D-I-TASSER O95831-D1

D-I-TASSER results for O95831-D1

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

Input Sequence in FASTA format

>O95831 (109 residues)
MFRCGGLAAGALKQKLVPLVRTVCVRSPRQRNRLPGNLFQRWHVPLELQMTRQMASSGAS
GGKIDNSVLVLIVGLSTVGAGAYAYKTMKEDEKRYNERISGLGLTPEQK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MFRCGGLAAGALKQKLVPLVRTVCVRSPRQRNRLPGNLFQRWHVPLELQMTRQMASSGASGGKIDNSVLVLIVGLSTVGAGAYAYKTMKEDEKRYNERISGLGLTPEQK
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCSSSSSSSSSSSSSSSSSSSSSCCCCHHHHHHHHHHHHCCCCCC
Confidence	9611013457899887689999974226665046766566667763333122321479999987636799997113431268898621241367899998873177779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MFRCGGLAAGALKQKLVPLVRTVCVRSPRQRNRLPGNLFQRWHVPLELQMTRQMASSGASGGKIDNSVLVLIVGLSTVGAGAYAYKTMKEDEKRYNERISGLGLTPEQK
Prediction	7341443414312540141044224443454354444215344343634334414444244452432100000322331123201311565553255335514644588
	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 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCSSSSSSSSSSSSSSSSSSSSSCCCCHHHHHHHHHHHHCCCCCC
MFRCGGLAAGALKQKLVPLVRTVCVRSPRQRNRLPGNLFQRWHVPLELQMTRQMASSGASGGKIDNSVLVLIVGLSTVGAGAYAYKTMKEDEKRYNERISGLGLTPEQK

5ctqA

0.07

2.96

1.17

DEthreader

--ALLQAEAPRLAVENCLVPNCPWTVAWYVEIWQLAIMQNWARAYLERAGHCRKLMEGSLEDWDIAVQKTETRLARVNEQRMKAAEKEAALVQQEEEKAEQRKRARAKK

6tntA

0.09

3.48

0.43

CEthreader

KFQESNDKTQLIFGSVTNIPAKDAAPVEKIDTMLVLVLYTGVVRVGKRDPVHNRVTLELSNGSMVRITIPEIATSELVQTCLQAIKFILPKEIAVQMLVKWYNVHSAPG

6fkfp

0.06

2.49

0.52

EigenThreader

FLFLMFALDKIYYTPLGDFMDKRDASIKEQLSGVKDTSSEVKQLEEQANAVMRAARAEISAALNKMKKETQLEVEAKLAEGRKKIEVELQEALGSLEQQKEDTIKSLDS

6b5bA5

0.10

0.09

3.36

0.44

FFAS-3D

---------QATVSSCGQLALTGL---FSSCFEFNSDDLAEAGVDEDEKLTTLLMSKFTAQRLRPVYRFLGPLFQEFLAA-VRLTELLSSDRNSFNIFLYYVSSHSSSK

4kt3B

0.09

0.08

3.18

0.77

SPARKS-K

LQPARIKDSGLTREQAEQVLRVALKHQDYQLQRPGVFIDGDLKPPHPGYYDFSLGYNDPKAGATEYWGLFSVSLNT-----GDTWEINSCDGAELRALQRRVARTGKSL

5m0nA

0.07

0.06

2.60

0.71

CNFpred

----------EARRRVEDWLEEQIIETRKGNIHPPEGTALYEFAHWEDYLGNPMDSRTCA-----IDLMNTFRPLIAINRFVSFGLHAMNENPITREKIKSEPDYAYKF

6djlB

0.06

2.37

1.00

DEthreader

--------FDSAWQEMLNHATQRVMEAEQTKTRSELVHKEAARYNAAMGRMR-E---IN-KSKPYFELKAKYYVQLEQLKKTVDDLQAKLTLAKGEYKMALKNLEMDEE

5u7pA

0.07

2.98

0.58

MapAlign

LRLLDGDASERILQAVRDMLNNKIKKIVLKGKPYDLYVHSYLHFGREASRAEILKVTHGSASPFKASAPTSGANFDKCKKIIQKALNIVPYACMDLIYQYELLVDGFGL

5fvcA1

0.13

4.43

0.58

MUSTER

MLRWGVIARSSNNIMLGHVSVQAELKQVTEVYDLVREMGPE----SGLLHLRQSPKAGLLSLANCPNFASVVLGNASGLGIIGMYRGRVPNTELFSAAESYAKSLKESN

6tgbA1

0.17

5.45

0.42

HHsearch

MCVCAEDGKTICAGDKPMEYRSVPRWMETVKVAVPIEDMQRIHLRFMFRHRSSLESK-DKGEKNFAMSYVKLKEDGTTLHDGFHDLVVKGDSKKMEDASAYLTLPSYRH

(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	0.4035

(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	6g3dA	0.56	4.00	0.037	0.936	model1_6g3dA.pdb.gz
2	3wdoA	0.53	3.76	0.087	0.807	model1_3wdoA.pdb.gz
3	6g9xA	0.52	4.28	0.020	0.853	model1_6g9xA.pdb.gz
4	5eixA	0.51	3.70	0.048	0.734	model1_5eixA.pdb.gz
5	3o7pA	0.51	4.17	0.040	0.817	model1_3o7pA.pdb.gz
6	2inrA	0.51	4.05	0.024	0.761	model1_2inrA.pdb.gz
7	5npkb	0.51	3.77	0.083	0.743	model1_5npkb.pdb.gz
8	2qjpE	0.51	3.85	0.062	0.807	model1_2qjpE.pdb.gz
9	1pquA	0.46	3.98	0.036	0.743	model1_1pquA.pdb.gz
10	1pv6A	0.46	4.42	0.092	0.789	model1_1pv6A.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:0016174	1.00	NAD(P)H oxidase activity
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0009055	0.56	electron carrier activity
GO:0036094	0.55	small molecule binding
GO:0000166	0.54	nucleotide binding
GO:0003676	0.50	nucleic acid 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:0050794	1.00	regulation of cellular process
GO:0009987	0.87	cellular process
GO:0044699	0.86	single-organism process
GO:0044763	0.82	single-organism cellular process
GO:0080090	0.78	regulation of primary metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0048522	0.78	positive regulation of cellular process
GO:0031323	0.78	regulation of cellular metabolic process
GO:0006950	0.78	response to stress
GO:0097193	0.77	intrinsic apoptotic signaling pathway
GO:0045862	0.77	positive regulation of proteolysis
GO:0043085	0.77	positive regulation of catalytic activity
GO:0042981	0.77	regulation of apoptotic process
GO:0034976	0.77	response to endoplasmic reticulum stress
GO:0070059	0.76	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0006919	0.76	activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0016043	0.55	cellular component organization
GO:0008152	0.55	metabolic process
GO:0006996	0.54	organelle organization
GO:0008219	0.53	cell death
GO:0006915	0.52	apoptotic 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:0044429	1.00	mitochondrial part
GO:0043226	0.83	organelle
GO:0043229	0.82	intracellular organelle
GO:0043227	0.82	membrane-bounded organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005829	0.79	cytosol
GO:0070013	0.78	intracellular organelle lumen
GO:0005739	0.78	mitochondrion
GO:0005634	0.78	nucleus
GO:0005758	0.76	mitochondrial intermembrane space
GO:0016020	0.61	membrane
GO:0031090	0.57	organelle membrane
GO:0031966	0.55	mitochondrial membrane

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	1mo7A	0.294	5.14	0.063	0.596	3.6.3.9	49
2	0.060	2jkvA	0.469	4.47	0.031	0.771	1.1.1.44	NA
3	0.060	1dquA	0.450	4.16	0.031	0.734	4.1.3.1	NA
4	0.060	3b8eC	0.444	4.30	0.071	0.752	3.6.3.9	NA
5	0.060	1ta4A	0.446	4.05	0.023	0.743	1.2.1.11	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	2e9x2	0.468	2.84	0.114	0.642	0.41	III	complex1.pdb.gz	2,3,4,23,26,79,82,83,86,89,90,92,93,96,97,100,101,103,104,105,106,108
2	0.01	2j9tA	0.424	3.85	0.022	0.697	0.55	BO3	complex2.pdb.gz	19,20,78,81
3	0.01	2jkvA	0.469	4.47	0.031	0.771	0.59	NAP	complex3.pdb.gz	17,77,81,83
4	0.01	3o01B	0.471	4.43	0.010	0.771	0.43	DXC	complex4.pdb.gz	79,82,86
5	0.01	3o02B	0.475	4.22	0.022	0.771	0.45	JN3	complex5.pdb.gz	80,83,84,87

	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.