NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2101188255|gb|KAH0621845|]
View 

hypothetical protein JD844_023513 [Phrynosoma platyrhinos]

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
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 59-138 1.34e-58

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411819  Cd Length: 80  Bit Score: 178.49  E-value: 1.34e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  59 DEMRKIPVPAHRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCKETKDISALTKAADFVKAFILGFQVEDALAL 138
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 140-194 2.42e-39

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


The actual alignment was detected with superfamily member cd22392:

Pssm-ID: 469614  Cd Length: 96  Bit Score: 130.40  E-value: 2.42e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2101188255 140 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADSK 194
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 59-138 1.34e-58

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 178.49  E-value: 1.34e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  59 DEMRKIPVPAHRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCKETKDISALTKAADFVKAFILGFQVEDALAL 138
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 140-194 2.42e-39

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 130.40  E-value: 2.42e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2101188255 140 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADSK 194
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 85-197 8.94e-15

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 69.13  E-value: 8.94e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  85 IVEHLQLQIRFNLKTRNVEIkTCKETKDISALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 164
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2101188255 165 AIGRIAGKGGKTKFTIENVTRTRIVLADSKSSI 197
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAI 137
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 85-197 8.97e-14

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 66.43  E-value: 8.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  85 IVEHLQLQIRFNLKTRNVEIKTCKETKDisALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 164
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPEDEDPL--AVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRR 98

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2101188255 165 AIGRIAGKGGKTKFTIENVTRTRIVLADSKSSI 197
Cdd:TIGR03665  99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGI 131
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 59-138 1.34e-58

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 178.49  E-value: 1.34e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  59 DEMRKIPVPAHRYTPLKENWMKIFTPIVEHLQLQIRFNLKTRNVEIKTCKETKDISALTKAADFVKAFILGFQVEDALAL 138
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 140-194 2.42e-39

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 130.40  E-value: 2.42e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2101188255 140 RLDDLFLESFEVTDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADSK 194
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 85-197 8.94e-15

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 69.13  E-value: 8.94e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  85 IVEHLQLQIRFNLKTRNVEIkTCKETKDISALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 164
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2101188255 165 AIGRIAGKGGKTKFTIENVTRTRIVLADSKSSI 197
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAI 137
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 85-197 8.97e-14

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 66.43  E-value: 8.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2101188255  85 IVEHLQLQIRFNLKTRNVEIKTCKETKDisALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEVTDVKPLKgDHLSR 164
Cdd:TIGR03665  23 IEERTGVKLDIDSETGEVKIEPEDEDPL--AVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRR 98

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2101188255 165 AIGRIAGKGGKTKFTIENVTRTRIVLADSKSSI 197
Cdd:TIGR03665  99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGI 131
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 163-192 3.32e-03

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 34.91  E-value: 3.32e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2101188255 163 SRAIGRIAGKGGKTKFTIENVTRTRIVLAD 192
Cdd:cd22403     8 SSMVGRIIGKGGQNVRELQRLTGAIIKLPR 37
 
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