I-TASSER results

Input Sequence in FASTA format

>protein (63 residues)
MERSIGLEAAAQQAGHSGSEITRRHYVERSVTVPDYTAALDEYSRPIRAFRPLKSNRPGD
IPT

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MERSIGLEAAAQQAGHSGSEITRRHYVERSVTVPDYTAALDEYSRPIRAFRPLKSNRPGDIPT
Prediction	CCHHHCHHHHHHHHCCCCCHHHEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Conf.Score	975666899999988998565435666645788877999999987777755566789998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MERSIGLEAAAQQAGHSGSEITRRHYVERSVTVPDYTAALDEYSRPIRAFRPLKSNRPGDIPT
Prediction	765544355224434444461344221555363552340154145314324415764557358
	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

CCHHHCHHHHHHHHCCCCCHHHEEEEEEHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
MERSIGLEAAAQQAGHSGSEITRRHYVERSVTVPDYTAALDEYSRPIRAFRPLKSNRPGDIPT

1rhcA

0.23

0.22

0.98

0.71

MUSTER

KNVTIPFEEGAREAGKDPSKMEHAMLIWYSV-DPDYDKAVEALRFWAGCLVPSMFKYKVYDPK

4hmwA1

0.16

0.14

0.87

0.72

dPPAS

----EESENDKLWFGRSVPMHAMSSASHQSDELVDREALRAHAAELLALGVALP--RPPRF--

1taeA1

0.30

0.27

0.90

0.77

wdPPAS

--QPLTLTAATTRAQELRKQLNQEYYVKDQPSVEDYDRLYKELVDIETEF-PLIT--P-DSPT

1v9pA1

0.29

0.27

0.92

0.83

wMUSTER

----MTREEARRRINELRDLIRYRYYVLADPEISDYDRLLRELKELEERF-PFKSDSPGARPL

1taeA1

0.32

0.27

0.84

0.76

wPPAS

--QPLTLTAATTRA----KQLNQEYYVKDQPSVEDYDRLYKELVDIETEF-PLIT--P-DSPT

2yb1A1

0.22

0.17

0.78

0.74

dPPAS2

IA--GCFDGAMRWCD-NPEMISRTHFVDSGA-VKDMRTVFRKY---------LTPGKPGYVS-

1taeA1

0.30

0.27

0.90

0.79

PPAS

--QPLTLTAATTRAQELRKQLNQEYYVKDQPSVEDYDRLYKELVDIETEF-PLIT--P-DSPT

4uz2A1

0.21

0.13

0.60

0.91

Env-PPAS

----------------------QATYTVAP---GDLYSIARRYVEELMRLNGLESFQPGQLPS

4y42A

0.22

1.00

0.67

MUSTER

IRKNLTFEAINQGTGLSLAFVTAALLGQHPLPEQAARVVAEKLEDAIRLLQPLRGSIPGGVPT

4r6iA5

0.12

0.11

0.89

0.66

dPPAS

---SLNLQICEELVFKKNSQSLAQ---KLHLQVGALYPIINQINYDIQSSHLNIKKKPLEIS-

(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=-1.83

Estimated TM-score = 0.49±0.15

Estimated RMSD = 6.8±4.0Å

Download Model 2

C-score=-2.87

Download Model 3

C-score=-3.90

Download Model 4

C-score=-2.43

Download Model 5

C-score=-4.40

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	5a9qA	0.608	2.83	0.121	0.873
2	3i5pA	0.599	2.93	0.068	0.889
3	3evyB	0.599	2.90	0.051	0.889
4	1lvfA	0.588	2.59	0.103	0.825
5	1taeA1	0.588	2.45	0.127	0.794
6	4knhA	0.587	3.16	0.065	0.921
7	3p5pA	0.579	3.34	0.033	0.936
8	2vxxB	0.578	3.07	0.067	0.873
9	2qr4A1	0.576	3.12	0.088	0.889
10	1b04B	0.575	2.65	0.179	0.809

(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	0.12	3	4h10B	NUC	Rep, Mult	42,45
2	0.11	3	1bgyC	HEM	Rep, Mult	7,10,11,18,19,21,22,25,40,43,47
3	0.08	2	1n9kA	BR	Rep, Mult	15,22,23
4	0.08	2	3pyoN	MG	Rep, Mult	35,39
5	0.08	2	3babA	NMN	Rep, Mult	21,22,40,43,44,47
6	0.04	1	3h1jC	CDL	Rep, Mult	8,9,10,50

	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	0.130	1fyjA	0.502	2.50	0.135	0.730	6.1.1.15,6.1.1.17	15,38
2	0.060	1gulA	0.545	2.84	0.052	0.873	2.5.1.18	NA
3	0.060	3m3mA	0.533	2.96	0.034	0.825	2.5.1.18	NA
4	0.060	3kkbB	0.534	3.28	0.052	0.825	2.7.13.3	15
5	0.060	2iirJ	0.553	3.39	0.136	0.905	2.7.2.1	24
6	0.060	1zc6B	0.543	2.88	0.086	0.889	2.7.1.59	47
7	0.060	1vf4A	0.535	2.86	0.053	0.873	2.5.1.18	NA
8	0.060	2w00B	0.571	3.79	0.161	0.968	3.1.21.3	NA
9	0.060	2ch5A	0.532	2.98	0.052	0.889	2.7.1.59	NA
10	0.060	3hxxA	0.553	3.22	0.070	0.905	6.1.1.7	NA
11	0.060	2a06C	0.467	3.28	0.035	0.809	1.10.2.2	10
12	0.060	1zauA	0.545	2.81	0.070	0.825	6.5.1.2	NA
13	0.060	2e20A	0.561	3.40	0.115	0.921	2.7.2.15	16
14	0.060	3lomA	0.547	2.92	0.051	0.825	2.5.1.10	NA
15	0.060	1ileA	0.505	3.11	0.068	0.889	6.1.1.5	NA
16	0.060	1qs1A	0.565	2.94	0.103	0.905	2.4.2.30	NA
17	0.060	1tuuA	0.550	3.24	0.164	0.905	2.7.2.1	NA
18	0.060	1gumG	0.543	2.84	0.069	0.873	2.5.1.18	NA
19	0.060	2iirA	0.554	3.39	0.136	0.905	2.7.2.1	NA
20	0.060	3m9uA	0.544	2.45	0.107	0.762	2.5.1.10	10,42

(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	0.575	2.59	0.10	0.83	4j2cA	GO:0000139 GO:0005484 GO:0005769 GO:0005794 GO:0005802 GO:0005829 GO:0005886 GO:0006810 GO:0006886 GO:0006906 GO:0007032 GO:0015031 GO:0016020 GO:0016021 GO:0016192 GO:0019905 GO:0030136 GO:0031201 GO:0032456 GO:0032588 GO:0032880 GO:0042147 GO:0043195 GO:0045335 GO:0048193 GO:0048278 GO:0048471 GO:0090161 GO:1903827
1	0.14	0.556	2.64	0.07	0.84	4iwbA	GO:0044780
2	0.11	0.464	3.22	0.08	0.81	1n1zA	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046211 GO:0046872 GO:0047926
3	0.07	0.575	2.65	0.18	0.81	1b04B	GO:0003677 GO:0003911 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006974 GO:0016874 GO:0046872
4	0.07	0.575	2.28	0.12	0.79	4lh6A	GO:0003911 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006974 GO:0016874 GO:0046872
5	0.07	0.599	2.93	0.07	0.89	3i5pA	GO:0000972 GO:0003682 GO:0005634 GO:0005643 GO:0006342 GO:0006405 GO:0006606 GO:0006810 GO:0006913 GO:0007059 GO:0015031 GO:0016020 GO:0016458 GO:0016584 GO:0017056 GO:0031965 GO:0032403 GO:0034398 GO:0036228 GO:0044611 GO:0051028 GO:0051292 GO:0070869 GO:1990841
6	0.07	0.526	3.00	0.07	0.83	3sgiA	GO:0000287 GO:0003911 GO:0005618 GO:0005829 GO:0005886 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006288 GO:0006974 GO:0016874 GO:0040007 GO:0046872
7	0.07	0.599	2.90	0.05	0.89	3evyB	GO:0003677 GO:0004519 GO:0005524 GO:0006304 GO:0009035 GO:0009307 GO:0016787 GO:0090305
8	0.07	0.550	2.82	0.24	0.79	1v9pA	GO:0003677 GO:0003911 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006974 GO:0016874 GO:0046872
9	0.07	0.550	2.35	0.09	0.78	4cc5A	GO:0003677 GO:0003911 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006974 GO:0016874 GO:0046872
10	0.07	0.587	3.16	0.07	0.92	4knhA	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
11	0.07	0.508	3.39	0.07	0.87	5hb1A	GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
12	0.07	0.537	2.32	0.09	0.76	2owoA	GO:0003677 GO:0003911 GO:0005829 GO:0006259 GO:0006260 GO:0006266 GO:0006281 GO:0006288 GO:0006974 GO:0016874 GO:0046872 GO:0070403
13	0.07	0.502	3.43	0.03	0.87	4knhB	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
14	0.07	0.468	3.52	0.12	0.83	4ifqA	GO:0000059 GO:0005634 GO:0005643 GO:0006810 GO:0006999 GO:0015031 GO:0017056 GO:0044611 GO:0046822 GO:0051028
15	0.07	0.577	2.88	0.12	0.86	5hayA	GO:0005634 GO:0005643 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0051028
16	0.07	0.497	3.84	0.07	0.89	5hb4B	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
17	0.07	0.433	3.82	0.00	0.75	5cheE	GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0016020 GO:0016021 GO:0031969
18	0.07	0.485	3.62	0.15	0.84	4mhcA	GO:0000972 GO:0000973 GO:0003677 GO:0003723 GO:0005634 GO:0005643 GO:0006405 GO:0006606 GO:0006810 GO:0006913 GO:0015031 GO:0016020 GO:0017056 GO:0031965 GO:0036228 GO:0044611 GO:0051028 GO:0051292

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0000149
GO-Score	0.47	0.40
Biological Processes	GO:0060341	GO:0007033	GO:0022406	GO:0045184	GO:0016482	GO:0032880	GO:0090174	GO:0016050	GO:0007030	GO:0034613	GO:0071702	GO:0016197
GO-Score	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40
Cellular Component	GO:0000139	GO:0030139	GO:0043679	GO:0005768	GO:0030135	GO:0098793	GO:0071944	GO:0098796	GO:0005802	GO:0031224
GO-Score	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	0.40	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 Rv3643

[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]