I-TASSER results

Input Sequence in FASTA format

>protein (103 residues)
MRPDSVNSAGIDIAAVYAVADRFSAAAELIDDAIGNHLTRLAFGGACAGRGHASRGDALR
CRLDRLAGELSVWSRAAVQIAFALRAGANRYAEADLCAAARIG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MRPDSVNSAGIDIAAVYAVADRFSAAAELIDDAIGNHLTRLAFGGACAGRGHASRGDALRCRLDRLAGELSVWSRAAVQIAFALRAGANRYAEADLCAAARIG
Prediction	CCHHHHCHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	9856654455669999999999999999999999999864677865444444677899999999999999999888899999999999999999999887769
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MRPDSVNSAGIDIAAVYAVADRFSAAAELIDDAIGNHLTRLAFGGACAGRGHASRGDALRCRLDRLAGELSVWSRAAVQIAFALRAGANRYAEADLCAAARIG
Prediction	7446437434131300330054144005303510464034141322323442364354024305511540452343444014203431532452444226548
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHCHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MRPDSVNSAGIDIAAVYAVADRFSAAAELIDDAIGNHLTRLAFGGACAGRGHASRGDALRCRLDRLAGELSVWSRAAVQIAFALRAGANRYAEADLCAAARIG

3gvmA

0.14

0.13

0.91

1.02

MUSTER

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQA-DENWDG----STFDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.13

0.12

0.88

0.80

dPPAS

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQAWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.13

0.12

0.88

1.09

wdPPAS

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQAWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.13

0.12

0.88

1.08

wMUSTER

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQAWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.12

0.11

0.88

1.19

wPPAS

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQNWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.13

0.12

0.88

1.05

dPPAS2

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQAWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.12

0.11

0.88

1.04

PPAS

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQNWDGST--------FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3gvmA

0.12

0.11

0.92

1.09

Env-PPAS

---GAMSQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQVIDENWDGST----FDSFEAQFNELSPKITEFAQLLEDINQQLLKVADIIEQTDADIASQI-

3zbhA

0.13

0.12

0.86

1.00

MUSTER

----------LTPEELRGVARQYNVESSNVTELIARLDQMSHLQGIWEG----ASSEAFIQQYQELRPSFEKMAVLLNEVGQQLHNSATILEDTDQQIASQIR

3zbhA

0.13

0.12

0.86

0.78

dPPAS

----------LTPEELRGVARQYNVESSNVTELIARLDQMSHLQGIWEG----ASSEAFIQQYQELRPSFEKMAVLLNEVGQQLHNSATILEDTDQQIASQIR

(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 3 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=-0.21

Estimated TM-score = 0.69±0.12

Estimated RMSD = 4.4±2.9Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-2.02

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	3gvmA	0.882	1.00	0.126	0.922
2	3zbhA	0.832	1.00	0.111	0.874
3	2vrzA	0.809	1.77	0.106	0.913
4	2ch7A	0.777	2.18	0.078	0.913
5	3fx7B	0.764	1.36	0.161	0.845
6	2d4cB	0.749	2.52	0.078	0.903
7	1l8dA	0.745	2.24	0.063	0.893
8	5j65A	0.742	2.80	0.059	0.971
9	2efkA	0.741	2.24	0.040	0.864
10	4iloA	0.741	2.39	0.029	0.913

(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	18	1s5lC	CLA	Rep, Mult	16,83,87,90,91
2	0.07	14	5e1uA	RIR	Rep, Mult	28,31,71,74,75,78
3	0.05	11	3vgxC	III	Rep, Mult	70,73,74,77,81,84,87,88,91
4	0.05	10	1t8zE	12P	Rep, Mult	59,63,66,70,73,77,80
5	0.05	10	1gd2E	NUC	Rep, Mult	52,55,56,59,60,63,67
6	0.05	10	1dgcA	NUC	Rep, Mult	60,63,64,67,68,71
7	0.04	7	4de6A	ACD	Rep, Mult	20,81,82,85,89
8	0.04	8	2g38B	MN	Rep, Mult	87,90,91
9	0.04	8	2jqkA	III	Rep, Mult	27,31,34,35,38,64,65,67,68,71,74,75
10	0.03	5	3f33A	PFL	Rep, Mult	17,20,21,24,85
11	0.03	7	3mgnF	DTR	Rep, Mult	89,90,93,94
12	0.01	1	2jizG	STL	Rep, Mult	71,74,75,78,79
13	0.01	1	2jj1G	PIT	Rep, Mult	23,26,27,30,31
14	0.01	3	2ck3G	III	Rep, Mult	25,73,74,77
15	0.00	1	1l8d0	III	Rep, Mult	36,39,43,46,59,63
16	0.00	1	2d32A	MG	Rep, Mult	93,95
17	0.00	1	1i4d1	III	Rep, Mult	28,31,34,35,38,39,41,42,43,45,46,64,67,71,74,75
18	0.00	1	3favC	ZN	Rep, Mult	8,12
19	0.00	1	2id3A	CA	Rep, Mult	12,76

	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	0.217	1urfA	0.553	2.56	0.087	0.699	2.7.11.13	18,30,79
2	0.112	1wu0A	0.502	2.44	0.056	0.650	3.6.3.14	NA
3	0.093	1cxzB	0.560	2.76	0.098	0.728	2.7.11.13	NA
4	0.060	1vdkA	0.609	2.88	0.052	0.806	4.2.1.2	52
5	0.060	1j3uA	0.586	2.97	0.051	0.806	4.3.1.1	52
6	0.060	2iw5A	0.672	2.39	0.060	0.845	1.-.-.-	NA
7	0.060	1u7lA	0.650	3.26	0.099	0.913	3.6.3.14	NA
8	0.060	1yfeA	0.590	3.05	0.073	0.806	4.2.1.2	NA
9	0.060	1serB	0.521	3.22	0.099	0.786	6.1.1.11	NA
10	0.060	3lssB	0.668	2.51	0.039	0.825	6.1.1.11	46,48,51
11	0.060	2fonB	0.633	2.61	0.082	0.796	1.3.3.6	NA
12	0.060	1dofA	0.592	3.36	0.129	0.825	4.3.2.2	NA
13	0.060	2dq3A	0.657	2.89	0.053	0.854	6.1.1.11	28,35
14	0.060	1tj7A	0.621	3.09	0.063	0.835	4.3.2.1	NA
15	0.060	3no9A	0.608	3.14	0.066	0.835	4.2.1.2	83
16	0.060	2occN	0.602	2.82	0.022	0.796	1.9.3.1	NA
17	0.060	1sesA	0.547	3.99	0.121	0.903	6.1.1.11	68
18	0.060	1occA	0.600	2.81	0.022	0.796	1.9.3.1	65
19	0.060	1k62B	0.597	3.07	0.061	0.825	4.3.2.1	NA
20	0.060	1i0aA	0.637	2.99	0.095	0.835	4.3.2.1	NA
21	0.060	3gtdA	0.597	3.01	0.032	0.806	4.2.1.2	NA
22	0.060	3g61A	0.677	2.90	0.020	0.922	3.6.3.44	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	0.36	0.828	1.85	0.10	0.94	2vrzA	GO:0005576 GO:0009405
1	0.25	0.720	2.43	0.06	0.92	3g67A	GO:0004871 GO:0007165 GO:0016020
2	0.21	0.771	2.46	0.08	0.93	3zx6A	GO:0004871 GO:0004888 GO:0005886 GO:0005887 GO:0006935 GO:0007165 GO:0016020 GO:0016021 GO:0043200 GO:0043424 GO:0046872 GO:0048870
3	0.18	0.550	2.68	0.04	0.74	3p30A
4	0.18	0.519	1.90	0.06	0.62	3cp1A	GO:0005198 GO:0019031
5	0.17	0.623	2.42	0.06	0.80	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
6	0.16	0.543	3.06	0.03	0.78	1envA	GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0002223 GO:0003677 GO:0003682 GO:0003700 GO:0005198 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0042802 GO:0043565 GO:0044174 GO:0044175 GO:0045899 GO:0046718 GO:0055036 GO:0060261 GO:0075509 GO:0075512 GO:1903833
7	0.15	0.459	1.76	0.06	0.53	4bl6C	GO:0003729 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0006810 GO:0007275 GO:0007293 GO:0007294 GO:0007309 GO:0007310 GO:0007312 GO:0007314 GO:0008103 GO:0008298 GO:0016325 GO:0017137 GO:0019233 GO:0030100 GO:0030154 GO:0030669 GO:0030727 GO:0032050 GO:0045502 GO:0048477 GO:0048488 GO:0050658 GO:0051028 GO:0070727 GO:2000302 GO:2000370
8	0.15	0.612	2.85	0.08	0.83	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	0.14	0.587	3.18	0.07	0.88	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
10	0.14	0.537	2.75	0.11	0.77	3k9aA
11	0.13	0.569	2.99	0.07	0.77	2oszA	GO:0005487 GO:0005634 GO:0005635 GO:0005643 GO:0006810 GO:0006913 GO:0008139 GO:0015031 GO:0016020 GO:0031965 GO:0042306 GO:0043234 GO:0051028 GO:0051260 GO:0051290 GO:0051291 GO:0070208
12	0.13	0.777	2.18	0.08	0.91	2ch7A	GO:0004871 GO:0005886 GO:0006935 GO:0007165 GO:0016020 GO:0016021
13	0.12	0.754	2.68	0.04	0.94	1y2oA	GO:0001726 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0007009 GO:0007409 GO:0008022 GO:0008093 GO:0008286 GO:0008360 GO:0009617 GO:0014069 GO:0015629 GO:0016020 GO:0016358 GO:0030141 GO:0030165 GO:0030175 GO:0030838 GO:0032956 GO:0038096 GO:0042802 GO:0042995 GO:0043005 GO:0043025 GO:0043197 GO:0048010 GO:0048167 GO:0051017 GO:0051764 GO:0061003 GO:0070062 GO:0070064 GO:0097481 GO:0098609 GO:0098641 GO:2000251
14	0.12	0.650	2.96	0.14	0.92	4rsjA	GO:0000166 GO:0003677 GO:0005524 GO:0005694 GO:0005737 GO:0006260 GO:0007059 GO:0007062 GO:0030261 GO:0051276
15	0.07	0.465	1.57	0.05	0.52	2npsD	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
16	0.07	0.529	2.95	0.09	0.70	2c2jA	GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0046872 GO:0055114
17	0.07	0.545	3.17	0.06	0.82	4uxvA	GO:0000921 GO:0005886 GO:0005940 GO:0007049 GO:0016020 GO:0016021 GO:0051301 GO:0051781
18	0.07	0.502	3.71	0.10	0.80	2jesA	GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
19	0.07	0.549	3.60	0.02	0.83	5a20A	GO:0019012 GO:0019028 GO:0019076 GO:0046718 GO:0046729
20	0.06	0.386	3.36	0.06	0.57	2eabA	GO:0003824 GO:0016020 GO:0016021 GO:0046872
21	0.06	0.353	3.64	0.02	0.50	4h1zB	GO:0003824 GO:0008152 GO:0009063 GO:0046872
22	0.06	0.297	3.97	0.02	0.47	4ic6A	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0009507 GO:0009534 GO:0009536 GO:0009543 GO:0009579 GO:0010206 GO:0016787 GO:0031977
23	0.06	0.258	5.40	0.08	0.59	2z9iA	GO:0004252 GO:0005576 GO:0006508 GO:0006950 GO:0008233 GO:0008236 GO:0009405 GO:0016020 GO:0016021 GO:0030163
24	0.06	0.277	3.21	0.01	0.40	2ogiB	GO:0046872
25	0.06	0.302	4.40	0.04	0.51	1j6uA	GO:0000166 GO:0005524 GO:0005737 GO:0007049 GO:0008360 GO:0008763 GO:0009058 GO:0009252 GO:0016874 GO:0051301 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0019901	GO:0099600	GO:0043169	GO:0038023
GO-Score	0.41	0.41	0.41	0.41
Biological Processes	GO:0010243	GO:0042330	GO:1901700	GO:0001101	GO:0051674	GO:0006928	GO:0007165	GO:0009405
GO-Score	0.41	0.41	0.41	0.41	0.41	0.41	0.40	0.36
Cellular Component	GO:0031226	GO:0005576	GO:0036338
GO-Score	0.41	0.36	0.36

(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 Rv3440c

[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]