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Conserved domains on  [gi|19115686|ref|NP_594774|]
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zinc finger ribosome biogenesis protein [Schizosaccharomyces pombe]

Protein Classification

UFD2 family protein( domain architecture ID 10009081)

ubiquitin fusion degradation protein 2 (UFD2) family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UFD2 COG5112
U1-like Zn-finger-containing protein [General function prediction only];
1-124 8.29e-73

U1-like Zn-finger-containing protein [General function prediction only];


:

Pssm-ID: 227443  Cd Length: 126  Bit Score: 212.63  E-value: 8.29e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115686   1 MGRVARKRKHHSNGNHALFRTRVYGRDLDQIHNDLTESEKFDKLPIDPDLPGLGQHYCIECARYFDSSQALLVHKKGKVH 80
Cdd:COG5112   1 MGRSDTKRKKRRSNRLRIKRTRLFGRDLDQIKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVH 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 19115686  81 KRRLKNLREEPYTQEEAEAAV--NIGQPKQSVASKLADNSNVVMAD 124
Cdd:COG5112  81 KRRAKELREVPYTQEDAEAAVglTVGPEKESNEALLKEHLDSTLAN 126
 
Name Accession Description Interval E-value
UFD2 COG5112
U1-like Zn-finger-containing protein [General function prediction only];
1-124 8.29e-73

U1-like Zn-finger-containing protein [General function prediction only];


Pssm-ID: 227443  Cd Length: 126  Bit Score: 212.63  E-value: 8.29e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115686   1 MGRVARKRKHHSNGNHALFRTRVYGRDLDQIHNDLTESEKFDKLPIDPDLPGLGQHYCIECARYFDSSQALLVHKKGKVH 80
Cdd:COG5112   1 MGRSDTKRKKRRSNRLRIKRTRLFGRDLDQIKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVH 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 19115686  81 KRRLKNLREEPYTQEEAEAAV--NIGQPKQSVASKLADNSNVVMAD 124
Cdd:COG5112  81 KRRAKELREVPYTQEDAEAAVglTVGPEKESNEALLKEHLDSTLAN 126
zf-C2H2_jaz pfam12171
Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, ...
 55-81 9.50e-08

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.


Pssm-ID: 432381 [Multi-domain]  Cd Length: 27  Bit Score: 44.85  E-value: 9.50e-08
                          10        20
                  ....*....|....*....|....*..
gi 19115686    55 QHYCIECARYFDSSQALLVHKKGKVHK 81
Cdd:pfam12171   1 QFYCVLCDKYFKSENALQNHLKSKKHK 27
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 54-85 2.94e-05

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.39  E-value: 2.94e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 19115686     54 GQHYCIECARYFDSSQALLVHKKGKVHKRRLK 85
Cdd:smart00451   2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVK 33
 
Name Accession Description Interval E-value
UFD2 COG5112
U1-like Zn-finger-containing protein [General function prediction only];
1-124 8.29e-73

U1-like Zn-finger-containing protein [General function prediction only];


Pssm-ID: 227443  Cd Length: 126  Bit Score: 212.63  E-value: 8.29e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115686   1 MGRVARKRKHHSNGNHALFRTRVYGRDLDQIHNDLTESEKFDKLPIDPDLPGLGQHYCIECARYFDSSQALLVHKKGKVH 80
Cdd:COG5112   1 MGRSDTKRKKRRSNRLRIKRTRLFGRDLDQIKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVH 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 19115686  81 KRRLKNLREEPYTQEEAEAAV--NIGQPKQSVASKLADNSNVVMAD 124
Cdd:COG5112  81 KRRAKELREVPYTQEDAEAAVglTVGPEKESNEALLKEHLDSTLAN 126
zf-C2H2_jaz pfam12171
Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, ...
 55-81 9.50e-08

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.


Pssm-ID: 432381 [Multi-domain]  Cd Length: 27  Bit Score: 44.85  E-value: 9.50e-08
                          10        20
                  ....*....|....*....|....*..
gi 19115686    55 QHYCIECARYFDSSQALLVHKKGKVHK 81
Cdd:pfam12171   1 QFYCVLCDKYFKSENALQNHLKSKKHK 27
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 54-85 2.94e-05

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.39  E-value: 2.94e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 19115686     54 GQHYCIECARYFDSSQALLVHKKGKVHKRRLK 85
Cdd:smart00451   2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVK 33
PRP9 COG5188
Splicing factor 3a, subunit 3 [RNA processing and modification];
57-94 3.91e-03

Splicing factor 3a, subunit 3 [RNA processing and modification];


Pssm-ID: 227515 [Multi-domain]  Cd Length: 470  Bit Score: 35.76  E-value: 3.91e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 19115686  57 YCIECARYFDSSQALLVHKKGKVHKRRLKNLREEPYTQ 94
Cdd:COG5188 240 YCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSE 277
 
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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