I-TASSER results

I-TASSER results for job id Rv2491

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

Input Sequence in FASTA format

>protein (207 residues)
MVDTSAPASRLDTDPRRAHVSLSKHPYQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILI
SGGMTGTMEASSRGASDADGLVVGVLPGDKFTDGNAYSTIKILSGMQFARNYITGLSCHG
AIVVGGSSGAYEEARRVWEGRGPVVVLANSGSPTGASAQMLSMQEIFGVAFPEDKPKPWR
VFSAATPAESVSLVIGLIRKGYAQHEP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVDTSAPASRLDTDPRRAHVSLSKHPYQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPGDKFTDGNAYSTIKILSGMQFARNYITGLSCHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSGSPTGASAQMLSMQEIFGVAFPEDKPKPWRVFSAATPAESVSLVIGLIRKGYAQHEP
Prediction	CCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHCCCEEEHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHCCCEEEHCCCHHHHHHHHHHHHHHHHHHCCC
Conf.Score	988778756667789999999865798699987999995999999999999999899899689987789999999998995899857998777789865899859989999999998997999799856899999999979998998589975589999999988876788645544556898499999999999999998876689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVDTSAPASRLDTDPRRAHVSLSKHPYQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPGDKFTDGNAYSTIKILSGMQFARNYITGLSCHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSGSPTGASAQMLSMQEIFGVAFPEDKPKPWRVFSAATPAESVSLVIGLIRKGYAQHEP
Prediction	745575446314520440242057343100000014255600510250042016460000000230002000400374613000001434464414203120305324420330043020030232332123000102436210000124311330033025424342323463453222012052043005202510562276368
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHCCEEEHCCCCCHHHHHHHHHHHHCCCEEEHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHCCCEEEHCCCHHHHHHHHHHHHHHHHHHCCC
MVDTSAPASRLDTDPRRAHVSLSKHPYQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPGDKFTDGNAYSTIKILSGMQFARNYITGLSCHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSGSPTGASAQMLSMQEIFGVAFPEDKPKPWRVFSAATPAESVSLVIGLIRKGYAQHEP

1wekA

0.25

0.23

0.92

2.81

MUSTER

HHEDSWRLFRILAEFVEGFETLSELVPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLRFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQL---FRLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

4.65

dPPAS

HHEDSWRLFRILAEFVEGFETLSELQPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQKNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLRFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQLF---RLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

4.39

wdPPAS

HHEDSWRLFRILAEFVEGFETLSELQPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVL-RFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQ---LFRLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

3.35

wMUSTER

HHEDSWRLFRILAEFVEGFETLSELVPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVL-RFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQL---FRLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

3.97

wPPAS

HHEDSWRLFRILAEFVEGFETLSELQPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLRFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQ---LFRLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

6.81

dPPAS2

HHEDSWRLFRILAEFVEGFETLSELQPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQKNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLRFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQLF---RLTDEPEEVVQALKA-----------

1wekA

0.25

0.23

0.92

3.36

PPAS

HHEDSWRLFRILAEFVEGFETLSELQPLVSVFGSARFGHPAYEAGYRLGRALAEAGFGVVTGGGPG-VEAVNRGAYEAGGVSVGLNIELPHEQPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLRFPVFLLDRGYWEGLVRWLAFLRDQK-AVGPEDLQ---LFRLTDEPEEVVQALKA-----------

3sbxA

0.23

0.19

0.81

4.81

Env-PPAS

-------------------------RWTVAVYCAAAPTPELLELAGAVGAAIAARGWTLVWGGGHSAMGAVSSAARAHGGWTVGVIPKMLVELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGKSIVVLDPWGHFDGLRAWLSELADT-GYVSRTAME---RLIVVDNLDDALQACA-----------P

3sbxA

0.23

0.19

0.81

2.57

MUSTER

-------------------------RWTVAVYCAAAPHPELLELAGAVGAAIAARGWTLVWGGGHSAMGAVSSAARAHGGWTVGVIPKMLVELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGKSIVVLDPWGHFDGLRAWLSELADT-GYVSRTAME---RLIVVDNLDDALQACA-----------P

3sbxA

0.23

0.18

0.81

4.48

dPPAS

-------------------------RWTVAVYCAAAPTPELLELAGAVGAAIAARGWTLVWGGGHSAMGAVSSAARAHGGWTVGVIPKMHRELADHDADELVVTETMWERKQVMEDRANAFITLPGGVGTLDELLDVWTEGKSIVVLDPWGHFDGLRAWLSELADT-GYVSRTAME---RLIVVDNLDDALQACAP-----------

(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=1.13

Estimated TM-score = 0.87±0.07

Estimated RMSD = 3.2±2.2Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.01

Download Model 5

C-score=-5.00

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	1wekA	0.875	1.40	0.246	0.923
2	3bq9A	0.812	2.43	0.146	0.937
3	3gh1A	0.780	2.64	0.156	0.908
4	3quaA	0.759	1.60	0.195	0.816
5	5itsA	0.748	1.94	0.174	0.821
6	3sbxA	0.744	1.69	0.210	0.807
7	5ajtA	0.728	2.27	0.207	0.821
8	2q4dA	0.705	2.03	0.205	0.783
9	3majA	0.700	3.66	0.186	0.874
10	1wehA	0.700	1.72	0.215	0.763

(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	0.56	16	3sbxF	AMP	Rep, Mult	33,34,35,68,107,110,111,127,128,129,130,132,133
2	0.10	5	2iegA	FRY	Rep, Mult	32,33,34,44,48,185,187
3	0.05	2	3sbxE	AMP	Rep, Mult	136,139
4	0.02	1	3maj0	III	Rep, Mult	44,148,151,183,185

	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	0.308	2q4dA	0.705	2.03	0.205	0.783	3.2.2.-	62,122,129,132
2	0.179	2a0kA	0.471	3.92	0.078	0.618	2.4.2.6	111,133
3	0.125	1f8xA	0.473	3.48	0.064	0.604	2.4.2.6	133
4	0.066	1e20A	0.526	3.88	0.081	0.705	4.1.1.36	NA
5	0.066	2o6lB	0.501	3.63	0.062	0.667	2.4.1.17	35,59
6	0.060	1q0lA	0.524	4.24	0.067	0.744	1.1.1.267	49,64,124,133
7	0.060	1ygpA	0.584	4.15	0.111	0.812	2.4.1.1	NA
8	0.060	1r0lC	0.538	4.23	0.079	0.749	1.1.1.267	58
9	0.060	3i39X	0.633	4.10	0.089	0.860	1.2.99.2	153
10	0.060	1fa9A	0.570	4.16	0.076	0.821	2.4.1.1	40
11	0.060	1e5dA	0.535	4.10	0.058	0.720	1.-.-.-	NA
12	0.060	1v4vA	0.549	3.88	0.101	0.734	5.1.3.14	NA
13	0.060	1e1yA	0.571	4.16	0.052	0.816	2.4.1.1	40
14	0.060	3cf4A	0.604	3.86	0.101	0.807	1.2.99.2	NA
15	0.060	2q4oA	0.695	1.79	0.205	0.758	3.2.2.-	63,126,133
16	0.060	1d7oA	0.528	4.67	0.103	0.758	1.3.1.9	68
17	0.060	3gpbA	0.585	4.14	0.076	0.816	2.4.1.1	NA
18	0.060	1chdA	0.525	3.94	0.087	0.710	3.1.1.61	NA
19	0.060	2z8yP	0.557	4.09	0.117	0.773	2.3.1.169	NA
20	0.060	2qllA	0.571	4.18	0.081	0.821	2.4.1.1	NA
21	0.060	1f6dA	0.564	3.82	0.124	0.744	5.1.3.14	73
22	0.060	3drwA	0.531	4.54	0.081	0.758	2.7.1.146	NA
23	0.060	1cjyA	0.544	5.03	0.093	0.850	3.1.1.4,3.1.1.5	NA
24	0.060	2r4uA	0.550	4.41	0.112	0.768	2.4.1.21	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	0.58	0.879	1.39	0.25	0.93	1wekA	GO:0009691 GO:0016787 GO:0016799
1	0.35	0.705	2.69	0.21	0.83	1t35E	GO:0005829 GO:0009691 GO:0016799
2	0.34	0.680	2.23	0.29	0.76	2iz7A	GO:0005829 GO:0009691 GO:0016799
3	0.33	0.759	1.60	0.20	0.82	3quaA	GO:0009691 GO:0016787 GO:0016799
4	0.32	0.735	2.03	0.20	0.82	2q4dA	GO:0005634 GO:0005737 GO:0005829 GO:0009691 GO:0016787 GO:0016799 GO:0042803
5	0.31	0.809	2.61	0.15	0.94	3gh1A	GO:0005829 GO:0009691 GO:0016799
6	0.29	0.709	1.72	0.22	0.77	1wehA	GO:0016020 GO:0016021
7	0.28	0.688	2.24	0.23	0.77	1rcuA	GO:0005829 GO:0009691 GO:0016799
8	0.28	0.715	1.77	0.20	0.78	2a33A	GO:0005634 GO:0005737 GO:0009691 GO:0016787 GO:0016799
9	0.12	0.497	3.73	0.11	0.64	1j2rA	GO:0003824 GO:0005829 GO:0006769 GO:0008152 GO:0008936 GO:0016787 GO:0019674
10	0.07	0.437	5.02	0.10	0.70	1g69B	GO:0000287 GO:0003824 GO:0004789 GO:0005737 GO:0009228 GO:0009229 GO:0016740 GO:0046872
11	0.06	0.429	5.33	0.07	0.69	2xtzC	GO:0000166 GO:0001789 GO:0003924 GO:0004871 GO:0005095 GO:0005525 GO:0005789 GO:0005834 GO:0005886 GO:0006571 GO:0007165 GO:0007186 GO:0008219 GO:0009094 GO:0009506 GO:0009738 GO:0009740 GO:0009749 GO:0009785 GO:0009788 GO:0009789 GO:0009845 GO:0010027 GO:0010119 GO:0010244 GO:0016020 GO:0016247 GO:0019001 GO:0031683 GO:0034260 GO:0042127 GO:0046872 GO:0071215 GO:0072593
12	0.06	0.372	5.30	0.02	0.59	3icqT	GO:0000049 GO:0003723 GO:0005525 GO:0005634 GO:0005635 GO:0005643 GO:0005737 GO:0005829 GO:0006409 GO:0006605 GO:0006810 GO:0008033 GO:0008536 GO:0015932 GO:0016363 GO:0071528
13	0.06	0.323	5.01	0.03	0.52	3o3fA	GO:0003676 GO:0003723 GO:0004518 GO:0004519 GO:0004523 GO:0005737 GO:0006298 GO:0006401 GO:0016787 GO:0030145 GO:0032299 GO:0043137 GO:0046872 GO:0090305 GO:0090502
14	0.06	0.290	5.30	0.02	0.47	1cbkA	GO:0000166 GO:0003848 GO:0005524 GO:0009396 GO:0016301 GO:0016310 GO:0016740 GO:0046654 GO:0046656
15	0.06	0.274	5.61	0.06	0.45	2l5aA	GO:0000086 GO:0000780 GO:0000786 GO:0000788 GO:0003677 GO:0005634 GO:0005694 GO:0006333 GO:0006334 GO:0007059 GO:0031298 GO:0034729 GO:0042393 GO:0043935 GO:0046982 GO:0051382 GO:0061587 GO:0071459 GO:0097030 GO:2000059
16	0.06	0.245	5.46	0.08	0.43	4chdA	GO:0003723 GO:0003968 GO:0006351 GO:0006370 GO:0006397 GO:0019012 GO:0042025 GO:0075526
17	0.06	0.211	4.61	0.04	0.31	2ly8A	GO:0000070 GO:0000775 GO:0000776 GO:0000777 GO:0000780 GO:0000786 GO:0003677 GO:0005634 GO:0005694 GO:0005727 GO:0019237 GO:0030543 GO:0043505 GO:0043565 GO:0046982
18	0.06	0.189	4.06	0.07	0.26	2l5fA	GO:0000398 GO:0003723 GO:0005634 GO:0005654 GO:0005685 GO:0005737 GO:0006397 GO:0007010 GO:0007049 GO:0008360 GO:0008380 GO:0016020 GO:0016363 GO:0016477 GO:0016607 GO:0032465 GO:0044822 GO:0051301 GO:0070064 GO:0071004
19	0.06	0.160	4.43	0.05	0.23	2hldQ	GO:0005739 GO:0005743 GO:0005756 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016787 GO:0016887 GO:0045261 GO:0046933 GO:0046961

Consensus prediction of GO terms

Molecular Function	GO:0016799	GO:0042803
GO-Score	0.92	0.32
Biological Processes	GO:0009691
GO-Score	0.92
Cellular Component	GO:0005829	GO:0005634
GO-Score	0.71	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.