D-I-TASSER Q9H2X0-D3

D-I-TASSER results for Q9H2X0-D3

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

Input Sequence in FASTA format

>Q9H2X0 (122 residues)
FSAILTLEGPPQQGVGGITLLTLSDTEDSLHFLLLFRGLLEPRSGGLTQVPLRLQILHQG
QLLRELQANVSAQEPGFAEVLPNLTVQEMDWLVLGELQMALEWAGRPGLRISGHIAARKS
CD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FSAILTLEGPPQQGVGGITLLTLSDTEDSLHFLLLFRGLLEPRSGGLTQVPLRLQILHQGQLLRELQANVSAQEPGFAEVLPNLTVQEMDWLVLGELQMALEWAGRPGLRISGHIAARKSCD
Prediction	CCCSSCCCCCCCCCCCCSSSSSSCCCCCCSSSSSSSSCCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCSSSSSCCCCHHHHHHHHCCCSSSSSSSCCCCCCSSSSSSSCCCCCC
Confidence	97314279987789871899994599982899999816668766776337999998167823444564125456866999668999999987608189999966899836899774242469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| FSAILTLEGPPQQGVGGITLLTLSDTEDSLHFLLLFRGLLEPRSGGLTQVPLRLQILHQGQLLRELQANVSAQEPGFAEVLPNLTVQEMDWLVLGELQMALEWAGRPGLRISGHIAARKSCD
Prediction	73140416446444110000011264443010000021114477543440202020356751144335514654441140345145722431341403020315644633030303435428
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSCCCCCCCCCCCCSSSSSSCCCCCCSSSSSSSSCCCCCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCSSSSSCCCCHHHHHHHHCCCSSSSSSSCCCCCCSSSSSSSCCCCCC
FSAILTLEGPPQQGVGGITLLTLSDTEDSLHFLLLFRGLLEPRSGGLTQVPLRLQILHQGQLLRELQANVSAQEPGFAEVLPNLTVQEMDWLVLGELQMALEWAGRPGLRISGHIAARKSCD

2jlpD

0.06

2.49

1.17

DEthreader

AACQVQPSATLQPRVTGVVLFRQLAPRAKLDAFFALEGF-PTEPN--SSSRAIHVHQFGTGHYHGDFGNFAVRSLWRYRAGLAASGPHS-IV---GRAVVVHAGEAGRRLACCVVGVCGPGE

4ts6A

0.13

0.11

3.98

0.73

SPARKS-K

-----------PIEGRLQLKLGYDQNTLQLIVTLVCAGLSLRQSGAGRNPYAKVFLLPDRSHKSKRRTKTVGTTCEPTFVYSGLRRCDLN---GRLLEVTLWDYVRGANDFIGEVVIDLAHH

1cf1C

0.06

2.48

0.68

MapAlign

RAEASWQFFMSDKPLRLAVSLSIYYHGEPIPVTVAVTNST------EKTVKIKVLVEQVTKTVAAEEAKVPPNSSTKTLTLVPEDTNLASSTILVSYQIKVKLTVSSEVATEVPFRLMHP--

4fxgA5

0.05

0.04

1.93

0.61

CEthreader

-----------SRRGHLFLQTPIYNPGQRVRYRVFALDQ----KMRPSTDTITVMVENHGLRVRKKEVYMPS---SIFQDDFVIPDIS----EPGTWKISARFSDGLESNSSTQFEVKKYGA

4es8A2

0.10

0.08

3.02

0.60

MUSTER

-------------NPSQLDKGVAYVGNKNVQLTLKS------DDGRTNFEGDEISLFNRGELLQTVTVTKDQQNP----ISITLSEDQAKSLKNKKLKVSIKQKQSKKTDFFFEVGIDPKVE

5kvmA1

0.11

0.09

3.24

0.57

HHsearch

------PREQRQTQQS---TLHYDQ-SSEPHIFVWNTEET---------LTIRAPFLAAPD--IPRFFPEPRGLYHFCLYWSRHTG-RL-HLRYGKHDYLLSSQASR-LLCFQKQEQSAPHK

2cm6A

0.12

0.11

3.79

0.55

FFAS-3D

--ALYEEEQVERIEERGKILVSLMTQQGGLIVGIICVHLAAMDANGYSDPFVKLWLKPKKAKHKTQIKKKTLNPEFNEEFFYDIKHSD---LAKKSLDISVWDYDIKSNDYIGGCQ------

1pzsA

0.06

0.05

2.21

0.62

EigenThreader

SLTSTLTAP--DGTKVATAKFEFAN--GYATVTIAT-TGVGKLT----PGFHGLHIHQTPASGDLASLQVRGDGSAMLVTTTDAFT--MDDLLSAKTAIIIHAGADNDAGVACGVIGSG---

6ankA

0.11

0.09

3.25

0.85

CNFpred

---------------ELLLSLCYNPSANSIIVNIIARNLKAMDIGGTSDPYVKVWLMYKDKRVEKKKTVTKNLNPIFNESAFDIPTEKLR---ETTIIITVMDKD-SRNDVIGKIYLSW---

1jk9B2

0.14

0.12

4.20

1.17

DEthreader

AVAILETFQ-KYDAVRGLARIVQV-GENKTLFDITVNGVPE------A-GNYHASIHKGTGKWHKFDEPIECNSGKTFLSA-PL-P--TWQL--IGRSFVISKSLNKDYSFLGVIARSAGVW

(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	0.7785

(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	2jlpD	0.73	2.72	0.061	0.934	model1_2jlpD.pdb.gz
2	1jk9B	0.70	2.43	0.147	0.885	model1_1jk9B.pdb.gz
3	6dtkA	0.68	2.67	0.104	0.861	model1_6dtkA.pdb.gz
4	1do5A	0.68	2.51	0.154	0.853	model1_1do5A.pdb.gz
5	1f1dA	0.68	2.50	0.096	0.853	model1_1f1dA.pdb.gz
6	1to4A	0.68	2.60	0.144	0.853	model1_1to4A.pdb.gz
7	6zs1A	0.68	2.52	0.096	0.853	model1_6zs1A.pdb.gz
8	1srdA	0.68	2.47	0.146	0.844	model1_1srdA.pdb.gz
9	6fonA	0.68	2.59	0.154	0.853	model1_6fonA.pdb.gz
10	2nnxA	0.68	2.50	0.107	0.844	model1_2nnxA.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:0097367	0.47	carbohydrate derivative binding
GO:0008201	0.46	heparin binding
GO:0045545	0.44	syndecan binding
GO:0019955	0.33	cytokine 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:0048856	1.00	anatomical structure development
GO:0044767	1.00	single-organism developmental process
GO:0065007	0.90	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0048523	0.85	negative regulation of cellular process
GO:0006355	0.85	regulation of transcription, DNA-templated
GO:0009968	0.84	negative regulation of signal transduction
GO:0006357	0.84	regulation of transcription from RNA polymerase II promoter
GO:0090288	0.83	negative regulation of cellular response to growth factor stimulus
GO:0090101	0.83	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0030510	0.83	regulation of BMP signaling pathway
GO:0051239	0.77	regulation of multicellular organismal process
GO:0030514	0.76	negative regulation of BMP signaling pathway
GO:0048522	0.73	positive regulation of cellular process
GO:0007165	0.71	signal transduction
GO:0044707	0.69	single-multicellular organism process
GO:0009653	0.69	anatomical structure morphogenesis
GO:0007167	0.69	enzyme linked receptor protein signaling pathway
GO:0030509	0.68	BMP signaling pathway
GO:0007389	0.67	pattern specification process
GO:0051241	0.61	negative regulation of multicellular organismal process
GO:0048731	0.61	system development
GO:0045596	0.61	negative regulation of cell differentiation
GO:0042127	0.61	regulation of cell proliferation
GO:0032879	0.61	regulation of localization
GO:0045785	0.60	positive regulation of cell adhesion
GO:0045668	0.60	negative regulation of osteoblast differentiation
GO:0030336	0.60	negative regulation of cell migration
GO:0021919	0.60	BMP signaling pathway involved in spinal cord dorsal/ventral patterning
GO:0002053	0.60	positive regulation of mesenchymal cell proliferation
GO:0001501	0.60	skeletal system development
GO:0009987	0.56	cellular process
GO:0048646	0.51	anatomical structure formation involved in morphogenesis

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:0044421	0.76	extracellular region part
GO:0005615	0.73	extracellular space
GO:0044464	0.61	cell part

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	0.086	2jlpD	0.730	2.72	0.061	0.934	1.15.1.1	110
2	0.068	1oztG	0.675	2.40	0.107	0.836	1.15.1.1	106
3	0.067	1srdA	0.678	2.47	0.146	0.844	1.15.1.1	106
4	0.067	3f7kA	0.648	2.60	0.149	0.828	1.15.1.1	31
5	0.067	1xsoA	0.674	2.44	0.127	0.836	1.15.1.1	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:

Click to view	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	1do50	0.680	2.51	0.154	0.853	0.78	III	complex1.pdb.gz	2,4,20,59,92,95,97,114,116,117,118,119
	2	0.03	1qup0	0.709	2.30	0.139	0.877	0.80	III	complex2.pdb.gz	2,4,59,93,96,97,114,116,117,118

	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.