I-TASSER results

Input Sequence in FASTA format

>protein (80 residues)
MVAASIVHHSAAPANRGRYHGIWSMTPVVASVVVPIMASYGPIHGAHLLAAVVVGSAGAA
LCLPLARALRRPTPSAMTTD

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MVAASIVHHSAAPANRGRYHGIWSMTPVVASVVVPIMASYGPIHGAHLLAAVVVGSAGAALCLPLARALRRPTPSAMTTD
Prediction	CCCHHHHHHCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHCCCCHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Conf.Score	97645677648876788577775335689999999898746554567899999999999999999999748898777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MVAASIVHHSAAPANRGRYHGIWSMTPVVASVVVPIMASYGPIHGAHLLAAVVVGSAGAALCLPLARALRRPTPSAMTTD
Prediction	74344233423444663423212333333333223222323334323211111233333321331343244444644568
	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

CCCHHHHHHCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHCCCCHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
MVAASIVHHSAAPANRGRYHGIWSMTPVVASVVVPIMASYGPIHGAHLLAAVVVGSAGAALCLPLARALRRPTPSAMTTD

5d92D2

0.12

0.11

0.94

1.00

MUSTER

KYARGLFAAIFLPIARLLAWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFRE-----

5d92D2

0.12

0.11

0.94

1.05

wMUSTER

KYARGLFAAIFLPIARLLAWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFRE-----

4x82B1

0.15

0.14

0.94

0.88

MUSTER

VALGGLLNTLAAHCTSGPCGKCLSVDDLLALHLARLSAAAALLSDPEGTCEDIRAGRWASRADHLLALLE--GPKAL---

5d92D2

0.09

0.94

0.72

dPPAS

YARGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFRE-----

4cj9A8

0.14

0.10

0.70

0.71

wdPPAS

--SQPDIVKIA--GNSG---G--AQALQAVLDLELTFRERGFS--QADIVKIAGN--GGTQALHAVLDL-----------

4x82B1

0.15

0.14

0.93

0.92

wMUSTER

VALGGLLNTLAA-CTSGPCGKCLSVDDLLALHLARLSAAAALLSDPEGTCEDIRAGRWASRADHLLALLE--GPKAL---

2k1lA

0.32

0.15

0.46

0.79

wPPAS

----------SPPVSRG------------------------LT-GGEIVAVIFGLLLGAALLLGILVFRRRA--------

2k1lA

0.29

0.14

0.47

0.74

dPPAS2

----------SPPVSRG------------------------LT-GGEIVAVIFGLLLGAALLLGILVFRSRRA-------

5d92D2

0.11

0.10

0.94

0.84

PPAS

KYARGLFAAIFLPIARLADWGVSPDAVTVVGTLGVMAGALIFYPMGQ-LFWGTVVITVFVFSDIIDGLMARLLFRE----

3ixqA1

0.14

0.12

0.89

0.90

Env-PPAS

KVAKEAVKLVKD----GMVIGLG--TGSTAALFIRELGNR-IREEELTVFGIPTSFEAKMLAMQYE--IPLVTLDEYDVD

(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=-2.14

Estimated TM-score = 0.46±0.15

Estimated RMSD = 8.0±4.4Å

Download Model 2

C-score=-2.18

Download Model 3

C-score=-3.09

Download Model 4

C-score=-4.21

Download Model 5

C-score=-3.73

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	5d92D	0.753	2.35	0.112	1.000
2	4o6mA2	0.736	2.12	0.139	0.988
3	4mndA2	0.704	2.34	0.077	0.975
4	2cjeA	0.682	2.69	0.101	0.988
5	2yxhB1	0.628	2.26	0.101	0.863
6	1oglA1	0.620	2.70	0.077	0.925
7	5aymA	0.619	3.23	0.051	0.950
8	2j2fA	0.618	3.69	0.076	0.938
9	4pypA	0.617	3.21	0.078	0.925
10	3obcA	0.617	2.35	0.051	0.850

(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	0.35	115	2htnA	HEM	Rep, Mult	28,31,32,35,55,59,62,63,65,66
2	0.09	31	1jkvA	MN3	Rep, Mult	27,61,64
3	0.03	9	4ryrA	MPG	Rep, Mult	33,34,42,50,53,54,57
4	0.02	6	3bvxA	MPD	Rep, Mult	59,60,63
5	0.02	7	5da5C	GOA	Rep, Mult	26,27,30,61
6	0.01	2	4zzcA	XE	Rep, Mult	56,57,60
7	0.01	5	2zg8X	PLL	Rep, Mult	40,43,48,51
8	0.01	2	3lw5A	PQN	Rep, Mult	33,34,41,42,54
9	0.01	3	3qbiD	22B	Rep, Mult	27,60,64,67,71
10	0.01	2	3nkoA	NKO	Rep, Mult	20,23,27
11	0.01	4	2jstA	HLT	Rep, Mult	30,57
12	0.00	1	1nd6A	UUU	Rep, Mult	7,8,9
13	0.00	1	3bwxA	CA	Rep, Mult	72,75
14	0.00	1	2np5C	NDS	Rep, Mult	30,31,34,38

	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	0.106	3c90A	0.584	2.67	0.051	0.850	3.6.1.31	NA
2	0.067	2a7wK	0.547	2.81	0.066	0.825	3.6.1.31	NA
3	0.066	1yxbG	0.542	2.55	0.067	0.800	3.6.1.31	32,68
4	0.060	1yvwC	0.586	2.38	0.039	0.825	3.6.1.31	NA
5	0.060	1jkuA	0.598	3.02	0.027	0.900	1.11.1.6	NA
6	0.060	3bvlF	0.585	2.16	0.070	0.713	1.16.3.1	NA
7	0.060	2wlaA	0.565	2.60	0.026	0.762	1.16.3.1	50
8	0.060	1jk0A	0.574	3.70	0.063	0.938	1.17.4.1	NA
9	0.060	1rtyC	0.575	2.55	0.027	0.762	2.5.1.17	NA
10	0.060	1biqB	0.571	3.73	0.051	0.938	1.17.4.1	NA
11	0.060	2uw1B	0.628	3.62	0.101	0.925	1.14.99.6	NA
12	0.060	1h0nA	0.574	3.67	0.038	0.950	1.17.4.1	NA
13	0.060	2cjeA	0.682	2.69	0.101	0.988	3.6.1.23	30,63
14	0.060	2jg0A	0.597	3.02	0.064	0.850	3.2.1.28	NA
15	0.060	3e6sF	0.584	1.93	0.092	0.700	1.16.3.1	NA
16	0.060	1bg7A	0.582	2.27	0.113	0.713	1.16.3.1	40
17	0.060	2vuxB	0.572	3.74	0.051	0.938	1.17.4.1	NA
18	0.060	1mfrW	0.576	2.28	0.085	0.713	1.16.3.1	NA
19	0.060	1r03A	0.582	2.24	0.111	0.700	1.16.3.1	NA
20	0.060	1l2aE	0.612	3.03	0.066	0.875	3.2.1.4	NA
21	0.060	3es3A	0.581	2.30	0.113	0.713	1.16.3.1	NA
22	0.060	1olpA	0.578	3.02	0.065	0.812	3.1.4.3	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	0.14	0.743	2.09	0.14	0.99	4o6mB	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
1	0.13	0.742	2.41	0.10	1.00	5d92B	GO:0000166 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016780 GO:0046872
2	0.13	0.704	2.34	0.08	0.97	4mndA	GO:0003824 GO:0008152 GO:0008654 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0016780 GO:0046872
3	0.12	0.577	2.66	0.03	0.78	2ah6B
4	0.10	0.685	2.68	0.10	0.99	2yb0E	GO:0004170 GO:0016787 GO:0046872
5	0.08	0.636	2.74	0.07	0.93	4dl8A	GO:0004170 GO:0016787 GO:0046872
6	0.07	0.542	3.06	0.10	0.85	1oglA
7	0.07	0.613	2.59	0.03	0.88	1w2yA	GO:0004170 GO:0016787 GO:0046872
8	0.07	0.548	3.08	0.06	0.88	4dk2A	GO:0004170 GO:0016787 GO:0046872
9	0.07	0.523	3.23	0.09	0.84	1q2vA	GO:0000166 GO:0005524 GO:0006457 GO:0051082
10	0.07	0.444	3.28	0.06	0.65	2vmbA	GO:0005886 GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628 GO:0016020 GO:0016021
11	0.06	0.430	3.54	0.05	0.69	5f1lB	GO:0003676 GO:0006351 GO:0006355 GO:0016568 GO:0070577
12	0.06	0.456	3.30	0.11	0.70	1rhgB	GO:0005125 GO:0005130 GO:0005576 GO:0005615 GO:0006955 GO:0007275 GO:0008083 GO:0008284 GO:0014068 GO:0019221 GO:0019899 GO:0030838 GO:0030851 GO:0032092 GO:0033138 GO:0042993 GO:0045639 GO:0045944 GO:0050731 GO:0051897 GO:0071222 GO:0071345 GO:1901215 GO:2000251
13	0.06	0.339	4.71	0.05	0.64	1c53A	GO:0005506 GO:0009055 GO:0020037 GO:0042597 GO:0046872 GO:0055114
14	0.06	0.345	4.65	0.00	0.72	3vp5A	GO:0003677 GO:0006351 GO:0006355 GO:0046872
15	0.06	0.410	3.92	0.03	0.78	1wvcA	GO:0000166 GO:0009058 GO:0009103 GO:0009243 GO:0016740 GO:0016779 GO:0046872 GO:0047343
16	0.06	0.359	3.92	0.03	0.61	4wj3M	GO:0000166 GO:0003676 GO:0004812 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0016874 GO:0050560
17	0.06	0.350	2.67	0.12	0.49	3beyD	GO:0051920 GO:0055114 GO:0098869
18	0.06	0.349	3.18	0.10	0.50	1ga3A	GO:0001774 GO:0002639 GO:0005125 GO:0005126 GO:0005144 GO:0005576 GO:0005615 GO:0005737 GO:0006928 GO:0006954 GO:0006955 GO:0007165 GO:0007267 GO:0009612 GO:0009897 GO:0010155 GO:0030890 GO:0032496 GO:0032723 GO:0033861 GO:0035094 GO:0042526 GO:0043032 GO:0043270 GO:0043306 GO:0045471 GO:0048661 GO:0050714 GO:0051281 GO:0071260 GO:0071345 GO:0071635 GO:1901215 GO:1901247 GO:1901251 GO:1903660 GO:2000231 GO:2000352

Consensus prediction of GO terms

Molecular Function	GO:1901265	GO:0036094	GO:0046872	GO:0016780
GO-Score	0.51	0.51	0.41	0.35
Biological Processes	GO:0008654
GO-Score	0.35
Cellular Component	GO:0016021
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 Rv0841

[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]