I-TASSER results

I-TASSER results for job id Rv1891

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

Input Sequence in FASTA format

>protein (135 residues)
MIRELVTTAAITGAAIGGAPVAGADPQRYDGDVPGMNYDASLGAPCSSWERFIFGRGPSG
QAEACHFPPPNQFPPAETGYWVISYPLYGVQQVGAPCPKPQAAAQSPDGLPMLCLGARGW
QPGWFTGAGFFPPEP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MIRELVTTAAITGAAIGGAPVAGADPQRYDGDVPGMNYDASLGAPCSSWERFIFGRGPSGQAEACHFPPPNQFPPAETGYWVISYPLYGVQQVGAPCPKPQAAAQSPDGLPMLCLGARGWQPGWFTGAGFFPPEP
Prediction	CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCEEHCCCCCCCCCCCCCCCCEEHCCCEHCEEHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCEHCCCCCCCCC
Conf.Score	867899998655444567888888988899999998888877888889875666658999867656788888998889857866874456655899999887667899856888778988787565788999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MIRELVTTAAITGAAIGGAPVAGADPQRYDGDVPGMNYDASLGAPCSSWERFIFGRGPSGQAEACHFPPPNQFPPAETGYWVISYPLYGVQQVGAPCPKPQAAAQSPDGLPMLCLGARGWQPGWFTGAGFFPPEP
Prediction	643320311133333333333342644526421121344241233136343010122553422203334445244544432242331221343546165473324334221000234733432224246333578
	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

CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCEEHCCCCCCCCCCCCCCCCEEHCCCEHCEEHCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCEHCCCCCCCCC
MIRELVTTAAITGAAIGGAPVAGADPQRYDGDVPGMNYDASLGAPCSSWERFIFGRGPSGQAEACHFPPPNQFPPAETGYWVISYPLYGVQQVGAPCPKPQAAAQSPDGLPMLCLGARGWQPGWFTGAGFFPPEP

4ut1A2

0.14

0.12

0.84

0.83

MUSTER

-------LAAGVATNSGTGVISQGS-VSAGYQLPSGTTTLAY----NAASKTLSGF-PVGTTVTIAGTPPTSINITSATTPVPYDPSKGASMTISS-TTQPAPSGVMNGVSVSLSGTPADGDQFTIG--------

5fhhA2

0.07

1.00

0.77

dPPAS

DDVALTNERRLQELPGKVHRFEAMDSNPELASTLDAQCPVSQLLQLKLGAQVMLVKNLSVSRGLVNGARGVVLPQVLCGVTEVIHADRWTVQATGGQLLSRQQLPLQLAWAMSIHKSQGMTLDCVEISLGRVFAS

1u34A

0.22

0.17

0.76

0.86

wdPPAS

------------GSGMKETAAAKFERQHMD--SPDLG-TTLLEQYCHRTTI----GNFSGPYTYC--------NTTLDQIWPQSAP--G-ALVERPCPEYNGIKYNTTRAYRECL-ENGWAS-RVNYSHCEPILD

5a9qA

0.16

0.15

0.91

0.85

wMUSTER

MSASV-SQNAIVSAAGNIARTIDRSV------FKIVQIAVI--ENSESLDCQLLAVTHAGVRLYFSTCPFRARPNTLTLVHVRLPP--G-FSASSTVEKPSKVHRASKGILLMAASENDNDILWCVNHDTFPFQK

1u34A

0.22

0.17

0.76

0.89

wPPAS

------------GSGM--KETAAAKFERQHMDSPDLG-TTLLEQYCHRTTI----GNFSGPYTYC--------NTTLDQIWPQSAP--G-ALVERPCPEYNGIKYNTTRAYRECL-ENGWAS-RYSHCEPILDDK

2rmsB

0.14

0.05

0.38

1.01

dPPAS2

MIALAGLLQMSQGEQTPNCVASSLPSTSCPDPVSVSEDPGPSGDQCSGTDT------------------------------------------------------------------------------------

1u34A

0.21

0.16

0.77

0.90

PPAS

--------------GSGMKETAAAKFERQHMDSPDLG-TTLLEQYCHRTTI----GNFSGPYTYC--------NTTLDQIWPQSAP--G-ALVERPCPENGIKYNTTRNAYRECLENGTWAS-RYSHCEPILDDK

2fflA1

0.20

0.18

0.88

0.69

Env-PPAS

DLRALMVTAQLMCDAKRLSDELSASLHGRMVATPEISWSVVLGIDSTQTSLSYFTRANESITYMRYYTAHNIHLRAADLPLVAAVRLDDLKDHQIPAPGSDDLA--PKLRFLLCL----LLPDEF----------

3twkA1

0.12

0.98

0.74

MUSTER

ELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSSILGKTIISARRNLWLELDSPPFPSFQFGAGAIYIKGVAVT--KYKRSAVKDSEEWPSKYSKFFVELDDGLELSFTDKRRFAKVRLL-ANPTSVSP

1u34A

0.19

0.15

0.77

0.76

dPPAS

--------------GSGMKETAAAKFERQHMDSPDLG-TTLLEQYCHRTTI----GNFSGPYTYCNTTLDQIGPQSAPGALVERP-----------CPENGIKYNTTRNAYRECL-ENGTWASRVNYSHCEPILD

(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=-4.12

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.3±3.8Å

Download Model 2

C-score=-4.61

Download Model 3

C-score=-4.83

Download Model 4

C-score=-4.62

Download Model 5

C-score=-5.00

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	4ojvA	0.465	4.85	0.057	0.837
2	4iv9A	0.460	4.89	0.088	0.815
3	3aboA2	0.458	4.94	0.092	0.822
4	2dy1A	0.458	5.21	0.055	0.904
5	4a69A	0.455	5.20	0.073	0.874
6	1g7sA	0.454	4.95	0.056	0.830
7	3e49A	0.454	5.05	0.118	0.822
8	3maxA	0.451	5.21	0.065	0.874
9	2dskA	0.451	5.16	0.058	0.844
10	3pt1A	0.451	4.93	0.050	0.815

(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	0.06	3	1wepA	ZN	Rep, Mult	46,65,97,114
2	0.06	3	3maxA	NA	Rep, Mult	84,85,87,90,119
3	0.06	3	2wsf3	CLA	Rep, Mult	52,53
4	0.04	2	1in0A	MMC	Rep, Mult	5,9,53
5	0.04	2	4jjfB	N2I	Rep, Mult	1,57,126
6	0.04	2	2pybA	FE	Rep, Mult	66,74
7	0.04	2	2vqvA	HA3	Rep, Mult	93,95,103
8	0.02	1	1d0cA	ZN	Rep, Mult	97,114
9	0.02	1	3m0fB	GSH	Rep, Mult	3,28,32
10	0.02	1	3fbyA	CA	Rep, Mult	30,32,37,39
11	0.02	1	3nt0A	CU1	Rep, Mult	1,5
12	0.02	1	1np1A	HSM	Rep, Mult	24,26,115,120
13	0.02	1	2b2jA	XE	Rep, Mult	42,52,54
14	0.02	1	1y4jA	UUU	Rep, Mult	70,71
15	0.02	1	3ppiA	MG	Rep, Mult	9,13,15

	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	1d2kA	0.448	4.97	0.057	0.800	3.2.1.14	50,85
2	0.060	3beqB	0.398	4.98	0.059	0.748	3.2.1.18	74
3	0.060	2nvrA	0.443	5.18	0.079	0.852	3.5.1.98	NA
4	0.060	1ptdA	0.414	4.99	0.042	0.763	4.6.1.13	NA
5	0.060	2a3eA	0.437	5.19	0.057	0.822	3.2.1.14	124
6	0.060	3maxA	0.451	5.21	0.065	0.874	3.5.1.98	NA
7	0.060	1f89A	0.441	5.02	0.110	0.807	3.5.-.-	NA
8	0.060	1t64A	0.445	5.33	0.046	0.881	3.5.1.98	NA
9	0.060	1cevA	0.440	5.43	0.073	0.874	3.5.3.1	39
10	0.060	2yr4A	0.450	5.14	0.050	0.822	1.13.12.9	NA
11	0.060	1onxA	0.446	5.24	0.076	0.822	3.4.19.-	NA
12	0.060	1wogA	0.440	5.30	0.105	0.867	3.5.3.11	NA
13	0.060	1pq3A	0.451	5.44	0.055	0.904	3.5.3.1	39
14	0.060	3egjA	0.433	5.21	0.048	0.822	3.5.1.25	15
15	0.060	1wb4B	0.439	4.97	0.018	0.793	3.2.1.8	NA
16	0.060	2vqjA	0.446	5.21	0.056	0.844	3.5.1.98	51
17	0.060	1ll6A	0.449	4.94	0.056	0.800	3.2.1.14	NA
18	0.060	1gq7E	0.436	5.22	0.049	0.859	3.5.3.22	NA
19	0.060	3iv8D	0.398	5.41	0.063	0.763	3.5.1.25	77

(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	0.465	4.85	0.06	0.84	4ojvA	GO:0004114 GO:0004115 GO:0005622 GO:0006198 GO:0008081 GO:0016787 GO:0019933 GO:0030818 GO:0043949 GO:0046069 GO:0047555 GO:1902660 GO:2000480
1	0.07	0.438	4.94	0.08	0.79	3we0A	GO:0000166 GO:0004497 GO:0016491 GO:0050067 GO:0055114
2	0.06	0.362	4.81	0.06	0.64	3ishA	GO:0004791 GO:0005737 GO:0016491 GO:0019430 GO:0055114
3	0.06	0.410	5.13	0.09	0.77	3r9uA	GO:0000166 GO:0004791 GO:0005737 GO:0016491 GO:0019430 GO:0055114
4	0.06	0.398	5.36	0.04	0.78	2gqfA	GO:0016491 GO:0055114
5	0.06	0.317	5.46	0.02	0.64	2jaeA	GO:0000166 GO:0001716 GO:0016491 GO:0055114
6	0.06	0.336	5.75	0.06	0.70	3lovA	GO:0000166 GO:0004729 GO:0006779 GO:0016491 GO:0055114
7	0.06	0.382	5.40	0.07	0.74	3qj4A	GO:0002931 GO:0005576 GO:0005615 GO:0016491 GO:0055114 GO:0071869 GO:0071871 GO:1902074
8	0.06	0.344	5.65	0.05	0.70	2z5xA	GO:0005739 GO:0005741 GO:0006576 GO:0006584 GO:0008131 GO:0016020 GO:0016021 GO:0016491 GO:0042133 GO:0042135 GO:0042420 GO:0042428 GO:0042443 GO:0050660 GO:0051378 GO:0055114
9	0.06	0.394	5.56	0.08	0.79	3ayiA	GO:0000166 GO:0004497 GO:0016491 GO:0050172 GO:0055114
10	0.06	0.303	6.08	0.05	0.67	2iveA	GO:0004729 GO:0005737 GO:0006779 GO:0006782 GO:0006783 GO:0016020 GO:0016491 GO:0055114
11	0.06	0.424	5.11	0.08	0.79	4gdpB	GO:0015940 GO:0016491 GO:0046208 GO:0046592 GO:0052901 GO:0052902 GO:0052903 GO:0052904 GO:0055114
12	0.06	0.310	4.80	0.07	0.55	4a79A	GO:0005739 GO:0005740 GO:0005741 GO:0005743 GO:0008131 GO:0009055 GO:0009636 GO:0010044 GO:0010269 GO:0014063 GO:0016020 GO:0016021 GO:0016491 GO:0021762 GO:0032496 GO:0042420 GO:0042493 GO:0042803 GO:0045471 GO:0045964 GO:0048545 GO:0050660 GO:0050665 GO:0051412 GO:0055114 GO:0070062
13	0.06	0.389	5.41	0.04	0.79	3nksA	GO:0004729 GO:0005739 GO:0005743 GO:0005758 GO:0006779 GO:0006782 GO:0006783 GO:0016020 GO:0016491 GO:0031304 GO:0031305 GO:0031966 GO:0042493 GO:0046501 GO:0050660 GO:0055114
14	0.06	0.415	5.26	0.07	0.79	3kpfA	GO:0016491 GO:0052893 GO:0052896 GO:0052897 GO:0052898 GO:0052900 GO:0055114
15	0.06	0.404	5.28	0.06	0.76	1reoA	GO:0001716 GO:0005576 GO:0006915 GO:0016491 GO:0019835 GO:0042742 GO:0044179 GO:0055114
16	0.06	0.310	5.32	0.04	0.59	3ng7X	GO:0000166 GO:0016491 GO:0018531 GO:0055114
17	0.06	0.336	5.37	0.02	0.69	1d7lA	GO:0004497 GO:0016491 GO:0018659 GO:0019439 GO:0043639 GO:0043640 GO:0044550 GO:0050660 GO:0055114 GO:0071949
18	0.06	0.320	5.43	0.05	0.63	4dsgA	GO:0000166 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003824
GO-Score	0.33
Biological Processes	GO:0044710
GO-Score	0.47
Cellular Component	GO:0005737
GO-Score	0.13

(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.