D-I-TASSER Q9H7Y0-D3

D-I-TASSER results for Q9H7Y0-D3

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

Input Sequence in FASTA format

>Q9H7Y0 (184 residues)
TRPLQEFYDAPPDQAADLAYQLLGVLESLRSNDLNYFFYFTHIDAGMFGVFNNGHLFIRD
ASAVGVIDKQEGSQEANRAGENKDIFSCLVSGCQAQLPSCESISEKQSLVLVCQKLLPRL
LQGRFPSPVQDDIDSILVQCGDSIRPDPEVLGAASQLKDILRPLRTCDSRFAYRYPDCKY
NDKF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| TRPLQEFYDAPPDQAADLAYQLLGVLESLRSNDLNYFFYFTHIDAGMFGVFNNGHLFIRDASAVGVIDKQEGSQEANRAGENKDIFSCLVSGCQAQLPSCESISEKQSLVLVCQKLLPRLLQGRFPSPVQDDIDSILVQCGDSIRPDPEVLGAASQLKDILRPLRTCDSRFAYRYPDCKYNDKF
Prediction	CCHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCSSSCCCCSSSSSSCCCSSSSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	9507988629899999999999999999761897828998527811336706984999947735998642145655567666640136630003678765663443419999999997662368998999999999998137777770599999999999997156896433348765456779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| TRPLQEFYDAPPDQAADLAYQLLGVLESLRSNDLNYFFYFTHIDAGMFGVFNNGHLFIRDASAVGVIDKQEGSQEANRAGENKDIFSCLVSGCQAQLPSCESISEKQSLVLVCQKLLPRLLQGRFPSPVQDDIDSILVQCGDSIRPDPEVLGAASQLKDILRPLRTCDSRFAYRYPDCKYNDKF
Prediction	8530551173425301500330040034045434401000011336201024623010111420000236435665555544231140345415244531543444210100023004522765226501630450054036444444412500530351055145144613142240524776
	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

CCHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCSSSCCCCSSSSSSCCCSSSSSCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
TRPLQEFYDAPPDQAADLAYQLLGVLESLRSNDLNYFFYFTHIDAGMFGVFNNGHLFIRDASAVGVIDKQEGSQEANRAGENKDIFSCLVSGCQAQLPSCESISEKQSLVLVCQKLLPRLLQGRFPSPVQDDIDSILVQCGDSIRPDPEVLGAASQLKDILRPLRTCDSRFAYRYPDCKYNDKF

3e3pA

0.13

0.12

4.16

1.17

DEthreader

PDTLHCCYAPPPILIKVFLFQLIRSIGCLHLPSV--NVCHRDIKPHNVLVNADGTLKLCDFGSAKKLSPSEPNGNQH-YTTAVDIWSVGCIFAEMLGEPI-FRGDNSAGQLHEIVRVLIPWSNVFSHSLDKEAYDLLSALLQ-YLP-EERM-KPYEALCHYFDELHDPA--TKLPN-NKD--E-

2ozoA3

0.11

0.10

3.72

1.41

SPARKS-K

GGPLHKFLEEPVSNVAELLHQVSMGMKYLEEKN----FVHRNLAARNVLLVNRHYAKISDFGLSK--ALGPLKWYAPECRKFSSRSDVWSYGVTMWEALSGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWI-YKWEDR--PDFLTVEQRMRACYYSLASKVEGGSALEVA---

3dkcA2

0.12

0.11

3.99

1.19

FFAS-3D

--DLRNFIRNTVKDLIGFGLQVAKGMKFLASKKFVHR----DLAARNCMLDEKFTVKVADFGLARDMYDKEFDSVHNKTGAKLPVKWMA-----LESLQTQKFTTKSDVWSFITVYLLQGRRLLQPEYCPDPLYEVMLKCWH---PKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVN--

4x3fA

0.12

0.10

3.63

1.51

CNFpred

GEPLNSVLK-SLRHALDMLEQTGRALQIAHAA----GLVHRDVKPGNILITPMGQVKITDFGIAKAVD-GTAQYIAPEQAL-SPASDVYSLGVVGYEAVSGKRPFAGGALMVAMKHIKEP-PPPLPPDLPPNVRELIEITLVKN-PAMRY-RSGGPFADAVAAVR-------------------

4e7wA

0.16

0.15

4.89

1.17

DEthreader

PETVYASYTMPMLLIKLYMYQLLRSLAYIHSI-G---ICHRDIKPQNLLLDPSGVLKLIDFGSAKILIGEPNVSGATNYTTNIDIWSTGCVMAELQGQPL-FPGESGIDQLVEIIKVLHPFSKVFRPRTPPDAIDLISRLLE-YTP-SARL-TAIEALCHFFDELRTGE--ARMPN-GREL---

4x3fA2

0.13

0.12

4.16

1.40

SPARKS-K

GEPLNSVLKRSLRHALDMLEQTGRALQIAHAAG----LVHRDVKPGNILITP-GQVKITDFGIAKAVDMGTAQYIAPEQHDASPASDVYSLGVVGYEAVSGKRPFAGDGALVAMKHIKEPPPPLPPD-LPPNVRELIEITLVKN-PAMR-YRSGGPFADAVAAVRAGR-----RPPRPSQTPPP

3kcfC2

0.13

0.11

3.98

0.37

MapAlign

HGSLFDYLTVTVEGMIKLALSTASGLAHLHMEIGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIFESFKRADIYAMGLVFWEDYQLPYYDLVPSDPVEEMRKVVRPNIPNRWQSCEALRVMAKIMRECWYANGAA--RL-TALRIKKTLSQLSQQEG---------------

6wppA2

0.13

0.12

4.33

0.28

CEthreader

GGSLGQLVKEPEDRALYYLGQALEGLEYLHS----RRILHGDVKADNVLLSSDGHAALCDFGHAVCLQPLTGDYIPRSCDAKVDVWSSCCMMLHMLNGCH-PWTQFFRGPLCLKIASEPPPVREIPPSCAPLTAQAIQEGLRKE-PIHRV--SAAELGGKVNRALQQVGGLKSPWRGEYKEPRH

5hesA

0.13

0.12

4.34

0.84

MUSTER

LGSLYDYINSDMDHIMTWATDVAKGMHYLHMEA-PVKVIHRDLKSRNVVIAADGVLKICDFGASRFHNHGTFPIQSLPVSETCDTYSY---GVVLWEMLTREVPKGLEGLQVAWLVVEKNERLTIPSSCPRSFAELLHQCWEAD-AKKRP--SFKQIISILESMSNDTSLPDKCNSFLHNKAEW

1k9aB

0.15

0.12

4.23

0.62

HHsearch

KGSLVDYLRSGGDCLLKFSLDVCEAMEYLEG----NNFVHRDLAARNVLVSEDNVAKVSDFGLTKEAGKLPVKWTAPEASTKSDVWSF---GILLWEIYSGRVPYRIPLKDVVPRVEKGYKMD---APCPPAVYDVMKNCWHLD-AATR--PTFLQLREQLEHIRTHELHL-------------

(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	0.7896

(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	6wppA	0.76	3.07	0.134	0.924	model1_6wppA.pdb.gz
2	1koaA1	0.75	2.74	0.112	0.908	model1_1koaA1.pdb.gz
3	3blrA2	0.75	2.94	0.079	0.891	model1_3blrA2.pdb.gz
4	3c0gB2	0.74	3.15	0.083	0.913	model1_3c0gB2.pdb.gz
5	6z3uB	0.74	3.04	0.113	0.908	model1_6z3uB.pdb.gz
6	3e3pA	0.74	3.00	0.131	0.897	model1_3e3pA.pdb.gz
7	4e7wA	0.74	3.05	0.128	0.897	model1_4e7wA.pdb.gz
8	7kpvA	0.74	2.97	0.126	0.902	model1_7kpvA.pdb.gz
9	7jv7A	0.74	2.79	0.123	0.886	model1_7jv7A.pdb.gz
10	1kobA	0.74	3.00	0.088	0.908	model1_1kobA.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	0.89	catalytic activity
GO:0016740	0.88	transferase activity
GO:0016772	0.87	transferase activity, transferring phosphorus-containing groups
GO:0004672	0.86	protein kinase activity
GO:0004713	0.80	protein tyrosine kinase activity
GO:1901363	0.68	heterocyclic compound binding
GO:0097159	0.68	organic cyclic compound binding
GO:0000166	0.61	nucleotide binding
GO:0004715	0.60	non-membrane spanning protein tyrosine kinase activity
GO:0035639	0.58	purine ribonucleoside triphosphate binding
GO:0032555	0.58	purine ribonucleotide binding
GO:0032550	0.58	purine ribonucleoside binding
GO:0005524	0.56	ATP binding
GO:0044877	0.52	macromolecular complex binding
GO:0019899	0.52	enzyme binding
GO:0098632	0.51	protein binding involved in cell-cell adhesion
GO:0046906	0.51	tetrapyrrole binding
GO:0045296	0.51	cadherin binding
GO:0035591	0.51	signaling adaptor activity
GO:0035258	0.51	steroid hormone receptor binding
GO:0030674	0.51	protein binding, bridging
GO:0019904	0.51	protein domain specific binding
GO:0019901	0.51	protein kinase binding
GO:0004674	0.50	protein serine/threonine kinase 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:0009966	1.00	regulation of signal transduction

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0044446	0.87	intracellular organelle part
GO:0043226	0.82	organelle
GO:0044425	0.80	membrane part
GO:0043229	0.77	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0032991	0.76	macromolecular complex
GO:0043234	0.75	protein complex
GO:0044421	0.71	extracellular region part
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0016020	0.71	membrane
GO:0044431	0.69	Golgi apparatus part
GO:0005737	0.69	cytoplasm
GO:0098796	0.68	membrane protein complex
GO:0044433	0.68	cytoplasmic vesicle part
GO:0005615	0.68	extracellular space
GO:0030126	0.67	COPI vesicle coat
GO:0005634	0.56	nucleus

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	0.067	2iwiB	0.671	2.55	0.110	0.788	2.7.11.1	44
2	0.067	2zv2A	0.688	2.95	0.144	0.832	2.7.11.17	53
3	0.067	3fqeA	0.722	3.06	0.135	0.875	2.7.10.2	NA
4	0.067	2z2wA	0.674	2.61	0.156	0.799	2.7.10.2	NA
5	0.066	1sm2A	0.658	2.91	0.142	0.788	2.7.10.2	30

	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	0.13	1pyxB	0.738	2.91	0.105	0.886	0.39	ANP	complex1.pdb.gz	44,46,47,49,60
2	0.13	1q4lA	0.735	2.86	0.104	0.880	0.23	679	complex2.pdb.gz	9,10,24,49,54,57
3	0.12	3fy0A	0.735	2.84	0.143	0.880	0.18	DW1	complex3.pdb.gz	56,57,58,59
4	0.12	3ckxA	0.736	2.89	0.123	0.875	0.21	STU	complex4.pdb.gz	16,17,20,23,49
5	0.11	3ggfB	0.661	3.21	0.118	0.815	0.21	GVD	complex5.pdb.gz	50,54,56
6	0.11	3i4bB	0.735	2.82	0.105	0.880	0.16	Z48	complex6.pdb.gz	49,59,60
7	0.05	2vn9B	0.734	3.39	0.103	0.924	0.39	GVD	complex7.pdb.gz	4,45,49,57
8	0.05	3a7hB	0.735	2.94	0.129	0.875	0.20	ATP	complex8.pdb.gz	23,49,51
9	0.05	3zrmB	0.742	2.71	0.105	0.880	0.39	III	complex9.pdb.gz	25,40,41,43,44,45,48,49,51
10	0.05	3mfuA	0.746	2.96	0.101	0.908	0.31	ANP	complex10.pdb.gz	49,55,57

	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.