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Conserved domains on  [gi|1958767101|ref|XP_038962685|]
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protein LSM14 homolog B isoform X6 [Rattus norvegicus]

Protein Classification

LSM14 family protein( domain architecture ID 10560089)

LSM14 family protein having an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, may be involved in essential RNA-processing tasks

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FDF super family cl09757
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 116-218 1.14e-21

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


The actual alignment was detected with superfamily member pfam09532:

Pssm-ID: 430668  Cd Length: 104  Bit Score: 86.35  E-value: 1.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958767101 116 IKFEGDFDFESANAQFNREELDKEFKKKLNFKDDKAEKGDEKDPAVmaqseetPPEEDLLGPNCYYDKSKSFFDNISSEL 195
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNENNATRV-------ATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958767101 196 KTSSRRT-------TWAEERKLNTETFGVS 218
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
 
Name Accession Description Interval E-value
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 116-218 1.14e-21

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 86.35  E-value: 1.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958767101 116 IKFEGDFDFESANAQFNREELDKEFKKKLNFKDDKAEKGDEKDPAVmaqseetPPEEDLLGPNCYYDKSKSFFDNISSEL 195
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNENNATRV-------ATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958767101 196 KTSSRRT-------TWAEERKLNTETFGVS 218
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
 
Name Accession Description Interval E-value
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 116-218 1.14e-21

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 86.35  E-value: 1.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958767101 116 IKFEGDFDFESANAQFNREELDKEFKKKLNFKDDKAEKGDEKDPAVmaqseetPPEEDLLGPNCYYDKSKSFFDNISSEL 195
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNENNATRV-------ATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958767101 196 KTSSRRT-------TWAEERKLNTETFGVS 218
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
 
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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