I-TASSER results

I-TASSER results for job id Rv1089

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (120 residues)
SFAGAEAANASQLQSIARQVRGAVNAVAGQVTGNGGSGNSGTSAAAANPNSDNTASIADR
GTSAIMTTASATASSTGVDGGIAATYAVASQWDGGYVANYTITQFGRDFDDRLAVAIHFA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| SFAGAEAANASQLQSIARQVRGAVNAVAGQVTGNGGSGNSGTSAAAANPNSDNTASIADRGTSAIMTTASATASSTGVDGGIAATYAVASQWDGGYVANYTITQFGRDFDDRLAVAIHFA
Prediction	CCCCHHHCCHHHHHHHHHHHHHHHHHHCEEEHCCCCCCCCCCCCHCCCCCCCCCCEEHCCCCCEEEEHCCCCCCCCCCCCCEEEEEEEEHCCCCCEEEEEEEEHCCCCCCCEEEEEEEHC
Conf.Score	976555456789999999997555544446656888888876544468888875444357775566655666666787765555666544568765766777544677664357787659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| SFAGAEAANASQLQSIARQVRGAVNAVAGQVTGNGGSGNSGTSAAAANPNSDNTASIADRGTSAIMTTASATASSTGVDGGIAATYAVASQWDGGYVANYTITQFGRDFDDRLAVAIHFA
Prediction	834445435364045105414321422243133544534433433444364643341354434122323434354442422122222214424332114231342055244303112427
	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                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHCCHHHHHHHHHHHHHHHHHHCEEEHCCCCCCCCCCCCHCCCCCCCCCCEEHCCCCCEEEEHCCCCCCCCCCCCCEEEEEEEEHCCCCCEEEEEEEEHCCCCCCCEEEEEEEHC
SFAGAEAANASQLQSIARQVRGAVNAVAGQVTGNGGSGNSGTSAAAANPNSDNTASIADRGTSAIMTTASATASSTGVDGGIAATYAVASQWDGGYVANYTITQFGRDFDDRLAVAIHFA

4ut1A2

0.21

0.19

0.90

0.88

MUSTER

-LAAGVATN----SGTGVISQGSV--SAGYQLPSGTTTNAASKTLSGFP-VGTTVTIAGTPPTSINITSATTPVPYDPSKGASMTISSTTQAPSGVMNGVSVSLSGTPADDQFTIG----

1hpwA

0.14

0.13

0.97

0.67

dPPAS

EFARAQLSEAMTLASGLKTKVSDIFSQDGSCPANTAATAGIEKDTDINGKYVAKVTTGGTAAASGGCTIVATMKASDVATPLKTLTLTLGNADKGSYTWACTSNADNKYLPK---TCQTA

5tgnA

0.34

0.26

0.77

0.59

wdPPAS

-AAAIDLAREYISRVNGRDGSGAAALFAGEIIAPVGRVYRGWDAIAAAPPA-TTAQIAERGTHRVVLH------------GVVQTFAPAQ-WDGDRIRRLTINHL-RD------------

3emoC

0.22

0.20

0.91

0.73

wMUSTER

SATSTDAINGSQLYAVAKGVTNLAGQVNGKVNKVGKRADAGTASALA------ASQLATMPGKSMVAIAGSSYQG---QNGLAIGVSRISD-NGKVIIRLSGTTNSQG-KTGVAAGVGYQ

1p9hA2

0.30

0.22

0.72

0.64

wPPAS

-Y-GA--ASTAQKDGVA----GADTGVAGKADAKNS-GH-SSHVAANHGYS-GDRSKTDRNSVSI--HESLNRQLTHLAAGTKDTDAV----------N--VAQL-KKEIEK--------

4q1qA1

0.25

0.18

0.73

0.62

dPPAS2

------------------------KAAYDQTIGRGETSSAGDTAKNTTINSGGKQYVSS-GGSATSTTINIGGVQHVSSGGSATSSTIGHQHSGGSATNTTVNNGG-------RQTVFSG

1p9hA2

0.26

0.20

0.76

0.80

PPAS

--YGA--ASTAQKDGVA---ARASTGVAGKADAKNSVGH-SSHVAANHGYSIGDRSKTDRENSVSIGHESLNRQLTHLAAGTKDTDAV------------NVAQL-KKEIEK--------

4uzmA

0.18

0.17

0.91

0.86

Env-PPAS

AFADAQTLTPEERSAVENYLESLTQVL--QVPGPTGASAAPISL-ALNAESNNVMMLT-H---AITRYGISTDDPNKLD---SVEVHLPPFWE-QYINDENTVELIHTDSLPLVISLHTL

1oqwA

0.21

0.20

0.94

0.78

MUSTER

AIIGILAA-QYQNYVARSEGASALASVNPLKTTRGWSVKSGTGTEDATKKEVPLGVAADANKLGTIALKPDPADGTAD---ITLTFTMGGA--GPKNKGKIITLT-RTAADLWKCTSDQD

3emoC

0.21

0.17

0.85

0.62

dPPAS

SATSTDAINGSQLYAVAKGVTNLAGQVEGKVNKVGKRADAGTASALAQATMPGKSMVAIQGQNGLAIGVSRISD----NGKVIIRLSGTTNSQGKTGVAAGVGYQW--------------

(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=-3.22

Estimated TM-score = 0.35±0.12

Estimated RMSD = 11.6±4.5Å

Download Model 2

C-score=-3.34

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.41

Download Model 5

C-score=-4.33

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	2oknA	0.581	3.70	0.047	0.875
2	4b28A	0.573	3.65	0.048	0.867
3	2bwxA	0.572	3.78	0.075	0.883
4	4egeA	0.572	3.65	0.114	0.867
5	1wy2A	0.570	3.81	0.075	0.883
6	5jqkA	0.570	3.77	0.047	0.875
7	2b3lA	0.569	3.76	0.065	0.875
8	4r60A	0.568	3.55	0.095	0.867
9	4km3A	0.567	4.00	0.045	0.900
10	3s6bA	0.567	3.76	0.057	0.867

(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	0.05	2	1swuA	MPD	Rep, Mult	11,83,104,113
2	0.05	2	3lmtA	IOD	Rep, Mult	21,25
3	0.05	2	1qpaA	CA	Rep, Mult	75,93,101,104,108
4	0.05	2	1o71B	GOL	Rep, Mult	37,73,76,77,104,105,108
5	0.05	2	2vveB	CA	Rep, Mult	104,108,110
6	0.05	2	4ogqA	8K6	Rep, Mult	20,24,57,87
7	0.05	2	5klgA	6UC	Rep, Mult	24,27
8	0.02	1	3t41B	CA	Rep, Mult	65,67,79
9	0.02	1	4ea2A	MG	Rep, Mult	25,96
10	0.02	1	3keuB	MG	Rep, Mult	31,108
11	0.02	1	1kv8A	PO4	Rep, Mult	81,106,107
12	0.02	1	1yvmA	NA	Rep, Mult	64,65,66,88
13	0.02	1	3s6lC	IOD	Rep, Mult	76,88,90
14	0.02	1	4matA	NA	Rep, Mult	24,30,31,65
15	0.02	1	3wmoO	CRT	Rep, Mult	14,24

	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	1imaA	0.409	4.66	0.078	0.750	3.1.3.25	NA
2	0.060	1ftaA	0.488	4.19	0.071	0.783	3.1.3.11	NA
3	0.060	1wn1A	0.564	3.90	0.055	0.883	3.4.-.-	110
4	0.060	2wefA	0.513	4.70	0.116	0.883	3.1.3.7	NA
5	0.060	1bk4A	0.487	4.17	0.071	0.792	3.1.3.11	NA
6	0.060	1wy2A	0.570	3.81	0.075	0.883	3.4.13.9	NA
7	0.060	1awbA	0.423	4.34	0.096	0.725	3.1.3.25	62
8	0.060	1fsaA	0.515	4.00	0.093	0.825	3.1.3.11	NA
9	0.060	3d1rA	0.506	4.19	0.046	0.817	3.1.3.11	NA
10	0.060	1qxwA	0.537	3.78	0.095	0.850	3.4.11.18	33
11	0.060	2b3lA	0.569	3.76	0.065	0.875	3.4.11.18	NA
12	0.060	2iw2A	0.581	3.70	0.047	0.875	3.4.13.9	NA
13	0.060	1pv9B	0.528	3.88	0.049	0.825	3.4.13.9	NA
14	0.060	3fmrB	0.554	3.81	0.067	0.850	3.4.11.18	NA
15	0.060	2gq1A	0.470	4.46	0.049	0.800	3.1.3.11	NA
16	0.060	2ea4A	0.547	3.95	0.084	0.867	3.4.11.18	100
17	0.060	1qxyA	0.537	3.77	0.095	0.850	3.4.11.18	NA
18	0.060	1lbvA	0.507	4.46	0.104	0.825	3.1.3.25,	62
19	0.060	2zsgA	0.548	4.04	0.111	0.892	3.4.11.9	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	0.13	0.568	3.78	0.07	0.88	3mx6B	GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
1	0.13	0.553	3.93	0.04	0.88	4matA	GO:0004177 GO:0005829 GO:0006508 GO:0008198 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
2	0.12	0.544	3.60	0.06	0.82	3iu7A	GO:0004177 GO:0005506 GO:0006508 GO:0006555 GO:0008233 GO:0008235 GO:0016151 GO:0016787 GO:0030145 GO:0035551 GO:0046872 GO:0050897 GO:0070006 GO:0070084
3	0.11	0.581	3.70	0.05	0.88	2iw2A	GO:0004177 GO:0004181 GO:0006508 GO:0006520 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0030145 GO:0030574 GO:0046872 GO:0070062 GO:0102009
4	0.08	0.537	3.78	0.10	0.85	1qxwA	GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
5	0.08	0.556	3.85	0.08	0.87	1pv9A	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
6	0.07	0.548	4.04	0.11	0.89	2zsgA	GO:0004177 GO:0006508 GO:0016787 GO:0046872
7	0.07	0.498	3.66	0.07	0.76	3j2iA	GO:0003677 GO:0003700 GO:0003723 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006351 GO:0006355 GO:0006364 GO:0006417 GO:0007050 GO:0008283 GO:0016020 GO:0030529 GO:0031625 GO:0043066 GO:0044822 GO:0045597 GO:0045892 GO:0070062
8	0.07	0.541	3.47	0.11	0.82	4qr8A	GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0016795 GO:0016805 GO:0030145 GO:0043171 GO:0046872 GO:0070573 GO:0102009
9	0.07	0.567	3.76	0.06	0.87	3s6bA	GO:0004177 GO:0005737 GO:0006464 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
10	0.07	0.567	4.00	0.04	0.90	4km3A	GO:0004177 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0046872 GO:0070006 GO:0070084
11	0.07	0.565	3.82	0.07	0.87	3ig4A	GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
12	0.07	0.570	3.81	0.07	0.88	1wy2A	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
13	0.07	0.574	3.77	0.07	0.88	2bh3A	GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0030145 GO:0042802 GO:0046872
14	0.06	0.399	5.49	0.03	0.82	3v1hA	GO:0004436 GO:0005576 GO:0006629 GO:0008081 GO:0009405 GO:0016042 GO:0016829
15	0.06	0.353	5.32	0.09	0.73	4dllA	GO:0004616 GO:0008679 GO:0016491 GO:0051287 GO:0055114
16	0.06	0.374	5.11	0.05	0.72	1nd1A	GO:0004222 GO:0005576 GO:0006508 GO:0006935 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
17	0.06	0.533	3.68	0.09	0.82	3l24B	GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
18	0.06	0.565	3.85	0.03	0.88	4s2rP	GO:0004177 GO:0006508 GO:0016787 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0070006
GO-Score	0.43	0.38
Biological Processes	GO:0006508	GO:0070084
GO-Score	0.45	0.38
Cellular Component	GO:0005829	GO:0070062
GO-Score	0.12	0.11

(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.