NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2559883506|pdb|8INE|i]
View 

Chain i, 60S ribosomal protein L27

Protein Classification

KOW domain-containing RNA-binding protein( domain architecture ID 55)

KOW domain-containing RNA-binding protein similar to the KOW motif in 60S ribosomal protein L27, which is a component of the large ribosomal subunit; the KOW domain is known as an RNA-binding motif that is shared among some families of ribosomal proteins

Gene Ontology:  GO:0003723|GO:0003735
PubMed:  8987397

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
KOW super family cl00354
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 1-136 2.75e-48

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


The actual alignment was detected with superfamily member PTZ00471:

Pssm-ID: 469738 [Multi-domain]  Cd Length: 134  Bit Score: 151.54  E-value: 2.75e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i         1 MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHL 80
Cdd:PTZ00471   1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
8INE_i        81 MPTRYSVDipLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF 136
Cdd:PTZ00471  81 LPTRYNMD--MSKELRGRINVSDASKKARSKQLVKKLFQARYNAGSSRWFFQRLRF 134
 
Name Accession Description Interval E-value
PTZ00471 PTZ00471
60S ribosomal protein L27; Provisional
 1-136 2.75e-48

60S ribosomal protein L27; Provisional


Pssm-ID: 240428 [Multi-domain]  Cd Length: 134  Bit Score: 151.54  E-value: 2.75e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i         1 MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHL 80
Cdd:PTZ00471   1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
8INE_i        81 MPTRYSVDipLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF 136
Cdd:PTZ00471  81 LPTRYNMD--MSKELRGRINVSDASKKARSKQLVKKLFQARYNAGSSRWFFQRLRF 134
KOW_RPL27 cd06090
KOW motif of eukaryotic Ribosomal Protein L27; RPL27e has a KOW motif at its N terminal. KOW ...
 6-88 1.46e-47

KOW motif of eukaryotic Ribosomal Protein L27; RPL27e has a KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4.


Pssm-ID: 240514  Cd Length: 83  Bit Score: 147.72  E-value: 1.46e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i        6 KPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRY 85
Cdd:cd06090   1 KPGKVVIVLSGRYAGKKAVIVKNNDEGTKDRPYGHALVAGIDRYPRKVTKKMSKKKIAKRSKVKPFVKVVNYNHLMPTRY 80


                ...
8INE_i       86 SVD 88
Cdd:cd06090  81 SVD 83
Ribosomal_L27e pfam01777
Ribosomal L27e protein family; The N-terminal region of the eukaryotic ribosomal L27 has the ...
 52-136 5.36e-46

Ribosomal L27e protein family; The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family.


Pssm-ID: 460322  Cd Length: 85  Bit Score: 143.87  E-value: 5.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i         52 KVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFF 131
Cdd:pfam01777   1 KVTKKMSKKKIAKRSKVKPFVKVVNYNHLMPTRYTVDVEDLKGVVTKDTFKDPSKRKEARKEVKKKFEERYKTGKNKWFF 80


                  ....*
8INE_i        132 QKLRF 136
Cdd:pfam01777  81 TKLRF 85
 
Name Accession Description Interval E-value
PTZ00471 PTZ00471
60S ribosomal protein L27; Provisional
 1-136 2.75e-48

60S ribosomal protein L27; Provisional


Pssm-ID: 240428 [Multi-domain]  Cd Length: 134  Bit Score: 151.54  E-value: 2.75e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i         1 MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHL 80
Cdd:PTZ00471   1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
8INE_i        81 MPTRYSVDipLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF 136
Cdd:PTZ00471  81 LPTRYNMD--MSKELRGRINVSDASKKARSKQLVKKLFQARYNAGSSRWFFQRLRF 134
KOW_RPL27 cd06090
KOW motif of eukaryotic Ribosomal Protein L27; RPL27e has a KOW motif at its N terminal. KOW ...
 6-88 1.46e-47

KOW motif of eukaryotic Ribosomal Protein L27; RPL27e has a KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4.


Pssm-ID: 240514  Cd Length: 83  Bit Score: 147.72  E-value: 1.46e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i        6 KPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRY 85
Cdd:cd06090   1 KPGKVVIVLSGRYAGKKAVIVKNNDEGTKDRPYGHALVAGIDRYPRKVTKKMSKKKIAKRSKVKPFVKVVNYNHLMPTRY 80


                ...
8INE_i       86 SVD 88
Cdd:cd06090  81 SVD 83
Ribosomal_L27e pfam01777
Ribosomal L27e protein family; The N-terminal region of the eukaryotic ribosomal L27 has the ...
 52-136 5.36e-46

Ribosomal L27e protein family; The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family.


Pssm-ID: 460322  Cd Length: 85  Bit Score: 143.87  E-value: 5.36e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i         52 KVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFF 131
Cdd:pfam01777   1 KVTKKMSKKKIAKRSKVKPFVKVVNYNHLMPTRYTVDVEDLKGVVTKDTFKDPSKRKEARKEVKKKFEERYKTGKNKWFF 80


                  ....*
8INE_i        132 QKLRF 136
Cdd:pfam01777  81 TKLRF 85
KOW_RPL14 cd06088
KOW motif of Ribosomal Protein L14; RPL14 is a component of the large ribosomal subunit in ...
 6-93 7.82e-03

KOW motif of Ribosomal Protein L14; RPL14 is a component of the large ribosomal subunit in both archaea and eukaryotes with KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. Auto-antibodies to RPL14 in humans have been associated with systemic lupus erythematosus . Although RPL14 is well conserved, it is not found in all archaea, and therefore it is presumably not essential.


Pssm-ID: 240512  Cd Length: 76  Bit Score: 33.22  E-value: 7.82e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
8INE_i        6 KPGKVVLVLAGRYSGRKAVIVKNIDDGTsdrpyshALVAGidryprkvtaamGKKKIAKRskiksfvKVYNYNHLMPTRY 85
Cdd:cd06088   2 EIGRVVLSKAGRDKGKLYVIVDIIDENV-------VLVDG------------PLRTGVKP-------KKKNLKHLQLTDF 55


                ....*...
8INE_i       86 SVDIPLDK 93
Cdd:cd06088  56 VIDIPRGA 63
 
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