D-I-TASSER O94880

D-I-TASSER results for O94880

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

Summary of the Protein

Uniprot ID: O94880
Protein Name: PHD finger protein 14
Gene Name: PHF14

Input Sequence in FASTA format

>O94880 (888 residues)
MDRSSKRRQVKPLAASLLEALDYDSSDDSDFKVGDASDSEGSGNGSEDASKDSGEGSCSD
SEENILEEELNEDIKVKEEQLKNSAEEEVLSSEKQLIKMEKKEEEENGERPRKKKEKEKE
KEKEKEKEKEREKEKEKATVSENVAASAAATTPATSPPAVNTSPSVPTTTTATEEQVSEP
KKWNLRRNRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVKRKGRSASQKEGSDGDNEDDE
DEGSGSDEDENDEGNDEDHSSPASEGGCKKKKSKVLSRNSADDEELTNDSLTLSQSKSNE
DSLILEKSQNWSSQKMDHILICCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSI
MSSASENSTEPWFCDACKCGVSPSCELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDI
DKLRPVTLTEMNYSKYGAKECSFCEDPRFARTGVCISCDAGMCRAYFHVTCAQKEGLLSE
AAAEEDIADPFFAYCKQHADRLDRKWKRKNYLALQSYCKMSLQEREKQLSPEAQARINAR
LQQYRAKAELARSTRPQAWVPREKLPRPLTSSASAIRKLMRKAELMGISTDIFPVDNSDT
SSSVDGRRKHKQPALTADFVNYYFERNMRMIQIQENMAEQKNIKDKLENEQEKLHVEYNK
LCESLEELQNLNGKLRSEGQGIWALLGRITGQKLNIPAILRAPKERKPSKKEGGTQKTST
LPAVLYSCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNSYWQCSECDQAG
SSDMEADMAMETLPDGTKRSRRQIKEPVKFVPQDVPPEPKKIPIRNTRTRGRKRSFVPEE
EKHEERVPRERRQRQSVLQKKPKAEDLRTECATCKGTGDNENLVRYPS

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 DeepPotential. 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	O94880-D1	1-888	888		MDRSSKRRQVKPLAASLLEALDYDSSDDSDFKVGDASDSEGSGNGSEDASKDSGEGSCSDSEENILEEELNEDIKVKEEQLKNSAEEEVLSSEKQLIKMEKKEEEENGERPRKKKEKEKEKEKEKEKEKEREKEKEKATVSENVAASAAATTPATSPPAVNTSPSVPTTTTATEEQVSEPKKWNLRRNRPLLDFVSMEELNDMDDYDSEDDNDWRPTVVKRKGRSASQKEGSDGDNEDDEDEGSGSDEDENDEGNDEDHSSPASEGGCKKKKSKVLSRNSADDEELTNDSLTLSQSKSNEDSLILEKSQNWSSQKMDHILICCVCLGDNSEDADEIIQCDNCGITVHEGCYGVDGESDSIMSSASENSTEPWFCDACKCGVSPSCELCPNQDGIFKETDAGRWVHIVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSFCEDPRFARTGVCISCDAGMCRAYFHVTCAQKEGLLSEAAAEEDIADPFFAYCKQHADRLDRKWKRKNYLALQSYCKMSLQEREKQLSPEAQARINARLQQYRAKAELARSTRPQAWVPREKLPRPLTSSASAIRKLMRKAELMGISTDIFPVDNSDTSSSVDGRRKHKQPALTADFVNYYFERNMRMIQIQENMAEQKNIKDKLENEQEKLHVEYNKLCESLEELQNLNGKLRSEGQGIWALLGRITGQKLNIPAILRAPKERKPSKKEGGTQKTSTLPAVLYSCGICKKNHDQHLLLLCDTCKLHYHLGCLDPPLTRMPRKTKNSYWQCSECDQAGSSDMEADMAMETLPDGTKRSRRQIKEPVKFVPQDVPPEPKKIPIRNTRTRGRKRSFVPEEEKHEERVPRERRQRQSVLQKKPKAEDLRTECATCKGTGDNENLVRYPS

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4588

(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 DeepPotential, 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	6yvuB	0.86	2.10	0.094	0.888	model1_6yvuB.pdb.gz
2	4rsiB	0.36	3.23	0.092	0.391	model1_4rsiB.pdb.gz
3	6z9lA	0.34	6.05	0.049	0.428	model1_6z9lA.pdb.gz
4	6yvuA	0.29	6.26	0.047	0.380	model1_6yvuA.pdb.gz
5	5xjyA	0.26	6.67	0.048	0.340	model1_5xjyA.pdb.gz
6	6ogdB	0.24	7.24	0.045	0.329	model1_6ogdB.pdb.gz
7	6rw8A	0.24	9.31	0.037	0.396	model1_6rw8A.pdb.gz
8	6rw9A	0.24	7.41	0.045	0.330	model1_6rw9A.pdb.gz
9	2ch7A	0.24	5.15	0.070	0.285	model1_2ch7A.pdb.gz
10	5nnvA	0.24	2.54	0.058	0.248	model1_5nnvA.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	0.52	heterocyclic compound binding
GO:0097159	0.52	organic cyclic compound 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	0.86	cellular process
GO:0065007	0.81	biological regulation
GO:0050794	0.80	regulation of cellular process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0010468	0.68	regulation of gene expression
GO:0008152	0.68	metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0044260	0.67	cellular macromolecule metabolic process
GO:0044238	0.67	primary metabolic process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0051252	0.66	regulation of RNA metabolic process
GO:0006355	0.65	regulation of transcription, DNA-templated
GO:0044699	0.59	single-organism process
GO:0016043	0.51	cellular component organization

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	0.80	intracellular organelle part
GO:0043226	0.80	organelle
GO:0043229	0.78	intracellular organelle
GO:0044428	0.75	nuclear part
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0032991	0.72	macromolecular complex
GO:0005634	0.72	nucleus
GO:0043234	0.55	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	2vumA	0.150	8.57	0.025	0.233	2.7.7.6	301,320
2	0.060	2vz9B	0.204	8.58	0.026	0.318	2.3.1.85	NA
3	0.060	1rw9A	0.166	7.95	0.025	0.249	4.2.2.5	NA
4	0.060	1b0pA	0.175	8.51	0.026	0.271	1.2.7.1	NA
5	0.060	3gtgB	0.166	8.75	0.023	0.260	2.7.7.6	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	2xzhA	0.122	7.06	0.025	0.170	0.33	VH2	complex1.pdb.gz	325,339,396
2	0.01	2xo8A	0.151	7.74	0.030	0.221	0.20	H70	complex2.pdb.gz	340,343,344
3	0.01	3bz9A	0.133	8.20	0.024	0.201	0.15	BL7	complex3.pdb.gz	324,344,345
4	0.01	2w6dB	0.194	6.11	0.044	0.247	0.15	CPL	complex4.pdb.gz	335,338,343,352
5	0.01	2aka0	0.154	8.13	0.046	0.232	0.23	III	complex5.pdb.gz	341,342,343,344,345,346,400,407
6	0.01	2jhrA	0.150	7.74	0.033	0.220	0.13	AD9	complex6.pdb.gz	343,351,375,384
7	0.01	3kllA	0.184	7.33	0.062	0.262	0.32	MAL	complex7.pdb.gz	337,338,408
8	0.01	1mneA	0.152	7.46	0.030	0.215	0.23	POP	complex8.pdb.gz	342,345,388
9	0.01	2dw4A	0.165	5.95	0.059	0.208	0.10	FAD	complex9.pdb.gz	342,352,356,357,358,359,360
10	0.01	1w9kA	0.140	8.30	0.020	0.214	0.13	UUU	complex10.pdb.gz	293,297,298

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.