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Conserved domains on  [gi|446355389|ref|WP_000433244|]
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MULTISPECIES: RNA 2',3'-cyclic phosphodiesterase [Bacillus]

Protein Classification

2'-5' RNA ligase family protein( domain architecture ID 11494094)

2'-5' RNA ligase family protein such as RNA 2',3'-cyclic phosphodiesterase hydrolyzes RNA 2',3'-cyclic phosphodiester to the RNA 2'-phosphomonoester

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 3-179 2.64e-65

2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing]


:

Pssm-ID: 274058 [Multi-domain]  Cd Length: 179  Bit Score: 197.89  E-value: 2.64e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    3 PHYFVAITLPNYIKEVLSNYKEDMEEELPFRSWVHKEDYHITLSFLGSATEEQLEGIKNGLQTlIEKKELPFTLQGFSTF 82
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAK-IAEPPFTLKLEGIGVF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   83 GMEDRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLETRPYHPHITVARKWMGEKKF--HLENIKEVPEVSFQADTITL 160
Cdd:TIGR02258  80 GNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVpeFLQEFANEEFGSFHVDEFHL 159

                         170       180
                  ....*....|....*....|
gi 446355389  161 YESHVKET-PKYKSIAEIKL 179
Cdd:TIGR02258 160 YSSTLTPGgPIYEPLARFQL 179
 
Name Accession Description Interval E-value
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 3-179 2.64e-65

2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing]


Pssm-ID: 274058 [Multi-domain]  Cd Length: 179  Bit Score: 197.89  E-value: 2.64e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    3 PHYFVAITLPNYIKEVLSNYKEDMEEELPFRSWVHKEDYHITLSFLGSATEEQLEGIKNGLQTlIEKKELPFTLQGFSTF 82
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAK-IAEPPFTLKLEGIGVF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   83 GMEDRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLETRPYHPHITVARKWMGEKKF--HLENIKEVPEVSFQADTITL 160
Cdd:TIGR02258  80 GNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVpeFLQEFANEEFGSFHVDEFHL 159

                         170       180
                  ....*....|....*....|
gi 446355389  161 YESHVKET-PKYKSIAEIKL 179
Cdd:TIGR02258 160 YSSTLTPGgPIYEPLARFQL 179
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 3-181 3.22e-45

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 147.10  E-value: 3.22e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   3 PHYFVAITLPNYIKEVLSNYKEDMEEELPFRsWVHKEDYHITLSFLGSATEEQLEGIKNGLQTLIEKKElPFTLQ--GFS 80
Cdd:COG1514    1 MRLFIALPPPEELREALAALRARLKAAPGGR-WVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAP-PFELRldGLG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389  81 TFGmEDRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLETRPYHPHITVARKWMGEKKF--HLENIKEVPEVSFQADTI 158
Cdd:COG1514   79 AFP-RPRPRVLWLGVEPSPELLALHRRLRAALARAGLPPERRPFVPHVTLARGKRPAPPLapALAELRDFEFPEFTVDEF 157

                        170       180
                 ....*....|....*....|....
gi 446355389 159 TLYESHVKET-PKYKSIAEIKLQK 181
Cdd:COG1514  158 VLYESELTPDgPRYEVLAEFPLGG 181
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 9-92 4.85e-15

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 66.67  E-value: 4.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    9 ITLPNYIKEVLSNYKEDMEEELPFR--SWVHKEDYHITLSFLGSATEEQLEGIKNGLQTLIEK-KELPFTLQGFSTFGME 85
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERALAKLgfKPVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGfPPFELKVDGVGLFPSR 80


                  ....*..
gi 446355389   86 DRPRIFW 92
Cdd:pfam02834  81 LRPRVIY 87
PRK13679 PRK13679
hypothetical protein; Provisional
 42-133 2.24e-05

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 42.62  E-value: 2.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389  42 HITLSFLGSATEEQLEGIKNGLQTLIEKKElPFTLQ--GFSTFgmedRP--RIFWAKVSENHELFQLQKQVHaicegNGF 117
Cdd:PRK13679  34 HITLKEPFEISDEQLDSIVEELRAIASETK-PFTLHvtKVSSF----APtnNVIYFKVEKTEELEELHERLH-----SGD 103

                         90
                 ....*....|....*...
gi 446355389 118 SLETRPYH--PHITVARK 133
Cdd:PRK13679 104 FYGEAEYAfvPHITIGQG 121
 
Name Accession Description Interval E-value
2_5_ligase TIGR02258
2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two ...
 3-179 2.64e-65

2'-5' RNA ligase; This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing]


Pssm-ID: 274058 [Multi-domain]  Cd Length: 179  Bit Score: 197.89  E-value: 2.64e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    3 PHYFVAITLPNYIKEVLSNYKEDMEEELPFRSWVHKEDYHITLSFLGSATEEQLEGIKNGLQTlIEKKELPFTLQGFSTF 82
Cdd:TIGR02258   1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAK-IAEPPFTLKLEGIGVF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   83 GMEDRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLETRPYHPHITVARKWMGEKKF--HLENIKEVPEVSFQADTITL 160
Cdd:TIGR02258  80 GNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKPGVpeFLQEFANEEFGSFHVDEFHL 159

                         170       180
                  ....*....|....*....|
gi 446355389  161 YESHVKET-PKYKSIAEIKL 179
Cdd:TIGR02258 160 YSSTLTPGgPIYEPLARFQL 179
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 3-181 3.22e-45

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 147.10  E-value: 3.22e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   3 PHYFVAITLPNYIKEVLSNYKEDMEEELPFRsWVHKEDYHITLSFLGSATEEQLEGIKNGLQTLIEKKElPFTLQ--GFS 80
Cdd:COG1514    1 MRLFIALPPPEELREALAALRARLKAAPGGR-WVRPENLHLTLAFLGEVDEERLEALAEALARAAAGAP-PFELRldGLG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389  81 TFGmEDRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLETRPYHPHITVARKWMGEKKF--HLENIKEVPEVSFQADTI 158
Cdd:COG1514   79 AFP-RPRPRVLWLGVEPSPELLALHRRLRAALARAGLPPERRPFVPHVTLARGKRPAPPLapALAELRDFEFPEFTVDEF 157

                        170       180
                 ....*....|....*....|....
gi 446355389 159 TLYESHVKET-PKYKSIAEIKLQK 181
Cdd:COG1514  158 VLYESELTPDgPRYEVLAEFPLGG 181
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 9-92 4.85e-15

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 66.67  E-value: 4.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    9 ITLPNYIKEVLSNYKEDMEEELPFR--SWVHKEDYHITLSFLGSATEEQLEGIKNGLQTLIEK-KELPFTLQGFSTFGME 85
Cdd:pfam02834   1 LGPPEEIAEELARLRAELERALAKLgfKPVRPFNPHITLAFLGEVDEEKLPELLEALAEIAFGfPPFELKVDGVGLFPSR 80


                  ....*..
gi 446355389   86 DRPRIFW 92
Cdd:pfam02834  81 LRPRVIY 87
2_5_RNA_ligase2 pfam13563
2'-5' RNA ligase superfamily; This family contains proteins related to pfam02834. These ...
 42-164 1.29e-09

2'-5' RNA ligase superfamily; This family contains proteins related to pfam02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity.


Pssm-ID: 433312 [Multi-domain]  Cd Length: 152  Bit Score: 53.97  E-value: 1.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   42 HITLSFLGSAtEEQLEGIKNGL-QTLIEKKELPFTLQGFSTFGMedRPRIFWAKVSENHELFQLQKQVHAICEGNGFSLE 120
Cdd:pfam13563  27 HITLLYPFVP-DELLPELLEALaEVAAETEPFELTLGGFGTFGH--RGGVVYLSVEGSEPLRALHAALREALPPCLLKQD 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446355389  121 TRPYHPHITVARKwmgEKKFHLENIKE-----VPEVSFQADTITLYESH 164
Cdd:pfam13563 104 SGPFTPHLTIAYK---VDDAPAAELLEklqraLPPLEFTVDELALLRRD 149
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 3-158 4.47e-08

AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function.


Pssm-ID: 402204 [Multi-domain]  Cd Length: 207  Bit Score: 50.73  E-value: 4.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389    3 PHYFVAITLPNY-IKEVLSNYKEDMEEELPfrswVHKEDY-------HITLSFLGSATEEQLEGIKNGLQTLIE--KKEL 72
Cdd:pfam10469   1 PTHFLSIPLNSPeLRKRLEEFQESVLKQLP----GLDESLfippeklHITLLVLVLLDDEEVARAKEALRECREeiKDIL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   73 P-----FTLQGFSTFGmeDRP---RIFWAKVSENHELFQLQK---QVHAICEGNGFSLE--TRPYHPHITVArkwmgeKK 139
Cdd:pfam10469  77 NgnplsLRFKGLETFN--DDPsavRVLYAKVEEDDHSPKLQEladRIIRRFQEAGLLVKenNSRVKLHMTLM------NT 148

                         170
                  ....*....|....*....
gi 446355389  140 FHLENIKEVPEVSFQADTI 158
Cdd:pfam10469 149 RYRKKKYAKSKESFDAREI 167
LigT_PEase pfam02834
LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that ...
 100-171 2.18e-07

LigT like Phosphoesterase; Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.


Pssm-ID: 397118 [Multi-domain]  Cd Length: 87  Bit Score: 46.64  E-value: 2.18e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446355389  100 ELFQLQKQVHAICEGNGFSLEtRPYHPHITVARKWMGEKKF------HLENI-KEVPEVSFQADTITLYESHVKETPKY 171
Cdd:pfam02834  10 ELARLRAELERALAKLGFKPV-RPFNPHITLAFLGEVDEEKlpelleALAEIaFGFPPFELKVDGVGLFPSRLRPRVIY 87
PRK13679 PRK13679
hypothetical protein; Provisional
 42-133 2.24e-05

hypothetical protein; Provisional


Pssm-ID: 184236  Cd Length: 168  Bit Score: 42.62  E-value: 2.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389  42 HITLSFLGSATEEQLEGIKNGLQTLIEKKElPFTLQ--GFSTFgmedRP--RIFWAKVSENHELFQLQKQVHaicegNGF 117
Cdd:PRK13679  34 HITLKEPFEISDEQLDSIVEELRAIASETK-PFTLHvtKVSSF----APtnNVIYFKVEKTEELEELHERLH-----SGD 103

                         90
                 ....*....|....*...
gi 446355389 118 SLETRPYH--PHITVARK 133
Cdd:PRK13679 104 FYGEAEYAfvPHITIGQG 121
PRK15124 PRK15124
RNA 2',3'-cyclic phosphodiesterase;
6-132 2.34e-04

RNA 2',3'-cyclic phosphodiesterase;


Pssm-ID: 185079  Cd Length: 176  Bit Score: 40.04  E-value: 2.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446355389   6 FVAITLPNYIKEVLSNYKEDMEEELPFRSwVHKEDYHITLSFLGSATEEQlegiKNGLQTLIEKKELP-FTLQgFSTFGM 84
Cdd:PRK15124   8 FFAIDLPDEIRQQIIHWRATHFPPEAGRP-VAAANLHLTLAFLGEVSAEK----QQALSQLAGRIRQPgFTLT-LDDAGQ 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446355389  85 EDRPRIFWAKVSEN-HELFQLQKQVHAICEGNGFSLETRPYHPHITVAR 132
Cdd:PRK15124  82 WPRSRVVWLGMRQPpRGLLQLANMLRSQAARSGCYQSPQPFHPHITLLR 130
 
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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