I-TASSER results

Input Sequence in FASTA format

>protein (56 residues)
MLIRWHIQLGNIVIPKSVNPMRIASNFDAFDFPRSMTEPGLVRIRKPSISQAGEMT

Predicted Secondary Structure

Sequence	20 40 \| \| MLIRWHIQLGNIVIPKSVNPMRIASNFDAFDFPRSMTEPGLVRIRKPSISQAGEMT
Prediction	CCCEEEHHHCCEHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCC
Conf.Score	63346545586666889999999999986489999989999998697888899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MLIRWHIQLGNIVIPKSVNPMRIASNFDAFDFPRSMTEPGLVRIRKPSISQAGEMT
Prediction	61012234443010221345721430251242613662253252554654664748
	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

                   |                   |

Sec.Str
Seq

CCCEEEHHHCCEHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCC
MLIRWHIQLGNIVIPKSVNPMRIASNFDAFDFPRSMTEPGLVRIRKPSISQAGEMT

4otkA2

0.36

1.00

2.57

MUSTER

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

4.81

dPPAS

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

4.44

wdPPAS

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

3.15

wMUSTER

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

2.77

wPPAS

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

6.39

dPPAS2

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

2.87

PPAS

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

4otkA2

0.36

1.00

3.62

Env-PPAS

VLLRWNLQLGNAVVVRSARPERIASNFDVFDFELAAEHMDALGGLNDGTRVREDPL

1q13A2

0.21

0.20

0.93

2.14

MUSTER

IALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYV----

1q13A2

0.21

0.20

0.93

4.15

dPPAS

IALRYQLQRGIVVLAKSFTEKRIKENIQVFEFQLPSEDMKVIDSLNRNFRYV----

(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=0.94

Estimated TM-score = 0.84±0.08

Estimated RMSD = 1.2±1.2Å

Download Model 2

C-score=-3.01

Download Model 3

C-score=-2.48

Download Model 4

C-score=-2.27

Download Model 5

C-score=-3.23

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	4f40A	0.898	0.93	0.304	1.000
2	1vbjA	0.895	0.95	0.304	1.000
3	3f7jA	0.887	0.98	0.286	1.000
4	4otkA	0.879	1.03	0.357	1.000
5	4fziA	0.875	1.05	0.321	1.000
6	1q13A	0.868	1.27	0.196	1.000
7	2wzmA	0.865	1.05	0.393	1.000
8	4q3mA	0.861	1.11	0.357	1.000
9	1mzrB	0.859	1.11	0.393	1.000
10	3wbwA	0.858	1.14	0.375	1.000

(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	0.32	64	2wzmA	NA7	Rep, Mult	14,16,17,18,22,25,26
2	0.22	46	4dbsB	0HV	Rep, Mult	52,53,54
3	0.17	36	3r8gA	IZP	Rep, Mult	52
4	0.06	12	3cmfA	PDN	Rep, Mult	53,55,56
5	0.05	9	2pq3A	ZN	Rep, Mult	35,38
6	0.01	2	1s2cA	FLF	Rep, Mult	7,10,11,30
7	0.00	1	4ck2A	NVU	Rep, Mult	1,4,29
8	0.00	1	1xjbA	ACT	Rep, Mult	30
9	0.00	1	3hk7A	CO3	Rep, Mult	45,46

	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	1q13A	0.868	1.27	0.196	1.000	1.1.1.189,1.1.1.149	NA
2	0.060	1vp5A	0.821	1.41	0.250	1.000	1.1.1.274	NA
3	0.060	3b3dA	0.859	1.11	0.268	1.000	1.-.-.-	NA
4	0.060	2p5nA	0.869	1.27	0.196	1.000	1.1.1.-	NA
5	0.060	1keuA	0.571	2.75	0.111	0.946	4.2.1.46	NA
6	0.060	1vbjA	0.895	0.95	0.304	1.000	1.1.1.188	NA
7	0.060	1afsA	0.844	1.39	0.161	1.000	1.1.1.213,1.1.1.50	NA
8	0.060	2clpA	0.715	1.83	0.132	0.946	1.-.-.-	NA
9	0.060	3h7rA	0.777	1.38	0.259	0.964	1.1.1.-	NA
10	0.060	1np3A	0.572	2.61	0.102	0.839	1.1.1.86	NA
11	0.060	1gveB	0.689	1.86	0.113	0.946	1.-.-.-	NA
12	0.060	1og6C	0.701	1.25	0.135	0.839	1.-.-.-	17
13	0.060	2d0tB	0.553	3.00	0.057	0.946	1.13.11.52	34,39
14	0.060	2fvlA	0.867	1.31	0.214	1.000	1.1.1.225,1.1.1.50	NA
15	0.060	1k8cB	0.776	1.38	0.255	0.982	1.1.1.21	NA
16	0.060	1mzrB	0.859	1.11	0.393	1.000	1.1.1.274	NA
17	0.060	3e08A	0.558	2.57	0.060	0.875	1.13.11.11	NA
18	0.060	1gveA	0.698	1.87	0.113	0.946	1.-.-.-	NA
19	0.060	3h7uA	0.777	1.44	0.278	0.964	1.1.1.-	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	0.22	0.882	1.01	0.32	1.00	4gieA	GO:0000166 GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0036131 GO:0047017 GO:0055114
1	0.22	0.879	1.03	0.36	1.00	4otkA	GO:0005618 GO:0005886 GO:0016491 GO:0040007 GO:0055114
2	0.21	0.857	1.11	0.20	0.98	3cv6A	GO:0004032 GO:0004033 GO:0005737 GO:0005829 GO:0006629 GO:0006694 GO:0008202 GO:0016491 GO:0016655 GO:0018636 GO:0031406 GO:0032052 GO:0033764 GO:0047023 GO:0047042 GO:0047086 GO:0047115 GO:0055114 GO:0070062
3	0.21	0.871	1.42	0.21	1.00	4zfcB	GO:0000060 GO:0001523 GO:0001758 GO:0004032 GO:0004033 GO:0004745 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0006693 GO:0007186 GO:0007584 GO:0008202 GO:0008284 GO:0008584 GO:0009267 GO:0010942 GO:0016488 GO:0016491 GO:0016655 GO:0018636 GO:0019371 GO:0030216 GO:0034614 GO:0035410 GO:0036130 GO:0036131 GO:0042448 GO:0042572 GO:0042574 GO:0044259 GO:0044597 GO:0044598 GO:0045550 GO:0045703 GO:0047017 GO:0047020 GO:0047023 GO:0047035 GO:0047045 GO:0047086 GO:0047115 GO:0047718 GO:0047787 GO:0048385 GO:0051897 GO:0052650 GO:0055114 GO:0061370 GO:0070062 GO:0070293 GO:0071276 GO:0071277 GO:0071379 GO:0071384 GO:0071395 GO:0071799 GO:1900053 GO:2000224 GO:2000353 GO:2000379
4	0.21	0.867	1.31	0.21	1.00	2fvlA	GO:0001523 GO:0001758 GO:0004033 GO:0005737 GO:0005829 GO:0006699 GO:0008202 GO:0008209 GO:0009055 GO:0015125 GO:0015721 GO:0016491 GO:0016655 GO:0044597 GO:0044598 GO:0047023 GO:0047743 GO:0055114 GO:0070062 GO:0071395
5	0.20	0.874	1.29	0.23	1.00	4l1wA	GO:0004032 GO:0005737 GO:0006629 GO:0006693 GO:0007186 GO:0007586 GO:0008202 GO:0008284 GO:0016491 GO:0016655 GO:0018636 GO:0030855 GO:0031406 GO:0032052 GO:0042448 GO:0044597 GO:0044598 GO:0047086 GO:0047115 GO:0051897 GO:0055114 GO:0071395 GO:0071799
6	0.20	0.856	1.10	0.36	0.98	3rx2A	GO:0001894 GO:0004032 GO:0004033 GO:0005615 GO:0005654 GO:0005737 GO:0005829 GO:0005975 GO:0005996 GO:0006061 GO:0006700 GO:0006950 GO:0009055 GO:0009414 GO:0010033 GO:0016491 GO:0018931 GO:0031098 GO:0032838 GO:0033010 GO:0042415 GO:0042629 GO:0043220 GO:0043795 GO:0044597 GO:0044598 GO:0046370 GO:0046427 GO:0048471 GO:0048661 GO:0055114 GO:0060135 GO:0070062 GO:0070301 GO:0072061 GO:0097066 GO:0097238 GO:0097454 GO:1901653
7	0.20	0.868	1.27	0.20	1.00	1q13A	GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0047006 GO:0050221 GO:0055114
8	0.20	0.850	1.47	0.39	1.00	4gq0A	GO:0001523 GO:0001758 GO:0004033 GO:0005576 GO:0005764 GO:0005829 GO:0006081 GO:0007586 GO:0008202 GO:0016488 GO:0016491 GO:0044597 GO:0044598 GO:0045550 GO:0047718 GO:0055114 GO:0070062
9	0.20	0.895	0.95	0.30	1.00	1vbjA	GO:0000166 GO:0001516 GO:0004033 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0019571 GO:0036131 GO:0045290 GO:0047017 GO:0055114
10	0.19	0.887	0.98	0.29	1.00	3f7jA	GO:0016491 GO:0043892 GO:0055114
11	0.19	0.894	0.95	0.30	1.00	4g5dA	GO:0000166 GO:0001516 GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0006693 GO:0016491 GO:0036131 GO:0047017 GO:0055114
12	0.19	0.844	1.39	0.16	1.00	1afsA	GO:0005737 GO:0008202 GO:0016229 GO:0016491 GO:0021766 GO:0047023 GO:0047042 GO:0055114
13	0.19	0.858	1.14	0.38	1.00	3wbwA	GO:0000166 GO:0016491 GO:0055114
14	0.19	0.859	1.11	0.27	1.00	3b3dA	GO:0016491 GO:0055114
15	0.19	0.824	1.54	0.34	1.00	3fx4A	GO:0008106 GO:0016491 GO:0055114
16	0.19	0.840	1.40	0.32	1.00	3burA	GO:0004033 GO:0005496 GO:0005737 GO:0005829 GO:0006629 GO:0006699 GO:0006707 GO:0007586 GO:0008202 GO:0008207 GO:0008209 GO:0016042 GO:0016491 GO:0030573 GO:0047787 GO:0055114 GO:0070062
17	0.18	0.802	1.50	0.34	1.00	3wczA	GO:0006629 GO:0008202 GO:0016491 GO:0055114
18	0.18	0.847	1.33	0.27	1.00	3up8A	GO:0016491 GO:0050580 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016655	GO:0047023	GO:1901265	GO:0036094	GO:0033293	GO:0005496	GO:0035671	GO:0005319	GO:1901618	GO:0008028	GO:0047017	GO:0036131	GO:0047115	GO:0004032	GO:0047086	GO:0018636	GO:0001758
GO-Score	0.51	0.51	0.45	0.45	0.42	0.42	0.42	0.42	0.42	0.42	0.39	0.39	0.38	0.38	0.38	0.38	0.38
Biological Processes	GO:0055114	GO:0046457	GO:0009913	GO:0034599	GO:2000377	GO:0044236	GO:1901617	GO:1900052	GO:0043588	GO:0008406	GO:0006606	GO:0016487	GO:0051592	GO:0016107	GO:0048384	GO:0031960	GO:0000302	GO:0046137	GO:0031325	GO:0071383	GO:0050810	GO:1904037	GO:0006081	GO:0031669	GO:0046686	GO:0010566	GO:2000351	GO:0042127	GO:0043170	GO:0019369	GO:0051055	GO:0051896	GO:1902533	GO:0046546	GO:0032351	GO:0003014	GO:0034310	GO:0071798	GO:0031327	GO:0045827	GO:0008207	GO:0071248	GO:0042594	GO:0016095	GO:0008206	GO:0015849	GO:0015718	GO:0006869	GO:0015850	GO:0006693	GO:0044597	GO:0044598	GO:0071395
GO-Score	0.70	0.45	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.42	0.39	0.38	0.38	0.38
Cellular Component	GO:0005829	GO:0070062	GO:0030312	GO:0043231	GO:0016020
GO-Score	0.51	0.51	0.44	0.42	0.33

(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 Rv2970A

[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]