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Conserved domains on  [gi|2499533017|ref|WP_280956781|]
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HNH endonuclease [Acetohalobium arabaticum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
guided_IscB super family cl45881
RNA-guided endonuclease IscB;
8-160 1.03e-47

RNA-guided endonuclease IscB;


The actual alignment was detected with superfamily member NF040563:

Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 161.18  E-value: 1.03e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017   8 GYNVREYLLYKHNHTCQYCGGEsgDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEwlqdlkeqdFRKKlp 87
Cdd:NF040563  181 GYEVREYLLERDGRTCQYCGAK--DVPLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVEE---------FLKG-- 247

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2499533017  88 kvrYKNVKQILeSKVDISLKDAGRVNSYRYKLLDQLKSICSNIETSTGAKTKYNRNQVaELEKTHYFDALCVG 160
Cdd:NF040563  248 ---PELLKRIL-KQAKAPLKDAAAVNATRWALFNRLKETGLPVETTSGGRTKYNRIRL-GLPKTHWNDAAIVG 315
 
Name Accession Description Interval E-value
guided_IscB NF040563
RNA-guided endonuclease IscB;
8-160 1.03e-47

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 161.18  E-value: 1.03e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017   8 GYNVREYLLYKHNHTCQYCGGEsgDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEwlqdlkeqdFRKKlp 87
Cdd:NF040563  181 GYEVREYLLERDGRTCQYCGAK--DVPLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVEE---------FLKG-- 247

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2499533017  88 kvrYKNVKQILeSKVDISLKDAGRVNSYRYKLLDQLKSICSNIETSTGAKTKYNRNQVaELEKTHYFDALCVG 160
Cdd:NF040563  248 ---PELLKRIL-KQAKAPLKDAAAVNATRWALFNRLKETGLPVETTSGGRTKYNRIRL-GLPKTHWNDAAIVG 315
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
10-65 1.33e-19

5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 80.03  E-value: 1.33e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2499533017  10 NVREYLLYKHNHTCQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDK 65
Cdd:COG1403     9 ALRRAVLKRDNGRCQYCGRPFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 15-65 8.05e-13

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 61.72  E-value: 8.05e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2499533017  15 LLYKHNHTCQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDK 65
Cdd:cd00085     6 VLLARDGLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKK 56
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 23-69 6.42e-11

HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.


Pssm-ID: 464124 [Multi-domain]  Cd Length: 56  Bit Score: 56.58  E-value: 6.42e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2499533017  23 CQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRT 69
Cdd:pfam14279   1 CIYCGKEFPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDV 47
HNHc smart00507
HNH nucleases;
10-63 2.29e-10

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 55.16  E-value: 2.29e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2499533017   10 NVREYLLYKHnHTCQYCGgESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQ 63
Cdd:smart00507   1 KLRRLLLHRD-GVCAYCG-KPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 10-107 7.54e-07

CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.


Pssm-ID: 273840  Cd Length: 805  Bit Score: 50.12  E-value: 7.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017  10 NVREYLLYKHNHTCQYCGGE------SGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEWLQDLKEQDF- 82
Cdd:TIGR01865 571 ILKLRLYYQQNGKCMYTGKEididdlFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEAEIVKKDSAFw 650

                          90       100       110
                  ....*....|....*....|....*....|
gi 2499533017  83 -----RKKLPKVRYKNVKQILESKVDISLK 107
Cdd:TIGR01865 651 nkfeaYVLISKRKSDKLTRAERGGLSDDDK 680
 
Name Accession Description Interval E-value
guided_IscB NF040563
RNA-guided endonuclease IscB;
8-160 1.03e-47

RNA-guided endonuclease IscB;


Pssm-ID: 468538 [Multi-domain]  Cd Length: 315  Bit Score: 161.18  E-value: 1.03e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017   8 GYNVREYLLYKHNHTCQYCGGEsgDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEwlqdlkeqdFRKKlp 87
Cdd:NF040563  181 GYEVREYLLERDGRTCQYCGAK--DVPLEVHHIVPRSKGGSDRVSNLILACEPCNQKKGNQPVEE---------FLKG-- 247

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2499533017  88 kvrYKNVKQILeSKVDISLKDAGRVNSYRYKLLDQLKSICSNIETSTGAKTKYNRNQVaELEKTHYFDALCVG 160
Cdd:NF040563  248 ---PELLKRIL-KQAKAPLKDAAAVNATRWALFNRLKETGLPVETTSGGRTKYNRIRL-GLPKTHWNDAAIVG 315
McrA COG1403
5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];
10-65 1.33e-19

5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms];


Pssm-ID: 441013 [Multi-domain]  Cd Length: 64  Bit Score: 80.03  E-value: 1.33e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2499533017  10 NVREYLLYKHNHTCQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDK 65
Cdd:COG1403     9 ALRRAVLKRDNGRCQYCGRPFSGDALEVDHIIPRSRGGTDTWENLVLLCRRCNRRK 64
HNHc cd00085
HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic ...
 15-65 8.05e-13

HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.


Pssm-ID: 238038 [Multi-domain]  Cd Length: 57  Bit Score: 61.72  E-value: 8.05e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2499533017  15 LLYKHNHTCQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDK 65
Cdd:cd00085     6 VLLARDGLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKK 56
Cas9 COG3513
CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein ...
 8-127 5.99e-12

CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]; CRISPR-Cas system type-II protein Cas9 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442735 [Multi-domain]  Cd Length: 812  Bit Score: 65.37  E-value: 5.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017   8 GYNVREYLLYKH-NHTCQYCGGESG-----DPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEWLQDLKEQD 81
Cdd:COG3513   527 RRDILKYRLWEEqNGRCPYTGKPISisdllDGSVEIDHILPRSRTLDDSFNNKVLCLADANREKGNRTPYEALGGDEAEK 606

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2499533017  82 FR------KKLPKVRYKNVKQILESKVDISLKDA--GR-VNSYRY---KLLDQLKSIC 127
Cdd:COG3513   607 WEeilarvENLKLIPQKKKKRFLKKELDRDDDEGfiARqLNDTRYisrLAAEYLKSLY 664
HNH_5 pfam14279
HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. ...
 23-69 6.42e-11

HNH endonuclease; This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function.


Pssm-ID: 464124 [Multi-domain]  Cd Length: 56  Bit Score: 56.58  E-value: 6.42e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2499533017  23 CQYCGGESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRT 69
Cdd:pfam14279   1 CIYCGKEFPEKNLTIEHIIPESLGGKNKISNLQTLCKKCNSKKGHDV 47
HNH pfam01844
HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic ...
 23-68 6.71e-11

HNH endonuclease; His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity.


Pssm-ID: 396422 [Multi-domain]  Cd Length: 47  Bit Score: 56.21  E-value: 6.71e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2499533017  23 CQYCGGE-SGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNR 68
Cdd:pfam01844   1 CQYCGRPfHISDALTVDHIIPLSDGGADDIENLILLCPSCHNKKHNR 47
HNHc smart00507
HNH nucleases;
10-63 2.29e-10

HNH nucleases;


Pssm-ID: 214702 [Multi-domain]  Cd Length: 52  Bit Score: 55.16  E-value: 2.29e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2499533017   10 NVREYLLYKHnHTCQYCGgESGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQ 63
Cdd:smart00507   1 KLRRLLLHRD-GVCAYCG-KPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52
HNH_4 pfam13395
HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.
 23-69 1.50e-08

HNH endonuclease; This HNH nuclease domain is found in CRISPR-related proteins.


Pssm-ID: 433172 [Multi-domain]  Cd Length: 55  Bit Score: 49.93  E-value: 1.50e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2499533017  23 CQYCGGE------SGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRT 69
Cdd:pfam13395   1 CPYTGEQisiddlFSEKNYDIDHILPYSRSFDDSFSNKVLVLRSANQEKGNRT 53
cas_Csn1 TIGR01865
CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile ...
 10-107 7.54e-07

CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1; CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.


Pssm-ID: 273840  Cd Length: 805  Bit Score: 50.12  E-value: 7.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017  10 NVREYLLYKHNHTCQYCGGE------SGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEWLQDLKEQDF- 82
Cdd:TIGR01865 571 ILKLRLYYQQNGKCMYTGKEididdlFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEAEIVKKDSAFw 650

                          90       100       110
                  ....*....|....*....|....*....|
gi 2499533017  83 -----RKKLPKVRYKNVKQILESKVDISLK 107
Cdd:TIGR01865 651 nkfeaYVLISKRKSDKLTRAERGGLSDDDK 680
Csn1 cd09643
CRISPR/Cas system-associated protein Cas9; CRISPR (Clustered Regularly Interspaced Short ...
 10-110 3.31e-06

CRISPR/Cas system-associated protein Cas9; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II


Pssm-ID: 187774 [Multi-domain]  Cd Length: 799  Bit Score: 48.19  E-value: 3.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2499533017  10 NVREYLLYKHNHTCQYCGGE------SGDPVLEVEHKIPSSRGGTDSIKNLTLSCKTCNQDKDNRTLKEWLQDlKEQDFR 83
Cdd:cd09643   567 ILKLRLYYQQNGKCMYTGKEididdlFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPYEEIVS-KMSAFW 645

                          90       100
                  ....*....|....*....|....*..
gi 2499533017  84 KKLpkVRYKNVKQILESKVDISLKDAG 110
Cdd:cd09643   646 NKL--EAAKLISQRGDSKKDRLLLEKG 670
 
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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