D-I-TASSER O75419-D2

D-I-TASSER results for O75419-D2

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

Input Sequence in FASTA format

>O75419 (143 residues)
KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRI
SFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYH
GLELAKKQLRATQQTIASCLCTN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCSSSSSSSSSSSSCCCCCSSHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	97178999999977889999999875204678889999986233000000122345321124541378886255522336899999999955677998899999999984578689999999999999999999999998339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN
Prediction	85322100000212034303531544413522542452144445456546534446444232313102333426340100020202201010356764445101400100337326304500530352043015304311658
	Values range from 0 (buried residue) to 8 (highly exposed residue)

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

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCSSSSSSSSSSSSCCCCCSSHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

0.87

0.86

24.22

1.33

DEthreader

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNRNEDEENT-SVDCTRISFEYVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

1.00

28.00

1.44

SPARKS-K

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

0.99

0.97

27.22

1.24

MapAlign

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCL---

5dgoA

0.99

27.62

1.31

CEthreader

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYDLFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA2

0.66

0.59

16.95

1.08

MUSTER

SVKRLQEFLADMGLPLKQVKQKFQA---ISLKENLREMIEESANKFGMKD-----------MRVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

1.00

28.00

4.41

HHsearch

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEYQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA2

0.66

0.61

17.34

1.27

FFAS-3D

VHGQKRLFLADMGLPLKQVKQKFQAMDISLKENLREMIEESANKFGMK------------DMRVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

0.70

0.69

19.69

1.03

EigenThreader

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNDEENTLSVDCTRISFEYDLRSIHFGFKHKFLASDVVFATMSLMES-PEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

5dgoA

0.99

27.81

1.23

CNFpred

KDLNDMLWWAIVGLTDQWVQDKITQMKYVTDVGVLQRHVSRHNHRNEDEENTLSVDCTRISFEVQTFSIHFGFKHKFLASDVVFATMSLMESPEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTN

3jc5c

0.24

0.22

6.98

1.17

DEthreader

ETNLSNLWLNILGTTSLD-IAYAQ--VYNRLYPLLQDEVKR-LTP-----SSRSTDTTLNIQPIRGFVRTLGYRGSISASEFVEALTALLEVGNLRKRWVSNFWLSWDALDDRKVELLNRGIQLAQDLQRAIFNTGVAILEKK

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7898

(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	5dgoA	0.99	0.43	1.000	1.000	model1_5dgoA.pdb.gz
2	3jc5c	0.81	2.14	0.217	0.909	model1_3jc5c.pdb.gz
3	6rawA	0.78	2.43	0.314	0.930	model1_6rawA.pdb.gz
4	6cc2A	0.75	2.19	0.204	0.874	model1_6cc2A.pdb.gz
5	1xwmA	0.54	3.87	0.060	0.776	model1_1xwmA.pdb.gz
6	5f54A	0.54	3.17	0.083	0.727	model1_5f54A.pdb.gz
7	5ghrA	0.54	3.83	0.079	0.790	model1_5ghrA.pdb.gz
8	3zc0A	0.54	4.03	0.043	0.790	model1_3zc0A.pdb.gz
9	3ripA2	0.54	4.51	0.064	0.846	model1_3ripA2.pdb.gz
10	2i0mA	0.52	3.69	0.059	0.762	model1_2i0mA.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:0003682	1.00	chromatin binding
GO:0043138	0.97	3'-5' DNA helicase activity
GO:0003697	0.97	single-stranded DNA binding
GO:0003688	0.97	DNA replication origin 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:1902977	1.00	mitotic DNA replication preinitiation complex assembly
GO:1900087	1.00	positive regulation of G1/S transition of mitotic cell cycle
GO:0031938	1.00	regulation of chromatin silencing at telomere
GO:0006270	1.00	DNA replication initiation
GO:0006267	1.00	pre-replicative complex assembly involved in nuclear cell cycle DNA replication
GO:0000727	1.00	double-strand break repair via break-induced replication

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:0044428	1.00	nuclear part
GO:0031298	0.97	replication fork protection complex
GO:0031261	0.97	DNA replication preinitiation complex
GO:0005656	0.97	nuclear pre-replicative 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	3g61A	0.484	4.55	0.067	0.776	3.6.3.44	15,77,81
2	0.060	1ia7A	0.485	4.94	0.030	0.804	3.2.1.4	NA
3	0.060	1g87B	0.488	5.01	0.059	0.832	3.2.1.4	NA
4	0.060	1gz7C	0.455	4.74	0.069	0.776	3.1.1.3	NA
5	0.060	1ksdA	0.490	5.04	0.030	0.832	3.2.1.4	77

	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	0.16	3du7B	0.501	4.81	0.077	0.839	0.35	CN2	complex1.pdb.gz	113,117,118,121,122
2	0.14	3ryhB	0.509	4.73	0.069	0.846	0.13	G2P	complex2.pdb.gz	58,69,70,71,72,83,123
3	0.13	3hkdB	0.500	4.66	0.078	0.825	0.12	N16	complex3.pdb.gz	115,118,122
4	0.01	1z2bB	0.511	4.56	0.053	0.825	0.16	CN2	complex4.pdb.gz	77,78,84,85
5	0.01	3hkbB	0.508	4.71	0.053	0.832	0.19	GDP	complex5.pdb.gz	70,72,79,82,110
6	0.01	3e22B	0.510	4.68	0.069	0.832	0.21	TZT	complex6.pdb.gz	101,117,118
7	0.01	1sa0D	0.509	4.62	0.046	0.825	0.24	CN2	complex7.pdb.gz	75,81,82,120
8	0.01	2btqA	0.495	4.53	0.055	0.804	0.19	GDP	complex8.pdb.gz	83,109,118,122,125
9	0.01	1ffxD	0.501	4.80	0.093	0.832	0.15	GDP	complex9.pdb.gz	121,122,125
10	0.01	3hkcB	0.509	4.62	0.054	0.825	0.13	GDP	complex10.pdb.gz	70,72,73,74,120

	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.