I-TASSER results

Input Sequence in FASTA format

>protein (90 residues)
MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAES
ARLTVADVVAEARGRIGEEAPLPAGARVDE

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAESARLTVADVVAEARGRIGEEAPLPAGARVDE
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Conf.Score	956788999999999987789999999998756655678899999876656789999999998999999999998755689998889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAESARLTVADVVAEARGRIGEEAPLPAGARVDE
Prediction	443322334323321322221311420352246331351313133221323443553155241422402340374347634436456688
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
MVTHELLVKAAGAVLTGLVGVSAYETLRKALGTAPIRRASVTVMEWGLRGTRRAEAAAESARLTVADVVAEARGRIGEEAPLPAGARVDE

5cwcA2

0.19

0.99

0.83

MUSTER

LAIRLIKECVENAQREGYDISEACRAAAEAFKRVAAKRAGITSSETLKRAIEEIRKRVEEAQREGND-ISEACRQAAEEFRKKAEELKRR

5hdaA1

0.12

0.11

0.89

0.66

dPPAS

------RMKSDHKRETERVVREALEKLRSEMEEEKRQAVNKAVANMQGEMDRKCKQVKEKCKEEFVEEIKKLATQHKQLISQTKKK----

1fewA1

0.15

0.12

0.83

0.67

wdPPAS

SLSSEALMRRAVSLVTDSTSTFLSQTTYALIE---LETTWMTAVGLSEMAAEAAYQTADQASITARNHIQLVKLQVEE------------

4aurA

0.14

1.00

0.65

wMUSTER

NAATEILKTNVPEVLLVKTGDVVKDIVIQRVTLASRHLDELNTFVEKNDEDHRFSNDIKQSRIEVKRLAGELFEELNLEKQLSQLRPLDL

5idxA1

0.21

0.16

0.74

0.69

wPPAS

M---GIAGKTA--LVCAGLGRGCAEALAAE--------VNLVIVA---RTRDTLERTADEIRAAACDI-PDGRAAALAACPQP------D

2n9bA

0.10

0.08

0.77

0.74

dPPAS2

-------GSHENKQVEEILRLEKEIEDLQRMKE--RQELSLTEASLQKLQLEDKVEELLSKNYHLENEVARLKKLVGE------------

5cwjA2

0.26

0.22

0.84

0.81

PPAS

-QDSEVLEEAIRVILRIAKESGSEEALRQAIRAAEIAKEAPRVLEEAIRVIRQIAEESEEARRQAERAEEEIRRRAQ-------------

1p6tA2

0.13

0.11

0.86

0.95

Env-PPAS

VTEKAEFD------IEGMTCAACANRIEKRLNKIEVANAPVNFA------LETVTVEYNPKEAS-VSDLKEAVDKLGYKLKLKGEQDSIE

5jqzA

0.16

0.13

0.81

MUSTER

IEANSRMLKALIEIAKAIWKALWANSLLLEATS----RGDTERMRQWAEEARKIYKEAEKIIDRADEIVEEAKKR--HD-----------

5cffA

0.08

0.92

0.63

dPPAS

FELRRQASNYQLTLTNTRATVNILERLKKSDADVEQYRAELESVQLAKGALEQSYLVLQADAEQLRQQLTESQDALNALRSSS-------

(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=-2.99

Estimated TM-score = 0.38±0.13

Estimated RMSD = 10.3±4.6Å

Download Model 2

C-score=-3.31

Download Model 3

C-score=-3.20

Download Model 4

C-score=-3.04

Download Model 5

C-score=-4.44

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	4cemA	0.658	2.93	0.115	0.933
2	4uvkA1	0.640	3.50	0.033	0.967
3	4d0pA	0.636	2.80	0.105	0.900
4	4kf7A3	0.636	2.71	0.082	0.889
5	5hb1A1	0.634	3.03	0.081	0.878
6	5haxA	0.623	3.12	0.079	0.867
7	3icqT1	0.622	2.95	0.046	0.933
8	4um2A2	0.619	3.12	0.070	0.944
9	5fvmA	0.618	2.95	0.107	0.922
10	4jspB	0.614	2.88	0.112	0.889

(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	0.12	11	3mjwA	WYF	Rep, Mult	44,46,54,65
2	0.07	6	3fggB	ZN	Rep, Mult	67,71
3	0.04	3	3pg9A	AZI	Rep, Mult	37,71
4	0.03	3	3q43A	D66	Rep, Mult	44,45,64,67,68,71,72,75
5	0.03	3	2chwA	039	Rep, Mult	45,46,49,54,55
6	0.03	3	3tl5A	980	Rep, Mult	20,23,27,30
7	0.02	2	1a0aA	NUC	Rep, Mult	52,59,62
8	0.02	2	1e8wA	QUE	Rep, Mult	72,73,76,77
9	0.02	2	3l08A	ZIG	Rep, Mult	48,54,70,71,72
10	0.01	1	3q44A	D50	Rep, Mult	38,41,45,46,49
11	0.01	1	3t8mA	3T8	Rep, Mult	14,25,65,70
12	0.01	1	1e7uA	KWT	Rep, Mult	33,35,37,41,76,77
13	0.01	1	3nzuA	NZU	Rep, Mult	8,24,52,56,66
14	0.01	1	3dbsA	GD9	Rep, Mult	20,23,30,43,49
15	0.01	1	3dpdA	41A	Rep, Mult	24,56,66
16	0.01	1	1e7vA	LY2	Rep, Mult	64,68,69
17	0.01	1	3csfA	DW2	Rep, Mult	9,10,11,15,16
18	0.01	1	3atsA	CA	Rep, Mult	77,79

	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	2x6fA	0.573	3.34	0.071	0.889	2.7.1.137,2.7.1.153,2.7.1.154	20,31
2	0.060	1fmiA	0.561	3.52	0.036	0.889	3.2.1.113	NA
3	0.060	1f1sA	0.574	3.59	0.058	0.922	4.2.2.1	NA
4	0.060	2vn4A	0.549	3.53	0.060	0.911	3.2.1.3	NA
5	0.060	1h12A	0.553	3.86	0.071	0.933	3.2.1.8	NA
6	0.060	1is9A	0.553	3.39	0.037	0.889	3.2.1.4	NA
7	0.060	1ujkB	0.492	3.61	0.076	0.800	3.4.23.46	6
8	0.060	2j2fA	0.549	3.53	0.047	0.867	1.14.19.2,1.14.99.6	67
9	0.060	1lwtA	0.566	3.29	0.084	0.867	3.6.3.14	NA
10	0.060	1cb8A	0.559	3.67	0.072	0.911	4.2.2.5	73
11	0.060	3d9dA	0.538	3.68	0.157	0.878	1.7.3.1	NA
12	0.060	2rd0A	0.586	3.18	0.049	0.900	2.7.1.153	NA
13	0.060	1i8qA	0.578	3.55	0.060	0.911	4.2.2.1	10
14	0.060	3ismC	0.560	3.42	0.080	0.911	3.6.1.3	12,52
15	0.060	3dpyA	0.533	2.81	0.038	0.756	2.5.1.58,2.5.1.59	24
16	0.060	2vtbA	0.559	3.46	0.082	0.867	4.1.99.3	NA
17	0.060	1dfaA	0.568	3.29	0.071	0.878	3.6.3.14,3.6.1.34	NA
18	0.060	1s5jA	0.552	3.96	0.034	0.933	2.7.7.7	NA
19	0.060	1fo2A	0.560	3.68	0.036	0.900	3.2.1.113	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	0.09	0.644	3.22	0.03	0.96	4pjwA	GO:0000775 GO:0000785 GO:0005634 GO:0005654 GO:0005694 GO:0005730 GO:0005829 GO:0005886 GO:0007049 GO:0007059 GO:0007062 GO:0007067 GO:0015629 GO:0016020 GO:0016925 GO:0032876 GO:0045111 GO:0051301 GO:0051321
1	0.09	0.609	3.16	0.15	0.93	4kf7A	GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
2	0.07	0.633	2.81	0.10	0.90	4d10D	GO:0000338 GO:0000715 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006283 GO:0008021 GO:0008180 GO:0010388 GO:0019784 GO:0030054 GO:0031410 GO:0045202 GO:0070062
3	0.07	0.566	3.22	0.09	0.88	3jcoP	GO:0000502 GO:0006511 GO:0008180 GO:0008541 GO:0010388 GO:0031595 GO:0034515 GO:0043161
4	0.07	0.592	2.73	0.04	0.83	3txmA	GO:0000502 GO:0005838 GO:0005875 GO:0008541 GO:0043161
5	0.07	0.658	2.89	0.12	0.93	4cemB	GO:0000184 GO:0001889 GO:0003723 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0031100 GO:0035145 GO:0042162 GO:0048471
6	0.07	0.564	3.61	0.09	0.93	4cekA	GO:0000184 GO:0001889 GO:0003723 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0031100 GO:0035145 GO:0042162 GO:0048471
7	0.07	0.569	3.55	0.10	0.88	5a9qA	GO:0000972 GO:0005215 GO:0005634 GO:0005635 GO:0005643 GO:0006405 GO:0006406 GO:0006409 GO:0006606 GO:0006810 GO:0006913 GO:0006998 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0031965 GO:0036228 GO:0044611 GO:0051028 GO:0075733 GO:0086014 GO:1900034
8	0.07	0.522	3.82	0.09	0.89	4lunU	GO:0000184 GO:0003723 GO:0005737 GO:0005844 GO:0006310 GO:0006452 GO:0070478
9	0.07	0.501	3.61	0.10	0.83	4f5xB	GO:0003723 GO:0019013
10	0.07	0.623	3.12	0.08	0.87	5haxA	GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
11	0.07	0.533	3.53	0.11	0.91	4uvkA	GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
12	0.07	0.476	3.89	0.10	0.84	4d10C	GO:0000715 GO:0001701 GO:0005634 GO:0005654 GO:0005737 GO:0006283 GO:0006511 GO:0007165 GO:0008180 GO:0009416 GO:0010388
13	0.07	0.634	3.03	0.08	0.88	5hb1A	GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
14	0.07	0.404	4.62	0.06	0.79	4ghnA	GO:0006508 GO:0008236 GO:0016020 GO:0016021
15	0.06	0.428	3.98	0.13	0.73	4ijcA	GO:0005737 GO:0005829 GO:0016491 GO:0044262 GO:0045290 GO:0055114
16	0.06	0.435	3.88	0.04	0.74	2kwiA	GO:0000145 GO:0000166 GO:0000910 GO:0001928 GO:0001934 GO:0003924 GO:0005525 GO:0005622 GO:0005776 GO:0005886 GO:0006915 GO:0007049 GO:0007165 GO:0007264 GO:0007265 GO:0009267 GO:0016020 GO:0019003 GO:0030496 GO:0031625 GO:0032091 GO:0032092 GO:0051117 GO:0051301 GO:0060178 GO:0070062 GO:0071360 GO:0071902 GO:2000786
17	0.06	0.478	4.07	0.06	0.86	5aijA	GO:0016787 GO:0042802 GO:0046872 GO:0046983
18	0.06	0.414	3.99	0.03	0.72	1nikA	GO:0001055 GO:0001172 GO:0003677 GO:0003899 GO:0003968 GO:0005634 GO:0005665 GO:0006351 GO:0006366 GO:0016740 GO:0016779 GO:0019985 GO:0043566 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0017056	GO:0019784
GO-Score	0.09	0.07
Biological Processes	GO:0010388	GO:0043161	GO:0032876	GO:0051321	GO:0007067	GO:0016925	GO:0007062	GO:0051301	GO:0006606	GO:0031990	GO:0006999	GO:0006283	GO:0000715
GO-Score	0.13	0.13	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.07	0.07
Cellular Component	GO:0005654	GO:0008180	GO:0008541	GO:0000785	GO:0005886	GO:0015629	GO:0005730	GO:0045111	GO:0000775	GO:0044611	GO:0008021	GO:0070062	GO:0030054	GO:0031595	GO:0005875	GO:0034515
GO-Score	0.15	0.13	0.13	0.09	0.09	0.09	0.09	0.09	0.09	0.09	0.07	0.07	0.07	0.07	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 Rv1993c

[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]