I-TASSER results

Input Sequence in FASTA format

>protein (68 residues)
MLVITMFRVLVARMTALAVDESGMSTVEYAIGTIAAAAFGAILYTVVTGDSIVSALNRII
GRALSTKV

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLVITMFRVLVARMTALAVDESGMSTVEYAIGTIAAAAFGAILYTVVTGDSIVSALNRIIGRALSTKV
Prediction	CCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHEEEEHCCHHHHHHHHHHHHHHHCCC
Conf.Score	99875678889989886678888657999999999999988654555587799999999999997689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLVITMFRVLVARMTALAVDESGMSTVEYAIGTIAAAAFGAILYTVVTGDSIVSALNRIIGRALSTKV
Prediction	74244324413430442246653132133220102133323211301447503510441055226567
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(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

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60

                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHEEEEHCCHHHHHHHHHHHHHHHCCC
MLVITMFRVLVARMTALAVDESGMSTVEYAIGTIAAAAFGAILYTVVTGDSIVSALNRIIGRALSTKV

3bniA

0.12

1.00

0.64

MUSTER

GRVAERLTELLSGYLGRRPDDDLRRVFLVAVETADTLVQLAFRVAPDGDEKIIEEARELLRAYLGRVL

4xdnA5

0.13

0.12

0.93

0.67

dPPAS

-HDLGEIYAISAKCFDMCRQQGGMRKVQYVIGIWHLMNCTVAMRG--KDVALTNAKLEALVKQITS--

2mqkA

0.11

0.10

0.91

0.69

wdPPAS

-GPMN-ISDIRAGLRTLV-ENEETTFKQIALESLSTGTISSFINDKYNGDRVSQTLQRWLEKYHA---

2mqkA

0.15

0.13

0.88

0.85

wMUSTER

MN----ISDIRAGLRTLVENE-ETTFKQIALESLSTGTISSFINDKYNGDRVSQTLQRWLEKYHA---

2mqkA

0.16

0.13

0.82

0.81

wPPAS

MN----ISDIRAGLRTLVENE-ETTFKQIALESLSTGTISSFI----NGDRVSQTLQRWLEKYHA---

3ifmA

0.09

0.06

0.66

0.70

dPPAS2

VIDTSAVESAITDGQGDMK-----AIGGYIVGALVILAVAGLIYSMLRKA------------------

2mqkA

0.15

0.13

0.88

0.87

PPAS

MN----ISDIRAGLRTLVENE-ETTFKQIALESLSTGTISSFINDKYNGDRVSQTLQRWLEKYHA---

4rg8A1

0.15

0.99

0.81

Env-PPAS

IDMLRLTRALRPEGIEWPVDGSGKPSLRLEALTVANGALADVRATIAVARLVRERQPKLFNFVFANR-

3f1bA

0.18

0.97

0.60

MUSTER

GSVQSSRDRLIELTAHLLESSTKQDFELIAIALVGAGEAVADRVA-IEVDAAADLLESLAWRGLAGK-

3h6pB

0.15

0.99

0.66

dPPAS

-SHTAFAAKAGLMRHTIGQAEQQAMSAQAFHQGESAAAFQGAHARFVAAAAKVNTLLDIAQANLGEAA

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

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 higher value signifies a model with a high 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.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-2.22

Estimated TM-score = 0.45±0.15

Estimated RMSD = 7.8±4.4Å

Download Model 2

C-score=-2.14

Download Model 3

C-score=-2.01

Download Model 4

C-score=-4.60

Download Model 5

C-score=-5.00

Proteins structureally close to the target in 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
1	2o8cB	0.628	2.78	0.108	0.956
2	3jrtA	0.614	2.76	0.032	0.912
3	3thwB	0.610	2.45	0.078	0.926
4	5tgzA1	0.600	2.64	0.030	0.882
5	2pedA	0.596	3.18	0.136	0.956
6	4qikA1	0.589	2.55	0.051	0.853
7	4ib4A	0.589	3.27	0.169	0.956
8	4wbeA	0.588	3.17	0.016	0.926
9	1he1A	0.584	3.16	0.077	0.912
10	4n6hA2	0.580	3.17	0.143	0.926

(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 COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results 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	0.10	5	1c61A	KR	Rep, Mult	26,29,30,33,59,62,63
2	0.08	4	2axtM	CLA	Rep, Mult	39,43
3	0.06	3	3glnA	XE	Rep, Mult	13,14,29
4	0.04	2	1jl7A	CYN	Rep, Mult	39,56,60
5	0.04	2	2v5kB	MG	Rep, Mult	28,50
6	0.04	2	1bjyB	CTC	Rep, Mult	56,60,63
7	0.04	2	1vd5A	GLY	Rep, Mult	39,53
8	0.02	1	3fk7A	4DM	Rep, Mult	63,67
9	0.02	1	1brrB	ARC	Rep, Mult	7,64
10	0.02	1	3jcuZ	CLA	Rep, Mult	17,21
11	0.02	1	3x0eA	MG	Rep, Mult	17,27,29,30
12	0.02	1	2xquB	CVM	Rep, Mult	12,16
13	0.02	1	4rkuJ	CLA	Rep, Mult	7,10

	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	0.060	3e6iA	0.527	3.58	0.067	0.838	1.14.13.-	NA
2	0.060	2ar0A	0.521	2.78	0.089	0.824	2.1.1.72	NA
3	0.060	1yqyA	0.476	4.23	0.103	0.868	3.4.24.83	25
4	0.060	1tqgA	0.528	3.37	0.031	0.941	2.7.13.3	33
5	0.060	1zxvA	0.517	2.95	0.016	0.882	3.4.24.83	44
6	0.060	3gqbA	0.545	2.94	0.030	0.868	3.6.3.14	56
7	0.060	2wpnB	0.543	3.30	0.078	0.926	1.12.7.2	NA
8	0.060	1w27A	0.519	3.35	0.095	0.853	4.3.1.24	NA
9	0.060	3d2rB	0.523	3.62	0.045	0.853	2.7.11.2	NA
10	0.060	1fftA	0.555	3.16	0.078	0.897	1.10.3.-	NA
11	0.060	2zdxA	0.518	3.70	0.060	0.853	2.7.11.2	NA
12	0.060	3bhgA	0.529	3.20	0.050	0.809	4.3.2.2	40
13	0.060	1yfeA	0.522	3.41	0.078	0.868	4.2.1.2	NA
14	0.060	2wyeB	0.521	3.41	0.119	0.853	3.5.1.97	NA
15	0.060	2nsmA	0.522	3.94	0.045	0.941	3.4.17.3	NA
16	0.060	2pdaA	0.527	2.23	0.096	0.765	1.2.7.1	NA
17	0.060	1ordA	0.549	3.28	0.083	0.882	4.1.1.17	NA
18	0.060	1g4uS	0.565	3.10	0.095	0.882	3.1.3.48	NA
19	0.060	1jtnA	0.401	3.58	0.067	0.647	3.2.1.17	NA

(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
Homologous GO templates in PDB
0	0.12	0.486	3.24	0.12	0.85	2l7aA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
1	0.07	0.316	3.80	0.06	0.56	1sgfA	GO:0004175 GO:0004252 GO:0005057 GO:0005615 GO:0005634 GO:0006508 GO:0007264 GO:0008083 GO:0016811 GO:0043234 GO:0043552 GO:0046872 GO:0070062
2	0.07	0.628	2.76	0.11	0.96	2o8eB	GO:0000166 GO:0000228 GO:0000287 GO:0000400 GO:0000710 GO:0000790 GO:0003677 GO:0003682 GO:0003684 GO:0003690 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005794 GO:0005886 GO:0006281 GO:0006298 GO:0006974 GO:0007131 GO:0008340 GO:0008630 GO:0009411 GO:0016032 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032142 GO:0032143 GO:0032301 GO:0032357 GO:0032405 GO:0035064 GO:0042803 GO:0043231 GO:0043531 GO:0043570 GO:0045190 GO:0045830 GO:0045910 GO:0051096 GO:0097193
3	0.07	0.586	2.98	0.08	0.96	1ng9A	GO:0000018 GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0005829 GO:0006281 GO:0006298 GO:0006974 GO:0008301 GO:0016887 GO:0030983 GO:0032136 GO:0032300 GO:0042802 GO:0043531
4	0.07	0.543	3.07	0.05	0.91	1ewrB	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
5	0.07	0.541	3.45	0.05	0.94	3thxA	GO:0000166 GO:0000287 GO:0000400 GO:0000403 GO:0000404 GO:0000406 GO:0000710 GO:0000784 GO:0001701 GO:0002204 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0006119 GO:0006281 GO:0006298 GO:0006301 GO:0006302 GO:0006311 GO:0006974 GO:0007050 GO:0007131 GO:0007281 GO:0008022 GO:0008340 GO:0008584 GO:0008630 GO:0010165 GO:0010224 GO:0016020 GO:0016446 GO:0016447 GO:0016887 GO:0019237 GO:0019724 GO:0019899 GO:0019901 GO:0030183 GO:0030983 GO:0031573 GO:0032137 GO:0032139 GO:0032142 GO:0032143 GO:0032181 GO:0032300 GO:0032301 GO:0032302 GO:0032357 GO:0032405 GO:0042771 GO:0042803 GO:0043524 GO:0043531 GO:0043570 GO:0045128 GO:0045190 GO:0045910 GO:0051096
6	0.07	0.610	2.45	0.08	0.93	3thwB	GO:0000166 GO:0000228 GO:0000710 GO:0003677 GO:0003684 GO:0003697 GO:0005524 GO:0005654 GO:0006281 GO:0006298 GO:0006974 GO:0007131 GO:0016020 GO:0019899 GO:0030983 GO:0032137 GO:0032139 GO:0032142 GO:0032181 GO:0032302 GO:0032357 GO:0042803 GO:0043570 GO:0045910 GO:0051096
7	0.07	0.533	2.74	0.13	0.88	5akbE	GO:0000018 GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0005829 GO:0006281 GO:0006298 GO:0006974 GO:0008301 GO:0016887 GO:0030983 GO:0032136 GO:0032300 GO:0042802 GO:0043531
8	0.07	0.540	3.03	0.07	0.88	1ewqA	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
9	0.07	0.395	4.35	0.03	0.82	3f6tB	GO:0003824 GO:0004069 GO:0008483 GO:0009058 GO:0016740 GO:0030170 GO:0080130
10	0.07	0.469	3.64	0.07	0.84	4ymsA	GO:0000166 GO:0003333 GO:0005524 GO:0015424 GO:0016887
11	0.07	0.513	3.40	0.08	0.93	1u89A	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
12	0.07	0.398	3.72	0.06	0.71	1ewrA	GO:0000166 GO:0003677 GO:0003684 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0030983
13	0.07	0.440	3.20	0.04	0.75	3p3qB	GO:0000160 GO:0005622
14	0.07	0.411	3.44	0.06	0.65	3nd2A	GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
15	0.06	0.420	4.27	0.04	0.78	1us2A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0031176 GO:0045493
16	0.06	0.359	3.66	0.08	0.62	3k8kA	GO:0000272 GO:0000287 GO:0003824 GO:0004556 GO:0005509 GO:0005975 GO:0005983 GO:0008152 GO:0009279 GO:0016020 GO:0016787 GO:0016798 GO:0019867 GO:0046872 GO:2001070
17	0.06	0.362	3.95	0.08	0.65	3e82D	GO:0008152 GO:0016491 GO:0055114
18	0.06	0.385	4.22	0.09	0.81	5a07A	GO:0000026 GO:0000030 GO:0000032 GO:0005794 GO:0006486 GO:0006487 GO:0006493 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0097502

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032559	GO:0032550	GO:0003690
GO-Score	0.37	0.37	0.37	0.37
Biological Processes	GO:0006281
GO-Score	0.37
Cellular Component	GO:0031988	GO:1903561	GO:0044424	GO:0071944
GO-Score	0.37	0.37	0.36	0.36

(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 result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.

I-TASSER results for job id Rv3656c

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

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