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Conserved domains on  [gi|1803229663|ref|WP_161747487|]
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MULTISPECIES: RNA-guided endonuclease TnpB family protein, partial [unclassified Proteus]

Protein Classification

RNA-guided endonuclease InsQ/TnpB family protein( domain architecture ID 11430747)

RNA-guided endonuclease InsQ/TnpB family protein such as the RNA-guided endonuclease TnpB from IS200/IS605 family elements and IS607 family elements; this protein is homologous to some CRISPR-associated (Cas) proteins such as the type V CRISPR-associated protein C2c8; TnpB proteins were described as accessory proteins in IS (insertion sequence) elements, present as one of just one or two proteins encoded in the element but not necessary for transposition. The programmable RNA-guided endonuclease TnpB proteins may provide a CRISPR-like, widespread form of phage defense by RNA-guided DNA degradation.

EC:  3.1.21.-
Gene Ontology:  GO:0003677|GO:0004519|GO:0046872|GO:0006310|GO:0032196
PubMed:  11276247|24499397|34619744

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
17-122 3.29e-39

Transposase [Mobilome: prophages, transposons];


:

Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 135.02  E-value: 3.29e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663  17 RNVKAKSGLNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRQSQSQFECLECGYTANADING 96
Cdd:COG0675   275 KGMKKNKKLNKSISDAGWGEFRRQLEYKAEKYGIKVVEVDPAYTSQTCSSCGHVVKKLRLSVRTFVCPKCGTVHDRDVNA 354

                          90       100
                  ....*....|....*....|....*..
gi 1803229663  97 ARNILAAGHAVLACGGRVQSD-RPSKQ 122
Cdd:COG0675   355 AINILRRGLRQLGLAGHSGGTvRPLRD 381
 
Name Accession Description Interval E-value
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
17-122 3.29e-39

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 135.02  E-value: 3.29e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663  17 RNVKAKSGLNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRQSQSQFECLECGYTANADING 96
Cdd:COG0675   275 KGMKKNKKLNKSISDAGWGEFRRQLEYKAEKYGIKVVEVDPAYTSQTCSSCGHVVKKLRLSVRTFVCPKCGTVHDRDVNA 354

                          90       100
                  ....*....|....*....|....*..
gi 1803229663  97 ARNILAAGHAVLACGGRVQSD-RPSKQ 122
Cdd:COG0675   355 AINILRRGLRQLGLAGHSGGTvRPLRD 381
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-103 8.65e-30

RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB from IS200/IS605 family elements (NF038281) and IS607 family elements (NF038280), but also many additional proteins. It exhibits homolog to or actually includes some CRISPR-associated (Cas) proteins such as the type V CRISPR-associated protein C2c8. For a long time, TnpB proteins were described as accessory proteins in IS (insertion sequence) elements, present as one of just one or two proteins encoded in the element but not necessary for transposition. The programmable RNA-guided endonuclease TnpB proteins may provide a CRISPR-like, widespread form of phage defense by RNA-guided DNA degradation.


Pssm-ID: 468544 [Multi-domain]  Cd Length: 384  Bit Score: 110.33  E-value: 8.65e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663   1 VSNMSKSakgtterhgrnvKAKSGLNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRQ-SQS 79
Cdd:NF040570  293 VKGMVKN------------KKKKKLAKSIHDWAFGQLRRMLEYKAEWYGIKVVKVDPAYTSSQCCSCGGHRKEKLLlSCR 360

                          90       100
                  ....*....|....*....|....
gi 1803229663  80 QFECLECGYTANADINGARNILAA 103
Cdd:NF040570  361 EWTCPECGYTVHRDINAAINILRR 384
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 34-101 1.32e-24

Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.


Pssm-ID: 284650 [Multi-domain]  Cd Length: 69  Bit Score: 89.20  E-value: 1.32e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1803229663  34 WYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRqSQSQFECLECGYTANADINGARNIL 101
Cdd:pfam07282   1 FRKFIEQLEYKAKEYGIKVVEVDPAYTSKTCSVCGHKNKESL-SGRTFVCPNCGFVADRDVNAAINIL 67
PHA02942 PHA02942
putative transposase; Provisional
 39-121 3.73e-03

putative transposase; Provisional


Pssm-ID: 165252 [Multi-domain]  Cd Length: 383  Bit Score: 36.15  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663  39 RQFEYKQLWR----GGQVLAIPPAYTSQKCACCGHTAKEnrQSQSQFECLECGYTANADINGARNILAAGHAVLACGGRV 114
Cdd:PHA02942  299 HRIQYWIEWQakkhGMIVEFVNPSYSSVSCPKCGHKMVE--IAHRYFHCPSCGYENDRDVIAIMNLNGRGSLTLSTAPQM 376


                  ....*..
gi 1803229663 115 QSDRPSK 121
Cdd:PHA02942  377 RDVAPNR 383
tspaseT_teng_C TIGR01766
transposase, IS605 OrfB family, central region; This model represents a region of a sequence ...
 25-61 6.87e-03

transposase, IS605 OrfB family, central region; This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins. [Mobile and extrachromosomal element functions, Transposon functions]


Pssm-ID: 273793 [Multi-domain]  Cd Length: 82  Bit Score: 33.46  E-value: 6.87e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1803229663  25 LNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTS 61
Cdd:TIGR01766  46 LRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS 82
 
Name Accession Description Interval E-value
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
17-122 3.29e-39

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 135.02  E-value: 3.29e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663  17 RNVKAKSGLNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRQSQSQFECLECGYTANADING 96
Cdd:COG0675   275 KGMKKNKKLNKSISDAGWGEFRRQLEYKAEKYGIKVVEVDPAYTSQTCSSCGHVVKKLRLSVRTFVCPKCGTVHDRDVNA 354

                          90       100
                  ....*....|....*....|....*..
gi 1803229663  97 ARNILAAGHAVLACGGRVQSD-RPSKQ 122
Cdd:COG0675   355 AINILRRGLRQLGLAGHSGGTvRPLRD 381
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-103 8.65e-30

RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB from IS200/IS605 family elements (NF038281) and IS607 family elements (NF038280), but also many additional proteins. It exhibits homolog to or actually includes some CRISPR-associated (Cas) proteins such as the type V CRISPR-associated protein C2c8. For a long time, TnpB proteins were described as accessory proteins in IS (insertion sequence) elements, present as one of just one or two proteins encoded in the element but not necessary for transposition. The programmable RNA-guided endonuclease TnpB proteins may provide a CRISPR-like, widespread form of phage defense by RNA-guided DNA degradation.


Pssm-ID: 468544 [Multi-domain]  Cd Length: 384  Bit Score: 110.33  E-value: 8.65e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663   1 VSNMSKSakgtterhgrnvKAKSGLNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRQ-SQS 79
Cdd:NF040570  293 VKGMVKN------------KKKKKLAKSIHDWAFGQLRRMLEYKAEWYGIKVVKVDPAYTSSQCCSCGGHRKEKLLlSCR 360

                          90       100
                  ....*....|....*....|....
gi 1803229663  80 QFECLECGYTANADINGARNILAA 103
Cdd:NF040570  361 EWTCPECGYTVHRDINAAINILRR 384
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 34-101 1.32e-24

Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.


Pssm-ID: 284650 [Multi-domain]  Cd Length: 69  Bit Score: 89.20  E-value: 1.32e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1803229663  34 WYEMRRQFEYKQLWRGGQVLAIPPAYTSQKCACCGHTAKENRqSQSQFECLECGYTANADINGARNIL 101
Cdd:pfam07282   1 FRKFIEQLEYKAKEYGIKVVEVDPAYTSKTCSVCGHKNKESL-SGRTFVCPNCGFVADRDVNAAINIL 67
PHA02942 PHA02942
putative transposase; Provisional
 39-121 3.73e-03

putative transposase; Provisional


Pssm-ID: 165252 [Multi-domain]  Cd Length: 383  Bit Score: 36.15  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1803229663  39 RQFEYKQLWR----GGQVLAIPPAYTSQKCACCGHTAKEnrQSQSQFECLECGYTANADINGARNILAAGHAVLACGGRV 114
Cdd:PHA02942  299 HRIQYWIEWQakkhGMIVEFVNPSYSSVSCPKCGHKMVE--IAHRYFHCPSCGYENDRDVIAIMNLNGRGSLTLSTAPQM 376


                  ....*..
gi 1803229663 115 QSDRPSK 121
Cdd:PHA02942  377 RDVAPNR 383
tspaseT_teng_C TIGR01766
transposase, IS605 OrfB family, central region; This model represents a region of a sequence ...
 25-61 6.87e-03

transposase, IS605 OrfB family, central region; This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins. [Mobile and extrachromosomal element functions, Transposon functions]


Pssm-ID: 273793 [Multi-domain]  Cd Length: 82  Bit Score: 33.46  E-value: 6.87e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1803229663  25 LNRSILEQGWYEMRRQFEYKQLWRGGQVLAIPPAYTS 61
Cdd:TIGR01766  46 LRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS 82
 
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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