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Conserved domains on  [gi|1872085762|ref|WP_180058446|]
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MULTISPECIES: zinc ribbon domain-containing protein, partial [unclassified Acinetobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
InsQ super family cl34004
Transposase [Mobilome: prophages, transposons];
1-35 8.93e-09

Transposase [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG0675:

Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 47.58  E-value: 8.93e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1872085762   1 EWSC-ECGVTHDRDLNSAMNILALGHKRLAVGITSV 35
Cdd:COG0675   338 TFVCpKCGTVHDRDVNAAINILRRGLRQLGLAGHSG 373
 
Name Accession Description Interval E-value
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
1-35 8.93e-09

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 47.58  E-value: 8.93e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1872085762   1 EWSC-ECGVTHDRDLNSAMNILALGHKRLAVGITSV 35
Cdd:COG0675   338 TFVCpKCGTVHDRDVNAAINILRRGLRQLGLAGHSG 373
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-22 9.30e-07

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: 42.15  E-value: 9.30e-07
                          10        20
                  ....*....|....*....|...
gi 1872085762   1 EWSC-ECGVTHDRDLNSAMNILA 22
Cdd:NF040570  361 EWTCpECGYTVHRDINAAINILR 383
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 1-21 7.59e-05

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: 34.88  E-value: 7.59e-05
                         10        20
                 ....*....|....*....|..
gi 1872085762  1 EWSCE-CGVTHDRDLNSAMNIL 21
Cdd:pfam07282 46 TFVCPnCGFVADRDVNAAINIL 67
 
Name Accession Description Interval E-value
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
1-35 8.93e-09

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 47.58  E-value: 8.93e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1872085762   1 EWSC-ECGVTHDRDLNSAMNILALGHKRLAVGITSV 35
Cdd:COG0675   338 TFVCpKCGTVHDRDVNAAINILRRGLRQLGLAGHSG 373
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 1-22 9.30e-07

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: 42.15  E-value: 9.30e-07
                          10        20
                  ....*....|....*....|...
gi 1872085762   1 EWSC-ECGVTHDRDLNSAMNILA 22
Cdd:NF040570  361 EWTCpECGYTVHRDINAAINILR 383
OrfB_Zn_ribbon pfam07282
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ...
 1-21 7.59e-05

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: 34.88  E-value: 7.59e-05
                         10        20
                 ....*....|....*....|..
gi 1872085762  1 EWSCE-CGVTHDRDLNSAMNIL 21
Cdd:pfam07282 46 TFVCPnCGFVADRDVNAAINIL 67
 
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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