I-TASSER results

Input Sequence in FASTA format

>protein (67 residues)
MGPMNGFLSWWDGVELWLSGLPFALQALAVMPVVLALAYFTAALLDALLGRVIQLIRRAR
RPDQAPR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MGPMNGFLSWWDGVELWLSGLPFALQALAVMPVVLALAYFTAALLDALLGRVIQLIRRARRPDQAPR
Prediction	CCCHHHHHHHHCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	9878989987554556665787589999999999999999999999999999999845557888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MGPMNGFLSWWDGVELWLSGLPFALQALAVMPVVLALAYFTAALLDALLGRVIQLIRRARRPDQAPR
Prediction	7542521142233223224434333323132133333233212213311430142044345468768
	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

CCCHHHHHHHHCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
MGPMNGFLSWWDGVELWLSGLPFALQALAVMPVVLALAYFTAALLDALLGRVIQLIRRARRPDQAPR

2d2sA1

0.17

0.15

0.88

1.00

wMUSTER

MSSTAQRLKFLDEIDIELARLRFESAVETLLDIESQLEDLSLMLLNLISLKIEQRREAI--------

2na8A

0.38

0.22

0.60

1.05

wPPAS

-----G----WDT-E-SV--LP--MWVLALIVIFLTIAVLLALRFCGIYG-------RLRRK-----

4eijA

0.10

0.09

0.94

1.11

dPPAS2

VISANEIMDLLRGMDARLQHLEQKVDKVLAQGSMVTQIKNELSTVKTTLATIEGMMATVKIMD----

4eijA

0.10

0.09

0.94

1.16

PPAS

VISANEIMDLLRGMDARLQHLEQKVDKVLAQGSMVTQIKNELSTVKTTLATIEGMMATVKIMD----

3dinD

0.25

0.21

0.82

1.01

wPPAS

VIAEAKKISWPSRKEL--------LTSFGVVLVILAVTSVYFFVLDFIFSGVVSAIFKALGIG----

3tsiA

0.26

0.19

0.75

1.09

dPPAS2

-SPSSGLGSITDLLNNILS---VANQIIYNSAVALPLQLDTLESTLLTAIKSLQ-------------

3dinD

0.25

0.21

0.82

1.04

PPAS

VIAEAKKISWPSRKEL--------LTSFGVVLVILAVTSVYFFVLDFIFSGVVSAIFKALGIG----

2lzrA

0.19

0.13

0.72

1.05

dPPAS2

------------------GGISIWQLLIIAVIVVLLFGPKKLGSIGSDLGASIKGFKKAMSDDEPK-

2d2sA1

0.17

0.15

0.88

1.01

PPAS

MSSTAQRLKFLDEIDIELARLRFESAVETLLDIESQLEDLSLMLLNLISLKIEQRREAI--------

3tsiA

0.26

0.19

0.75

1.01

PPAS

-SPSSGLGSITDLLNNILS---VANQIIYNSAVALPLQLDTLESTLLTAIKSLQ-------------

(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=-2.31

Estimated TM-score = 0.44±0.14

Estimated RMSD = 8.0±4.4Å

Download Model 2

C-score=-2.50

Download Model 3

C-score=-3.58

Download Model 4

C-score=-3.97

Download Model 5

C-score=-2.52

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	4d8mA1	0.746	1.50	0.045	0.910
2	1u4qA	0.731	1.96	0.104	0.940
3	4gyoA	0.717	2.08	0.078	0.940
4	4xngA	0.717	1.60	0.016	0.881
5	4ev6A	0.715	2.39	0.061	0.940
6	1y1uA4	0.714	1.96	0.164	0.940
7	5ah5A	0.712	1.87	0.121	0.925
8	1fewA1	0.711	1.69	0.082	0.910
9	4uicA1	0.709	2.32	0.094	0.925
10	1w99A	0.708	2.34	0.134	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	0.10	9	3ze3A	78N	Rep, Mult	34,38,45
2	0.07	7	5fjyA	III	Rep, Mult	15,18,19,55
3	0.05	5	4wfdE	III	Rep, Mult	11,15,18,30,33,34,37
4	0.05	5	1xvfD	3CL	Rep, Mult	11,12,15
5	0.04	4	1ow8C	III	Rep, Mult	4,7,8,11,15,18,30,33,37,40,41
6	0.04	4	4eneA	DMU	Rep, Mult	30,34
7	0.03	3	3bz1L	PL9	Rep, Mult	31,34,35,37,38
8	0.03	3	4tnwS	POV	Rep, Mult	26,29,30,33,55,59
9	0.02	2	2d2cA	CLA	Rep, Mult	34,56
10	0.02	2	4o6mB	MPG	Rep, Mult	27,28
11	0.02	2	1hz40	III	Rep, Mult	29,51,54,58
12	0.02	2	4xzwA	O4B	Rep, Mult	15,18,54,55
13	0.01	1	3locA	URA	Rep, Mult	23,26
14	0.01	1	2wssX	III	Rep, Mult	10,14
15	0.01	1	2vl8B	CTS	Rep, Mult	7,11,13,44
16	0.01	1	3b6cA	SDN	Rep, Mult	2,34,37,38,41

	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	0.215	3eabA	0.582	2.78	0.078	0.895	3.6.4.3	7,18
2	0.148	1r1bA	0.529	2.83	0.135	0.776	6.1.1.15,6.1.1.17	30
3	0.134	1fyjA	0.528	2.01	0.137	0.702	6.1.1.15,6.1.1.17	30,38
4	0.066	2e2aA	0.607	2.86	0.106	0.940	2.7.1.69	NA
5	0.060	1u7lA	0.618	2.57	0.062	0.806	3.6.3.14	16
6	0.060	1gaxA	0.658	2.69	0.077	0.970	6.1.1.9	NA
7	0.060	1chuA	0.621	2.77	0.104	0.985	1.4.3.16	NA
8	0.060	3lomA	0.616	2.37	0.133	0.895	2.5.1.10	35
9	0.060	1fyzF	0.630	2.40	0.048	0.910	1.14.13.25	27
10	0.060	1qz2A	0.637	2.74	0.104	0.985	5.2.1.8	16
11	0.060	3i9wA	0.611	2.69	0.106	0.940	2.7.13.3	61
12	0.060	2ewgA	0.618	2.43	0.100	0.895	2.5.1.10	NA
13	0.060	1qlaD	0.610	2.78	0.090	0.970	1.3.99.1	NA
14	0.060	1mhyG	0.639	2.37	0.032	0.925	1.14.13.25	16
15	0.060	1k04A	0.498	2.21	0.061	0.657	2.7.10.2	27,29
16	0.060	1ihgA	0.667	2.70	0.060	1.000	5.2.1.8	5,37
17	0.060	1wz2A	0.622	2.58	0.061	0.940	6.1.1.4	NA
18	0.060	1d8dA	0.635	2.60	0.076	0.955	2.5.1.58	NA
19	0.060	2htnG	0.591	2.92	0.095	0.925	1.16.3.1	44
20	0.060	1wcrA	0.639	2.36	0.060	0.940	2.7.1.69	NA
21	0.060	2epoA	0.613	2.55	0.060	0.970	3.2.1.52	NA
22	0.060	1i8qA	0.666	2.75	0.063	0.940	4.2.2.1	30,32
23	0.060	1e7pA	0.608	2.81	0.104	0.970	1.3.99.1	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	0.30	0.637	2.73	0.09	0.93	3f31B	GO:0000165 GO:0003779 GO:0005088 GO:0005200 GO:0005509 GO:0005516 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0005938 GO:0006888 GO:0007411 GO:0008091 GO:0015630 GO:0016020 GO:0019905 GO:0031532 GO:0032403 GO:0043231 GO:0043234 GO:0043547 GO:0046872 GO:0047485 GO:0051693 GO:0070062 GO:0098609 GO:0098641 GO:1903561
1	0.24	0.604	2.07	0.07	0.85	3uunA	GO:0002027 GO:0002162 GO:0003779 GO:0005200 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0007517 GO:0008270 GO:0008307 GO:0009986 GO:0010880 GO:0010881 GO:0010976 GO:0014809 GO:0014819 GO:0015629 GO:0016010 GO:0016013 GO:0016020 GO:0016203 GO:0016328 GO:0017022 GO:0017166 GO:0030018 GO:0030049 GO:0030054 GO:0030055 GO:0030175 GO:0031527 GO:0033137 GO:0034613 GO:0035994 GO:0042383 GO:0043034 GO:0043043 GO:0043234 GO:0043623 GO:0044306 GO:0044458 GO:0045121 GO:0045202 GO:0045211 GO:0045666 GO:0046716 GO:0046872 GO:0048747 GO:0050998 GO:0060048 GO:0060314 GO:0086001 GO:0090287 GO:1901385 GO:1902083 GO:2000651
2	0.24	0.617	2.74	0.11	0.94	3fb2B	GO:0000165 GO:0003779 GO:0005088 GO:0005200 GO:0005509 GO:0005516 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0005938 GO:0006888 GO:0007411 GO:0008091 GO:0015630 GO:0016020 GO:0019905 GO:0031532 GO:0032403 GO:0043231 GO:0043234 GO:0043547 GO:0046872 GO:0047485 GO:0051693 GO:0070062 GO:0098609 GO:0098641 GO:1903561
3	0.22	0.731	1.96	0.10	0.94	1u4qA	GO:0003779 GO:0005509 GO:0005516 GO:0005737 GO:0005856 GO:0005938 GO:0046872 GO:0051693
4	0.21	0.607	2.79	0.03	0.96	1s35A	GO:0000165 GO:0003779 GO:0005088 GO:0005200 GO:0005737 GO:0005829 GO:0005856 GO:0005938 GO:0006888 GO:0007411 GO:0008091 GO:0009986 GO:0014731 GO:0015629 GO:0030506 GO:0031235 GO:0043234 GO:0043547 GO:0051015 GO:0051693
5	0.21	0.619	2.75	0.06	0.99	3lbxB	GO:0000165 GO:0003779 GO:0005088 GO:0005200 GO:0005737 GO:0005829 GO:0005856 GO:0005938 GO:0006888 GO:0007411 GO:0008091 GO:0009986 GO:0014731 GO:0015629 GO:0030506 GO:0031235 GO:0043234 GO:0043547 GO:0051015 GO:0051693
6	0.20	0.624	2.05	0.08	0.85	3uumB	GO:0003779 GO:0007528 GO:0008270 GO:0030426 GO:0030864 GO:0031594 GO:0046872 GO:0051015
7	0.17	0.628	2.46	0.08	0.91	3edvA	GO:0000165 GO:0000281 GO:0003779 GO:0005088 GO:0005200 GO:0005516 GO:0005543 GO:0005634 GO:0005730 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005913 GO:0006888 GO:0007009 GO:0007182 GO:0007184 GO:0007411 GO:0008091 GO:0014731 GO:0016020 GO:0030506 GO:0030673 GO:0030863 GO:0031430 GO:0032437 GO:0043001 GO:0043547 GO:0044822 GO:0051020 GO:0051693 GO:0070062 GO:0071709 GO:0072661 GO:0097481 GO:0098609 GO:0098641 GO:1900042 GO:1903076 GO:1903078
8	0.14	0.714	2.09	0.08	0.94	4gyoB	GO:0004721 GO:0006470 GO:0016787
9	0.10	0.620	2.44	0.09	0.93	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
10	0.10	0.568	3.20	0.07	1.00	4i1aB	GO:0004721 GO:0006470 GO:0016787
11	0.10	0.582	2.74	0.04	0.97	4d8mA	GO:0009405 GO:0030435
12	0.10	0.667	2.27	0.06	0.93	3uq3A	GO:0003729 GO:0005737 GO:0006457 GO:0008104 GO:0030544 GO:0042030 GO:0043086 GO:0051879
13	0.10	0.673	2.42	0.03	0.94	4i9eA	GO:0004721 GO:0006470 GO:0016787
14	0.09	0.536	2.52	0.10	0.87	2iakA	GO:0001725 GO:0003779 GO:0005509 GO:0005634 GO:0005635 GO:0005737 GO:0005783 GO:0005789 GO:0005856 GO:0005874 GO:0005882 GO:0005886 GO:0005925 GO:0005938 GO:0007010 GO:0007050 GO:0007155 GO:0007409 GO:0008090 GO:0008092 GO:0009898 GO:0014704 GO:0015629 GO:0015630 GO:0016020 GO:0016021 GO:0016023 GO:0030018 GO:0030054 GO:0030056 GO:0030424 GO:0031673 GO:0035371 GO:0042383 GO:0042803 GO:0042995 GO:0045104 GO:0046872 GO:0046907 GO:0048471 GO:0051010 GO:0097038 GO:0097481 GO:1904115
15	0.08	0.644	2.38	0.04	0.94	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
16	0.08	0.654	2.55	0.04	0.94	3q15A	GO:0004721 GO:0006470 GO:0016787
17	0.08	0.598	2.68	0.06	0.93	1sjjA	GO:0001725 GO:0001726 GO:0003779 GO:0005509 GO:0005623 GO:0005737 GO:0005856 GO:0005886 GO:0005915 GO:0005923 GO:0005925 GO:0016020 GO:0016328 GO:0017166 GO:0030018 GO:0030027 GO:0030054 GO:0030274 GO:0030486 GO:0031252 GO:0042383 GO:0042803 GO:0042995 GO:0045214 GO:0046872 GO:0048741 GO:0051015 GO:0051017 GO:0051219 GO:0051393 GO:0051764 GO:0090636 GO:0090637 GO:0097433 GO:1990357
18	0.07	0.579	2.69	0.00	0.88	1g8xA	GO:0000146 GO:0000166 GO:0000281 GO:0000331 GO:0001931 GO:0003774 GO:0003779 GO:0005200 GO:0005509 GO:0005516 GO:0005524 GO:0005737 GO:0005773 GO:0005826 GO:0005829 GO:0005856 GO:0005884 GO:0005938 GO:0006909 GO:0006935 GO:0006971 GO:0006972 GO:0007275 GO:0008104 GO:0008360 GO:0009267 GO:0009612 GO:0016459 GO:0016460 GO:0030038 GO:0030554 GO:0030587 GO:0030674 GO:0030837 GO:0030866 GO:0030898 GO:0031034 GO:0031143 GO:0031152 GO:0031154 GO:0031252 GO:0031254 GO:0031270 GO:0031410 GO:0032009 GO:0032060 GO:0032154 GO:0032982 GO:0033275 GO:0033298 GO:0034461 GO:0042542 GO:0042641 GO:0042803 GO:0044351 GO:0045179 GO:0045335 GO:0046847 GO:0046872 GO:0048870 GO:0051015 GO:0051017 GO:0051764 GO:0060328 GO:0071889 GO:0097204 GO:1990753

Consensus prediction of GO terms

Molecular Function	GO:0003779	GO:0005200	GO:0005516	GO:0005509	GO:0005088	GO:0001948	GO:0019899	GO:0046914	GO:0047485	GO:0019905	GO:0032403	GO:0098641
GO-Score	0.75	0.68	0.58	0.58	0.58	0.48	0.48	0.48	0.47	0.47	0.47	0.47
Biological Processes	GO:0051693	GO:0006888	GO:0043547	GO:0007411	GO:0000165	GO:0010975	GO:0001508	GO:0060538	GO:2000169	GO:0006518	GO:0050848	GO:0071363	GO:2001257	GO:0033275	GO:0001933	GO:0033135	GO:0070727	GO:0055002	GO:0014722	GO:0032414	GO:0009612	GO:0008104	GO:1901019	GO:0042384	GO:0031346	GO:0010469	GO:2000649	GO:0060249	GO:1901566	GO:1902307	GO:0050769	GO:0043604	GO:0051279	GO:0010882	GO:0014808	GO:0031532	GO:0098609
GO-Score	0.67	0.58	0.58	0.58	0.58	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.47	0.47
Cellular Component	GO:0005829	GO:0008091	GO:0016010	GO:0098857	GO:0031674	GO:0030175	GO:0031253	GO:0043005	GO:0098794	GO:0097060	GO:0043231	GO:0070062	GO:0015630	GO:0005913	GO:0031226	GO:0009898	GO:0009986
GO-Score	0.68	0.58	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.47	0.47	0.47	0.47	0.41	0.41	0.40

(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 Rv2401A

[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]