  81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIID 125
Cdd:PRK05559  334 EGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIK 378
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-113 3.04e-21

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 88.40  E-value: 3.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDG-FQENIYCFTNNIpQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPK 79
Cdd:PTZ00109  410 EVSLSWSLEsYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAE 488

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2508193483  80 FSSQTKDKLVSSEVKSAVEQQMNELLSEYLLENP 113
Cdd:PTZ00109  489 FDGQTKTKLGNHLLKTILESIVFEQLSEILEFEP 522
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 1-88 1.26e-17

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 73.06  E-value: 1.26e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWND---GFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNaymdkegyskkakvsatGDDAREGLIAVVSVKVPD 77
Cdd:cd00329    30 EGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPP 92

                          90
                  ....*....|....
gi 2508193483  78 --PKFS-SQTKDKL 88
Cdd:cd00329    93 slVDVNvHPTKEEV 106
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 8-95 4.42e-05

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 42.05  E-value: 4.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   8 DGFQENiyCFTNNIPQRDGGTHLAGFRAAMTRTLnaymdKEGYSKKAKVSATGDDAREGLIAVVSVK-VPDPKFSSQTKD 86
Cdd:PHA02569  257 DGFRQL--SFVNGLHTKNGGHHVDCVMDDICEEL-----IPMIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKE 329

                          90
                  ....*....|.
gi 2508193483  87 KLVSS--EVKS 95
Cdd:PHA02569  330 RLTSPfgEIRN 340
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 1-113 6.06e-04

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 38.87  E-value: 6.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483    1 EVALQWNDGfQENIYCFTNNIPQRDGGTHLagfRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF 80
Cdd:PTZ00108   279 EVVVSLSDG-QFQQVSFVNSICTTKGGTHV---NYILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCLIVNPSF 354

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2508193483   81 SSQTKDKLVSSEVKSAVEQQMNELLSEYLLENP 113
Cdd:PTZ00108   355 DSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP 387
TopoIIA_Trans_ScTopoIIA cd03481
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 1-119 6.18e-03

TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 239563 [Multi-domain]  Cd Length: 153  Bit Score: 34.96  E-value: 6.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2508193483   1 EVALQWNDG-FQenIYCFTNNIPQRDGGTHLagfRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPK 79
Cdd:cd03481    34 EVAVALSDGqFQ--QVSFVNSIATTKGGTHV---DYVADQIVKKLDEVVKKKNKGGINVKPFQVKNHLWIFVNCLIENPS 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2508193483  80 FSSQTKDKLVsSEVKSAVEQQmneLLSEYLLENPSDAKIV 119
Cdd:cd03481   109 FDSQTKETLT-TKPKSFGSKC---ELSEKFLKKAVKSGIV 144
 
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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