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Conserved domains on  [gi|1063706351|ref|NP_001325110|]
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initiator tRNA phosphoribosyl transferase family protein [Arabidopsis thaliana]

Protein Classification

protein-tyrosine phosphatase family protein; phosphatase PAP2/dual specificity phosphatase family protein( domain architecture ID 11977874)

cys-based protein-tyrosine phosphatase (PTP) family protein may be a PTP or a dual-specificity phosphatase (DUSP or DSP), and may catalyze the dephosphorylation of target phosphoproteins at tyrosine or tyrosine and serine/threonine residues, respectively| bifunctional phosphatase PAP2/dual specificity phosphatase (DSP) family protein containing a C-terminal DSP domain that may dephosphorylate phosphotyrosine, phosphoserine, and phosphothreonine residues in target proteins, and an N-terminal phosphatase PAP2 domain that may be a histidine phosphatase that catalyzes the dephosphorylation of phospholipids

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rit1_C super family cl28847
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 1-187 9.86e-79

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


The actual alignment was detected with superfamily member pfam17184:

Pssm-ID: 435771  Cd Length: 273  Bit Score: 244.01  E-value: 9.86e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351   1 MSKTIPMWSCVVNRSIFNHWNRLcnidagltsdddgdnirkllDKWDCSLHL---PLWVSNTERASIEARLDEWTRELDE 77
Cdd:pfam17184 103 LSKTIPIWCAVLNRALFPRLGKS--------------------LPWDHDLHLftpPSWVSASEHAQIEARIPGFVKSLKA 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351  78 SGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNRTSSEFSWNYIPGAGDDEESWAR 156
Cdd:pfam17184 163 LGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDGVDSRGGFTYIQGAGDDHELWAR 242

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1063706351 157 GLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 187
Cdd:pfam17184 243 GLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 281-390 5.98e-37

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


:

Pssm-ID: 427764  Cd Length: 110  Bit Score: 130.01  E-value: 5.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 281 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 358
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1063706351 359 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 390
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
 
Name Accession Description Interval E-value
Rit1_C pfam17184
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 1-187 9.86e-79

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


Pssm-ID: 435771  Cd Length: 273  Bit Score: 244.01  E-value: 9.86e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351   1 MSKTIPMWSCVVNRSIFNHWNRLcnidagltsdddgdnirkllDKWDCSLHL---PLWVSNTERASIEARLDEWTRELDE 77
Cdd:pfam17184 103 LSKTIPIWCAVLNRALFPRLGKS--------------------LPWDHDLHLftpPSWVSASEHAQIEARIPGFVKSLKA 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351  78 SGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNRTSSEFSWNYIPGAGDDEESWAR 156
Cdd:pfam17184 163 LGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDGVDSRGGFTYIQGAGDDHELWAR 242

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1063706351 157 GLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 187
Cdd:pfam17184 243 GLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 281-390 5.98e-37

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


Pssm-ID: 427764  Cd Length: 110  Bit Score: 130.01  E-value: 5.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 281 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 358
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1063706351 359 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 390
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 245-341 9.27e-09

dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in typical and atypical dual-specificity phosphatases (DUSPs), which function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Atypical DUSPs contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Also included in this family are dual specificity phosphatase-like domains of catalytically inactive members such as serine/threonine/tyrosine-interacting protein (STYX) and serine/threonine/tyrosine interacting like 1 (STYXL1), as well as active phosphatases with substrates that are not phosphoproteins such as PTP localized to the mitochondrion 1 (PTPMT1), which is a lipid phosphatase, and laforin, which is a glycogen phosphatase.


Pssm-ID: 350348 [Multi-domain]  Cd Length: 135  Bit Score: 53.32  E-value: 9.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 245 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 319
Cdd:cd14498     7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84

                          90       100
                  ....*....|....*....|..
gi 1063706351 320 CCQDGEDISICVCLAILMSLFN 341
Cdd:cd14498    85 HCQAGVSRSATIVIAYLMKKYG 106
DSPc smart00195
Dual specificity phosphatase, catalytic domain;
240-341 1.12e-03

Dual specificity phosphatase, catalytic domain;


Pssm-ID: 214551 [Multi-domain]  Cd Length: 138  Bit Score: 38.80  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351  240 WLSSTNLAVGASQVacKETSIDCILNC-DQNPISVPVSYleEHLHLPMkgSKFDRFSISRNLPPAVNFAKLKMSSGKKVL 318
Cdd:smart00195   9 YLGSYSDALNLALL--KKLGITHVINVtNEVPNYNGSDF--TYLGVPI--DDNTETKISPYFPEAVEFIEDAESKGGKVL 82

                           90       100
                   ....*....|....*....|...
gi 1063706351  319 VCCQDGEDISICVCLAILMSLFN 341
Cdd:smart00195  83 VHCQAGVSRSATLIIAYLMKTRN 105
 
Name Accession Description Interval E-value
Rit1_C pfam17184
Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) ...
 1-187 9.86e-79

Rit1 N-terminal domain; This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein.


Pssm-ID: 435771  Cd Length: 273  Bit Score: 244.01  E-value: 9.86e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351   1 MSKTIPMWSCVVNRSIFNHWNRLcnidagltsdddgdnirkllDKWDCSLHL---PLWVSNTERASIEARLDEWTRELDE 77
Cdd:pfam17184 103 LSKTIPIWCAVLNRALFPRLGKS--------------------LPWDHDLHLftpPSWVSASEHAQIEARIPGFVKSLKA 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351  78 SGADIASLASCLRKPLRPLWVSQKTVIWLNEVPEHDSWDFTPLILVSAS-ASGELQNRTSSEFSWNYIPGAGDDEESWAR 156
Cdd:pfam17184 163 LGLDLPSLRGKLGKPLRPLWITPGSSLPLPSVDDFTSLDFHPIILCSASrASSEAQDGVDSRGGFTYIQGAGDDHELWAR 242

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1063706351 157 GLSPNVFWTHVDDLIHSGPDLCNQKVAEIVE 187
Cdd:pfam17184 243 GLTPDLFWKHKDDLLSTPEDELPELIAELVE 273
Init_tRNA_PT pfam04179
Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in ...
 281-390 5.98e-37

Rit1 DUSP-like domain; This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.


Pssm-ID: 427764  Cd Length: 110  Bit Score: 130.01  E-value: 5.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 281 HLHLPMKGSKFDRFSISRNLPPAVNFAKLKMSSGK--KVLVCCQDGEDISICVCLAILMSLFNEEGAFDggkSFEEKSIT 358
Cdd:pfam04179   2 YLHLPLPSGKKGSRNLRTALPEIIQFVRSRLSEDKskKILVCCETGKDLSVGVALAILCLLFDDGTLDD---DPSRPQIT 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1063706351 359 KMDMRRMLIFICKYAVNARPSRGNLKQVFGFL 390
Cdd:pfam04179  79 KDDIRQRLAWIITSSPDANPSRATLQSVNSFL 110
DSP cd14498
dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in ...
 245-341 9.27e-09

dual-specificity phosphatase domain; The dual-specificity phosphatase domain is found in typical and atypical dual-specificity phosphatases (DUSPs), which function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Atypical DUSPs contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Also included in this family are dual specificity phosphatase-like domains of catalytically inactive members such as serine/threonine/tyrosine-interacting protein (STYX) and serine/threonine/tyrosine interacting like 1 (STYXL1), as well as active phosphatases with substrates that are not phosphoproteins such as PTP localized to the mitochondrion 1 (PTPMT1), which is a lipid phosphatase, and laforin, which is a glycogen phosphatase.


Pssm-ID: 350348 [Multi-domain]  Cd Length: 135  Bit Score: 53.32  E-value: 9.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 245 NLAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGSkfDRFSISRNLPPAVNFAKLKMSSGKKVLV 319
Cdd:cd14498     7 GLYLGSLDAAQdkellKKLGITHILNVAGEPPPNKFPDGIKYLRIPIEDS--PDEDILSHFEEAIEFIEEALKKGGKVLV 84

                          90       100
                  ....*....|....*....|..
gi 1063706351 320 CCQDGEDISICVCLAILMSLFN 341
Cdd:cd14498    85 HCQAGVSRSATIVIAYLMKKYG 106
DSPc pfam00782
Dual specificity phosphatase, catalytic domain; Ser/Thr and Tyr protein phosphatases. The ...
 256-341 9.41e-06

Dual specificity phosphatase, catalytic domain; Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.


Pssm-ID: 395632 [Multi-domain]  Cd Length: 127  Bit Score: 44.56  E-value: 9.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 256 KETSIDCILNCDQNPISVPVSYLeeHLHLPMKgsKFDRFSISRNLPPAVNFAKLKMSSGKKVLVCCQDGEDISICVCLAI 335
Cdd:pfam00782  15 SKLGITAVINVTREVDLYNSGIL--YLRIPVE--DNHETNISKYLEEAVEFIDDARQKGGKVLVHCQAGISRSATLIIAY 90


                  ....*.
gi 1063706351 336 LMSLFN 341
Cdd:pfam00782  91 LMKTRN 96
DSPc smart00195
Dual specificity phosphatase, catalytic domain;
240-341 1.12e-03

Dual specificity phosphatase, catalytic domain;


Pssm-ID: 214551 [Multi-domain]  Cd Length: 138  Bit Score: 38.80  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351  240 WLSSTNLAVGASQVacKETSIDCILNC-DQNPISVPVSYleEHLHLPMkgSKFDRFSISRNLPPAVNFAKLKMSSGKKVL 318
Cdd:smart00195   9 YLGSYSDALNLALL--KKLGITHVINVtNEVPNYNGSDF--TYLGVPI--DDNTETKISPYFPEAVEFIEDAESKGGKVL 82

                           90       100
                   ....*....|....*....|...
gi 1063706351  319 VCCQDGEDISICVCLAILMSLFN 341
Cdd:smart00195  83 VHCQAGVSRSATLIIAYLMKTRN 105
DSP_STYXL1 cd14517
dual specificity phosphatase-like domain of serine/threonine/tyrosine interacting like 1; ...
 246-385 1.63e-03

dual specificity phosphatase-like domain of serine/threonine/tyrosine interacting like 1; Serine/threonine/tyrosine interacting like 1 (STYXL1), also known as DUSP24 and MK-STYX, is a catalytically inactive phosphatase with homology to the mitogen-activated protein kinase (MAPK) phosphatases (MKPs). STYXL1 plays a role in regulating pathways by competing with active phosphatases for binding to MAPKs. Similar to MKPs, STYXL1 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, however its C-terminal dual specificity phosphatase-like domain is a pseudophosphatase missing the catalytic cysteine.


Pssm-ID: 350367 [Multi-domain]  Cd Length: 155  Bit Score: 38.80  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063706351 246 LAVGASQVAC-----KETSIDCILNCDQNPISVPVSYLEEHLHLPMKGS-KFDRFSisrNLPPAVNFAKLKMSSGKKVLV 319
Cdd:cd14517    19 LYMGNYKQACdkkiqKDLKIKAHINVSMDADELFKSGNDQVLHIPVEDSvEADLLS---FFERACSFIDKHKNNGSRVLV 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063706351 320 CCQDGEDISICVCLAILMSLFneegafdggksfeeksitKMDMRRMLIFICKYAVNARPSRGNLKQ 385
Cdd:cd14517    96 FSTLGISRSVAVAIAYLMYHY------------------KWSLKDAWKYLLKCKNNMRPNRGFVKQ 143
 
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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