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I-TASSER results for job id S776237

(Click on S776237_results.tar.bz2 to download the tarball file including all modeling results listed on this page. Click on Annotation of I-TASSER Output to read the instructions for how to interpret the results on this page. Model results are kept on the server for 60 days, there is no way to retrieve the modeling data older than 2 months)

Submitted Sequence in FASTA format

>protein
VAQYTGGISRPLEAAAKTVEGIYKIVTGYLVSLSEAAAKSMKYAVWNQPIAAAIDAEAAA
KSKTKEGVVHGVATVAEKTKKYVGSKTKEGVVHGVATKKAVAQKTVEGAGSIAAATG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VAQYTGGISRPLEAAAKTVEGIYKIVTGYLVSLSEAAAKSMKYAVWNQPIAAAIDAEAAAKSKTKEGVVHGVATVAEKTKKYVGSKTKEGVVHGVATKKAVAQKTVEGAGSIAAATG
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSCCHHHHHHHHHHCCCCHHHHCC
Conf.Score	950046657256898878878999877765127788886536787367458999999986435456688879999887789871155675687420048999998862454332039
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VAQYTGGISRPLEAAAKTVEGIYKIVTGYLVSLSEAAAKSMKYAVWNQPIAAAIDAEAAAKSKTKEGVVHGVATVAEKTKKYVGSKTKEGVVHGVATKKAVAQKTVEGAGSIAAATG
Prediction	744344314431531253042013103321331352335414323243623220311341254244211431352264346314453443113223444412442374344246468
	Values range from 0 (buried residue) to 9 (highly exposed residue)

Predicted normalized B-factor

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

(I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each threading program can generate tens of thousands of template alignments. I-TASSER only uses the templates of the highest significance in the threading alignments, the significance of which are measured by the Z-score, i.e. the difference between the raw and average scores in the unit of standard deviation. The templates in this section are the 10 best templates selected from the LOMETS threading programs. Usually, one template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.)

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Z-score

Download
Align.

                  20                  40                  60                  80                 100
                   |                   |                   |                   |                   |                 

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSCCHHHHHHHHHHCCCCHHHHCC
VAQYTGGISRPLEAAAKTVEGIYKIVTGYLVSLSEAAAKSMKYAVWNQPIAAAIDAEAAAKSKTKEGVVHGVATVAEKTKKYVGSKTKEGVVHGVATKKAVAQKTVEGAGSIAAATG

1xq8

0.76

0.46

0.54

6.98

Download

-----------------------------------------------------MDVFMKGLSKAKEGVVQGVAEAAGKTKEYVGSKTKEGVVHGVATVTAVAQKTVEGAGSIAAAT-

1xq8

0.62

0.46

0.61

6.78

Download

------------------------------------------MDVFMKGLSKAKEGVVAAAEKTKQGVVHGVATVAEKTKEQVTNV-GGAVVTGV---TAVAQKTVEGAGSIAAATG

1xq8

0.77

0.46

0.55

5.04

Download

-----------------------------------------------------MDVFMKGLSKAKEGVVQGVAEAAGKTKEYVGSKTKEGVVHGVATVTAVAQKTVEGAGSIAAATG

1xq8

0.60

0.46

0.34

2.39

Download

---------------------------------------------------------LYVGSKTKEGVVHGVATVAEKTKEQV-TNVGGAVVTGVTAV-------------------

1xq8

0.56

0.46

0.52

2.99

Download

-----------------------------------------------------MDVFMKGLSKAKEGVVQGVAEAAGKTKEGVGSKTKEGVVHGV---ATVAEKTKEQVTNVGGAVV

1xq8

0.36

0.46

0.76

1.49

Download

MDVF--------------MKGLSKAKEGVVAAAAEAAGKT-------------KEGVLYVGSKTKEGVVHGVATVAEKTKEQV-TNVGGAVVTGVTAVAQKTVEGAAATGFVKKDQL

1qsdA

0.13

0.14

0.85

0.92

Download

---------TQLDIKVKALKRLTKEEGYYQQELKDQEAHVAKLKEDKSVDPYDLKKQEEVLDDTKRLLYEKIREFKEDLEQFLKTYQGTEDVSDARSAITSAQELLDS---------

8ugcA

0.23

0.34

1.00

0.69

Download

VAQAAGASEAAFEAFAAIAAAAAEAAAAAFEAFSETVAEAVAKALKAAAFAEIAKAVAQAAKQASEEAFEKFAAIAAEAAEAAAASTGETEAEKVAKLKQLMEEFAERAKSVAEQAK

6yrlA

0.11

0.20

0.91

0.70

Download

---------YELDTKVSELSHKLGSSEGSNRSLEEETARLRSLNQQLSSSKHELEIQLNEAKAKVLALDEKAQSQGDVIEQQRGRLRDEAALRQTEQRCADLRDTLASAEGRAKEA-

3d1bA

0.48

0.10

0.21

0.95

Download

---------------AKAVSSIYKLVTGKNLSLDFASQIL-----------------------------------------------------------------------------

(a)	All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)	Rank of templates represents the top ten threading templates used by I-TASSER.
(c)	Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)	Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)	Cov represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)	Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)	Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)	The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
	1: HHSEARCH 2: HHSEARCH2 3: HHSEARCH I 4: HHSEARCH 5: HHSEARCH2 6: HHSEARCH I 7: FFAS-3D 8: SPARKS-X 9: SP3 10: HHSEARCH

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of a higher value signifies a model with a higher confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated; this is usually an indication that the models have a good quality because of the converged simulations.)

(By right-click on the images, you can export image file or change the configurations, e.g. modifying the background color or stopping the spin of your models)

Download Model 1 C-score=-2.76 (Read more about C-score) Estimated TM-score = 0.40±0.13 Estimated RMSD = 10.4±4.6Å	Download Model 2 C-score = -3.00	Download Model 3 C-score = -2.87	Download Model 4 C-score = -3.84	Download Model 5 C-score = -2.92

Proteins structurally close to the target in the PDB (as identified by TM-align)

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	Alignment
1	8ga6A2	0.611	4.02	0.104	0.983	Download
2	7zrdB	0.595	3.59	0.037	0.906	Download
3	7y3gR	0.585	3.78	0.019	0.914	Download
4	8iwpA	0.585	4.06	0.053	0.940	Download
5	7w47A	0.582	3.43	0.049	0.863	Download
6	8u8fR	0.582	3.61	0.029	0.889	Download
7	2zxeA	0.581	3.63	0.029	0.880	Download
8	7qkrA	0.580	4.38	0.026	0.957	Download
9	6lcpA4	0.579	3.59	0.079	0.846	Download
10	8ijmA	0.579	4.01	0.115	0.914	Download

(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 function using COFACTOR and COACH

(This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.09	5	4clvB	ZN	Rep, Mult	73,77
2	0.07	4	2q6qA	CO	Rep, Mult	66,70
3	0.06	3	1mz9B	VDY	Rep, Mult	65,68,72
4	0.06	3	1y66C	DIO	Rep, Mult	54,57
5	0.04	2	4j4qA	BOG	Rep, Mult	79,96,101

	Download the residue-specific ligand binding probability, which is estimated by SVM.
	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.113	3c6gB	0.521	4.52	0.035	0.855	1.14.13.15	109
2	0.113	1po5A	0.527	4.24	0.027	0.855	1.14.14.1	NA
3	0.110	3b8eC	0.541	4.31	0.045	0.914	3.6.3.9	96
4	0.100	3ixzA	0.547	4.29	0.124	0.940	3.6.3.10	NA
5	0.099	1mhsA	0.529	3.83	0.097	0.863	3.6.3.6	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Top 10 homologous GO templates in PDB
1	0.16	0.2753	4.37	0.06	0.45	1xq8A	GO:0030426 GO:0016044 GO:0051585 GO:0070555 GO:0042802 GO:0043524 GO:0046928 GO:0045920 GO:0032026 GO:0001963 GO:0042493 GO:0050544 GO:0045202 GO:0034341 GO:0034599 GO:0042775 GO:0031623 GO:0010642 GO:0008344 GO:0042393 GO:0048156 GO:0048488 GO:0005634 GO:0071902 GO:0031092 GO:0032496 GO:0000287 GO:0045502 GO:0051622 GO:0050806 GO:0005504 GO:0035067 GO:0040012 GO:0042417 GO:0033138 GO:0008198 GO:0010040 GO:0055074 GO:0006916 GO:0008270 GO:0051612 GO:0005515 GO:0006638 GO:0060079 GO:0032410 GO:0060732 GO:0006644 GO:0050812 GO:0014048 GO:0016020 GO:0030054 GO:0042416 GO:0010517 GO:0048169 GO:0006919 GO:0008219 GO:0048168 GO:0001956 GO:0043154 GO:0045807 GO:0031115 GO:0030544 GO:0043030 GO:0005739 GO:0019717 GO:0014059 GO:0005737 GO:0001774 GO:0005886 GO:0030424 GO:0019894 GO:0001921 GO:0032769 GO:0005509 GO:0006631 GO:0048489 GO:0005829 GO:0015629 GO:0070495 GO:0051281 GO:0051219 GO:0005938 GO:0043014 GO:0060961 GO:0043027 GO:0005856 GO:0043205 GO:0007006 GO:0060291
2	0.12	0.5604	4.24	0.04	0.92	3ajbA	GO:0005779 GO:0007031
3	0.12	0.5811	3.63	0.03	0.88	2zxeA	GO:0006810 GO:0016820 GO:0015672 GO:0006812 GO:0046872 GO:0006754 GO:0000166 GO:0015077 GO:0016021 GO:0006811 GO:0015662 GO:0016020 GO:0008152 GO:0005524 GO:0003824 GO:0016787
4	0.11	0.5399	4.18	0.09	0.91	3emlA	GO:0003796 GO:0007186 GO:0009253 GO:0016021 GO:0016998 GO:0016798 GO:0008152 GO:0042742 GO:0019835 GO:0016787 GO:0003824
5	0.11	0.5504	4.18	0.09	0.91	3oduA	GO:0019835 GO:0016998 GO:0003796 GO:0016798 GO:0008152 GO:0042742 GO:0016787 GO:0003824 GO:0009253 GO:0007186 GO:0016021
6	0.11	0.5528	3.56	0.04	0.83	3ljbA	GO:0003924 GO:0005525
7	0.11	0.5568	4.19	0.05	0.93	2ydvA	GO:0001609 GO:0001973 GO:0007186 GO:0016021
8	0.10	0.5316	4.32	0.03	0.92	1iwoA	GO:0033017 GO:0006810 GO:0046872 GO:0000166 GO:0005388 GO:0005524 GO:0006816 GO:0005789 GO:0005515 GO:0016021 GO:0005783 GO:0005509 GO:0016787 GO:0031448 GO:0016529 GO:0016020 GO:0006811 GO:0003824 GO:0006754 GO:0006812 GO:0008152 GO:0015662
9	0.10	0.5468	4.29	0.12	0.94	3ixzA	GO:0008900 GO:0016787 GO:0016820 GO:0015077 GO:0015662 GO:0046872 GO:0016021 GO:0000287 GO:0006810 GO:0005524 GO:0015991 GO:0006754 GO:0015672 GO:0000166 GO:0006813 GO:0006812 GO:0008152 GO:0006811 GO:0015992 GO:0016020 GO:0003824
10	0.10	0.5218	4.42	0.06	0.92	3b8eA	GO:0016323 GO:0002026 GO:0005886 GO:0006814 GO:0006813 GO:0016021 GO:0003869 GO:0006811 GO:0042383 GO:0016787 GO:0005792 GO:0008217 GO:0042470 GO:0045989 GO:0045822 GO:0000166 GO:0042493 GO:0016020 GO:0031947 GO:0006810 GO:0045823 GO:0005524 GO:0046872 GO:0005391 GO:0003824 GO:0006754 GO:0006812 GO:0008152 GO:0015077 GO:0015662 GO:0015672 GO:0016820

Consensus prediction of GO terms

Molecular Function GO:0004869 GO:0050543 GO:0004859 GO:0015631 GO:0043167 GO:0043028 GO:0016787

GO-Score 0.33 0.33 0.33 0.33 0.33 0.33 0.31

Biological Process GO:0000270 GO:0006027 GO:0044036 GO:0060191 GO:0043066 GO:0045860 GO:0045744 GO:0007005 GO:0043523 GO:2000757

GO-Score 0.43 0.43 0.43 0.33 0.33 0.33 0.33 0.33 0.33 0.33

Cellular Component GO:0031091 GO:0030427 GO:0044420 GO:0030667 GO:0043232 GO:0071944 GO:0044463 GO:0043005 GO:0005624 GO:0016021

GO-Score 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.31

(a) Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.

(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.

(f) The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on S776237_results.tar.bz2 to download the tarball file including all modeling results listed on this page]

Please cite the following articles when you use the I-TASSER server:

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. Cell Reports Methods, 1: 100014 (2021).
Chengxin Zhang, Peter L. Freddolino, and Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017).
Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.