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Conserved domains on  [gi|74870304|sp|Q9VPU8|]
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RecName: Full=KRR1 small subunit processome component homolog; AltName: Full=KRR-R motif-containing protein 1; AltName: Full=Protein dribble

Protein Classification

KRR1 small subunit processome component( domain architecture ID 16910090)

KRR1 small subunit (SSU) processome component is involved in the assembly of the SSU processome; contains two K-homology (KH) RNA-binding domains, the first one is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor

CATH:  3.30.1370.10
Gene Ontology:  GO:0003723|GO:0032040|GO:0042274|GO:0006364
PubMed:  11160884|18422648
SCOP:  4001190

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 122-214 2.75e-63

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411822  Cd Length: 93  Bit Score: 195.86  E-value: 2.75e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304 122 IGCDIIKIGNLVHKKEKFVKRRQRLIGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRDIVLETMNNVHPIYNI 201
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 74870304 202 KALMIKRELMKDP 214
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 36-118 2.88e-54

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


:

Pssm-ID: 411821  Cd Length: 83  Bit Score: 172.72  E-value: 2.88e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304  36 MVEESSFATLFPKYRERYLKEVWPLVEQCLAEHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAK 115
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 74870304 116 RVL 118
Cdd:cd22393  81 KIL 83
 
Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 122-214 2.75e-63

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411822  Cd Length: 93  Bit Score: 195.86  E-value: 2.75e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304 122 IGCDIIKIGNLVHKKEKFVKRRQRLIGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRDIVLETMNNVHPIYNI 201
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 74870304 202 KALMIKRELMKDP 214
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 36-118 2.88e-54

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


Pssm-ID: 411821  Cd Length: 83  Bit Score: 172.72  E-value: 2.88e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304  36 MVEESSFATLFPKYRERYLKEVWPLVEQCLAEHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAK 115
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 74870304 116 RVL 118
Cdd:cd22393  81 KIL 83
KH_8 pfam17903
Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ...
 40-120 1.31e-30

Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1.


Pssm-ID: 407755  Cd Length: 81  Bit Score: 111.29  E-value: 1.31e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304    40 SSFATLFPKYRERYLKEVWPLVEQCLAEHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQ 119
Cdd:pfam17903   1 SSFEILFPKHREQYLKGVEEYIRELLEEKKIKCEVDYDERSIKVSTTEKTRDPYVILKARDFIKLVSRGVPLEEAVKVFE 80


                  .
gi 74870304   120 D 120
Cdd:pfam17903  81 D 81
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 67-186 4.52e-16

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: 74.91  E-value: 4.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304    67 EHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQDDIGCDIIKIGNLVHKKEKFVKRRQRL 146
Cdd:TIGR03665  24 EERTGVKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRI 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 74870304   147 IGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRD 186
Cdd:TIGR03665 104 IGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIARE 143
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 69-186 1.53e-13

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 67.97  E-value: 1.53e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304   69 HLKAELDLMEGSMVVkTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQDDIGCDIIKIGNLVHKKEKFVKRRQRLIG 148
Cdd:PRK13763  33 GVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIG 111

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 74870304  149 PNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRD 186
Cdd:PRK13763 112 EGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIARE 149
KH smart00322
K homology RNA-binding domain;
140-190 1.52e-03

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 36.50  E-value: 1.52e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 74870304    140 VKRRQRLIGPNGATLKSIELLTDCYVLVQG-----NTVSALGPYKGLQQVRDIVLE 190
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIPGpgseeRVVEITGPPENVEKAAELILE 66
 
Name Accession Description Interval E-value
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 122-214 2.75e-63

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411822  Cd Length: 93  Bit Score: 195.86  E-value: 2.75e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304 122 IGCDIIKIGNLVHKKEKFVKRRQRLIGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRDIVLETMNNVHPIYNI 201
Cdd:cd22394   1 VACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKAIELLTKCYILVQGNTVSAIGPYKGLKEVRKIVEDCMKNIHPIYNI 80

                        90
                ....*....|...
gi 74870304 202 KALMIKRELMKDP 214
Cdd:cd22394  81 KTLMIKRELEKDP 93
KH-I_KRR1_rpt1 cd22393
first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 36-118 2.88e-54

first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 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 and is involved in binding another assembly factor, Kri1.


Pssm-ID: 411821  Cd Length: 83  Bit Score: 172.72  E-value: 2.88e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304  36 MVEESSFATLFPKYRERYLKEVWPLVEQCLAEHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAK 115
Cdd:cd22393   1 FLEESSFATLFPKYREKYLKEVWPLVTKALKEHGIKCELDLVEGSMTVKTTRKTRDPYIIIKARDLIKLLARSVPFEQAV 80


                ...
gi 74870304 116 RVL 118
Cdd:cd22393  81 KIL 83
KH_8 pfam17903
Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ...
 40-120 1.31e-30

Krr1 KH1 domain; This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1.


Pssm-ID: 407755  Cd Length: 81  Bit Score: 111.29  E-value: 1.31e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304    40 SSFATLFPKYRERYLKEVWPLVEQCLAEHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQ 119
Cdd:pfam17903   1 SSFEILFPKHREQYLKGVEEYIRELLEEKKIKCEVDYDERSIKVSTTEKTRDPYVILKARDFIKLVSRGVPLEEAVKVFE 80


                  .
gi 74870304   120 D 120
Cdd:pfam17903  81 D 81
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 67-186 4.52e-16

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: 74.91  E-value: 4.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304    67 EHHLKAELDLMEGSMVVKTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQDDIGCDIIKIGNLVHKKEKFVKRRQRL 146
Cdd:TIGR03665  24 EERTGVKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRI 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 74870304   147 IGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRD 186
Cdd:TIGR03665 104 IGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIARE 143
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 69-186 1.53e-13

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 67.97  E-value: 1.53e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74870304   69 HLKAELDLMEGSMVVkTSRKTWDPYIIIKARDMIKLMARSVPFEQAKRVLQDDIGCDIIKIGNLVHKKEKFVKRRQRLIG 148
Cdd:PRK13763  33 GVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIG 111

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 74870304  149 PNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRD 186
Cdd:PRK13763 112 EGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIARE 149
KH-I_Dim2p_like_rpt2 cd22390
second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 115-188 5.64e-12

second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411818  Cd Length: 96  Bit Score: 61.08  E-value: 5.64e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 74870304 115 KRVLQDDIGCDIIKIGNLVHKKEKFVKR-RQRLIGPNGATLKSIELLTDCYVLVQGNTVSALGPYKGLQQVRDIV 188
Cdd:cd22390   1 LLLLDDDYVLEVIDLRDYAGRSKKALRRvKGRVIGSGGKTRRLIEELTGCYISVYGKTVSIIGDFENLQIAKEAI 75
KH smart00322
K homology RNA-binding domain;
140-190 1.52e-03

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 36.50  E-value: 1.52e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 74870304    140 VKRRQRLIGPNGATLKSIELLTDCYVLVQG-----NTVSALGPYKGLQQVRDIVLE 190
Cdd:smart00322  11 ADKVGLIIGKGGSTIKKIEEETGVKIDIPGpgseeRVVEITGPPENVEKAAELILE 66
 
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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