I-TASSER results

Input Sequence in FASTA format

>protein (108 residues)
MRVVSTLLSIPLMIGLAVPAHAGPSGDDAVFLASLERAGITYSHPDQAIASGKAVCALVE
SGESGLQVVNELRTRNPGFSMDGCCKFAAISAHVYCPHQITKTSVSAK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MRVVSTLLSIPLMIGLAVPAHAGPSGDDAVFLASLERAGITYSHPDQAIASGKAVCALVESGESGLQVVNELRTRNPGFSMDGCCKFAAISAHVYCPHQITKTSVSAK
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHCCCCCCC
Conf.Score	975999999999998657778889987699999999869999999999999999999998599999999999986899999999999999999959788645788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MRVVSTLLSIPLMIGLAVPAHAGPSGDDAVFLASLERAGITYSHPDQAIASGKAVCALVESGESGLQVVNELRTRNPGFSMDGCCKFAAISAHVYCPHQITKTSVSAK
Prediction	433101223323320112113134664244004204746052634730142033005305765424400430376347143530130012004321242267455668
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHHCCCCCCC
MRVVSTLLSIPLMIGLAVPAHAGPSGDDAVFLASLERAGITYSHPDQAIASGKAVCALVESGESGLQVVNELRTRNPGFSMDGCCKFAAISAHVYCPHQITKTSVSAK

1z96A

0.21

0.07

0.35

1.12

dPPAS2

-------------------------------------------------GLNSKIAQLVSMGFDPLEAAQALDAANG--DLDVAASFLL-------------------

4yy2A

0.13

0.10

0.76

1.07

dPPAS2

TTREEVKEKFLKELRKGK------SPTEVLLELIAEASGTT------KEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL--------------

4k82A2

0.16

0.96

0.84

MUSTER

DETVFNAVCDVTKKMLDNKCLPKIQGDLVKFLKDLKYK-IEGGDPELIIKDLKIILERLPC-VGLDDLFKNIFVKDGILSEGIAKPLGDLLILVLCPNVKN-INVSS-

3h20A2

0.11

0.09

0.82

0.71

dPPAS

-RRTALDEYRSEMAGLVKRFGDDLSKCDFIAAQKLASRGR---SAEEIGKAMAEASPALAERKHEADYIERTVSKVMGLPSVQLARAELARAP---------------

3quqA2

0.16

0.09

0.58

0.80

wdPPAS

----------------SMPYH------SEAWHQVMKTHGLDL-SREEAYMH----------GRTGASTINIVFQRELGATQEEIESIYHEKSILF-P-----------

4k82A2

0.17

0.16

0.94

0.85

wMUSTER

-ETVFNAVCDVTKKMLDNKCLPK-QGDLVKFLKDLKYK-IEGGDPELIIKDLKIILERLPC-VGLDDLFKNIFVKDGILSEGIAKPLGDLLILVLCPNVKN-INVSS-

4k82A2

0.17

0.16

0.95

0.77

wPPAS

DETVFNAVCDVTKKMLDNKCLPK-QGDLVKFLKDLKYK-IEGGDPELIIKDLKIILERLPC-VGLDDLFKNIFVKDGILSEGIAKPLGDLLILVLCPNVKN-INVSS-

4jkzA2

0.14

0.12

0.83

1.05

dPPAS2

VTADLASWAGTLAAALTTR-------RGHAMLKTLMAASLEHEDEGFSRPLIESVRDRLRDDIDLGAVVNAVLSEGRSYSRQRAETSARIIVAGLRP-----------

2mqaA

0.09

0.08

0.94

0.81

PPAS

SSNLLSSGDFVQMISSTTSTDQAVSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISISSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA------

2kzzA3

0.17

0.15

0.88

0.93

Env-PPAS

LRIMAHLSRDKGLLTAFA------EGKDIHRATAAEVFGLPLETTSEQRRSAKAINFGLIYGMSAFGLARQLN-----IPRKEAQKYMDLYFERY-PGVLEYMERTA-

(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=-1.79

Estimated TM-score = 0.50±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-2.82

Download Model 3

C-score=-3.47

Download Model 4

C-score=-4.08

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	4k82A	0.834	1.73	0.170	0.982
2	3cucB	0.567	3.68	0.058	0.898
3	5jj6A	0.561	3.70	0.075	0.870
4	5i6cA	0.537	3.95	0.066	0.843
5	3m5fA	0.531	4.10	0.095	0.852
6	1z6aA	0.531	4.09	0.043	0.861
7	1t5jA	0.531	4.28	0.109	0.926
8	2r8qA	0.529	3.79	0.028	0.861
9	3g9dA	0.528	4.30	0.097	0.944
10	3p3lA	0.527	3.92	0.042	0.833

(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	0.11	6	3qbiB	22B	Rep, Mult	31,35,38,51,52,55
2	0.06	3	3b99A	U51	Rep, Mult	48,49,51,52,55,56,72,75,77,91
3	0.06	3	3b6aD	ZCT	Rep, Mult	13,16,18,35,49,50,52,54,61,62,65,66,86,89
4	0.06	3	2jjoA	EY5	Rep, Mult	35,48,52,92,95,96,100
5	0.04	2	2bfnA	CA	Rep, Mult	27,28
6	0.04	2	3rovB	III	Rep, Mult	58,59
7	0.02	1	3ehbB	HEA	Rep, Mult	18,90
8	0.02	1	1o83B	PO4	Rep, Mult	95,99,102
9	0.02	1	2nunA	ADP	Rep, Mult	28,31,52,72
10	0.02	1	4bntD	36E	Rep, Mult	4,8
11	0.02	1	4o6mA	MPG	Rep, Mult	16,31
12	0.02	1	3serA	CA	Rep, Mult	36,39
13	0.02	1	1s32G	UUU	Rep, Mult	53,54

	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	1cleA	0.501	4.28	0.072	0.880	3.1.1.3	NA
2	0.060	1vb3A	0.504	4.14	0.040	0.870	4.2.3.1	NA
3	0.060	1lpsA	0.500	4.25	0.052	0.870	3.1.1.3	45
4	0.060	3kb9A	0.507	4.28	0.067	0.935	4.2.3.37	NA
5	0.060	3hf2A	0.472	4.04	0.118	0.787	1.14.14.1,1.6.2.4	36,56
6	0.060	1fsaA	0.500	4.60	0.078	0.907	3.1.3.11	NA
7	0.060	1gz7A	0.506	4.21	0.031	0.880	3.1.1.3	NA
8	0.060	2wm4A	0.509	3.67	0.098	0.796	1.14.-.-	NA
9	0.060	3dsiA	0.496	4.00	0.062	0.833	4.2.1.92	NA
10	0.060	2zbzA	0.501	3.64	0.120	0.796	1.14.14.1	NA
11	0.060	1gz7C	0.503	4.38	0.041	0.898	3.1.1.3	NA
12	0.060	1jpzB	0.489	3.65	0.113	0.796	1.14.14.1,1.6.2.4	85
13	0.060	1crlA	0.501	4.21	0.021	0.870	3.1.1.3	NA
14	0.060	3hxxA	0.493	3.30	0.069	0.750	6.1.1.7	NA
15	0.060	2z3tA	0.468	4.08	0.084	0.824	1.-.-.-	36,56
16	0.060	1p2yA	0.503	3.50	0.067	0.768	1.14.15.1	NA
17	0.060	1osnA	0.495	4.03	0.067	0.815	2.7.1.21	NA
18	0.060	3letA	0.523	3.56	0.050	0.833	2.7.7.-	62,65
19	0.060	2jjpA	0.514	3.76	0.077	0.787	1.14.-.-	49,85

(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	0.530	4.40	0.12	0.94	4betA	GO:0005576 GO:0008152 GO:0009405 GO:0016740 GO:0030430 GO:0043087 GO:0044605
1	0.07	0.463	4.09	0.05	0.77	2vh3A	GO:0005576 GO:0046872
2	0.07	0.560	3.95	0.07	0.90	5jj6B	GO:0000166 GO:0005524 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0018117 GO:0070733
3	0.06	0.418	3.53	0.05	0.63	3zecB	GO:0000166 GO:0000287 GO:0005524 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
4	0.06	0.431	3.92	0.05	0.70	3zc7A	GO:0000166 GO:0000287 GO:0005524 GO:0009405 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
5	0.06	0.501	4.05	0.04	0.86	4itrA	GO:0000166 GO:0003824 GO:0004197 GO:0005524 GO:0005576 GO:0006464 GO:0006508 GO:0008152 GO:0008233 GO:0008234 GO:0009279 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0018117 GO:0034260 GO:0070733
6	0.06	0.391	3.63	0.04	0.60	5cklA	GO:0000166 GO:0005524 GO:0016740 GO:0016779 GO:0018117 GO:0042803 GO:0070733
7	0.06	0.422	4.23	0.03	0.64	2vzaA	GO:0000166 GO:0005524 GO:0005576 GO:0009405 GO:0016740 GO:0016779 GO:0018117 GO:0070733
8	0.06	0.386	4.54	0.06	0.69	2ky4A	GO:0009579 GO:0015979 GO:0016020 GO:0016829 GO:0018298 GO:0030089 GO:0042651 GO:0055114
9	0.06	0.395	3.87	0.06	0.56	5a01A	GO:0006486 GO:0006493 GO:0008375 GO:0016740 GO:0016757 GO:0035220 GO:0045475
10	0.06	0.402	4.33	0.07	0.69	2d5kB	GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0055114
11	0.06	0.385	4.61	0.03	0.62	5a31C	GO:0004842 GO:0005622 GO:0005654 GO:0005680 GO:0005829 GO:0006511 GO:0007049 GO:0007067 GO:0007080 GO:0007091 GO:0007096 GO:0016567 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
12	0.06	0.549	4.06	0.02	0.94	4u0uA	GO:0000166 GO:0005524 GO:0016020 GO:0016021 GO:0016740 GO:0016779 GO:0018117 GO:0034260 GO:0070733
13	0.06	0.380	4.00	0.06	0.56	4xifA	GO:0000123 GO:0000791 GO:0001933 GO:0001934 GO:0005547 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006041 GO:0006110 GO:0006486 GO:0006493 GO:0006915 GO:0007165 GO:0007584 GO:0008047 GO:0008134 GO:0008289 GO:0008375 GO:0010628 GO:0010801 GO:0016020 GO:0016262 GO:0016568 GO:0016740 GO:0016757 GO:0019904 GO:0030854 GO:0030900 GO:0031397 GO:0032868 GO:0032869 GO:0032922 GO:0033137 GO:0035020 GO:0042277 GO:0042588 GO:0043005 GO:0043025 GO:0043085 GO:0043981 GO:0043982 GO:0043984 GO:0043995 GO:0043996 GO:0045793 GO:0045862 GO:0045944 GO:0046626 GO:0046972 GO:0048015 GO:0048029 GO:0048312 GO:0048511 GO:0051571 GO:0060548 GO:0061087 GO:0070207 GO:0070208 GO:0070688 GO:0071222 GO:0071300 GO:0071333 GO:0080182 GO:0090315 GO:0090526 GO:0097237 GO:0097363 GO:1900038 GO:1900182 GO:1903428
14	0.06	0.349	4.34	0.09	0.59	3ooqF	GO:0016787 GO:0016810 GO:0019239
15	0.06	0.357	4.31	0.08	0.55	2fo7A
16	0.06	0.369	4.71	0.05	0.71	3d8uB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
17	0.06	0.352	4.79	0.07	0.67	2yj4B	GO:0000166 GO:0005887 GO:0006812 GO:0008900 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0035434 GO:0043231 GO:0043682 GO:0046872 GO:0098655 GO:1902600
18	0.06	0.390	4.00	0.03	0.63	1npdB	GO:0000166 GO:0004764 GO:0008652 GO:0009073 GO:0009423 GO:0016491 GO:0030266 GO:0050661 GO:0051287 GO:0052733 GO:0052734 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0070566	GO:0032559	GO:0032550
GO-Score	0.36	0.36	0.36	0.36
Biological Processes	GO:0018175
GO-Score	0.36
Cellular Component	GO:0005576	GO:0030430	GO:0016021
GO-Score	0.13	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 Rv1804c

[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]