NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2428050239|ref|WP_270823100|]
View 

helix-turn-helix domain-containing protein, partial [Bacillus cereus group sp. Bc002]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
IS200_TnpB super family cl45733
IS200/IS605 family element RNA-guided endonuclease TnpB;
5-46 1.14e-19

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: 79.45  E-value: 1.14e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2428050239   5 NKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEK 46
Cdd:NF038281    1 HKAYKFRIYPNKEQEILINKTIGCSRFVYNHFLAKWNEAYEE 42
 
Name Accession Description Interval E-value
IS200_TnpB NF038281
IS200/IS605 family element RNA-guided endonuclease TnpB;
5-46 1.14e-19

IS200/IS605 family element RNA-guided endonuclease TnpB;


Pssm-ID: 468448 [Multi-domain]  Cd Length: 359  Bit Score: 79.45  E-value: 1.14e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2428050239   5 NKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEK 46
Cdd:NF038281    1 HKAYKFRIYPNKEQEILINKTIGCSRFVYNHFLAKWNEAYEE 42
HTH_OrfB_IS605 pfam12323
Helix-turn-helix domain; This is the N terminal helix-turn-helix domain of Transposase_2 ...
 4-48 5.86e-19

Helix-turn-helix domain; This is the N terminal helix-turn-helix domain of Transposase_2 pfam01385.


Pssm-ID: 432479 [Multi-domain]  Cd Length: 47  Bit Score: 71.45  E-value: 5.86e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2428050239  4 QNKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHK 48
Cdd:pfam12323  2 VLKAYKYRLYPTPEQEELLARTFGCARFVYNKALAERKEAYKEGG 46
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
5-57 7.35e-15

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 66.46  E-value: 7.35e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2428050239   5 NKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHKD--DKEQLKKQ 57
Cdd:COG0675     2 LRTYKFRLYPTKEQEELLERTLGCCRFVYNYALAERRQAYKETGKslSYYELQKL 56
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 8-58 8.13e-10

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: 52.16  E-value: 8.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2428050239   8 YKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHKDDKEQLKKQK 58
Cdd:NF040570    1 YKYRLYPTKEQKRELAELFGAARFLYNAALAERKEAYEKNGKFLSYKALLK 51
 
Name Accession Description Interval E-value
IS200_TnpB NF038281
IS200/IS605 family element RNA-guided endonuclease TnpB;
5-46 1.14e-19

IS200/IS605 family element RNA-guided endonuclease TnpB;


Pssm-ID: 468448 [Multi-domain]  Cd Length: 359  Bit Score: 79.45  E-value: 1.14e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2428050239   5 NKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEK 46
Cdd:NF038281    1 HKAYKFRIYPNKEQEILINKTIGCSRFVYNHFLAKWNEAYEE 42
HTH_OrfB_IS605 pfam12323
Helix-turn-helix domain; This is the N terminal helix-turn-helix domain of Transposase_2 ...
 4-48 5.86e-19

Helix-turn-helix domain; This is the N terminal helix-turn-helix domain of Transposase_2 pfam01385.


Pssm-ID: 432479 [Multi-domain]  Cd Length: 47  Bit Score: 71.45  E-value: 5.86e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2428050239  4 QNKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHK 48
Cdd:pfam12323  2 VLKAYKYRLYPTPEQEELLARTFGCARFVYNKALAERKEAYKEGG 46
InsQ COG0675
Transposase [Mobilome: prophages, transposons];
5-57 7.35e-15

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 440439 [Multi-domain]  Cd Length: 381  Bit Score: 66.46  E-value: 7.35e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2428050239   5 NKAYKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHKD--DKEQLKKQ 57
Cdd:COG0675     2 LRTYKFRLYPTKEQEELLERTLGCCRFVYNYALAERRQAYKETGKslSYYELQKL 56
guided_TnpB NF040570
RNA-guided endonuclease TnpB family protein; This family includes RNA-guided endonuclease TnpB ...
 8-58 8.13e-10

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: 52.16  E-value: 8.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2428050239   8 YKFRLYPTDDQAHLMRKTFGCVRFVYNRMLAERKEAYEKHKDDKEQLKKQK 58
Cdd:NF040570    1 YKYRLYPTKEQKRELAELFGAARFLYNAALAERKEAYEKNGKFLSYKALLK 51
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH