I-TASSER results

Input Sequence in FASTA format

>protein (65 residues)
MNCALGFDTKPILLASYVTHGARRATANQFERPAKGAGVLMALLILGEMAGFAVVVTGVV
FGQLV

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MNCALGFDTKPILLASYVTHGARRATANQFERPAKGAGVLMALLILGEMAGFAVVVTGVVFGQLV
Prediction	CCCCCCCCCCCHHHHHHHHHCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC
Conf.Score	98767778875689999998555567554578875578999999999875557888888887749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MNCALGFDTKPILLASYVTHGARRATANQFERPAKGAGVLMALLILGEMAGFAVVVTGVVFGQLV
Prediction	75134425343221121132023332543165344313220111132333233113223344337
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCHHHHHHHHHCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC
MNCALGFDTKPILLASYVTHGARRATANQFERPAKGAGVLMALLILGEMAGFAVVVTGVVFGQLV

3v5sA1

0.21

0.20

0.97

1.03

MUSTER

VILGVGYFLLGLILLYYGSDWFVLGSERHFNVPS--VVFSLVLLIIGLIGGAELFVDGAKKIALA

2x2vA

0.23

0.22

0.92

1.05

wMUSTER

LGAAIGLAAVAGAIAVAIIV-TIEGTTRQ---PE-LRGTLQTLMFIGVPLAEAVPIIAIVISLLI

1q90R

0.16

0.09

0.57

1.43

dPPAS2

----------------------------SSEVPDMNKRNIMNLILAGGAGLPITTLALGYGAFFV

2x2vA

0.23

0.22

0.92

1.03

MUSTER

LGAAIGLAAVAGAIAVAIIV-TIEGTTRQ---PE-LRGTLQTLMFIGVPLAEAVPIIAIVISLLI

3v5sA1

0.21

0.20

0.97

1.02

wMUSTER

VILGVGYFLLGLILLYYGSDWFVLGSERHFNVPS--VVFSLVLLIIGLIGGAELFVDGAKKIALA

2jwaA

0.34

0.18

0.54

1.27

dPPAS2

------------------------------GCPAEQRASPLTSIISAVVGILLVVVLGVVFGILI

2axtZ

0.18

0.17

0.92

1.02

MUSTER

M--TILFQ---LALAALVILSMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV

5jynA

0.16

0.08

0.49

1.18

dPPAS2

---------------------------------NWLWYIRIFIIIVGSLIGLRIVFAVLSLVNRV

2l2tA

0.26

0.14

0.52

1.16

dPPAS2

-----------------------------STLPQHARTPLIAAGVIGGL--FILVIVGLTFAVYV

1spfA

0.17

0.09

0.54

1.09

dPPAS2

-----------------------------LRIPCCPVNLKRLLVVVVVVVLVVVVIVGALLMGL-

(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=-1.44

Estimated TM-score = 0.54±0.15

Estimated RMSD = 6.0±3.7Å

Download Model 2

C-score=-3.05

Download Model 3

C-score=-2.22

Download Model 4

C-score=-2.58

Download Model 5

C-score=-3.87

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	4mh6A	0.860	1.20	0.077	1.000
2	2fefB	0.831	1.56	0.000	0.985
3	4ry2A	0.831	1.32	0.016	0.985
4	2nrjA	0.819	1.37	0.031	0.985
5	2onjA1	0.814	1.36	0.031	0.985
6	3hhmB	0.811	1.46	0.062	1.000
7	4pl0A	0.810	1.42	0.031	0.985
8	1yewC	0.808	1.87	0.031	1.000
9	1ciiA1	0.807	1.33	0.063	0.969
10	4dk0A	0.799	1.44	0.031	0.985

(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	0.19	179	3bknC	HEM	Rep, Mult	15,18,19,22,41,45,48,49,51,52
2	0.07	64	4ub6X	CLA	Rep, Mult	41,43,44,45,47,48,50
3	0.06	54	1aijL	BPH	Rep, Mult	47,50,51,54,55
4	0.06	55	1z6oM	FE	Rep, Mult	14,47,50
5	0.04	38	5b0wB	22B	Rep, Mult	18,22,25,37,40,41,44,48,51
6	0.04	37	5bqjK	E21	Rep, Mult	14,17,18,21,22,24,25
7	0.03	31	4pj0h	CLA	Rep, Mult	17,20,21,24,25
8	0.03	25	4wfdE	III	Rep, Mult	15,19,22,48,51,52,55
9	0.03	29	2q7mD	2CS	Rep, Mult	13,15,16,17,19,20,47,52
10	0.03	28	5d56C	78M	Rep, Mult	54,55,58,59,62
11	0.02	23	4f4sE	EFO	Rep, Mult	11,45,48,49,52,53,56
12	0.01	11	3dd3B	RUC	Rep, Mult	16,17,20
13	0.00	1	2pyhB	CA	Rep, Mult	23,26
14	0.00	1	1f61A	MG	Rep, Mult	8,48
15	0.00	5	1egcC	FAD	Rep, Mult	28,37,39,40
16	0.00	1	1q9sA	MG	Rep, Mult	26,28

	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	0.395	2w5jA	0.662	2.38	0.161	0.954	3.6.3.14	48
2	0.291	1qleD	0.472	1.47	0.024	0.523	1.9.3.1	50,52,58
3	0.217	2jwaA	0.471	2.04	0.098	0.554	2.7.10.1	43
4	0.191	1urfA	0.654	2.20	0.111	0.969	2.7.11.13	18
5	0.162	1cxzB	0.688	1.85	0.079	0.969	2.7.11.13	25
6	0.124	1fyjA	0.528	2.01	0.093	0.708	6.1.1.15,6.1.1.17	NA
7	0.105	1vp7B	0.609	2.23	0.048	0.815	3.1.11.6	15
8	0.087	1a91A	0.682	2.16	0.108	1.000	3.6.3.14	NA
9	0.060	1sc7A	0.767	1.63	0.094	0.985	5.99.1.2	NA
10	0.060	1c3cA	0.735	1.86	0.048	0.969	4.3.2.2	NA
11	0.060	2ix6A	0.720	2.20	0.094	0.969	1.3.3.6	NA
12	0.060	3ii9C	0.710	2.24	0.078	0.969	1.3.99.7	48
13	0.060	3no9A	0.696	1.97	0.097	0.954	4.2.1.2	NA
14	0.060	1ukwA	0.731	2.10	0.063	0.969	1.3.99.3	48
15	0.060	1rr8C	0.487	3.33	0.032	0.785	5.99.1.2	NA
16	0.060	1ivhA	0.706	2.10	0.047	0.969	1.3.99.10	50
17	0.060	1eiyA	0.723	1.94	0.138	1.000	6.1.1.20	53
18	0.060	1jqiA	0.746	2.12	0.094	0.969	1.3.99.2	21
19	0.060	3e6sF	0.725	2.07	0.062	1.000	1.16.3.1	NA
20	0.060	1wu0A	0.707	2.29	0.094	0.985	3.6.3.14	NA
21	0.060	2iw5A	0.714	1.92	0.078	0.985	1.-.-.-	NA
22	0.060	3mddA	0.776	2.02	0.078	0.969	1.3.99.3	22
23	0.060	1olpA	0.733	2.31	0.063	0.954	3.1.4.3	NA
24	0.060	1a31A	0.483	2.99	0.109	0.862	5.99.1.2	24
25	0.060	1qd1B	0.467	3.20	0.096	0.708	2.1.2.5,4.3.1.4	NA
26	0.060	1w27A	0.702	2.02	0.033	0.923	4.3.1.24	NA
27	0.060	3gm1B	0.743	1.84	0.063	0.985	2.7.10.2	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	0.20	0.720	1.77	0.03	0.97	3cp1A	GO:0005198 GO:0019031
1	0.19	0.459	1.17	0.09	0.51	1ce9A	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
2	0.16	0.464	1.37	0.09	0.52	3ck4C	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
3	0.14	0.705	2.01	0.11	0.98	3qf4B	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
4	0.14	0.700	2.04	0.06	0.98	5c73A	GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
5	0.13	0.831	1.32	0.02	0.98	4ry2A	GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
6	0.13	0.685	2.11	0.05	0.98	3k9aA
7	0.12	0.712	2.05	0.10	0.97	3b5xA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085
8	0.11	0.751	1.70	0.09	1.00	1qbzA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
9	0.11	0.690	1.97	0.12	0.98	3b5wA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
10	0.11	0.660	2.16	0.08	0.98	4m1mA	GO:0000086 GO:0000166 GO:0002481 GO:0002485 GO:0002489 GO:0002591 GO:0005524 GO:0005886 GO:0006810 GO:0006855 GO:0008559 GO:0009986 GO:0015893 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042623 GO:0042626 GO:0042908 GO:0046581 GO:0055085 GO:0070062 GO:0072089
11	0.10	0.811	1.39	0.03	0.98	4a82A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0042626 GO:0055085
12	0.10	0.721	1.84	0.05	0.95	3wfvA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
13	0.10	0.466	0.68	0.03	0.49	1untB	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
14	0.10	0.676	2.18	0.08	0.98	3p30A
15	0.10	0.456	0.95	0.00	0.51	1w5jA	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
16	0.10	0.770	1.58	0.06	0.97	4q4aA	GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
17	0.09	0.648	2.33	0.05	1.00	5da9A	GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547
18	0.09	0.811	1.47	0.12	0.98	4mrrA	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0046689 GO:0055085
19	0.09	0.582	2.97	0.07	0.91	2ezoA	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
20	0.08	0.461	0.90	0.03	0.51	2bniB	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0003677 GO:0003682 GO:0003700 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0042802 GO:0043565 GO:0045899 GO:0060261 GO:1903833
21	0.08	0.812	1.41	0.03	0.98	4pl0B	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
22	0.08	0.632	2.29	0.03	0.98	3wmgA	GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
23	0.07	0.594	2.80	0.06	0.95	5da9B	GO:0000723 GO:0005089 GO:0005524 GO:0005634 GO:0006281 GO:0016887 GO:0030870 GO:0035023 GO:0043547
24	0.07	0.562	3.23	0.05	0.89	1dflB	GO:0000166 GO:0003774 GO:0003779 GO:0005516 GO:0005524 GO:0005737 GO:0016459 GO:0030016 GO:0032982
25	0.07	0.643	2.62	0.06	0.95	4uelA	GO:0000502 GO:0004843 GO:0004866 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0006281 GO:0006310 GO:0006351 GO:0006355 GO:0006508 GO:0006511 GO:0006974 GO:0008233 GO:0008234 GO:0010951 GO:0016579 GO:0016787 GO:0021670 GO:0030901 GO:0031011 GO:0036459 GO:0044822 GO:0048853 GO:0061136 GO:0070628
26	0.07	0.630	2.30	0.08	0.98	4f4cA	GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
27	0.07	0.772	1.55	0.08	0.97	4mycA	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0006811 GO:0006879 GO:0016020 GO:0016021 GO:0016887 GO:0022857 GO:0042626 GO:0044281 GO:0055072 GO:0055085
28	0.07	0.803	1.49	0.06	0.98	4ayxA	GO:0000166 GO:0005215 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0032592 GO:0042626 GO:0042803 GO:0055085
29	0.07	0.499	2.94	0.15	0.88	5do7A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045177 GO:0045796 GO:0046982 GO:0055085

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0043492	GO:0016820	GO:0032550	GO:0015405	GO:0032559	GO:0001084	GO:0000978	GO:0042802	GO:0003682	GO:0000981	GO:0001190	GO:0001135
GO-Score	0.52	0.52	0.52	0.52	0.52	0.52	0.32	0.32	0.32	0.32	0.32	0.32	0.32
Biological Processes	GO:0044765	GO:0008652	GO:0045899	GO:0010691	GO:1903833	GO:0001080
GO-Score	0.52	0.32	0.32	0.32	0.32	0.32
Cellular Component	GO:0031224	GO:0036338	GO:0005667	GO:0000790
GO-Score	0.41	0.39	0.32	0.32

(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 Rv3857c

[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]