I-TASSER results

Input Sequence in FASTA format

>protein (100 residues)
MPGSVPGKAPEEPPVKFTRAAAVWSALIVGFLILILLLIFIAQNTASAQFAFFGWRWSLP
LGVAILLAAVGGGLITVFAGTARILQLRRAAKKTHAAALR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MPGSVPGKAPEEPPVKFTRAAAVWSALIVGFLILILLLIFIAQNTASAQFAFFGWRWSLPLGVAILLAAVGGGLITVFAGTARILQLRRAAKKTHAAALR
Prediction	CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	9999999999888888874689999999999999999999998698589999989997437999999999999999999999999999999999988759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MPGSVPGKAPEEPPVKFTRAAAVWSALIVGFLILILLLIFIAQNTASAQFAFFGWRWSLPLGVAILLAAVGGGLITVFAGTARILQLRRAAKKTHAAALR
Prediction	8466556655777535423012233233333333333310011144514030123433322221133233331330132332212302341464456678
	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                  80                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MPGSVPGKAPEEPPVKFTRAAAVWSALIVGFLILILLLIFIAQNTASAQFAFFGWRWSLPLGVAILLAAVGGGLITVFAGTARILQLRRAAKKTHAAALR

2l35A

0.24

0.15

0.62

0.97

wPPAS

---------------CSTVSPGVLAGIVVGDLVLTVLIALAVY--------FLG------LGTAEVLGIISIVLVATVLKTIVLIPFLEQN---------

2k1lA

0.21

0.08

0.38

1.44

dPPAS2

-------SPPVSRGLTGGEIVAVIFGLLLGAALLLGILVFRSRRA-------------------------------------------------------

2yevC

0.21

0.12

0.56

1.29

dPPAS2

----------------------VYIALFALGAALVTLFFYLILNGETFDLRF------VLFMLLLILLAAGTVALMLLIGKAHH----------------

3j2wE

0.22

0.10

0.46

1.23

dPPAS2

--------HTTLGVQDISTTAMSWVQKITG-------------------------------GVGLIVAVAALILIVVLCVSFSRH---------------

3tsiA

0.14

0.07

0.50

1.23

dPPAS2

---------------SPSSGLGSITDLLNNILSVANQIIYNSA-------------VALPLQLDTLESTLLTAIKSLQ----------------------

2ifoA

0.38

0.13

0.34

1.17

dPPAS2

---------------------------------------------------------SAIQGAAGPIAAIGGAVLTVMVGIKVYKWVRRAM---------

5ezmA

0.18

0.16

0.89

0.91

MUSTER

ASPVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLL-----------RRGVLPSVAVYAMGMYLGFTVALLGHETVGRPASADIAPQIAQKLT

2n64A

0.08

0.06

0.75

0.88

dPPAS

------GHMEGKPKMEPAASSQAAVEELRTQVRELRSIIETMKDQQ-------------KREIKQLLSELDEEKKIRLRLQMEVNDIKKALQSK------

2l35A

0.24

0.15

0.62

0.93

wdPPAS

---------------CSTVSPGVLAGIVVGDLVLTVLIALAVY--------FLG------LGTAEVLGIISIVLVATVLKTIVLIPFLEQN---------

5ezmA

0.18

0.16

0.88

wMUSTER

L-PVVATLNANHIPNSFYRAYAVWVAVAFVVMLLGIAVARLLL-----------RRGVLPSVAVYAMGMYLGFTVALLGHETVGRPASADIAPQIAQKLT

(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=-2.38

Estimated TM-score = 0.44±0.14

Estimated RMSD = 9.1±4.6Å

Download Model 2

C-score=-2.95

Download Model 3

C-score=-3.03

Download Model 4

C-score=-3.54

Download Model 5

C-score=-3.11

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	4f4cA	0.663	2.69	0.040	0.910
2	4nqiA	0.663	3.21	0.020	0.890
3	3pltA	0.661	2.94	0.061	0.870
4	2d4cB	0.653	2.77	0.092	0.880
5	1yc9A	0.652	2.96	0.105	0.820
6	1i49A	0.651	2.37	0.085	0.840
7	4akkA	0.648	3.03	0.061	0.920
8	4uosA	0.646	2.87	0.067	0.890
9	4akvA	0.644	3.10	0.092	0.910
10	1uruA	0.643	3.18	0.100	0.910

(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	0.11	16	2r5bA	III	Rep, Mult	84,87,90,91,94,95
2	0.09	12	1kb9D	PIE	Rep, Mult	77,80,81,84,85
3	0.07	10	3m4oA	C7P	Rep, Mult	83,84,87
4	0.05	7	2dyrB	TGL	Rep, Mult	36,39,40,43,45
5	0.05	7	1sofB	HEM	Rep, Mult	32,35,36,39,62,66,69
6	0.03	5	3klzD	FMT	Rep, Mult	40,42,62
7	0.03	4	2agvA	PTY	Rep, Mult	25,76,80,83,84
8	0.02	3	2c9lY	NUC	Rep, Mult	63,64,67,68,70,71,74
9	0.02	3	2voyK	III	Rep, Mult	24,28,31,32,39
10	0.02	3	5l26C	6ZL	Rep, Mult	69,76,77
11	0.02	3	5m9eD	III	Rep, Mult	81,85,86,88,89,90,92
12	0.01	1	3zciA	BU9	Rep, Mult	42,43,59
13	0.01	1	1m18G	UUU	Rep, Mult	18,19
14	0.01	2	4qi1C	MPG	Rep, Mult	19,20,23,24,27,31,34,75
15	0.01	1	3a0bL	CLA	Rep, Mult	32,36,40
16	0.01	1	2zt9G	III	Rep, Mult	66,74

	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	0.155	1joyA	0.458	2.42	0.121	0.590	2.7.13.3	22,32,35
2	0.089	1a91A	0.516	2.31	0.067	0.640	3.6.3.14	NA
3	0.066	1wu0A	0.466	2.54	0.097	0.620	3.6.3.14	NA
4	0.066	2w5jA	0.467	2.83	0.065	0.650	3.6.3.14	NA
5	0.060	1m56A	0.559	3.45	0.102	0.830	1.9.3.1	NA
6	0.060	2pfmA	0.563	4.17	0.082	0.940	4.3.2.2	NA
7	0.060	2z4yB	0.548	3.24	0.044	0.790	2.5.1.29	NA
8	0.060	2nztA	0.592	3.59	0.042	0.870	2.7.1.1	NA
9	0.060	1kkcX	0.555	3.63	0.112	0.800	1.15.1.1	32
10	0.060	1ig8A	0.552	3.66	0.104	0.810	2.7.1.1	NA
11	0.060	3f9mA	0.530	3.44	0.063	0.740	2.7.1.2	NA
12	0.060	3no9A	0.558	3.63	0.084	0.900	4.2.1.2	NA
13	0.060	2f89F	0.560	3.15	0.061	0.820	2.5.1.1,2.5.1.10	31
14	0.060	2azkA	0.554	3.31	0.052	0.830	2.5.1.1,2.5.1.29,2.5.1.10	NA
15	0.060	1b8fA	0.556	3.50	0.041	0.870	4.3.1.3	NA
16	0.060	1yfeA	0.581	4.01	0.063	0.930	4.2.1.2	NA
17	0.060	1v4tA	0.572	3.68	0.094	0.850	2.7.1.2,2.7.1.1	NA
18	0.060	2azjA	0.559	3.35	0.052	0.830	2.5.1.1	NA
19	0.060	3hm8A	0.594	3.43	0.073	0.860	2.7.1.1	NA
20	0.060	3kkbB	0.586	2.65	0.085	0.770	2.7.13.3	34,38
21	0.060	1qleA	0.541	3.82	0.090	0.840	1.9.3.1	83
22	0.060	2pfdB	0.602	2.88	0.084	0.810	2.1.2.5,4.3.1.4	67
23	0.060	1k04A	0.560	3.48	0.108	0.830	2.7.10.2	27,69

(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	0.07	0.663	2.69	0.04	0.91	4f4cA	GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
1	0.07	0.603	3.75	0.03	0.92	3j83A	GO:0005576 GO:0009405 GO:0044315
2	0.07	0.635	2.82	0.06	0.85	4mrrA	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0046689 GO:0055085
3	0.07	0.570	3.21	0.09	0.85	4q4aA	GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
4	0.07	0.566	3.04	0.03	0.80	3auyA	GO:0000166 GO:0005524 GO:0006281 GO:0006302 GO:0006974 GO:0008270 GO:0016787 GO:0016887 GO:0046872
5	0.07	0.619	2.70	0.06	0.81	5da9A	GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547
6	0.07	0.527	3.36	0.03	0.79	3zgxB	GO:0000166 GO:0003677 GO:0005524 GO:0005694 GO:0005737 GO:0006260 GO:0007059 GO:0007062 GO:0030261 GO:0042802 GO:0051276
7	0.07	0.490	3.57	0.06	0.80	3wmgA	GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
8	0.07	0.585	2.94	0.07	0.80	3b5wA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
9	0.07	0.551	3.75	0.02	0.89	4a82A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
10	0.07	0.492	3.23	0.08	0.75	5do7A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045177 GO:0045796 GO:0046982 GO:0055085
11	0.07	0.633	3.09	0.10	0.91	4m1mA	GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
12	0.07	0.615	3.24	0.09	0.85	4ry2A	GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
13	0.07	0.587	2.34	0.07	0.75	5da9B	GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547
14	0.07	0.634	2.90	0.13	0.86	4mycA	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0006811 GO:0006879 GO:0016020 GO:0016021 GO:0016887 GO:0022857 GO:0042626 GO:0044281 GO:0055072 GO:0055085
15	0.07	0.624	3.05	0.05	0.87	5c73A	GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
16	0.07	0.601	3.28	0.05	0.81	3b5xA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
17	0.07	0.448	3.73	0.04	0.74	5do7D	GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
18	0.07	0.499	3.26	0.04	0.73	4ux3A	GO:0000166 GO:0003682 GO:0005524 GO:0005634 GO:0005694 GO:0006281 GO:0007049 GO:0007064 GO:0007067 GO:0007130 GO:0007131 GO:0008280 GO:0016887 GO:0030437 GO:0034990 GO:0042802 GO:0051177 GO:0051276 GO:0051301 GO:1990414

Consensus prediction of GO terms

Molecular Function	GO:0032559	GO:0035639	GO:0032550	GO:0043492	GO:0015405	GO:0016820
GO-Score	0.48	0.48	0.48	0.37	0.37	0.37
Biological Processes	GO:0044765	GO:0044763
GO-Score	0.37	0.37
Cellular Component	GO:0016021	GO:0005576	GO:0016324
GO-Score	0.19	0.07	0.07

(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 Rv3760

[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]