I-TASSER results

Input Sequence in FASTA format

>protein (128 residues)
MGAWQTADTMGIFQALPDVWGGWRTECWEDRFEEQLIRCNGALRLPELDLAAGMDSAREW
LRDRIFQRFSDSPAGQILKLSELLADVGPGLVVSDDAVTNGGARPNNEEWARFVAACDLV
RGAHAESA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGAWQTADTMGIFQALPDVWGGWRTECWEDRFEEQLIRCNGALRLPELDLAAGMDSAREWLRDRIFQRFSDSPAGQILKLSELLADVGPGLVVSDDAVTNGGARPNNEEWARFVAACDLVRGAHAESA
Prediction	CEEEHCCCCCHHHHHHHHHCCCCCEEEHCHHHHHHHHHHCCCEHCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCEEEHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	95676689874899999877876567753578999999879766787655777999999999998655678867699999999999799975656765444368999999999999999987665469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MGAWQTADTMGIFQALPDVWGGWRTECWEDRFEEQLIRCNGALRLPELDLAAGMDSAREWLRDRIFQRFSDSPAGQILKLSELLADVGPGLVVSDDAVTNGGARPNNEEWARFVAACDLVRGAHAESA
Prediction	63314436332014203711540423114541562146134204134252544164035204640254347432341340141036324423144531342234345641430440044144444668
	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                 120

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEHCCCCCHHHHHHHHHCCCCCEEEHCHHHHHHHHHHCCCEHCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCEEEHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
MGAWQTADTMGIFQALPDVWGGWRTECWEDRFEEQLIRCNGALRLPELDLAAGMDSAREWLRDRIFQRFSDSPAGQILKLSELLADVGPGLVVSDDAVTNGGARPNNEEWARFVAACDLVRGAHAESA

3fkdA

0.14

0.13

0.96

0.88

MUSTER

NAILVTNGPTAAFYQIAQAFRGSRSLIAIPSFAEYEDACRYEHEVCFYPSNEDIGEADFS--DFCWLCNPNNPDGRRTEILRLLNDHPDTTFVLDQSYVSFTTEEV---IRPADIKGRKNLVVYSFSH

5cwiA2

0.11

0.09

0.88

0.54

dPPAS

-----ADIAKLCIKAASEA-----AEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEA-----SKAAEEAQRHPDSQKARDEIKEASQKAEEVKERCE

4luqA1

0.18

0.16

0.85

0.54

wdPPAS

----HMTATSDLIESLISYWDDWQV-------RQEARRVIAAIRVP--DATIAALDKS--SLIKLFQR---GPPELARSLIASIAGRTTM-QARNALIRSLINNPQTDNWIYFTITFFDICADLADAA

4elnA1

0.16

0.15

0.91

0.73

wMUSTER

LSPLVELNTSDLIKQKKQLWAQFRS---TPEERKQFKTA--LITLWGEQYRPERQQRWNGMMQRMAQMKWNHPELKTEDLVALQAWTTDDYEVVQD-VLEKEARPT---AHGLAFAKCIISALHSL--

4luqA1

0.22

0.19

0.84

0.64

wPPAS

---HMTA-TSDLIESLISYWDDWQV-------RQEARRVIAAIRVP--DATIAALDKS--SLIKLFQR---GPPELARSLIASIAGRT---TMQRYQARNALIRPQTDNWIYFTITFFDICADLADAA

3ojcA2

0.09

0.08

0.84

0.58

dPPAS2

IGLLGTRYT---------EQGF--------YRGRLTEKHGIEVITPD---DTDREAVNRIIYEELCLGISETSRDAYRRVIKKLEAQGVQGIIFGCTEITLLVNAQDASVPVFDTTAIHASAAADYAL

4elnA1

0.17

0.16

0.94

0.69

PPAS

LSPLVELNTSDLIKQKKQLWQ--RVQHDGAQFPEERKQFKTAITLWGEQYRPERQQRWNGMMQRMAQMKWNHPELKTEDLVALQAWTTDDYEVVQD-VLEKEARPTAHGLAFAKCIISALHSL-----

3lloA

0.19

0.17

0.90

0.70

Env-PPAS

------SPSYTVLGQLP------DTDVYIDAYEE-VKEIPGIKIFAPIYYANSDLYSSANIHTVILDNFMDVGVKTLAGIVKEYGDVGCSAQVVNDLTSNRFFENPALKELLFHSIHDAVLGSQVREA

3getA

0.15

1.00

0.88

MUSTER

VQIIIGAGSDQVIEFAIHSKSKNAFLQAGVAYEIYAKQCGACYKTQSITNLDEFKKLYETHKDEIFLCLPNNPLGEASEATEFIKGVNEDLVVIDAAYNEFASFKDSKKPCELIKEFDNVLYLGTFSL

5cwpA1

0.14

0.12

0.87

0.53

dPPAS

--------MSSDEEEARELIERAKEA--AERAQEAAERTGDPRV---RELARELKRLAQEAAEEVKRDPSSSDVNEALKLIVEAIEA----AVRALEAAERTGDPEVRELARELVRLAVEAAEEVQRN

(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=-3.18

Estimated TM-score = 0.36±0.12

Estimated RMSD = 11.6±4.5Å

Download Model 2

C-score=-3.34

Download Model 3

C-score=-2.20

Download Model 4

C-score=-3.88

Download Model 5

C-score=-3.86

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	4elnA	0.622	3.68	0.107	0.938
2	3pjzA	0.506	4.35	0.064	0.812
3	3u0jB1	0.506	3.56	0.042	0.734
4	4j7cI	0.501	4.00	0.040	0.781
5	4zh0A	0.492	4.86	0.017	0.891
6	3d2rB	0.492	4.36	0.025	0.812
7	3mkhA	0.491	4.87	0.089	0.859
8	4z11A	0.490	5.04	0.104	0.883
9	4he8M2	0.489	4.51	0.050	0.781
10	1og4A	0.489	4.13	0.096	0.812

(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	5	2y04B	2CV	Rep, Mult	119,120
2	0.10	5	2fjcA	FE	Rep, Mult	30,34
3	0.04	2	3pfdA	FDA	Rep, Mult	102,113,114,117
4	0.04	2	2bq8X	ZN	Rep, Mult	26,30
5	0.04	2	2q8gA	AZX	Rep, Mult	14,16,19,31,32,35,36,112,115
6	0.04	2	4xk8l	CLA	Rep, Mult	61,84,88
7	0.02	1	4rvyT	CLA	Rep, Mult	113,117
8	0.02	1	2v54B	MG	Rep, Mult	8,109
9	0.02	1	3cyzB	9OD	Rep, Mult	36,57,89,113
10	0.02	1	3v09A	UNK	Rep, Mult	60,84
11	0.02	1	1xvbD	3BR	Rep, Mult	118,121,122,125
12	0.02	1	3m9iA	3PE	Rep, Mult	123,127
13	0.02	1	3ak1C	EDO	Rep, Mult	108,111
14	0.02	1	3r4iB	CA	Rep, Mult	29,49

	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	2pnrB	0.479	4.55	0.033	0.828	2.7.11.2	82
2	0.060	2fonB	0.437	4.84	0.076	0.797	1.3.3.6	NA
3	0.060	2zdxA	0.485	4.12	0.034	0.789	2.7.11.2	82
4	0.060	1ga0A	0.402	5.32	0.033	0.773	3.5.2.6	NA
5	0.060	1bucA	0.470	5.08	0.073	0.836	1.3.99.2	NA
6	0.060	1cc1L	0.452	4.64	0.047	0.781	1.12.99.6	NA
7	0.060	1rx0A	0.453	4.97	0.078	0.859	1.3.99.-	NA
8	0.060	2ix6A	0.463	5.10	0.048	0.852	1.3.3.6	NA
9	0.060	1h54B	0.454	5.10	0.032	0.828	2.4.1.8	NA
10	0.060	1w07B	0.454	4.60	0.077	0.797	1.3.3.6	NA
11	0.060	1up8A	0.466	4.85	0.053	0.797	1.11.1.18	NA
12	0.060	1r5zA	0.484	4.57	0.086	0.781	3.6.3.14	80,86
13	0.060	1vncA	0.485	4.69	0.059	0.805	1.11.1.10	3
14	0.060	1ci8A	0.464	4.67	0.079	0.797	3.1.1.1	NA
15	0.060	3d2rB	0.492	4.36	0.025	0.812	2.7.11.2	82
16	0.060	2ix6E	0.463	5.10	0.048	0.852	1.3.3.6	78
17	0.060	1xvgC	0.473	3.86	0.039	0.695	1.14.13.25	NA
18	0.060	3hq2B	0.456	5.19	0.063	0.883	3.4.24.-	82
19	0.060	2pnrF	0.481	4.58	0.033	0.828	2.7.11.2	84,90

(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	0.08	0.622	3.68	0.11	0.94	4elnA	GO:0003956 GO:0006471
1	0.07	0.486	4.47	0.03	0.82	1y8pA	GO:0000166 GO:0004672 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035357 GO:0071333 GO:0071398 GO:0097411 GO:2000377
2	0.07	0.492	4.36	0.03	0.81	3d2rB	GO:0000166 GO:0002230 GO:0004672 GO:0004740 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0005975 GO:0006006 GO:0006468 GO:0006885 GO:0008286 GO:0009267 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0042304 GO:0042593 GO:0042594 GO:0045124 GO:0046320 GO:0071398 GO:0072593 GO:0098792 GO:2000811
3	0.07	0.505	3.53	0.03	0.73	3u0jB	GO:0005576 GO:0009405 GO:0018120
4	0.07	0.475	4.41	0.03	0.81	2q8gA	GO:0000166 GO:0004672 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005967 GO:0005975 GO:0006006 GO:0006468 GO:0008283 GO:0008631 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0097411 GO:0098779
5	0.07	0.486	4.18	0.02	0.77	5butI	GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0022820 GO:0055085 GO:0071805
6	0.07	0.395	5.31	0.09	0.81	1gkzA	GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005739 GO:0005759 GO:0005947 GO:0006468 GO:0009083 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0047323
7	0.07	0.485	4.12	0.03	0.79	2zdxA	GO:0000166 GO:0002230 GO:0004672 GO:0004740 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0005975 GO:0006006 GO:0006468 GO:0006885 GO:0008286 GO:0009267 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0042304 GO:0042593 GO:0042594 GO:0045124 GO:0046320 GO:0071398 GO:0072593 GO:0098792 GO:2000811
8	0.07	0.479	4.55	0.03	0.83	2pnrB	GO:0000166 GO:0004672 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035357 GO:0071333 GO:0071398 GO:0097411 GO:2000377
9	0.07	0.399	5.23	0.04	0.80	3crlB	GO:0000166 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005967 GO:0005975 GO:0006006 GO:0006111 GO:0006468 GO:0006885 GO:0008286 GO:0010510 GO:0010565 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0031670 GO:0032403 GO:0042593 GO:0042803 GO:0045254 GO:0046982
10	0.06	0.506	4.35	0.06	0.81	3pjzA	GO:0005267 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006812 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0022820 GO:0030955 GO:0035826 GO:0035827 GO:0042803 GO:0055085 GO:0071805
11	0.06	0.403	5.01	0.02	0.77	4javA	GO:0000155 GO:0000160 GO:0000166 GO:0005524 GO:0005622 GO:0007165 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0023014
12	0.06	0.363	4.70	0.16	0.63	4urmB	GO:0000166 GO:0000287 GO:0003677 GO:0003916 GO:0003918 GO:0005524 GO:0005694 GO:0005737 GO:0006261 GO:0006265 GO:0016853 GO:0046677 GO:0046872
13	0.06	0.391	5.08	0.02	0.75	3d36B
14	0.06	0.360	4.98	0.03	0.66	2a1dD	GO:0010952 GO:0016504
15	0.06	0.365	5.33	0.04	0.73	4bivA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0043708 GO:0046777
16	0.06	0.357	4.85	0.05	0.66	4ykbA	GO:0009507 GO:0010019 GO:0019899 GO:0046906
17	0.06	0.379	4.69	0.08	0.65	1sqfA	GO:0003723 GO:0005737 GO:0005829 GO:0006355 GO:0006364 GO:0008168 GO:0008649 GO:0009383 GO:0016434 GO:0016740 GO:0031167 GO:0032259 GO:0070475
18	0.06	0.340	4.93	0.05	0.63	1id0A	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0006470 GO:0007165 GO:0010350 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016787 GO:0018106 GO:0023014 GO:0046777 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0032559	GO:0004672	GO:0035639	GO:0032550
GO-Score	0.37	0.37	0.37	0.37
Biological Processes	GO:0006796	GO:0019318	GO:0006086	GO:0050812	GO:0010675
GO-Score	0.37	0.37	0.37	0.37	0.37
Cellular Component	GO:0044429	GO:0070013
GO-Score	0.37	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 Rv0607

[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]