NCBI Conserved Domain Search

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Conserved domains on [gi\|49258844\|pdb\|1S1I\|F]
Chain F, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h.

Graphical summary show options »	Show site features Horizontal zoom: ×	?



List of domain hits		?

References:

Marchler-Bauer A et al. (2007), "CDD: a conserved domain database for interactive domain family analysis.", Nucleic Acids Res.35(D)237-240.

Marchler-Bauer A et al. (2005), "CDD: a Conserved Domain Database for protein classification.", Nucleic Acids Res.33(D)192-196.

Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.

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of the residues that compose this conserved feature have been mapped to the query sequence.

Click on the triangle to view details about the feature, including a multiple sequence alignment of your query sequence and the protein sequences used to curate the domain model, where hash marks (#) above the aligned sequences show the location of the conserved feature residues.

The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions. Click on the triangle for interactive 3D structure viewing options.

This image shows a graphical summary of conserved domains identified on the query sequence. The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits (labeled illustration) or all hits (labeled illustration).
Domains are color coded according to superfamilies to which they have been assigned. Hits with scores that pass a domain-specific threshold (specific hits) are drawn in bright colors. Others (non-specific hits) and superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features), they are mapped to the query sequence and indicated through sets of triangles with the same color and shade of the domain or superfamily that provides the annotation.
Mouse over the colored bars or triangles to see descriptions of the domains and features. click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.

The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores. Click on the PssmId to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.

To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page, or click on the triangles, if present, that represent functional sites (conserved features) mapped to the query sequence.

Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence. (labeled illustration)
Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance. (labeled illustration)
Four types of hits can be shown, as available, for each region on the query sequence:

specific hits meet or exceed a domain-specific e-value threshold (illustrated example) and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains

The CD-Search help document provides more detail about the tool and its features.

Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool (CDART).

100099

cd01657

Ribosomal_L7_archeal_euk

Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes.

Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes,...

true

false

true

159

1e-62

233.96

100.00

                    10        20        30        40        50        60        70        80
            ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1S1I_F    1 LVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVP 80
cd01657   1 LYAVVRIRGIVGVPPKIRKTLQLLRLRRINNAVFVKLTKATIGMLKKVEPYVTWGEPNLETLRELIYKRGRLKGNGQRIP 80

                    90       100       110       120       130       140       150       160
            ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1S1I_F   81 LSDNAIIEANLgKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGvpRKFKHFIQGGSFGNREEFINKLVKS 160
cd01657  81 LTDNYLVEKTL-KKGIICIEDLAHEIYTGGPNFKEVNNFLPPFRLHPPRGGFK--GKKRHFSEGGELGYRGEDINELIRR 157


            ..
1S1I_F  161 MN 162
cd01657 158 MI 159

cl00203

119616

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea.

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

100098

cd00355

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

false

2e-12

67.05

100.00

                    10        20        30        40        50
            ....*....|....*....|....*....|....*....|....*....|...
1S1I_F    3 FVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYG 55
cd00355   1 KVTRVRSLIGRPPKQRKTLKALGLRKINQTVFVKDTPSIRGMLRKVKHLVTVG 53

cl00203

119616

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

-1

102141

PRK06049

rpl30p

50S ribosomal protein L30P; Reviewed

false

155

6e-16

78.37

96.77

                     10        20        30        40        50        60        70        80
             ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1S1I_F     4 VVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKqrvPLSD 83
PRK06049   5 VIRIRGRVGVRPDIADTLKMLRLHRVNHCVLVPETPSYKGMLQKVKDYVTWGEIDADTLAELLEKRGRLSGNK---KLTD 81

                     90       100       110       120       130       140       150
             ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1S1I_F    84 NAIIEanlgKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKfKHFIQGGSFGNREEFINKLVKSM 161
PRK06049  82 EYVKE----NTGYDSIEELAEALVEGEIKLKDLPGLKPVFRLHPPRGGFKGGIK-RPFKEGGELGYRGEKINELLRRM 154

cl00203

119616

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

-1

109387

pfam00327

Ribosomal_L30

Ribosomal protein L30p/L7e

false

1e-15

77.29

100.00

                      10        20        30        40        50
              ....*....|....*....|....*....|....*....|....*....|..
1S1I_F      1 LVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYV 52
pfam00327   1 LLFVVRVRGVVGIPPKHRKTLRLLRLRRINHGVFVKLTKAVRGMLKLVEPYV 52

cl00203

119616

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

-1

32026

COG1841

RpmD

Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]

false

4e-10

58.97

100.00

                    10        20        30        40        50
            ....*....|....*....|....*....|....*....|....*....|....*
1S1I_F    2 VFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGY 56
COG1841   1 LKVTLIRSPIGRPPKIRKTLRLLGLRKINHTVIVEDTPAVRGMLNKVKHLVTVGE 55

cl00203

119616

Ribosomal_L30_like

Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea,...

-1

23S rRNA binding site	0	41	41	true	100099	cd01657	Ribosomal_L7_archeal_euk
5S rRNA binding site	1	9	9	true	100099	cd01657	Ribosomal_L7_archeal_euk