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Conserved domains on  [gi|17559978|ref|NP_506865|]
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Trichohyalin-like [Caenorhabditis elegans]

Protein Classification

DNA topoisomerase 1( domain architecture ID 1904900)

DNA topoisomerase 1 releases the supercoiling and torsional tension of DNA introduced during DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOPEUc super family cl42960
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 130-224 1.38e-03

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


The actual alignment was detected with superfamily member smart00435:

Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 39.25  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    130 VQRMREEIDyrrhLHKQQLKDLKLDCDREEEKceywNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKMLEELEM 209
Cdd:smart00435 279 MEKLQEKIK----ALKYQLKRLKKMILLFEMI----SDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEE 350

                           90
                   ....*....|....*
gi 17559978    210 LLKKTGKKRQILDEN 224
Cdd:smart00435 351 RIEKLEVQATDKEEN 365
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-208 6.46e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 37.34  E-value: 6.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978     44 EKKLQLSNRIDVVQSQVTELwDRVDKARRRESDISCRVTAWAQHLSEMMNEVKLKKAKMGTTMEisatlsaEIQESLDLL 123
Cdd:TIGR02168  222 LRELELALLVLRLEELREEL-EELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIE-------ELQKELYAL 293

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    124 AEKRVIVQRMREEIDYRRHLHKQQLKDLKLDCDREEEKCEYWNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKM 203
Cdd:TIGR02168  294 ANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESR 373


                   ....*
gi 17559978    204 LEELE 208
Cdd:TIGR02168  374 LEELE 378
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 130-224 1.38e-03

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 39.25  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    130 VQRMREEIDyrrhLHKQQLKDLKLDCDREEEKceywNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKMLEELEM 209
Cdd:smart00435 279 MEKLQEKIK----ALKYQLKRLKKMILLFEMI----SDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEE 350

                           90
                   ....*....|....*
gi 17559978    210 LLKKTGKKRQILDEN 224
Cdd:smart00435 351 RIEKLEVQATDKEEN 365
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-208 6.46e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 37.34  E-value: 6.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978     44 EKKLQLSNRIDVVQSQVTELwDRVDKARRRESDISCRVTAWAQHLSEMMNEVKLKKAKMGTTMEisatlsaEIQESLDLL 123
Cdd:TIGR02168  222 LRELELALLVLRLEELREEL-EELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIE-------ELQKELYAL 293

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    124 AEKRVIVQRMREEIDYRRHLHKQQLKDLKLDCDREEEKCEYWNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKM 203
Cdd:TIGR02168  294 ANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESR 373


                   ....*
gi 17559978    204 LEELE 208
Cdd:TIGR02168  374 LEELE 378
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 42-223 7.47e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 37.05  E-value: 7.47e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978  42 EMEKKL-QLSNRIDVVQSQVTELWDRVDKARRRESDISCRVTAWAQHLSEMMNEVklkkAKMGTTMEISATLSAEiqESL 120
Cdd:COG4942  59 ALERRIaALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRAL----YRLGRQPPLALLLSPE--DFL 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978 121 DLLAekrvIVQRMREEIDYRRhlhkQQLKDLKLDCDREEEKCEYWNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQ 200
Cdd:COG4942 133 DAVR----RLQYLKYLAPARR----EQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARL 204

                       170       180
                ....*....|....*....|...
gi 17559978 201 KKMLEELEMLLKKTGKKRQILDE 223
Cdd:COG4942 205 EKELAELAAELAELQQEAEELEA 227
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 130-224 1.38e-03

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 39.25  E-value: 1.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    130 VQRMREEIDyrrhLHKQQLKDLKLDCDREEEKceywNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKMLEELEM 209
Cdd:smart00435 279 MEKLQEKIK----ALKYQLKRLKKMILLFEMI----SDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEE 350

                           90
                   ....*....|....*
gi 17559978    210 LLKKTGKKRQILDEN 224
Cdd:smart00435 351 RIEKLEVQATDKEEN 365
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-208 6.46e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 37.34  E-value: 6.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978     44 EKKLQLSNRIDVVQSQVTELwDRVDKARRRESDISCRVTAWAQHLSEMMNEVKLKKAKMGTTMEisatlsaEIQESLDLL 123
Cdd:TIGR02168  222 LRELELALLVLRLEELREEL-EELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIE-------ELQKELYAL 293

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978    124 AEKRVIVQRMREEIDYRRHLHKQQLKDLKLDCDREEEKCEYWNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQKKM 203
Cdd:TIGR02168  294 ANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESR 373


                   ....*
gi 17559978    204 LEELE 208
Cdd:TIGR02168  374 LEELE 378
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 42-223 7.47e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 37.05  E-value: 7.47e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978  42 EMEKKL-QLSNRIDVVQSQVTELWDRVDKARRRESDISCRVTAWAQHLSEMMNEVklkkAKMGTTMEISATLSAEiqESL 120
Cdd:COG4942  59 ALERRIaALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRAL----YRLGRQPPLALLLSPE--DFL 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17559978 121 DLLAekrvIVQRMREEIDYRRhlhkQQLKDLKLDCDREEEKCEYWNDKSAEIEKVVEMLKEQRKSLGERVEEEKRMEQEQ 200
Cdd:COG4942 133 DAVR----RLQYLKYLAPARR----EQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARL 204

                       170       180
                ....*....|....*....|...
gi 17559978 201 KKMLEELEMLLKKTGKKRQILDE 223
Cdd:COG4942 205 EKELAELAAELAELQQEAEELEA 227
 
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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