I-TASSER results

Input Sequence in FASTA format

>protein (90 residues)
MDDLTRLRRELLDRFDVRDFTDWPPASLRALIATYDPWIDMTASPPQPVSPGGPRLRLVR
LTTNPSARAAPIGNGGDSSVCAGEKQCRPP

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MDDLTRLRRELLDRFDVRDFTDWPPASLRALIATYDPWIDMTASPPQPVSPGGPRLRLVRLTTNPSARAAPIGNGGDSSVCAGEKQCRPP
Prediction	CCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCEHCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	858999999999874756688899799999999848755567899999999998589999679976555667888877644566666899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MDDLTRLRRELLDRFDVRDFTDWPPASLRALIATYDPWIDMTASPPQPVSPGGPRLRLVRLTTNPSARAAPIGNGGDSSVCAGEKQCRPP
Prediction	874345135512641425524724343032103334321424453454355734313114134446344243364444421334662668
	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

CCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCEHCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MDDLTRLRRELLDRFDVRDFTDWPPASLRALIATYDPWIDMTASPPQPVSPGGPRLRLVRLTTNPSARAAPIGNGGDSSVCAGEKQCRPP

1kezA

0.19

0.17

0.88

MUSTER

QDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRL---TGQWRPRETG--LP-TLLVS-----GEPMGPWPDDSWKPTWPFEHDTVAP

2rmsB

0.17

0.11

0.64

0.70

dPPAS

-------------------SSTWSEAEMIALAGL----LQMSQGEQTPNCVA---------SSLPSTSCPDPVSVSEDPGPSGDQSCSGT

2rmsB

0.26

0.16

0.60

0.62

wdPPAS

-------------------SSTWSEAEMIALAGL----LQMSQGEQTPNCPSTS-------CPDPSVSEDPGPSGDQS--CSGTDT----

4g2nA1

0.18

0.17

0.93

0.62

wMUSTER

IRRFPAIEAELRQRFDLLEDTVLTPSGIASRAHGAE--LFVTATEA--ITA-QPGLKTIATLSH-RSLGIKVLHTPGWLLIQGEAQSDVP

3ojyB2

0.40

0.18

0.44

0.63

wPPAS

-------RKN------I-DWNCW---S---------NW-----SS----S-GRRKTR--RQCNNP----PP--NSGPA--SETL-DC---

2rmsB

0.29

0.18

0.61

0.73

dPPAS2

-------------------SSTWSEAEMIALAGL----LQMSQGEQTPVASSLPS------TSCPSVSEDPGPSGDQS--CSGTDT----

1wj9A1

0.28

0.23

0.82

0.66

PPAS

M--LTKLVLNPASR-AAR--RD--LANPYEMHRT------SKAVSRALEEGRE-RL-LWRLEPARGLEPPVV-TEPDSVLDEGYAQVFPP

1r6bX4

0.24

0.19

0.78

0.71

Env-PPAS

VDFIVELQVQLDQK-GVSEVSQ--EARNWLAEKGYDR--AMGARP----------MRVIDNLKKPLANFGSLVDGGDKGFQSAQK-----

3umcA

0.15

0.14

0.97

0.86

MUSTER

QAHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGHALKAD--YWLAALS-NGNTALLDVRHAGWDLLCADLFGHYKP

2i0xA

0.10

0.08

0.78

0.66

dPPAS

VERVNKVKKFLRMHLNWVQNSEVTLAEFERIKEGLKKIIDENSD----------SVIIYKLRSMPPRETLGIEKNPIEEI----------

(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=-4.09

Estimated TM-score = 0.28±0.09

Estimated RMSD = 13.1±4.2Å

Download Model 2

C-score=-4.12

Download Model 3

C-score=-4.39

Download Model 4

C-score=-4.55

Download Model 5

C-score=-4.59

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	5fruA	0.545	3.74	0.038	0.856
2	2qflA	0.537	3.81	0.091	0.922
3	1ddtA3	0.534	3.83	0.072	0.900
4	1xi6A	0.533	3.74	0.057	0.922
5	5kbeA	0.532	3.64	0.013	0.878
6	3uksA	0.529	4.03	0.047	0.922
7	2pfvA	0.528	3.60	0.085	0.844
8	1d9qB	0.525	3.71	0.080	0.878
9	4a01A	0.524	3.96	0.057	0.944
10	1vdwA	0.522	3.83	0.047	0.922

(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	7	3op2A	MG	Rep, Mult	19,40,84
2	0.06	3	3c63D	CA	Rep, Mult	2,3
3	0.04	2	3pfdD	FDA	Rep, Mult	11,15,16,57,58
4	0.04	2	1w25A	MG	Rep, Mult	2,3,40,49
5	0.04	2	2hsjA	MG	Rep, Mult	32,35,39
6	0.04	2	3vbgC	03M	Rep, Mult	4,7,72
7	0.02	1	2ox3A	PEP	Rep, Mult	27,28,29,43
8	0.02	1	2p2nC	ASP	Rep, Mult	19,64,67
9	0.02	1	2qflA	EEE	Rep, Mult	76,77,78
10	0.02	1	3a8eB	CE5	Rep, Mult	30,33,34,35
11	0.02	1	2dttC	H4B	Rep, Mult	21,22,66
12	0.02	1	2h1iB	CA	Rep, Mult	10,13
13	0.02	1	3t7dB	MG	Rep, Mult	6,9
14	0.02	1	2ptfA	FMN	Rep, Mult	28,31,32

	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	3hfwA	0.508	4.17	0.057	0.889	3.2.2.19	NA
2	0.060	2cjbB	0.492	3.95	0.093	0.789	6.1.1.11	NA
3	0.060	2pg0A	0.495	3.83	0.075	0.822	1.3.99.3	10
4	0.060	1g0iA	0.522	3.93	0.023	0.911	3.1.3.25	14,20
5	0.060	1e6yA	0.502	3.25	0.089	0.767	2.8.4.1	NA
6	0.060	2gq1A	0.519	3.95	0.080	0.933	3.1.3.11	NA
7	0.060	1wsaB	0.488	3.49	0.054	0.811	3.5.1.1	NA
8	0.060	1ivhA	0.495	4.24	0.059	0.878	1.3.99.10	10
9	0.060	2i4nB	0.497	3.81	0.057	0.800	6.1.1.15	NA
10	0.060	2qflA	0.537	3.81	0.091	0.922	3.1.3.25	NA
11	0.060	1spiA	0.515	3.93	0.068	0.900	3.1.3.11	NA
12	0.060	1awbA	0.524	3.92	0.057	0.911	3.1.3.25	NA
13	0.060	1djoA	0.483	3.27	0.085	0.767	3.5.1.38	35
14	0.060	1rx0A	0.494	3.66	0.063	0.822	1.3.99.-	NA
15	0.060	2himD	0.503	3.19	0.085	0.789	3.5.1.1	NA
16	0.060	2p3nA	0.502	3.93	0.086	0.867	3.1.3.25	NA
17	0.060	1dk4A	0.502	4.12	0.023	0.900	3.1.3.25	NA
18	0.060	1ec9D	0.495	3.63	0.077	0.767	4.2.1.40	NA
19	0.060	1ho3A	0.497	3.18	0.100	0.778	3.5.1.1	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	0.19	0.502	4.07	0.08	0.93	2cziA	GO:0000287 GO:0005737 GO:0005829 GO:0006020 GO:0006021 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0042803 GO:0043647 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
1	0.07	0.519	4.12	0.04	0.93	1lbvA	GO:0005975 GO:0006094 GO:0008934 GO:0016311 GO:0016787 GO:0042132 GO:0046854 GO:0046872 GO:0052832 GO:0052833 GO:0052834
2	0.07	0.521	4.12	0.08	0.93	4he0A	GO:0003824 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006000 GO:0006094 GO:0008152 GO:0016311 GO:0016787 GO:0030018 GO:0030054 GO:0042132 GO:0042578 GO:0046872 GO:0070062
3	0.07	0.425	4.67	0.07	0.87	5eygB	GO:0000287 GO:0005737 GO:0006020 GO:0007165 GO:0008934 GO:0046854 GO:0046855
4	0.07	0.489	4.08	0.05	0.89	4n81A	GO:0046854
5	0.07	0.457	4.36	0.08	0.89	5djfA	GO:0000103 GO:0000287 GO:0005737 GO:0005886 GO:0006020 GO:0007165 GO:0008441 GO:0008934 GO:0016787 GO:0030145 GO:0040007 GO:0042132 GO:0046854 GO:0046855 GO:0046872 GO:0050427 GO:0050897 GO:0052832 GO:0052833 GO:0052834
6	0.07	0.501	4.08	0.05	0.93	5et5A	GO:0003824 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006000 GO:0006094 GO:0008152 GO:0016311 GO:0016787 GO:0030018 GO:0030054 GO:0042132 GO:0042578 GO:0046872 GO:0070062
7	0.07	0.522	3.83	0.05	0.92	1vdwA	GO:0046854
8	0.07	0.533	3.74	0.06	0.92	1xi6A	GO:0046854
9	0.07	0.361	4.56	0.05	0.71	4hxvA	GO:0000103 GO:0000166 GO:0000287 GO:0005737 GO:0008441 GO:0009086 GO:0016311 GO:0046854 GO:0046872
10	0.07	0.519	4.18	0.07	0.93	3t0jA	GO:0046854
11	0.07	0.502	3.93	0.09	0.87	2p3nA	GO:0000287 GO:0005737 GO:0005975 GO:0006020 GO:0006094 GO:0007165 GO:0008934 GO:0016787 GO:0042132 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
12	0.07	0.490	4.08	0.10	0.87	3luzB	GO:0008934 GO:0046854 GO:0046855
13	0.07	0.537	3.81	0.09	0.92	2qflA	GO:0000287 GO:0005737 GO:0005829 GO:0006020 GO:0007165 GO:0008934 GO:0016787 GO:0031403 GO:0046854 GO:0046855 GO:0046872 GO:0047954 GO:0052832 GO:0052833 GO:0052834
14	0.07	0.495	4.07	0.06	0.89	2q74A	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0007165 GO:0008934 GO:0016787 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
15	0.07	0.456	4.62	0.07	0.89	1k9yA	GO:0000103 GO:0000287 GO:0005634 GO:0005737 GO:0006790 GO:0008441 GO:0009086 GO:0016311 GO:0016787 GO:0042538 GO:0046854 GO:0046872
16	0.07	0.513	4.07	0.04	0.92	3lv0A	GO:0008934 GO:0046854 GO:0046855
17	0.07	0.496	4.19	0.06	0.92	4as5A	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0006661 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0030145 GO:0031403 GO:0042802 GO:0042803 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834 GO:0070062
18	0.07	0.494	4.10	0.06	0.91	2bjiA	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0006661 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0030145 GO:0031403 GO:0042802 GO:0042803 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0052834	GO:0046983	GO:0042802
GO-Score	0.59	0.59	0.38	0.38
Biological Processes	GO:0071545	GO:0051716	GO:0044700	GO:0007154	GO:0046838	GO:0050794	GO:0034637	GO:0046173	GO:0046854
GO-Score	0.49	0.49	0.49	0.49	0.49	0.49	0.38	0.38	0.34
Cellular Component	GO:0044444
GO-Score	0.49

(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 Rv2662

[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]