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Conserved domains on  [gi|446838985|ref|WP_000916241|]
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MULTISPECIES: RtcB family protein [Bacillus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RtcB super family cl40686
tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate ...
 40-71 9.81e-05

tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyze the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage.


The actual alignment was detected with superfamily member pfam01139:

Pssm-ID: 460080 [Multi-domain]  Cd Length: 416  Bit Score: 38.26  E-value: 9.81e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446838985   40 IRIMPDTHAGAGCTIGTTM-TIQDKIVPNLVGV 71
Cdd:pfam01139  15 VAAMPDVHWGYGFPIGGVAaTDEGVISPGGVGV 47
 
Name Accession Description Interval E-value
RtcB pfam01139
tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate ...
 40-71 9.81e-05

tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyze the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage.


Pssm-ID: 460080 [Multi-domain]  Cd Length: 416  Bit Score: 38.26  E-value: 9.81e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446838985   40 IRIMPDTHAGAGCTIGTTM-TIQDKIVPNLVGV 71
Cdd:pfam01139  15 VAAMPDVHWGYGFPIGGVAaTDEGVISPGGVGV 47
PRK09588 PRK09588
hypothetical protein; Reviewed
 43-70 3.71e-03

hypothetical protein; Reviewed


Pssm-ID: 181972  Cd Length: 376  Bit Score: 33.79  E-value: 3.71e-03
                         10        20
                 ....*....|....*....|....*...
gi 446838985  43 MPDTHAGAGCTIGTTMTIQDKIVPNLVG 70
Cdd:PRK09588  45 MPDLHPGRGYPIGAAFFSVGRFYPALVG 72
 
Name Accession Description Interval E-value
RtcB pfam01139
tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate ...
 40-71 9.81e-05

tRNA-splicing ligase RtcB; This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyze the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage.


Pssm-ID: 460080 [Multi-domain]  Cd Length: 416  Bit Score: 38.26  E-value: 9.81e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446838985   40 IRIMPDTHAGAGCTIGTTM-TIQDKIVPNLVGV 71
Cdd:pfam01139  15 VAAMPDVHWGYGFPIGGVAaTDEGVISPGGVGV 47
PRK09588 PRK09588
hypothetical protein; Reviewed
 43-70 3.71e-03

hypothetical protein; Reviewed


Pssm-ID: 181972  Cd Length: 376  Bit Score: 33.79  E-value: 3.71e-03
                         10        20
                 ....*....|....*....|....*...
gi 446838985  43 MPDTHAGAGCTIGTTMTIQDKIVPNLVG 70
Cdd:PRK09588  45 MPDLHPGRGYPIGAAFFSVGRFYPALVG 72
 
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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