D-I-TASSER Q6P2P2-D4

D-I-TASSER results for Q6P2P2-D4

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

Input Sequence in FASTA format

>Q6P2P2 (185 residues)
LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERT
LGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKS
GRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVS
ITVKQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ
Prediction	CCCCCSCCSSSSCHHHHHHHHHHCCCCCSSSSCCSCSSSSSSSCCHHHHHHCCCCCCCCCCCSCHHHHHHHHHCCSSCCCSSCCCCCSSCCCCSSSSSSSCCCCCCCCCCSSSSSSSSCCCSSSSSSSSSSSSSCCCSSSSCCCCCCCCCSSSSSCCCCSSSCCCCSSSSSSSSCCCSSSSSSSC
Confidence	99642547256352578998864159991998672299999975999987503467655455130676666515504452320147447268679999978999764232379999921866899999999995798599169999863209997499547389929999999969658999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ
Prediction	76243314002122020102023104450303123020000000055015434045354110010220352043342341414424243015303013020442535536451404034513000000001030377130212244300200001055515045624030303136330303168
	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                 120                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSCCSSSSCHHHHHHHHHHCCCCCSSSSCCSCSSSSSSSCCHHHHHHCCCCCCCCCCCSCHHHHHHHHHCCSSCCCSSCCCCCSSCCCCSSSSSSSCCCCCCCCCCSSSSSSSSCCCSSSSSSSSSSSSSCCCSSSSCCCCCCCCCSSSSSCCCCSSSCCCCSSSSSSSSCCCSSSSSSSC
LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ

3b3fA

0.16

5.21

1.33

DEthreader

LSEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKNWYQPFDLSRGAAVDEYFRQPV-VDTFD--IRILMAKSVK-YTVNFLEAKDLRIEIPFKFHMLHSGLVHGLAFWFDVAFIGTVWLSTAPPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIASYISIVAQV

6pdmA2

1.00

28.00

2.50

SPARKS-K

LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ

6pdmA

0.22

6.82

1.16

MapAlign

---TVDAGLFGEGIVESLIHAWEHKTKYGKVIPASAVIFGMAVECAEIRRHHRV-GIKDIAGIHLVKFQSPAYIEPYTTEKMSRVGYLALTECFEIMTVDFNLKSLATKPDKIGIPVIKEGILDAIMVWFVLQLDDEHSLSTSPEETCWEQAVYPVQDLYWIKPGDHVMMEVSCQDCYLRIQISV

4c4aA

0.16

5.38

0.77

CEthreader

ITELFDTELIGEGALPSYEHAHKHVQEDCEAVPHRATVYAQLVESRRMWSWNKLFPVRVRTSLGEQVIVRCPGAPSVCDIQLNQVDFTVLSDVLPMFSVDFSKVSSSAACHSRQFVPLASGQAQVVLSWWDIEMDPEIKCTMAPFWAHWMQCVYFLPQEEPVVQGSPRCLVAHHDDYCVWYSLQR

6pdmA2

1.00

28.00

1.85

MUSTER

LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ

6pdmA2

1.00

28.00

2.18

HHsearch

LDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ

6pdmA2

1.00

0.99

27.85

2.04

FFAS-3D

-DVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ

2fytA2

0.17

5.50

1.50

EigenThreader

SEWMGYFLLFESMLDSVLYAKNKYLAKGGSVYPDICTISLVAVSDVNKHADRIAFWDDVY--GFKMSCMKKAVIPEAVVEVL--DPKTLISEPCGIKHIDCTSISDLEFSSDFTLKITRTSMCTAIAGYFDIYFEKNVVFSTGSTKTHWKQTVFLLEKPFSVKAGEALKGKTVHKNSLTVTLLNN

1g6q1

0.17

0.16

5.34

2.99

CNFpred

---WMGYFLLYESMMDTVLYARHYLVEGGLIFPDKCSIHLAGLEDSQYKDEKL-NYWQDVYGFDYSPFVPLVLHEPIVDTVE---RNNVNTTSDKLIEFDLNTVKDLAFKSNFKLTAKRQDMINGIVTWFDIVFPAPVEFSTGPPYTHWKQTIFYFPDDLDAETGDTIEGELVCSPRDLNIKISY

6cu3A

0.15

4.91

1.33

DEthreader

ISEWMGYFLLYESMLQTVLSARRWLRPGGYLFPDKCTMYICGIEDSEYKRDKIDFDNVYGF--NFSAIKADALREPLVD-FVE--SQQIITTQSKFLEIDLNTIQDLQITTSFEFTSQYQEYCQAFVAWFDCVFSRPVEFSTGTEGTHWKQTVFYLENDLPLKPNDVIKGTITISQDLISMKYTV

(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	0.8854

(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	6pdmA2	0.89	2.28	0.902	0.995	model1_6pdmA2.pdb.gz
2	3b3fA	0.86	2.25	0.155	0.978	model1_3b3fA.pdb.gz
3	6cu3A	0.86	2.18	0.149	0.978	model1_6cu3A.pdb.gz
4	2fytA	0.86	2.16	0.193	0.978	model1_2fytA.pdb.gz
5	1orhA	0.85	2.18	0.160	0.978	model1_1orhA.pdb.gz
6	4lwoB2	0.58	2.96	0.145	0.714	model1_4lwoB2.pdb.gz
7	1zpuA	0.32	5.77	0.033	0.584	model1_1zpuA.pdb.gz
8	2xriA	0.31	5.30	0.079	0.524	model1_2xriA.pdb.gz
9	2oxtA	0.28	5.75	0.019	0.481	model1_2oxtA.pdb.gz
10	2zwvA	0.28	5.25	0.097	0.470	model1_2zwvA.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:0008757	1.00	S-adenosylmethionine-dependent methyltransferase activity
GO:0016274	0.98	protein-arginine N-methyltransferase activity
GO:0042054	0.95	histone methyltransferase activity
GO:0008469	0.94	histone-arginine N-methyltransferase activity
GO:0035242	0.92	protein-arginine omega-N asymmetric methyltransferase activity
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0003676	0.58	nucleic acid binding
GO:0035241	0.52	protein-arginine omega-N monomethyltransferase activity

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:0065007	0.97	biological regulation
GO:0050794	0.96	regulation of cellular process
GO:2000112	0.95	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.95	regulation of primary metabolic process
GO:0010468	0.95	regulation of gene expression
GO:0009987	0.94	cellular process
GO:0006355	0.94	regulation of transcription, DNA-templated
GO:0044260	0.90	cellular macromolecule metabolic process
GO:0044238	0.90	primary metabolic process
GO:0019538	0.81	protein metabolic process
GO:0006464	0.80	cellular protein modification process
GO:0006479	0.77	protein methylation
GO:0018195	0.75	peptidyl-arginine modification
GO:0018216	0.74	peptidyl-arginine methylation
GO:0035247	0.67	peptidyl-arginine omega-N-methylation
GO:0034641	0.60	cellular nitrogen compound metabolic process
GO:0090304	0.59	nucleic acid metabolic process
GO:0016070	0.57	RNA metabolic process
GO:0019919	0.56	peptidyl-arginine methylation, to asymmetrical-dimethyl arginine
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:0005829	0.99	cytosol
GO:0043229	0.70	intracellular organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0005634	0.67	nucleus
GO:0032991	0.50	macromolecular 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	0.106	1orhA	0.853	2.18	0.160	0.978	2.1.1.125	NA
2	0.086	1f3lA	0.847	2.26	0.188	0.978	2.1.1.-	NA
3	0.060	1b6sB	0.377	5.52	0.069	0.659	4.1.1.21	NA
4	0.060	1v8bC	0.372	5.34	0.026	0.632	3.3.1.1	156
5	0.060	3fimB	0.394	4.70	0.040	0.622	1.1.3.7	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	0.07	3smqA	0.848	2.22	0.188	0.978	0.37	TDU	complex1.pdb.gz	115,117,122,166,167
2	0.07	2fytA	0.856	2.16	0.193	0.978	0.16	SAH	complex2.pdb.gz	39,82,89,90,91,123
3	0.04	3r0qG	0.832	2.55	0.188	0.978	0.13	SAH	complex3.pdb.gz	43,44,119
4	0.03	2v74B	0.864	2.16	0.155	0.978	0.14	SAH	complex4.pdb.gz	8,9,14,40
5	0.03	2y1wC	0.868	2.10	0.155	0.978	0.12	UUU	complex5.pdb.gz	8,11,13,14,19,22,132,150
6	0.03	3q7eA	0.854	2.18	0.155	0.978	0.13	SAH	complex6.pdb.gz	162,163,164,165
7	0.01	1mnnA	0.406	4.15	0.066	0.605	0.11	QNA	complex7.pdb.gz	39,101,102,133
8	0.01	3bvtA	0.418	5.43	0.069	0.746	0.33	MPD	complex8.pdb.gz	164,165,167
9	0.01	3gdnA	0.425	4.85	0.057	0.686	0.23	MXN	complex9.pdb.gz	17,18,30,34,35

	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.