D-I-TASSER Q9UNY4

D-I-TASSER results for Q9UNY4

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

Summary of the Protein

Uniprot ID: Q9UNY4
Protein Name: Transcription termination factor 2
Gene Name: TTF2

Input Sequence in FASTA format

>Q9UNY4 (1162 residues)
MEEVRCPEHGTFCFLKTGVRDGPNKGKSFYVCRADTCSFVRATDIPVSHCLLHEDFVVEL
QGLLLPQDKKEYRLFFRCIRSKAEGKRWCGSIPWQDPDSKEHSVSNKSQHASETFHHSSN
WLRNPFKVLDKNQEPALWKQLIKGEGEEKKADKKQREKGDQLFDQKKEQKPEMMEKDLSS
GLVPKKKQSVVQEKKQEEGAEIQCEAETGGTHKRDFSEIKSQQCQGNELTRPSASSQEKS
SGKSQDVQRESEPLREKVTQLLPQNVHSHNSISKPQKGGPLNKEYTNWEAKETKAKDGPS
IQATQKSLPQGHFQERPETHSVPAPGGPAAQAAPAAPGLSLGEGREAATSSDDEEEDDVV
FVSSKPGSPLLFDSTLDLETKENLQFPDRSVQRKVSPASGVSKKVEPSDPVARRVYLTTQ
LKQKKSTLASVNIQALPDKGQKLIKQIQELEEVLSGLTLSPEQGTNEKSNSQVPQQSHFT
KTTTGPPHLVPPQPLPRRGTQPVGSLELKSACQVTAGGSSQCYRGHTNQDHVHAVWKITS
EAIGQLHRSLESCPGETVVAEDPAGLKVPLLLHQKQALAWLLWRESQKPQGGILADDMGL
GKTLTMIALILTQKNQEKKEEKEKSTALTWLSKDDSCDFTSHGTLIICPASLIHHWKNEV
EKRVNSNKLRVYLYHGPNRDSRARVLSTYDIVITTYSLVAKEIPTNKQEAEIPGANLNVE
GTSTPLLRIAWARIILDEAHNVKNPRVQTSIAVCKLQACARWAVTGTPIQNNLLDMYSLL
KFLRCSPFDEFNLWRSQVDNGSKKGGERLSILTKSLLLRRTKDQLDSTGRPLVILPQRKF
QLHHLKLSEDEETVYNVFFARSRSALQSYLKRHESRGNQSGRSPNNPFSRVALEFGSEEP
RHSEAADSPRSSTVHILSQLLRLRQCCCHLSLLKSALDPMELKGEGLVLSLEEQLSALTL
SELRDSEPSSTVSLNGTFFKMELFEGMRESTKISSLLAELEAIQRNSASQKSVIVSQWTN
MLKVVALHLKKHGLTYATIDGSVNPKQRMDLVEAFNHSRGPQVMLISLLAGGVGLNLTGG
NHLFLLDMHWNPSLEDQACDRIYRVGQQKDVVIHRFVCEGTVEEKILQLQEKKKDLAKQV
LSGSGESVTKLTLADLRVLFGI

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	Q9UNY4-D1	1-253,984-1162	432		MEEVRCPEHGTFCFLKTGVRDGPNKGKSFYVCRADTCSFVRATDIPVSHCLLHEDFVVELQGLLLPQDKKEYRLFFRCIRSKAEGKRWCGSIPWQDPDSKEHSVSNKSQHASETFHHSSNWLRNPFKVLDKNQEPALWKQLIKGEGEEKKADKKQREKGDQLFDQKKEQKPEMMEKDLSSGLVPKKKQSVVQEKKQEEGAEIQCEAETGGTHKRDFSEIKSQQCQGNELTRPSASSQEKSSGKSQDVQRESEPFEGMRESTKISSLLAELEAIQRNSASQKSVIVSQWTNMLKVVALHLKKHGLTYATIDGSVNPKQRMDLVEAFNHSRGPQVMLISLLAGGVGLNLTGGNHLFLLDMHWNPSLEDQACDRIYRVGQQKDVVIHRFVCEGTVEEKILQLQEKKKDLAKQVLSGSGESVTKLTLADLRVLFGI
2	Q9UNY4-D2	254-332,550-592	122		LREKVTQLLPQNVHSHNSISKPQKGGPLNKEYTNWEAKETKAKDGPSIQATQKSLPQGHFQERPETHSVPAPGGPAAQALESCPGETVVAEDPAGLKVPLLLHQKQALAWLLWRESQKPQGG
3	Q9UNY4-D3	333-403,522-549	99		APAAPGLSLGEGREAATSSDDEEEDDVVFVSSKPGSPLLFDSTLDLETKENLQFPDRSVQRKVSPASGVSKCYRGHTNQDHVHAVWKITSEAIGQLHRS
4	Q9UNY4-D4	404-457,502-521	74		KVEPSDPVARRVYLTTQLKQKKSTLASVNIQALPDKGQKLIKQIQELEEVLSGLPVGSLELKSACQVTAGGSSQ
5	Q9UNY4-D5	458-501	44		TLSPEQGTNEKSNSQVPQQSHFTKTTTGPPHLVPPQPLPRRGTQ
6	Q9UNY4-D6	593-841	249		ILADDMGLGKTLTMIALILTQKNQEKKEEKEKSTALTWLSKDDSCDFTSHGTLIICPASLIHHWKNEVEKRVNSNKLRVYLYHGPNRDSRARVLSTYDIVITTYSLVAKEIPTNKQEAEIPGANLNVEGTSTPLLRIAWARIILDEAHNVKNPRVQTSIAVCKLQACARWAVTGTPIQNNLLDMYSLLKFLRCSPFDEFNLWRSQVDNGSKKGGERLSILTKSLLLRRTKDQLDSTGRPLVILPQRKFQ
7	Q9UNY4-D7	842-983	142		LHHLKLSEDEETVYNVFFARSRSALQSYLKRHESRGNQSGRSPNNPFSRVALEFGSEEPRHSEAADSPRSSTVHILSQLLRLRQCCCHLSLLKSALDPMELKGEGLVLSLEEQLSALTLSELRDSEPSSTVSLNGTFFKMEL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.44

(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	1z3iX	0.33	4.16	0.194	0.367	model1_1z3iX.pdb.gz
2	5h3zA	0.29	9.34	0.049	0.445	model1_5h3zA.pdb.gz
3	6ryrW	0.28	5.42	0.172	0.329	model1_6ryrW.pdb.gz
4	2vdcA	0.28	9.58	0.037	0.438	model1_2vdcA.pdb.gz
5	6tdaS	0.28	5.63	0.161	0.330	model1_6tdaS.pdb.gz
6	6fmlG	0.28	5.24	0.091	0.320	model1_6fmlG.pdb.gz
7	6g7eB	0.28	7.03	0.126	0.348	model1_6g7eB.pdb.gz
8	6kw5Q	0.28	5.38	0.156	0.325	model1_6kw5Q.pdb.gz
9	6vz4K	0.28	5.35	0.153	0.324	model1_6vz4K.pdb.gz
10	6ne3W	0.28	5.04	0.167	0.318	model1_6ne3W.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:0003824	0.76	catalytic activity
GO:0016787	0.71	hydrolase activity
GO:0017111	0.69	nucleoside-triphosphatase activity
GO:1901363	0.68	heterocyclic compound binding
GO:0097159	0.68	organic cyclic compound binding
GO:0016887	0.60	ATPase activity
GO:0003676	0.52	nucleic acid binding
GO:0042623	0.50	ATPase activity, coupled

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	0.89	cellular process
GO:0065007	0.70	biological regulation
GO:0050789	0.67	regulation of biological process
GO:0071704	0.65	organic substance metabolic process
GO:0050794	0.64	regulation of cellular process
GO:0044238	0.64	primary metabolic process
GO:0044237	0.64	cellular metabolic process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:0019222	0.60	regulation of metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0080090	0.57	regulation of primary metabolic process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0019219	0.55	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.55	regulation of gene expression
GO:0090304	0.54	nucleic acid metabolic process
GO:0051252	0.52	regulation of RNA metabolic process
GO:0044699	0.51	single-organism process

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:0044446	0.77	intracellular organelle part
GO:0043226	0.74	organelle
GO:0043229	0.73	intracellular organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0044428	0.66	nuclear part
GO:0005634	0.64	nucleus
GO:0032991	0.57	macromolecular complex
GO:0043234	0.50	protein complex

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	1h0hA	0.239	9.02	0.019	0.362	1.2.1.2	NA
2	0.060	3b9jJ	0.150	6.31	0.053	0.191	1.17.1.4 1.17.3.2	975
3	0.060	1llwA	0.256	10.36	0.048	0.427	1.4.7.1	869
4	0.060	2nyaA	0.240	8.88	0.031	0.361	1.7.99.4	NA
5	0.060	1ea0A	0.280	9.64	0.039	0.442	1.4.1.13	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	0.01	3cmvH	0.204	9.90	0.032	0.330	0.12	ANP	complex1.pdb.gz	564,568,569
2	0.01	1tllA	0.259	7.35	0.028	0.350	0.14	NAP	complex2.pdb.gz	335,336,563,564,578,966,967
3	0.01	3cmvG	0.205	9.42	0.027	0.318	0.11	ANP	complex3.pdb.gz	336,337,582
4	0.01	1ea0A	0.280	9.64	0.039	0.442	0.17	FMN	complex4.pdb.gz	348,561,569,1073
5	0.01	1tllA	0.259	7.35	0.028	0.350	0.16	FMN	complex5.pdb.gz	36,37,581,582,583
6	0.01	3cmxA	0.242	9.74	0.040	0.388	0.21	ALF	complex6.pdb.gz	346,519,1124
7	0.01	1tllB	0.256	7.34	0.046	0.344	0.17	NAP	complex7.pdb.gz	548,600,819
8	0.01	3cmxD	0.246	9.89	0.039	0.401	0.21	ALF	complex8.pdb.gz	346,578,1118
9	0.01	3cmvA	0.212	9.40	0.040	0.329	0.27	ANP	complex9.pdb.gz	574,575,578,579
10	0.01	3cmvD	0.215	8.31	0.060	0.308	0.24	ANP	complex10.pdb.gz	343,344,345,346,347,559

	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.