D-I-TASSER Q9BXT4

D-I-TASSER results for Q9BXT4

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: Q9BXT4
Protein Name: Tudor domain-containing protein 1
Gene Name: TDRD1

Input Sequence in FASTA format

>Q9BXT4 (1180 residues)
MSVKSPFNVMSRNNLEAPPCKMTEPFNFEKNENKLPPHESLRSPGTLPNHPNFRLKSSEN
GNKKNNFLLCEQTKQYLASQEDNSVSSNPNGINGEVVGSKGDRKKLPAGNSVSPPSAESN
SPPKEVNIKPGNNVRPAKSKKLNKLVENSLSISNPGLFTSLGPPLRSTTCHRCGLFGSLR
CSQCKQTYYCSTACQRRDWSAHSIVCRPVQPNFHKLENKSSIETKDVEVNNKSDCPLGVT
KEIAIWAERIMFSDLRSLQLKKTMEIKGTVTEFKHPGDFYVQLYSSEVLEYMNQLSASLK
ETYANVHEKDYIPVKGEVCIAKYTVDQTWNRAIIQNVDVQQKKAHVLYIDYGNEEIIPLN
RIYHLNRNIDLFPPCAIKCFVANVIPAEGNWSSDCIKATKPLLMEQYCSIKIVDILEEEV
VTFAVEVELPNSGKLLDHVLIEMGYGLKPSGQDSKKENADQSDPEDVGKMTTENNIVVDK
SDLIPKVLTLNVGDEFCGVVAHIQTPEDFFCQQLQSGRKLAELQASLSKYCDQLPPRSDF
YPAIGDICCAQFSEDDQWYRASVLAYASEESVLVGYVDYGNFEILSLMRLCPIIPKLLEL
PMQAIKCVLAGVKPSLGIWTPEAICLMKKLVQNKIITVKVVDKLENSSLVELIDKSETPH
VSVSKVLLDAGFAVGEQSMVTDKPSDVKETSVPLGVEGKVNPLEWTWVELGVDQTVDVVV
CVIYSPGEFYCHVLKEDALKKLNDLNKSLAEHCQQKLPNGFKAEIGQPCCAFFAGDGSWY
RALVKEILPNGHVKVHFVDYGNIEEVTADELRMISSTFLNLPFQGIRCQLADIQSRNKHW
SEEAITRFQMCVAGIKLQARVVEVTENGIGVELTDLSTCYPRIISDVLIDEHLVLKSASP
HKDLPNDRLVNKHELQVHVQGLQATSSAEQWKTIELPVDKTIQANVLEIISPNLFYALPK
GMPENQEKLCMLTAELLEYCNAPKSRPPYRPRIGDACCAKYTSDDFWYRAVVLGTSDTDV
EVLYADYGNIETLPLCRVQPITSSHLALPFQIIRCSLEGLMELNGSSSQLIIMLLKNFML
NQNVMLSVKGITKNVHTVSVEKCSENGTVDVADKLVTFGLAKNITPQRQSALNTEKMYRM
NCCCTELQKQVEKHEHILLFLLNNSTNQNKFIEMKKLLKS

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	Q9BXT4-D1	1-84,114-146,447-508,607-700,901-1124	497		MSVKSPFNVMSRNNLEAPPCKMTEPFNFEKNENKLPPHESLRSPGTLPNHPNFRLKSSENGNKKNNFLLCEQTKQYLASQEDNSPPSAESNSPPKEVNIKPGNNVRPAKSKKLNKLVLKPSGQDSKKENADQSDPEDVGKMTTENNIVVDKSDLIPKVLTLNVGDEFCGVVAHIQTPEDCVLAGVKPSLGIWTPEAICLMKKLVQNKIITVKVVDKLENSSLVELIDKSETPHVSVSKVLLDAGFAVGEQSMVTDKPSDVKETSVPLGVEGKVHKDLPNDRLVNKHELQVHVQGLQATSSAEQWKTIELPVDKTIQANVLEIISPNLFYALPKGMPENQEKLCMLTAELLEYCNAPKSRPPYRPRIGDACCAKYTSDDFWYRAVVLGTSDTDVEVLYADYGNIETLPLCRVQPITSSHLALPFQIIRCSLEGLMELNGSSSQLIIMLLKNFMLNQNVMLSVKGITKNVHTVSVEKCSENGTVDVADKLVTFGLAKNI
2	Q9BXT4-D2	85-113,701-746,823-900	153		VSSNPNGINGEVVGSKGDRKKLPAGNSVSNPLEWTWVELGVDQTVDVVVCVIYSPGEFYCHVLKEDALKKLNDLNFQGIRCQLADIQSRNKHWSEEAITRFQMCVAGIKLQARVVEVTENGIGVELTDLSTCYPRIISDVLIDEHLVLKSASP
3	Q9BXT4-D3	147-291,373-446,1125-1180	275		ENSLSISNPGLFTSLGPPLRSTTCHRCGLFGSLRCSQCKQTYYCSTACQRRDWSAHSIVCRPVQPNFHKLENKSSIETKDVEVNNKSDCPLGVTKEIAIWAERIMFSDLRSLQLKKTMEIKGTVTEFKHPGDFYVQLYSSEVLEYPPCAIKCFVANVIPAEGNWSSDCIKATKPLLMEQYCSIKIVDILEEEVVTFAVEVELPNSGKLLDHVLIEMGYGTPQRQSALNTEKMYRMNCCCTELQKQVEKHEHILLFLLNNSTNQNKFIEMKKLLKS
4	Q9BXT4-D4	292-372	81		MNQLSASLKETYANVHEKDYIPVKGEVCIAKYTVDQTWNRAIIQNVDVQQKKAHVLYIDYGNEEIIPLNRIYHLNRNIDLF
5	Q9BXT4-D5	509-606	98		FFCQQLQSGRKLAELQASLSKYCDQLPPRSDFYPAIGDICCAQFSEDDQWYRASVLAYASEESVLVGYVDYGNFEILSLMRLCPIIPKLLELPMQAIK
6	Q9BXT4-D6	747-822	76		KSLAEHCQQKLPNGFKAEIGQPCCAFFAGDGSWYRALVKEILPNGHVKVHFVDYGNIEEVTADELRMISSTFLNLP

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.46

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3bdlA	0.34	3.51	0.149	0.360	model1_3bdlA.pdb.gz
2	5amqA	0.27	9.67	0.020	0.421	model1_5amqA.pdb.gz
3	3cmuA	0.27	9.39	0.034	0.412	model1_3cmuA.pdb.gz
4	6eqoA	0.27	9.31	0.050	0.405	model1_6eqoA.pdb.gz
5	4bgdA	0.26	9.48	0.029	0.414	model1_4bgdA.pdb.gz
6	6fb3A	0.26	9.78	0.042	0.418	model1_6fb3A.pdb.gz
7	6um1A	0.26	9.79	0.041	0.419	model1_6um1A.pdb.gz
8	6u5vB	0.26	9.85	0.052	0.415	model1_6u5vB.pdb.gz
9	7alpU	0.26	9.67	0.028	0.406	model1_7alpU.pdb.gz
10	2uvcG	0.25	9.95	0.048	0.409	model1_2uvcG.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0003676	0.61	nucleic acid binding
GO:0003723	0.57	RNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.96	cellular process
GO:0044699	0.89	single-organism process
GO:0044763	0.79	single-organism cellular process
GO:0065007	0.78	biological regulation
GO:0050789	0.76	regulation of biological process
GO:0022414	0.76	reproductive process
GO:0044702	0.74	single organism reproductive process
GO:0008152	0.72	metabolic process
GO:0044767	0.71	single-organism developmental process
GO:0071704	0.70	organic substance metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044238	0.69	primary metabolic process
GO:0044260	0.67	cellular macromolecule metabolic process
GO:0048869	0.65	cellular developmental process
GO:0019222	0.65	regulation of metabolic process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0010468	0.63	regulation of gene expression
GO:0034641	0.61	cellular nitrogen compound metabolic process
GO:0090304	0.60	nucleic acid metabolic process
GO:0007276	0.60	gamete generation
GO:0007283	0.59	spermatogenesis
GO:0016070	0.55	RNA metabolic process
GO:0048856	0.54	anatomical structure development
GO:0048519	0.50	negative regulation of biological process
GO:0022412	0.50	cellular process involved in reproduction in multicellular organism

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0043226	0.97	organelle
GO:0043229	0.96	intracellular organelle
GO:0032991	0.87	macromolecular complex
GO:0044444	0.85	cytoplasmic part
GO:0043232	0.85	intracellular non-membrane-bounded organelle
GO:0030529	0.85	intracellular ribonucleoprotein complex
GO:0035770	0.82	ribonucleoprotein granule
GO:0036464	0.68	cytoplasmic ribonucleoprotein granule
GO:0043186	0.63	P granule
GO:0043227	0.50	membrane-bounded organelle

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2e1qA	0.230	10.07	0.025	0.376	1.17.3.2 1.17.1.4	NA
2	0.060	1hn0A	0.235	9.25	0.039	0.361	4.2.2.20	NA
3	0.060	1dmtA	0.228	7.91	0.039	0.320	3.4.24.11	NA
4	0.060	1b0pA	0.238	9.72	0.046	0.380	1.2.7.1	NA
5	0.060	1l9mB	0.225	8.06	0.047	0.320	2.3.2.13	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.06	3cmvC	0.254	9.56	0.046	0.395	0.33	ANP	complex1.pdb.gz	315,316,317,318,319,717
2	0.01	3q24B	0.244	9.26	0.039	0.374	0.17	POP	complex2.pdb.gz	316,334,335
3	0.01	3cmvH	0.253	9.58	0.049	0.394	0.31	ANP	complex3.pdb.gz	315,316,317,318,319,717
4	0.01	3cmxD	0.265	9.33	0.039	0.408	0.19	ALF	complex4.pdb.gz	228,276,317
5	0.01	2uvaG	0.253	9.81	0.035	0.401	0.13	FMN	complex5.pdb.gz	202,203,334,335
6	0.01	3q22B	0.245	9.30	0.039	0.377	0.12	GTP	complex6.pdb.gz	316,348,349
7	0.01	3cmvE	0.251	9.45	0.034	0.387	0.18	ANP	complex7.pdb.gz	318,319,320,321
8	0.01	3cmvB	0.243	9.43	0.038	0.375	0.16	ANP	complex8.pdb.gz	315,316,317,318,319,351
9	0.01	2vu9A	0.139	7.60	0.039	0.193	0.22	UUU	complex9.pdb.gz	319,321,353,717

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.