I-TASSER results

Input Sequence in FASTA format

>protein (133 residues)
MQPGGDMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPK
VVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRPPAPPAAPPGAPGMPGMPG
MPGAPGAPPVPGI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MQPGGDMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRPPAPPAAPPGAPGMPGMPGMPGAPGAPPVPGI
Prediction	CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEHCCCEEEEEEHCCCEEEEEEHCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9999999999999999999999999999875678998799799999758879999869888687788999999999999999999999999999998678999887788888888888887888888998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MQPGGDMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRPPAPPAAPPGAPGMPGMPGMPGAPGAPPVPGI
Prediction	7476441450153045226415622650573414051553202020305441450504551156732520240033014402530463257435523661513444433443431462672344463464678
	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

CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEHCCCEEEEEEHCCCEEEEEEHCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MQPGGDMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRPPAPPAAPPGAPGMPGMPGMPGAPGAPPVPGI

1pugA

0.37

0.26

0.71

2.83

MUSTER

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

3.81

dPPAS

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

4.29

wdPPAS

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

3.47

wMUSTER

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

3.91

wPPAS

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

7.76

dPPAS2

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

3.64

PPAS

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1pugA

0.37

0.26

0.71

3.60

Env-PPAS

----------MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG----------------------------

1ybxB

0.36

0.24

0.66

2.40

MUSTER

-----NINNLVKQAQKQRD--ERVQEELKEKTVEASAGGGAVTVVATGRKDIKEITIKPEVVDPDD-VELQDLILAAVNEALRKADEVTAEISKIT-------------------------------------

1ybxB

0.36

0.24

0.66

3.22

dPPAS

-----NINNLVKQAQKQRD--ERVQEELKEKTVEASAGGGAVTVVATGRKDIKEITIKPEVVDPDD-VELQDLILAAVNEALRKADEVTAEISKIT-------------------------------------

(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=-0.26

Estimated TM-score = 0.68±0.12

Estimated RMSD = 5.0±3.3Å

Download Model 2

C-score=-2.04

Download Model 3

C-score=-2.35

Download Model 4

C-score=-3.95

Download Model 5

C-score=-3.61

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	1pugA	0.668	1.25	0.362	0.707
2	5bqnA	0.613	3.29	0.078	0.835
3	3v0aB	0.594	3.60	0.034	0.850
4	1f31A3	0.578	3.29	0.036	0.804
5	3tnfB	0.575	4.06	0.064	0.857
6	2j69A	0.571	3.75	0.094	0.835
7	3ffzA3	0.560	3.59	0.060	0.820
8	4whjA	0.559	4.15	0.076	0.880
9	2w6dA2	0.555	3.92	0.043	0.812
10	4zktB4	0.553	3.88	0.061	0.827

(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	0.08	4	1jb0M	CLA	Rep, Mult	77,81
2	0.06	3	1gw9A	IOD	Rep, Mult	91,92,95
3	0.06	3	2izoC	ZN	Rep, Mult	68,72
4	0.04	2	2zxeA	K	Rep, Mult	28,29,30,31,32,33,48
5	0.04	2	1s0dA	CA	Rep, Mult	59,60,62
6	0.04	2	1mz9B	VDY	Rep, Mult	78,81,85
7	0.04	2	2h9dC	PYR	Rep, Mult	70,71,74
8	0.03	1	1pug0	III	Rep, Mult	50,51,52,55,56,57,59,62,67,70,71,74,75,78,79
9	0.02	1	1q0kE	THJ	Rep, Mult	18,21
10	0.02	1	1swiC	BNZ	Rep, Mult	10,14
11	0.02	1	1w46B	ADP	Rep, Mult	40,41,43
12	0.02	1	1fbmD	RTL	Rep, Mult	21,28
13	0.02	1	4mhlA	ARF	Rep, Mult	89,92
14	0.02	1	3u24A	ZN	Rep, Mult	84,87

	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	1fo4A	0.504	4.00	0.071	0.714	1.17.1.4	NA
2	0.060	3fwnA	0.533	3.92	0.055	0.782	1.1.1.44	NA
3	0.060	3b9jI	0.236	5.10	0.063	0.444	1.17.1.4,1.17.3.2	98
4	0.060	1hbmA	0.477	4.83	0.098	0.850	2.8.4.1	NA
5	0.060	1eulA	0.455	4.42	0.033	0.767	3.6.3.8	NA
6	0.060	1rr8C	0.348	4.28	0.067	0.587	5.99.1.2	NA
7	0.060	2r8jA	0.489	4.47	0.045	0.782	2.7.7.7	126
8	0.060	2w90B	0.530	4.05	0.082	0.782	1.1.1.44	50
9	0.060	3g61A	0.499	4.12	0.059	0.774	3.6.3.44	95
10	0.060	1e6vA	0.485	5.05	0.099	0.865	2.8.4.1	NA
11	0.060	1sc7A	0.485	4.08	0.085	0.729	5.99.1.2	NA
12	0.060	2vuaA	0.362	4.85	0.038	0.632	3.4.24.69	53
13	0.060	1w27A	0.491	4.33	0.069	0.789	4.3.1.24	NA
14	0.060	1wydB	0.482	4.50	0.044	0.789	6.1.1.12	NA
15	0.060	1a31A	0.316	4.73	0.031	0.474	5.99.1.2	NA
16	0.060	2ix6A	0.475	4.58	0.047	0.820	1.3.3.6	NA
17	0.060	3btaA	0.542	3.76	0.070	0.797	3.4.24.69	NA
18	0.060	1z0hB	0.362	4.18	0.008	0.556	3.4.24.69	43
19	0.060	1e6yA	0.481	4.94	0.077	0.857	2.8.4.1	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	0.38	0.621	1.82	0.35	0.69	1j8bA	GO:0003677 GO:0005737 GO:0009295 GO:0043590
1	0.37	0.570	2.10	0.37	0.65	1ybxB	GO:0003677 GO:0005737 GO:0009295 GO:0043590
2	0.29	0.668	1.25	0.36	0.71	1pugA	GO:0003677 GO:0005737 GO:0005829 GO:0009295 GO:0043590
3	0.17	0.550	2.36	0.23	0.68	3f42A	GO:0003677 GO:0005737 GO:0009295 GO:0043590
4	0.07	0.558	3.47	0.05	0.82	2np0A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
5	0.07	0.594	3.60	0.03	0.85	3v0aB	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
6	0.07	0.613	3.29	0.08	0.83	5bqnA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
7	0.06	0.548	3.77	0.07	0.79	3vuoA	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
8	0.06	0.415	4.67	0.04	0.69	1zb7A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0046872 GO:0050827 GO:0051609 GO:0071806
9	0.06	0.372	4.33	0.03	0.56	3mzoB	GO:0046872
10	0.06	0.367	4.75	0.06	0.59	3debA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
11	0.06	0.521	3.52	0.04	0.75	3ffzA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
12	0.06	0.352	4.53	0.06	0.58	5cfcA	GO:0000166 GO:0001172 GO:0003723 GO:0003724 GO:0003968 GO:0004197 GO:0004386 GO:0005198 GO:0005216 GO:0005524 GO:0006351 GO:0006508 GO:0006810 GO:0006811 GO:0008233 GO:0008234 GO:0016020 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0018144 GO:0019012 GO:0019028 GO:0019030 GO:0019062 GO:0030430 GO:0033644 GO:0034220 GO:0039694 GO:0039707 GO:0044161 GO:0044162 GO:0044385 GO:0046718 GO:0051259
13	0.06	0.393	4.34	0.05	0.64	1zkxB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
14	0.06	0.368	4.76	0.02	0.62	2imcB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
15	0.06	0.394	4.52	0.03	0.66	1z7hA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
16	0.06	0.559	3.36	0.04	0.80	3v0aA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
17	0.06	0.332	4.62	0.06	0.50	2bkrA	GO:0006508 GO:0008233 GO:0008234 GO:0016787
18	0.06	0.388	4.71	0.03	0.67	1yvgA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.77
Biological Processes	GO:0009405	GO:0051609	GO:0071806	GO:0006508
GO-Score	0.07	0.07	0.07	0.07
Cellular Component	GO:0043590	GO:0044444
GO-Score	0.77	0.58

(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 Rv3716c

[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]