I-TASSER results

Input Sequence in FASTA format

>protein (28 residues)
MTLSVVPEGLAAASAAVEALTARLAAAH

Predicted Secondary Structure

Sequence	20 \| MTLSVVPEGLAAASAAVEALTARLAAAH
Prediction	CCEEHCCCHHHHHHHHHHHHHHHHHHCC
Conf.Score	9566666456788899999999987659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| MTLSVVPEGLAAASAAVEALTARLAAAH
Prediction	7524333532432433143134424568
	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

                   |

Sec.Str
Seq

CCEEHCCCHHHHHHHHHHHHHHHHHHCC
MTLSVVPEGLAAASAAVEALTARLAAAH

3eabI

0.38

0.36

0.93

1.06

wdPPAS

LDLGSV--GTSVASAEQDELSQRLARLR

4yt2A3

0.46

0.43

0.93

1.20

wPPAS

-TLSLVKEGGAAAEGAIKRSARKLFE-H

2rmgA

0.33

0.32

0.96

1.26

PPAS

IVLSLVPQARARAAREQATTNARILA-R

2elnA

0.22

0.21

0.96

1.39

Env-PPAS

ILLKCPTDGCDYSTPDKYKLQAHLKV-H

2rmgA

0.33

0.32

0.96

1.20

wPPAS

IVLSLVPQARARAAREQATTNARILA-R

3s0rA

0.27

0.25

0.93

1.17

PPAS

SALEYAQQALEKAQLALQAARQALKA--

1rooA

0.14

1.00

1.36

Env-PPAS

SCIDTIPKSRCTAFQCKHSMKYRLSFCR

3eabI

0.44

0.39

0.89

1.07

wPPAS

LDLSV---GTSVASAEQDELSQRLARLR

4yt2A3

0.46

0.43

0.93

1.16

PPAS

-TLSLVKEGGAAAEGAIKRSARKLFE-H

1csbA

0.29

1.00

1.32

Env-PPAS

PTIKEIRDGSCWAFGAVEAISDRICIHT

(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=-0.79

Estimated TM-score = 0.61±0.14

Estimated RMSD = 3.0±2.2Å

Download Model 2

C-score=-2.80

Download Model 3

C-score=-2.42

Download Model 4

C-score=-3.18

Download Model 5

C-score=-3.79

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	4gytA	0.853	1.26	0.071	1.000
2	3pieA	0.847	0.82	0.107	1.000
3	3tqtA3	0.845	1.14	0.036	1.000
4	3fx7B	0.839	1.44	0.179	1.000
5	3vthA2	0.838	0.91	0.071	1.000
6	3tixA	0.835	0.95	0.074	0.964
7	4l8jA	0.835	0.73	0.071	1.000
8	3o6cA2	0.831	1.10	0.143	1.000
9	3s3uA	0.831	1.47	0.143	0.964
10	5ekaA	0.830	1.14	0.185	0.964

(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	0.14	688	2dysT	CDL	Rep, Mult	12,16,19,20,22,23,26,27
2	0.11	554	5ejiA	POP	Rep, Mult	11,12,13,14
3	0.11	573	4eoyA	CA	Rep, Mult	8,9,10,11,12,13
4	0.11	506	3bz1X	CLA	Rep, Mult	14,15,18,19
5	0.11	499	2wgmA	NA	Rep, Mult	21,22,24,26
6	0.10	525	1i94T	MG	Rep, Mult	12,13,14,15,16,17
7	0.04	227	2vbnB	CA	Rep, Mult	24,25,26,27
8	0.04	201	3lyaA	RHE	Rep, Mult	6,7,8,9
9	0.00	2	4z1mF	ATP	Rep, Mult	1,3,10
10	0.00	20	4utgA	MG	Rep, Mult	3,4,6,9,10
11	0.00	4	4p1eA	IOD	Rep, Mult	2,10,13

	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	0.303	3brvC	0.777	0.73	0.160	0.893	2.7.11.10	12,20
2	0.230	3brtA	0.694	0.53	0.111	0.821	2.7.11.10	19
3	0.189	3e7kH	0.747	1.77	0.107	0.893	2.7.11.1	NA
4	0.154	1vzjF	0.565	1.03	0.000	0.786	3.1.1.7	11
5	0.145	2k9yA	0.580	0.82	0.107	0.821	2.7.10.1	9
6	0.137	1qleD	0.708	1.85	0.071	0.893	1.9.3.1	16
7	0.136	1rklA	0.507	2.13	0.154	0.929	2.4.1.119	26
8	0.135	1xtcC	0.679	1.46	0.125	0.857	2.4.2.36	14
9	0.131	1r7cA	0.535	1.70	0.043	0.821	3.6.1.15	NA
10	0.104	2jwaA	0.712	0.47	0.036	0.821	2.7.10.1	NA
11	0.081	1z8yN	0.554	0.94	0.130	0.821	3.4.21.90	NA
12	0.066	2o98P	0.740	1.39	0.120	0.857	3.6.3.6	16,24
13	0.060	2b5uA	0.800	1.31	0.185	0.964	3.1.-.-	NA
14	0.060	1xzpA	0.806	0.85	0.036	1.000	3.6.5.-	NA
15	0.060	1uu1C	0.773	1.33	0.111	0.964	2.6.1.9	NA
16	0.060	2fuaA	0.805	1.13	0.179	1.000	4.1.2.17	NA
17	0.060	2a87A	0.803	1.52	0.214	0.964	1.8.1.9	NA
18	0.060	2f8jC	0.797	1.32	0.111	0.964	2.6.1.9	NA
19	0.060	1q6xA	0.761	1.26	0.179	1.000	2.3.1.6	NA
20	0.060	3fg0C	0.791	0.96	0.148	0.964	1.2.1.8	NA
21	0.060	3n2oA	0.809	0.95	0.143	1.000	4.1.1.19	NA
22	0.060	1sesA	0.753	1.26	0.250	0.893	6.1.1.11	13
23	0.060	2q8nB	0.807	1.46	0.214	1.000	5.3.1.9	NA
24	0.060	2fy3A	0.798	1.64	0.036	1.000	2.3.1.6	NA
25	0.060	2q8nC	0.806	1.46	0.214	1.000	5.3.1.9	NA
26	0.060	1serB	0.718	1.52	0.107	1.000	6.1.1.11	NA
27	0.060	3cxhR	0.800	0.81	0.036	0.964	1.10.2.2	3,7
28	0.060	3i12A	0.808	1.14	0.071	1.000	6.3.2.4	NA
29	0.060	3o6cA	0.831	1.10	0.143	1.000	2.6.99.2	NA
30	0.060	2eabA	0.790	1.28	0.036	1.000	3.2.1.63	NA
31	0.060	1q0lA	0.722	2.01	0.143	1.000	1.1.1.267	3

(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	0.23	0.796	1.14	0.04	1.00	2i80B	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
1	0.21	0.748	1.20	0.04	0.96	3k3pB	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
2	0.19	0.845	1.14	0.04	1.00	3tqtA	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
3	0.19	0.808	1.14	0.07	1.00	3i12A	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
4	0.17	0.747	2.41	0.00	0.96	5f5wA	GO:0000166 GO:0004812 GO:0004820 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006426 GO:0016874
5	0.16	0.747	1.94	0.04	0.96	3fqdA	GO:0003676 GO:0004518 GO:0004527 GO:0004534 GO:0005634 GO:0006139 GO:0006351 GO:0006353 GO:0006355 GO:0006364 GO:0006397 GO:0006402 GO:0016787 GO:0030846 GO:0090305 GO:0090503
6	0.15	0.753	1.72	0.07	1.00	5iy6K	GO:0000398 GO:0001055 GO:0003677 GO:0003899 GO:0005634 GO:0005654 GO:0005665 GO:0006283 GO:0006351 GO:0006366 GO:0006367 GO:0006368 GO:0006370 GO:0008543 GO:0010467 GO:0030275 GO:0031047 GO:0035019 GO:0042795 GO:0046983 GO:0050434
7	0.15	0.737	1.61	0.00	0.96	3pieC	GO:0000184 GO:0000932 GO:0000956 GO:0003676 GO:0003682 GO:0003723 GO:0004518 GO:0004527 GO:0004534 GO:0005634 GO:0005737 GO:0007089 GO:0008409 GO:0010494 GO:0016787 GO:0032968 GO:0046872 GO:0060261 GO:0070651 GO:0090503
8	0.15	0.775	1.40	0.04	0.86	2x7rC	GO:0002223 GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512
9	0.14	0.745	1.31	0.04	1.00	1ehiB	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
10	0.14	0.681	1.71	0.15	0.89	4c5aA	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0005829 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
11	0.14	0.771	1.84	0.07	1.00	5firA	GO:0000738 GO:0003676 GO:0004518 GO:0004527 GO:0004534 GO:0005634 GO:0005730 GO:0006139 GO:0006351 GO:0006353 GO:0006355 GO:0006397 GO:0007275 GO:0008409 GO:0010587 GO:0016787 GO:0040028 GO:0040034 GO:0046872 GO:0060965 GO:0090503
12	0.13	0.766	1.24	0.04	1.00	1ehiA	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
13	0.13	0.796	1.13	0.07	1.00	3rfcA	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
14	0.13	0.684	1.61	0.11	0.89	3lwbB	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0005886 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0040007 GO:0046872 GO:0071555
15	0.13	0.749	0.48	0.04	0.86	5bw9g	GO:0000221 GO:0000329 GO:0006810 GO:0006811 GO:0007035 GO:0015992 GO:0042626 GO:0046961 GO:0055085 GO:1902600
16	0.13	0.661	1.93	0.00	0.89	4s3kA	GO:0004553 GO:0004568 GO:0005975 GO:0006032 GO:0008152 GO:0016787 GO:0016798
17	0.12	0.772	0.82	0.07	0.96	3pieD	GO:0000184 GO:0000932 GO:0000956 GO:0003676 GO:0003682 GO:0003723 GO:0004518 GO:0004527 GO:0004534 GO:0005634 GO:0005737 GO:0007089 GO:0008409 GO:0010494 GO:0016787 GO:0032968 GO:0046872 GO:0060261 GO:0070651 GO:0090503
18	0.11	0.626	2.02	0.07	0.93	2fb9A	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0046872 GO:0071555
19	0.11	0.689	1.60	0.11	0.89	3lwbA	GO:0000166 GO:0000287 GO:0003824 GO:0005524 GO:0005737 GO:0005886 GO:0008360 GO:0008716 GO:0009252 GO:0016874 GO:0030145 GO:0040007 GO:0046872 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0000287	GO:0008716	GO:0030145	GO:0004812
GO-Score	0.67	0.60	0.60	0.60	0.35
Biological Processes	GO:0071555	GO:0008360	GO:0009252	GO:0006418
GO-Score	0.60	0.60	0.60	0.35
Cellular Component	GO:0044444
GO-Score	0.35

(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 Rv3018A

[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]