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Conserved domains on  [gi|1002302944|ref|XP_015614856|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NUMOD3 super family cl17841
NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. ...
 100-128 3.54e-05

NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (pfam01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease.


The actual alignment was detected with superfamily member pfam07460:

Pssm-ID: 429472 [Multi-domain]  Cd Length: 37  Bit Score: 40.86  E-value: 3.54e-05
                          10        20
                  ....*....|....*....|....*....
gi 1002302944 100 RMRISKANKGNTPWNKGRKHTPETLQRIR 128
Cdd:pfam07460   9 KAKISKALKGENNPNYGKKHSEETKKKIS 37
GIY-YIG_Cterm super family cl29963
GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing ...
 103-210 6.28e-03

GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing site at a fixed distance from the intron insertion site.


The actual alignment was detected with superfamily member cd00283:

Pssm-ID: 238175 [Multi-domain]  Cd Length: 113  Bit Score: 36.68  E-value: 6.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302944 103 ISKANKG-----NTPWnKGRKHTpetlqrirERTRIAMQDPKVKKKLMHLGHAQSEETRIKISMGVRRGWNLRLQKLMIQ 177
Cdd:cd00283     2 AKNKMSAsysgeKNPM-FGKTHS--------EETKAKISKNRSGENNPMFGKKHSDETKAKISAKKKGRKNLNAKKKQSD 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1002302944 178 DGCFVEWRDMIADAAR--KGFAGGISLQWNSYKIL 210
Cdd:cd00283    73 TDGYIGIFDSTTEAARflKVHSGTISKNIKSGKLL 107
 
Name Accession Description Interval E-value
NUMOD3 pfam07460
NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. ...
 100-128 3.54e-05

NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (pfam01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease.


Pssm-ID: 429472 [Multi-domain]  Cd Length: 37  Bit Score: 40.86  E-value: 3.54e-05
                          10        20
                  ....*....|....*....|....*....
gi 1002302944 100 RMRISKANKGNTPWNKGRKHTPETLQRIR 128
Cdd:pfam07460   9 KAKISKALKGENNPNYGKKHSEETKKKIS 37
GIY-YIG_Cterm cd00283
GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing ...
 103-210 6.28e-03

GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing site at a fixed distance from the intron insertion site.


Pssm-ID: 238175 [Multi-domain]  Cd Length: 113  Bit Score: 36.68  E-value: 6.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302944 103 ISKANKG-----NTPWnKGRKHTpetlqrirERTRIAMQDPKVKKKLMHLGHAQSEETRIKISMGVRRGWNLRLQKLMIQ 177
Cdd:cd00283     2 AKNKMSAsysgeKNPM-FGKTHS--------EETKAKISKNRSGENNPMFGKKHSDETKAKISAKKKGRKNLNAKKKQSD 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1002302944 178 DGCFVEWRDMIADAAR--KGFAGGISLQWNSYKIL 210
Cdd:cd00283    73 TDGYIGIFDSTTEAARflKVHSGTISKNIKSGKLL 107
 
Name Accession Description Interval E-value
NUMOD3 pfam07460
NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. ...
 100-128 3.54e-05

NUMOD3 motif; NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (pfam01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease.


Pssm-ID: 429472 [Multi-domain]  Cd Length: 37  Bit Score: 40.86  E-value: 3.54e-05
                          10        20
                  ....*....|....*....|....*....
gi 1002302944 100 RMRISKANKGNTPWNKGRKHTPETLQRIR 128
Cdd:pfam07460   9 KAKISKALKGENNPNYGKKHSEETKKKIS 37
GIY-YIG_Cterm cd00283
GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing ...
 103-210 6.28e-03

GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing site at a fixed distance from the intron insertion site.


Pssm-ID: 238175 [Multi-domain]  Cd Length: 113  Bit Score: 36.68  E-value: 6.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002302944 103 ISKANKG-----NTPWnKGRKHTpetlqrirERTRIAMQDPKVKKKLMHLGHAQSEETRIKISMGVRRGWNLRLQKLMIQ 177
Cdd:cd00283     2 AKNKMSAsysgeKNPM-FGKTHS--------EETKAKISKNRSGENNPMFGKKHSDETKAKISAKKKGRKNLNAKKKQSD 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1002302944 178 DGCFVEWRDMIADAAR--KGFAGGISLQWNSYKIL 210
Cdd:cd00283    73 TDGYIGIFDSTTEAARflKVHSGTISKNIKSGKLL 107
 
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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