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Conserved domains on  [gi|1777659011|ref|WP_154319811|]
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zinc ribbon domain-containing protein, partial [Metabacillus idriensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IS200_TnpB super family cl45733
IS200/IS605 family element RNA-guided endonuclease TnpB;
1-79 1.22e-57

IS200/IS605 family element RNA-guided endonuclease TnpB;


The actual alignment was detected with superfamily member NF038281:

Pssm-ID: 468448 [Multi-domain]  Cd Length: 359  Bit Score: 180.37  E-value: 1.22e-57
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFASSQLCSRCGYQNKAVKNLALREWDCPSCGTHHNRDLNAGLNLRNEAK 79
Cdd:NF038281  281 ISDVSWSEFRTMLEYKAKWYGRTVVKVGKFFPSSQLCSCCGYKNKEVKNLALREWTCPSCGTHHDRDINASKNILNEGL 359
 
Name Accession Description Interval E-value
IS200_TnpB NF038281
IS200/IS605 family element RNA-guided endonuclease TnpB;
1-79 1.22e-57

IS200/IS605 family element RNA-guided endonuclease TnpB;


Pssm-ID: 468448 [Multi-domain]  Cd Length: 359  Bit Score: 180.37  E-value: 1.22e-57
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFASSQLCSRCGYQNKAVKNLALREWDCPSCGTHHNRDLNAGLNLRNEAK 79
Cdd:NF038281  281 ISDVSWSEFRTMLEYKAKWYGRTVVKVGKFFPSSQLCSCCGYKNKEVKNLALREWTCPSCGTHHDRDINASKNILNEGL 359
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
1-85 3.88e-32

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 114.61  E-value: 3.88e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQNKAVKnLALREWDCPSCGTHHNRDLNAGLNLRNEAKR 80
Cdd:COG0675   287 ISDAGWGEFRRQLEYKAEKYGIKVVEVDPAY-TSQTCSSCGHVVKKLR-LSVRTFVCPKCGTVHDRDVNAAINILRRGLR 364


                  ....*
gi 1777659011  81 ISTAG 85
Cdd:COG0675   365 QLGLA 369
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 6-76 3.33e-26

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: 91.51  E-value: 3.33e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1777659011  6 WSQFRTMLEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQNKavKNLALREWDCPSCGTHHNRDLNAGLNLRN 76
Cdd:pfam07282  1 FRKFIEQLEYKAKEYGIKVVEVDPAY-TSKTCSVCGHKNK--ESLSGRTFVCPNCGFVADRDVNAAINILK 68
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-77 4.07e-26

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: 98.77  E-value: 4.07e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFASSQLCSrCGYQNKAVKNLALREWDCPSCGTHHNRDLNAGLNLRNE 77
Cdd:NF040570  309 IHDWAFGQLRRMLEYKAEWYGIKVVKVDPAYTSSQCCS-CGGHRKEKLLLSCREWTCPECGYTVHRDINAAINILRR 384
tspaseT_teng_C TIGR01766
transposase, IS605 OrfB family, central region; This model represents a region of a sequence ...
 1-33 5.62e-06

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: 40.39  E-value: 5.62e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1777659011  1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFAS 33
Cdd:TIGR01766 50 LHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS 82
PHA02942 PHA02942
putative transposase; Provisional
 13-84 1.62e-05

putative transposase; Provisional


Pssm-ID: 165252 [Multi-domain]  Cd Length: 383  Bit Score: 41.16  E-value: 1.62e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1777659011  13 LEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQnkaVKNLALREWDCPSCGTHHNRDLNAGLNLRNEAK-RISTA 84
Cdd:PHA02942  305 IEWQAKKHGMIVEFVNPSY-SSVSCPKCGHK---MVEIAHRYFHCPSCGYENDRDVIAIMNLNGRGSlTLSTA 373
 
Name Accession Description Interval E-value
IS200_TnpB NF038281
IS200/IS605 family element RNA-guided endonuclease TnpB;
1-79 1.22e-57

IS200/IS605 family element RNA-guided endonuclease TnpB;


Pssm-ID: 468448 [Multi-domain]  Cd Length: 359  Bit Score: 180.37  E-value: 1.22e-57
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFASSQLCSRCGYQNKAVKNLALREWDCPSCGTHHNRDLNAGLNLRNEAK 79
Cdd:NF038281  281 ISDVSWSEFRTMLEYKAKWYGRTVVKVGKFFPSSQLCSCCGYKNKEVKNLALREWTCPSCGTHHDRDINASKNILNEGL 359
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
1-85 3.88e-32

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 114.61  E-value: 3.88e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQNKAVKnLALREWDCPSCGTHHNRDLNAGLNLRNEAKR 80
Cdd:COG0675   287 ISDAGWGEFRRQLEYKAEKYGIKVVEVDPAY-TSQTCSSCGHVVKKLR-LSVRTFVCPKCGTVHDRDVNAAINILRRGLR 364


                  ....*
gi 1777659011  81 ISTAG 85
Cdd:COG0675   365 QLGLA 369
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 6-76 3.33e-26

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: 91.51  E-value: 3.33e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1777659011  6 WSQFRTMLEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQNKavKNLALREWDCPSCGTHHNRDLNAGLNLRN 76
Cdd:pfam07282  1 FRKFIEQLEYKAKEYGIKVVEVDPAY-TSKTCSVCGHKNK--ESLSGRTFVCPNCGFVADRDVNAAINILK 68
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-77 4.07e-26

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: 98.77  E-value: 4.07e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1777659011   1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFASSQLCSrCGYQNKAVKNLALREWDCPSCGTHHNRDLNAGLNLRNE 77
Cdd:NF040570  309 IHDWAFGQLRRMLEYKAEWYGIKVVKVDPAYTSSQCCS-CGGHRKEKLLLSCREWTCPECGYTVHRDINAAINILRR 384
tspaseT_teng_C TIGR01766
transposase, IS605 OrfB family, central region; This model represents a region of a sequence ...
 1-33 5.62e-06

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: 40.39  E-value: 5.62e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1777659011  1 ISEVSWSQFRTMLEYKAKWYGKQVIVVSKTFAS 33
Cdd:TIGR01766 50 LHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS 82
PHA02942 PHA02942
putative transposase; Provisional
 13-84 1.62e-05

putative transposase; Provisional


Pssm-ID: 165252 [Multi-domain]  Cd Length: 383  Bit Score: 41.16  E-value: 1.62e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1777659011  13 LEYKAKWYGKQVIVVSKTFaSSQLCSRCGYQnkaVKNLALREWDCPSCGTHHNRDLNAGLNLRNEAK-RISTA 84
Cdd:PHA02942  305 IEWQAKKHGMIVEFVNPSY-SSVSCPKCGHK---MVEIAHRYFHCPSCGYENDRDVIAIMNLNGRGSlTLSTA 373
 
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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