NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1008852358|gb|KYK35094|]
View 

hypothetical protein AYK22_08805 [Thermoplasmatales archaeon SG8-52-3]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Translation_Factor_II_like super family cl02787
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 18-72 6.47e-04

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


The actual alignment was detected with superfamily member cd01342:

Pssm-ID: 445922 [Multi-domain]  Cd Length: 80  Bit Score: 34.93  E-value: 6.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGatTDFKQKIDSMEINRVPVQSVKPGDDVGIKVKE 72
Cdd:cd01342   17 VAGGRVESGTLKVGDEIRILP--KGITGRVTSIERFHEEVDEAKAGDIVGIGILG 69
 
Name Accession Description Interval E-value
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 18-72 6.47e-04

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


Pssm-ID: 293888 [Multi-domain]  Cd Length: 80  Bit Score: 34.93  E-value: 6.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGatTDFKQKIDSMEINRVPVQSVKPGDDVGIKVKE 72
Cdd:cd01342   17 VAGGRVESGTLKVGDEIRILP--KGITGRVTSIERFHEEVDEAKAGDIVGIGILG 69
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 18-71 1.98e-03

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 33.39  E-value: 1.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGATTDFK---QKIDSMEINRVPVQSVKPGDDVGIKVK 71
Cdd:pfam03144  3 VATGRVESGTLKKGDKVRILPNGTGKKkivTRVTSLLMFHAPLREAVAGDNAGLILA 59
 
Name Accession Description Interval E-value
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 18-72 6.47e-04

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


Pssm-ID: 293888 [Multi-domain]  Cd Length: 80  Bit Score: 34.93  E-value: 6.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGatTDFKQKIDSMEINRVPVQSVKPGDDVGIKVKE 72
Cdd:cd01342   17 VAGGRVESGTLKVGDEIRILP--KGITGRVTSIERFHEEVDEAKAGDIVGIGILG 69
EFTU_II cd03697
Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ...
 18-68 1.34e-03

Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven alpha helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Both non-catalytic domains are composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA; and an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher affinity for GDP than for GTP.


Pssm-ID: 293898 [Multi-domain]  Cd Length: 87  Bit Score: 34.42  E-value: 1.34e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGATTDFKQKIDSMEINRVPVQSVKPGDDVGI 68
Cdd:cd03697   17 VVTGRIERGVIKVGDEVEIVGFKETLKTTVTGIEMFRKTLDEAEAGDNVGV 67
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 18-71 1.98e-03

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 33.39  E-value: 1.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1008852358 18 VAAIKITDGELKVGDTVHFVGATTDFK---QKIDSMEINRVPVQSVKPGDDVGIKVK 71
Cdd:pfam03144  3 VATGRVESGTLKKGDKVRILPNGTGKKkivTRVTSLLMFHAPLREAVAGDNAGLILA 59
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH