I-TASSER results

I-TASSER results for job id Rv2018

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (239 residues)
MAGDQELELRFDVPLYTLAEASRYLVVPRATLATWADGYERRPANAPAVQGQPIITALPH
PTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEV
LWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGD
ANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDAIAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAGDQELELRFDVPLYTLAEASRYLVVPRATLATWADGYERRPANAPAVQGQPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDAIAA
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCEHCCCCCCCCCCCCCEEEHCCCCCCCCCEHCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHCEEHCCEEEEEEHHHHCCHHHHHHHHHHHEEHCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEHCCCCCCCCEEHCCCCCCCEEEHCCCCCCHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHC
Conf.Score	99876666656788889999999989999999987655555777887655686677567888987566588899999999999989999999999999999969887555433446646877534545645666665544344577557899999999887435766654566568898887898676557656884888779999999998999999999989999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAGDQELELRFDVPLYTLAEASRYLVVPRATLATWADGYERRPANAPAVQGQPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDAIAA
Prediction	75555524341723303152023217043720320031232444644444442103234566654120101100001003303747042640250052037315732003330312034001421653454434532443133345233103400440043031446412530414637533020113212020104634030320141154654153007417043720340051058
	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                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHCCEHCCCCCCCCCCCCCEEEHCCCCCCCCCEHCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHCEEHCCEEEEEEHHHHCCHHHHHHHHHHHEEHCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEHCCCCCCCCEEHCCCCCCCEEEHCCCCCCHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHC
MAGDQELELRFDVPLYTLAEASRYLVVPRATLATWADGYERRPANAPAVQGQPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDAIAA

5af3A

1.00

0.90

2.64

MUSTER

--------LRFDVPLYTLAEASRYLVVPRATLATWAD--------------QPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

0.90

2.96

dPPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWADQ--------------PIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.90

3.93

wdPPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWAD--------------QPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

3.07

wMUSTER

---------RFDVPLYTLAEASRYLVVPRATLATWAD--------------QPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

0.90

4.67

wPPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWADQ--------------PIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

0.90

7.03

dPPAS2

--------LRFDVPLYTLAEASRYLVVPRATLATWADQ--------------PIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

0.90

4.01

PPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWADQ--------------PIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A

1.00

0.89

0.90

5.74

Env-PPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWADQ--------------PIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASMIRLPQYGDANVVLDPRRGYGQPVFDGSGVRVADVLGPLRAGATFQAVADDYGVTPDQLRDALDA---

5af3A1

0.99

0.62

0.63

1.53

MUSTER

--------LRFDVPLYTLAEASRYLVVPRATLATWA--------------DQPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASM-------------------------------------------------------------------

5af3A1

0.99

0.62

0.63

1.81

dPPAS

--------LRFDVPLYTLAEASRYLVVPRATLATWA--------------DQPIITALPHPTGSHARLPFVGIAEAYVLNAFRRAGVPMQRIRPSLDWLIKNVGPHALASQDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYVFKEIVEHYLQQISFADDNLASM-------------------------------------------------------------------

(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=0.72

Estimated TM-score = 0.81±0.09

Estimated RMSD = 4.2±2.8Å

Download Model 2

C-score=-1.26

Download Model 3

C-score=0.12

Download Model 4

C-score=-5.00

Download Model 5

C-score=-1.07

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	5af3A	0.886	0.59	0.995	0.895
2	5amqA	0.498	5.35	0.055	0.803
3	3hjeA	0.449	6.11	0.064	0.791
4	1e9xA	0.447	5.38	0.052	0.703
5	4m5dA	0.446	5.71	0.055	0.753
6	5a22A	0.445	5.89	0.101	0.745
7	5ifiA	0.443	5.53	0.065	0.728
8	3i6mA	0.441	5.76	0.061	0.728
9	1iv8A	0.441	5.96	0.056	0.766
10	1q83A	0.439	5.83	0.050	0.736

(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	0.06	3	5hhjA	GLY	Rep, Mult	113,117
2	0.04	2	1uvxA	XE	Rep, Mult	74,75,78,107,159
3	0.04	2	4wlsA	NUC	Rep, Mult	28,30,31,34,35,63,65,83,88,89
4	0.04	2	3n97A	NUC	Rep, Mult	202,225,226,227,228,229,232,236
5	0.04	2	4xlsF	NUC	Rep, Mult	210,215,216,217,227,228,231
6	0.04	2	2zhcA	MG	Rep, Mult	186,190
7	0.02	1	3hosA	MG	Rep, Mult	116,197
8	0.02	1	1bjyA	CTC	Rep, Mult	230,234
9	0.02	1	4ewlA	GOL	Rep, Mult	205,212,213,224,226
10	0.02	1	1u65A	UUU	Rep, Mult	199,223,224,225
11	0.02	1	3d5bG	MG	Rep, Mult	86,88
12	0.02	1	3kylA	MG	Rep, Mult	116,221,222
13	0.02	1	1mioB	CA	Rep, Mult	228,232
14	0.02	1	1maaD	UUU	Rep, Mult	104,106,113
15	0.02	1	2qb0B	MN	Rep, Mult	156,192
16	0.02	1	2vkuA	DBE	Rep, Mult	78,82,87,99
17	0.02	1	2ha5A	AT3	Rep, Mult	78,95,113
18	0.02	1	2y2vB	P15	Rep, Mult	75,79,82

	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	1qleA	0.397	5.76	0.067	0.669	1.9.3.1	202
2	0.060	3debA	0.414	5.82	0.045	0.711	3.4.24.69	158
3	0.060	1po5A	0.407	5.76	0.047	0.678	1.14.14.1	NA
4	0.060	1b41A	0.438	5.89	0.051	0.732	3.1.1.7	NA
5	0.060	1aorB	0.409	6.16	0.065	0.732	1.2.7.5	NA
6	0.060	2occN	0.434	5.41	0.051	0.695	1.9.3.1	68
7	0.060	1qksB	0.419	5.93	0.032	0.724	1.7.2.1	97
8	0.060	1fziA	0.427	6.21	0.025	0.749	1.14.13.25	NA
9	0.060	2ebsB	0.422	5.38	0.077	0.674	3.2.1.150	NA
10	0.060	2pm8A	0.439	5.91	0.025	0.741	3.1.1.8	NA
11	0.060	1s9rA	0.411	5.88	0.031	0.720	3.5.3.6	101
12	0.060	1t3tA	0.426	6.36	0.048	0.766	6.3.5.3	86
13	0.060	3b6hB	0.419	5.79	0.050	0.703	5.3.99.4	113
14	0.060	1maaD	0.440	5.83	0.050	0.732	3.1.1.7	NA
15	0.060	3b98A	0.429	5.31	0.060	0.682	5.3.99.4	NA
16	0.060	1iv8A	0.441	5.96	0.056	0.766	5.4.99.15	75
17	0.060	1eveA	0.442	5.79	0.060	0.732	3.1.1.7	NA
18	0.060	3a2pA	0.412	5.95	0.051	0.720	3.5.2.12	NA
19	0.060	1jxaA	0.419	6.09	0.043	0.745	2.6.1.16	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	0.68	0.886	0.59	0.99	0.90	5af3A	GO:0003677
1	0.06	0.371	6.71	0.05	0.71	3bh4A	GO:0003824 GO:0004553 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
2	0.06	0.373	6.13	0.03	0.68	1bliA	GO:0003824 GO:0004553 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
3	0.06	0.409	6.03	0.06	0.73	4tvuA	GO:0003824 GO:0005975 GO:0016853 GO:0046872 GO:0047471
4	0.06	0.364	6.53	0.08	0.69	3ucqA	GO:0003824 GO:0005975
5	0.06	0.375	6.14	0.04	0.67	1ud2A	GO:0003824 GO:0004553 GO:0005509 GO:0005975
6	0.06	0.378	5.96	0.06	0.65	4h8vA	GO:0003824 GO:0005975 GO:0046872
7	0.06	0.323	6.27	0.03	0.59	1d7fA	GO:0003824 GO:0005576 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0043169 GO:0043895 GO:0046872 GO:2001070
8	0.06	0.364	6.28	0.04	0.67	3eddA	GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0047798
9	0.06	0.397	5.86	0.05	0.66	3aibC	GO:0005576 GO:0005975 GO:0009250 GO:0016740 GO:0016757 GO:0046527 GO:0047849
10	0.06	0.386	6.10	0.07	0.67	4xr7A	GO:0000288 GO:0000289 GO:0000932 GO:0003676 GO:0004518 GO:0004527 GO:0004535 GO:0005737 GO:0006301 GO:0006397 GO:0016787 GO:0031251 GO:0090305 GO:0090503
11	0.06	0.377	6.16	0.06	0.67	4howA	GO:0003824 GO:0005975 GO:0016853 GO:0046872
12	0.06	0.371	6.09	0.04	0.66	1v9lA	GO:0000166 GO:0006520 GO:0016491 GO:0016639 GO:0055114
13	0.06	0.363	6.40	0.06	0.68	1bagA	GO:0003824 GO:0004556 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
14	0.06	0.441	5.96	0.06	0.77	1iv8A	GO:0003824 GO:0005975
15	0.06	0.357	6.44	0.06	0.66	5e70C	GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757 GO:0043169
16	0.06	0.361	6.13	0.06	0.63	2dh2A	GO:0003725 GO:0003824 GO:0005432 GO:0005634 GO:0005737 GO:0005886 GO:0005913 GO:0005975 GO:0006810 GO:0006816 GO:0006865 GO:0009986 GO:0015175 GO:0015827 GO:0016020 GO:0016021 GO:0016049 GO:0016324 GO:0035725 GO:0042470 GO:0043330 GO:0044822 GO:0050900 GO:0060356 GO:0070062 GO:0098609 GO:0098641
17	0.06	0.364	5.92	0.07	0.63	1m53A	GO:0003824 GO:0005975
18	0.06	0.383	5.96	0.04	0.68	3amlA	GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005978 GO:0005982 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0043169

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0043169
GO-Score	0.68	0.36
Biological Processes	GO:0044238	GO:0071704
GO-Score	0.40	0.38
Cellular Component	GO:0005576
GO-Score	0.12

(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.