I-TASSER results

Input Sequence in FASTA format

>protein (78 residues)
MAAYQKFGQEHAAAIRGGAVLHPTATATTVRVTGARGGDVVTGDGPYEAADLDEQGPFPM
ETVYLWEDGPNGTTRMTL

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MAAYQKFGQEHAAAIRGGAVLHPTATATTVRVTGARGGDVVTGDGPYEAADLDEQGPFPMETVYLWEDGPNGTTRMTL
Prediction	CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEHCCCCCCEEEHCCCCCCCCHHHCCCCHCCCCCCCCCCCCCCEEHCC
Conf.Score	867999999999975547777888765799985678986898578875445455575333477666788877555569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MAAYQKFGQEHAAAIRGGAVLHPTATATTVRVTGARGGDVVTGDGPYEAADLDEQGPFPMETVYLWEDGPNGTTRMTL
Prediction	755255135623531444342334433331304445614112342325345246624233434233643453344357
	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

CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEHCCCCCCEEEHCCCCCCCCHHHCCCCHCCCCCCCCCCCCCCEEHCC
MAAYQKFGQEHAAAIRGGAVLHPTATATTVRVTGARGGDVVTGDGPYEAADLDEQGPFPMETVYLWEDGPNGTTRMTL

1s7iA

0.19

0.18

0.92

1.12

MUSTER

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQ---GGRLAMTDGPFAETDLNQALQIAAKIPPGRLGC---VRPVEW

1s7iA

0.23

0.22

0.94

1.11

dPPAS

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQG---GRLAMTDGPFEARDLNQALQIAAKIPPGRLGC--VEVRPVK

1s7iA

0.20

0.18

0.88

1.64

wdPPAS

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQ---GGRLAMTDGPFAETDLNQALQIAAKIPPGRLG------CVEV

1s7iA

0.19

0.18

0.95

1.45

wMUSTER

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQ---GGRLAMTDGPFAETDLNQALQIAAKIPPGRLGC-VEVRPVEW

1s7iA

0.20

0.18

0.91

1.79

wPPAS

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQ---GGRLAMTDGPFAETDLNQALQIAAKIPPGRLGC----RPVEW

1s7iA

0.24

0.22

0.90

1.90

dPPAS2

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQG---GRLAMTDGPFEARDLNQALQIAAKIPPGRLGCWEGS-----

1s7iA

0.22

0.21

0.92

1.73

PPAS

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQG---GRLAMTDGPFEARDLNQALQIAAKIPPGRLGC---VRPKEW

1s7iA

0.23

0.22

0.94

1.52

Env-PPAS

VDECMTYSDQLGKAYIASHALQSVQTATTLRHQG---GRLAMTDGPFEARDLNQALQIAAKIPPGRLGC--VEVRPVK

4bhrA

0.12

0.92

0.81

MUSTER

-TAAQAYVRNVATAVEATGAL--PQLPQACD-QFVANPPASVTQCNVTANN--DGVNFTVTAQLTYGSSSTGQFSFQL

1uspA1

0.22

0.12

0.53

0.86

dPPAS

-----------------------NVYTAEATATGGRAGTTRSSDD---------RLNLDLSVPAEGGDGGPGT-----

(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=-2.70

Estimated TM-score = 0.40±0.14

Estimated RMSD = 9.2±4.6Å

Download Model 2

C-score=-2.78

Download Model 3

C-score=-3.09

Download Model 4

C-score=-3.04

Download Model 5

C-score=-3.93

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	1rsrB	0.549	3.83	0.039	0.923
2	4d0nB1	0.535	3.55	0.042	0.885
3	1rf8A	0.535	3.20	0.087	0.885
4	3ky9B	0.526	3.67	0.027	0.923
5	2gpqA2	0.525	3.30	0.072	0.872
6	4dr0A	0.525	3.74	0.056	0.859
7	1rj1A	0.523	3.60	0.082	0.833
8	1vgyA2	0.520	3.46	0.059	0.859
9	4gs1A	0.519	3.36	0.101	0.885
10	1be3A2	0.519	3.45	0.069	0.923

(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	0.16	8	3pciA	IHB	Rep, Mult	28,45,46,47
2	0.08	4	4ryoA	MPG	Rep, Mult	12,15,62
3	0.08	4	1xk0A	NO	Rep, Mult	14,18
4	0.04	2	2ydoA	SOG	Rep, Mult	56,57,58,59,62
5	0.02	1	3pcaO	DHB	Rep, Mult	21,36
6	0.02	1	4plrA	CA	Rep, Mult	17,18
7	0.02	1	2ih9A	5AX	Rep, Mult	31,34,37
8	0.02	1	4unpA	TXW	Rep, Mult	7,11,62,66
9	0.02	1	3zbyF	BCD	Rep, Mult	1,32
10	0.02	1	4ro2B	GLY	Rep, Mult	7,8
11	0.02	1	4m9vC	MPD	Rep, Mult	11,14

	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	1cg2A	0.473	3.60	0.030	0.821	3.4.17.11	48
2	0.060	3k1dA	0.487	3.84	0.075	0.833	2.4.1.18	NA
3	0.060	2zdoD	0.484	3.90	0.045	0.846	1.14.99.3	16,32,49,52,74
4	0.060	1biqB	0.543	3.79	0.039	0.923	1.17.4.1	7
5	0.060	1i19A	0.502	3.41	0.029	0.872	1.1.3.6	NA
6	0.060	2fgeA	0.502	3.76	0.095	0.910	3.4.24.-	NA
7	0.060	2d0tB	0.490	3.84	0.041	0.910	1.13.11.52	10
8	0.060	1jtnA	0.417	3.66	0.031	0.705	3.2.1.17	53
9	0.060	2pnrF	0.417	4.00	0.056	0.833	2.7.11.2	NA
10	0.060	1ad3A	0.494	3.17	0.079	0.795	1.2.1.5	NA
11	0.060	3bxvA	0.271	4.51	0.000	0.577	1.13.11.55	30
12	0.060	3d2rB	0.498	3.63	0.054	0.859	2.7.11.2	10
13	0.060	3cskA	0.485	3.64	0.031	0.821	3.4.14.4	57
14	0.060	1r0sA	0.492	3.76	0.053	0.910	3.2.2.5	NA
15	0.060	2gv9B	0.473	4.09	0.079	0.923	2.7.7.7	53,55
16	0.060	1cfrA	0.472	3.35	0.048	0.756	3.1.21.4	NA
17	0.060	1jk0A	0.498	3.93	0.053	0.936	1.17.4.1	NA
18	0.060	2pnrB	0.419	4.00	0.056	0.833	2.7.11.2	10
19	0.060	2rccA	0.477	4.12	0.041	0.910	1.17.4.1	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	0.07	0.373	4.14	0.01	0.64	3kz1A	GO:0000910 GO:0001558 GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005622 GO:0005737 GO:0005829 GO:0006928 GO:0006941 GO:0007186 GO:0007266 GO:0016020 GO:0030010 GO:0030036 GO:0035023 GO:0043065 GO:0043547 GO:0045893 GO:0051056
1	0.07	0.420	4.06	0.04	0.79	2pz1A	GO:0005085 GO:0005089 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0019904 GO:0030032 GO:0030676 GO:0032587 GO:0035023 GO:0035556 GO:0042995 GO:0043065 GO:0043547 GO:0046847 GO:0051056
2	0.07	0.434	3.90	0.06	0.77	4bmqA	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
3	0.07	0.351	3.61	0.04	0.60	4m1hB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
4	0.07	0.470	4.06	0.04	0.83	3gf9A	GO:0005070 GO:0005089 GO:0005509 GO:0005737 GO:0005813 GO:0006897 GO:0009967 GO:0030154 GO:0035023 GO:0043547 GO:0046872 GO:0070062 GO:1903861
5	0.07	0.417	4.26	0.03	0.78	3odxB	GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0005886 GO:0007266 GO:0008283 GO:0016020 GO:0035023 GO:0043547 GO:0044822 GO:0050771
6	0.07	0.492	3.82	0.07	0.88	4n83A	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
7	0.07	0.493	4.07	0.07	0.90	4dr0B	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
8	0.07	0.404	5.03	0.04	0.82	2bq1I	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
9	0.07	0.432	4.07	0.01	0.82	4yonA	GO:0005085 GO:0005089 GO:0005096 GO:0005543 GO:0005737 GO:0005829 GO:0005886 GO:0006801 GO:0007186 GO:0016020 GO:0019899 GO:0030041 GO:0030217 GO:0030426 GO:0030593 GO:0030833 GO:0035023 GO:0035556 GO:0042119 GO:0043198 GO:0043231 GO:0043547 GO:0045785 GO:0048471 GO:0050773 GO:0072593 GO:1900026
10	0.07	0.411	3.76	0.01	0.72	4ac8A	GO:0004748 GO:0005506 GO:0005829 GO:0005971 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
11	0.07	0.509	3.44	0.10	0.90	3jv3A	GO:0005085 GO:0005089 GO:0005509 GO:0005829 GO:0005886 GO:0005905 GO:0006897 GO:0007264 GO:0012505 GO:0016020 GO:0019209 GO:0030027 GO:0030054 GO:0030139 GO:0032947 GO:0035023 GO:0035556 GO:0042327 GO:0042995 GO:0043005 GO:0043524 GO:0043547 GO:0045202 GO:0046872 GO:0048013 GO:0051897 GO:0070064
12	0.07	0.447	4.08	0.05	0.91	1uzrB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0040007 GO:0046872 GO:0055114
13	0.07	0.364	4.04	0.00	0.67	4d0nB	GO:0004691 GO:0004871 GO:0005078 GO:0005085 GO:0005089 GO:0005634 GO:0005737 GO:0005829 GO:0005938 GO:0006468 GO:0007186 GO:0007507 GO:0010611 GO:0016020 GO:0017048 GO:0030864 GO:0032947 GO:0035023 GO:0035025 GO:0035556 GO:0043065 GO:0043123 GO:0043547 GO:0045859 GO:0046872 GO:0048471 GO:0051018 GO:0051056 GO:0051168 GO:0055007 GO:0060297 GO:0060348 GO:0071875 GO:0086023 GO:1900169
14	0.07	0.495	3.96	0.10	0.94	1x86A	GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0007186 GO:0016020 GO:0035023 GO:0035556 GO:0043065 GO:0043547 GO:0051056 GO:0070062
15	0.07	0.420	4.41	0.03	0.79	2rccA	GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
16	0.07	0.497	3.94	0.12	0.92	1x86E	GO:0001664 GO:0005085 GO:0005089 GO:0005096 GO:0005737 GO:0005829 GO:0007186 GO:0016020 GO:0035023 GO:0035556 GO:0043065 GO:0043547 GO:0051056 GO:0070062
17	0.07	0.554	3.78	0.04	0.92	5cnvH	GO:0004748 GO:0005506 GO:0005737 GO:0005829 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0015949 GO:0016491 GO:0042802 GO:0046872 GO:0055114
18	0.07	0.506	3.71	0.03	0.88	1f5xA	GO:0005085 GO:0005089 GO:0005829 GO:0005911 GO:0006909 GO:0006955 GO:0007186 GO:0007229 GO:0007264 GO:0008361 GO:0030168 GO:0030217 GO:0030593 GO:0030676 GO:0035023 GO:0035556 GO:0042110 GO:0043087 GO:0043547 GO:0045785 GO:0045954 GO:0046872 GO:0048010 GO:0072593

Consensus prediction of GO terms

Molecular Function	GO:0005088	GO:0043169
GO-Score	0.37	0.37
Biological Processes	GO:0046578	GO:0043087	GO:0051345	GO:0007266
GO-Score	0.37	0.37	0.37	0.37
Cellular Component	GO:0044424
GO-Score	0.37

(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 Rv1134

[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]