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Conserved domains on  [gi|550794328|gb|ERS91911|]
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hypothetical protein Q671_14395 [Halomonas sp. PBN3]

Protein Classification

protein kinase family protein( domain architecture ID 229378)

protein kinase family protein may catalyze the transfer of the gamma-phosphoryl group from ATP to substrates such as serine/threonine and/or tyrosine residues on proteins, or may be a pseudokinase

CATH:  1.10.510.10
PubMed:  16244704
SCOP:  4003661

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
prot_kin_PA4780 super family cl46025
PA4780 family RIO1-like protein kinase; Members of this family are putative serine ...
 10-108 1.88e-59

PA4780 family RIO1-like protein kinase; Members of this family are putative serine/threonine-protein kinases, closely related to founding member PA4780 from Pseudomonas aeruginosa PAO1, which was shown to be upregulated by and important for the biodegradation of phenanthrene and naphthalene. Members belong more generally to the RIO1 atypical kinase family (see PF01163).


The actual alignment was detected with superfamily member NF041645:

Pssm-ID: 469527  Cd Length: 274  Bit Score: 184.38  E-value: 1.88e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550794328  10 LAADGPVIIDLPQAVDAAGNNGAEWMFERDVDNMRRYFGRFAPELLATDYGKEIWALYEAGELHPESRLTGRFVHDTTPV 89
Cdd:NF041645 176 VDADGPVIIDLPQAVDAAGNNNARRMLERDVNNLAAYFGQFAPELLDTQYAKEIWALYEAGELTPDTELTGHFEESTGPA 255

                         90
                 ....*....|....*....
gi 550794328  90 DVDELMTVIDDVRDEEARR 108
Cdd:NF041645 256 DVDSVLREIDAAREEEEAR 274
 
Name Accession Description Interval E-value
prot_kin_PA4780 NF041645
PA4780 family RIO1-like protein kinase; Members of this family are putative serine ...
 10-108 1.88e-59

PA4780 family RIO1-like protein kinase; Members of this family are putative serine/threonine-protein kinases, closely related to founding member PA4780 from Pseudomonas aeruginosa PAO1, which was shown to be upregulated by and important for the biodegradation of phenanthrene and naphthalene. Members belong more generally to the RIO1 atypical kinase family (see PF01163).


Pssm-ID: 469527  Cd Length: 274  Bit Score: 184.38  E-value: 1.88e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550794328  10 LAADGPVIIDLPQAVDAAGNNGAEWMFERDVDNMRRYFGRFAPELLATDYGKEIWALYEAGELHPESRLTGRFVHDTTPV 89
Cdd:NF041645 176 VDADGPVIIDLPQAVDAAGNNNARRMLERDVNNLAAYFGQFAPELLDTQYAKEIWALYEAGELTPDTELTGHFEESTGPA 255

                         90
                 ....*....|....*....
gi 550794328  90 DVDELMTVIDDVRDEEARR 108
Cdd:NF041645 256 DVDSVLREIDAAREEEEAR 274
RIO1 COG1718
Serine/threonine-protein kinase RIO1 [Signal transduction mechanisms];
12-65 8.85e-22

Serine/threonine-protein kinase RIO1 [Signal transduction mechanisms];


Pssm-ID: 441324  Cd Length: 252  Bit Score: 86.78  E-value: 8.85e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 550794328  12 ADGPVIIDLPQAVDAAgNNGAEWMFERDVDNMRRYFGRFAPELLATDYGKEIWA 65
Cdd:COG1718  200 DGGPVIIDLPQAVDVA-HPNAKEFLERDVENIARFFARFGPELDPEELLKEIWA 252
RIO1 pfam01163
RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria ...
 13-59 8.45e-11

RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined.


Pssm-ID: 460091 [Multi-domain]  Cd Length: 184  Bit Score: 56.47  E-value: 8.45e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 550794328   13 DGPVIIDLPQAVDAAgNNGAEWMFERDVDNMRRYFGRFAPELLATDY 59
Cdd:pfam01163 139 DKPVIIDVPQAVETD-HPNALEFLERDVENIINFFRRKGVDEVDERK 184
RIO1_like cd05145
Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar ...
 13-50 3.72e-10

Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar proteins; RIO1 is present in archaea, bacteria and eukaryotes. In addition, RIO3 is present in multicellular eukaryotes. Both RIO1 and RIO3 are associated with precursors of 40S ribosomal subunits, just like RIO2. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and chromosome maintenance. Although depletion of either RIO1 and RIO2 results in similar effects, the two kinases are not fully interchangeable. The specific function of RIO3 is unknown. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K).


Pssm-ID: 270696 [Multi-domain]  Cd Length: 189  Bit Score: 54.87  E-value: 3.72e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 550794328  13 DGPVIIDLPQAVDAAGNNGAEwMFERDVDNMRRYFGRF 50
Cdd:cd05145  153 GKPVIIDVSQAVTLDHPNAEE-FLRRDIRNINRFFSRK 189
RIO smart00090
RIO-like kinase;
13-49 1.20e-05

RIO-like kinase;


Pssm-ID: 214511 [Multi-domain]  Cd Length: 237  Bit Score: 43.06  E-value: 1.20e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 550794328    13 DGPVIIDLPQAVDaAGNNGAEWMFERDVDNMRRYFGR 49
Cdd:smart00090 185 GKVVIIDVSQSVE-LDHPMALEFLERDIRNIIRFFRR 220
 
Name Accession Description Interval E-value
prot_kin_PA4780 NF041645
PA4780 family RIO1-like protein kinase; Members of this family are putative serine ...
 10-108 1.88e-59

PA4780 family RIO1-like protein kinase; Members of this family are putative serine/threonine-protein kinases, closely related to founding member PA4780 from Pseudomonas aeruginosa PAO1, which was shown to be upregulated by and important for the biodegradation of phenanthrene and naphthalene. Members belong more generally to the RIO1 atypical kinase family (see PF01163).


Pssm-ID: 469527  Cd Length: 274  Bit Score: 184.38  E-value: 1.88e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 550794328  10 LAADGPVIIDLPQAVDAAGNNGAEWMFERDVDNMRRYFGRFAPELLATDYGKEIWALYEAGELHPESRLTGRFVHDTTPV 89
Cdd:NF041645 176 VDADGPVIIDLPQAVDAAGNNNARRMLERDVNNLAAYFGQFAPELLDTQYAKEIWALYEAGELTPDTELTGHFEESTGPA 255

                         90
                 ....*....|....*....
gi 550794328  90 DVDELMTVIDDVRDEEARR 108
Cdd:NF041645 256 DVDSVLREIDAAREEEEAR 274
RIO1 COG1718
Serine/threonine-protein kinase RIO1 [Signal transduction mechanisms];
12-65 8.85e-22

Serine/threonine-protein kinase RIO1 [Signal transduction mechanisms];


Pssm-ID: 441324  Cd Length: 252  Bit Score: 86.78  E-value: 8.85e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 550794328  12 ADGPVIIDLPQAVDAAgNNGAEWMFERDVDNMRRYFGRFAPELLATDYGKEIWA 65
Cdd:COG1718  200 DGGPVIIDLPQAVDVA-HPNAKEFLERDVENIARFFARFGPELDPEELLKEIWA 252
RIO1 pfam01163
RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria ...
 13-59 8.45e-11

RIO1 family; This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined.


Pssm-ID: 460091 [Multi-domain]  Cd Length: 184  Bit Score: 56.47  E-value: 8.45e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 550794328   13 DGPVIIDLPQAVDAAgNNGAEWMFERDVDNMRRYFGRFAPELLATDY 59
Cdd:pfam01163 139 DKPVIIDVPQAVETD-HPNALEFLERDVENIINFFRRKGVDEVDERK 184
RIO1_like cd05145
Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar ...
 13-50 3.72e-10

Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar proteins; RIO1 is present in archaea, bacteria and eukaryotes. In addition, RIO3 is present in multicellular eukaryotes. Both RIO1 and RIO3 are associated with precursors of 40S ribosomal subunits, just like RIO2. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and chromosome maintenance. Although depletion of either RIO1 and RIO2 results in similar effects, the two kinases are not fully interchangeable. The specific function of RIO3 is unknown. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K).


Pssm-ID: 270696 [Multi-domain]  Cd Length: 189  Bit Score: 54.87  E-value: 3.72e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 550794328  13 DGPVIIDLPQAVDAAGNNGAEwMFERDVDNMRRYFGRF 50
Cdd:cd05145  153 GKPVIIDVSQAVTLDHPNAEE-FLRRDIRNINRFFSRK 189
RIO2_C cd05144
C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase; RIO2 is ...
 13-49 2.25e-07

C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase; RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO2 kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K).


Pssm-ID: 270695 [Multi-domain]  Cd Length: 183  Bit Score: 47.11  E-value: 2.25e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 550794328  13 DGPVIIDLPQAVDAAGNNgAEWMFERDVDNMRRYFGR 49
Cdd:cd05144  147 EKITVIDFPQMVSTSHPN-AEEYFDRDVECIIKFFRR 182
RIO smart00090
RIO-like kinase;
13-49 1.20e-05

RIO-like kinase;


Pssm-ID: 214511 [Multi-domain]  Cd Length: 237  Bit Score: 43.06  E-value: 1.20e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 550794328    13 DGPVIIDLPQAVDaAGNNGAEWMFERDVDNMRRYFGR 49
Cdd:smart00090 185 GKVVIIDVSQSVE-LDHPMALEFLERDIRNIIRFFRR 220
RIO2 COG0478
RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction ...
 13-53 2.92e-05

RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms];


Pssm-ID: 440246 [Multi-domain]  Cd Length: 183  Bit Score: 41.43  E-value: 2.92e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 550794328  13 DGPVIIDLPQAVDAAGNNGAEWMfERDVDNMRRYFGRFAPE 53
Cdd:COG0478  127 GGVWIIDWPQAVPRDHPNAEELL-ERDLENLLRSFRKKYGL 166
RIO cd05119
Catalytic domain of the atypical protein serine kinases, RIO kinases; RIO kinases are atypical ...
 10-50 1.36e-03

Catalytic domain of the atypical protein serine kinases, RIO kinases; RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K).


Pssm-ID: 270689  Cd Length: 192  Bit Score: 36.93  E-value: 1.36e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 550794328  10 LAADGPVIIDLPQAVDAaGNNGAEWMFERDVDNMRRYFGRF 50
Cdd:cd05119  153 LYIDKVYFIDFGQAVTL-RHPGAESYLERDVRNIIRFFSKY 192
 
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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