I-TASSER results

I-TASSER results for job id Rv2186c

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

Input Sequence in FASTA format

>protein (129 residues)
MNSIQIADETYVAADAARVSAAVADRCSWRRWWPDLRLQVTEDRADKGIRWTVTGALTGT
MEIWLEPSMDGVLLHYFLHAEPTGVAAWQLARMNLARMTHHRRVAGKKMAFEVKTVLERS
RPIGVSPVT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNSIQIADETYVAADAARVSAAVADRCSWRRWWPDLRLQVTEDRADKGIRWTVTGALTGTMEIWLEPSMDGVLLHYFLHAEPTGVAAWQLARMNLARMTHHRRVAGKKMAFEVKTVLERSRPIGVSPVT
Prediction	CCEEEEEEEEEEHCCHHHHHHHHCCHHHHHHHCCCEEEEEEHCCCCCCCEEEHCCCCCEEEEEEEEHCCCCEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	985567765677769999999985766567769977999986555678589986887656888875445867899988655689986446778999999999999999999999999858999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MNSIQIADETYVAADAARVSAAVADRCSWRRWWPDLRLQVTEDRADKGIRWTVTGALTGTMEIWLEPSMDGVLLHYFLHAEPTGVAAWQLARMNLARMTHHRRVAGKKMAFEVKTVLERSRPIGVSPVT
Prediction	564242213211203353025314446404411240303035532653230305342422032103321200001100203356255562445504531543433044102403531564454644458
	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

CCEEEEEEEEEEHCCHHHHHHHHCCHHHHHHHCCCEEEEEEHCCCCCCCEEEHCCCCCEEEEEEEEHCCCCEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
MNSIQIADETYVAADAARVSAAVADRCSWRRWWPDLRLQVTEDRADKGIRWTVTGALTGTMEIWLEPSMDGVLLHYFLHAEPTGVAAWQLARMNLARMTHHRRVAGKKMAFEVKTVLERSRPIGVSPVT

2m47A

0.17

0.16

0.97

1.22

MUSTER

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEGPVVGAHFTGRTDGNVKWIYSMEPLEEGTVLTESWEFTPKGQKFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV-HHHHHH---

2m47A

0.16

0.99

1.35

dPPAS

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPERTWETRTDGNVKWIYSMEPLEEGTVLTESWEFTPKGQKFGDKSIEEIEKRRLAAITGIPETLVAIQRILEVELEHHHHHH-

2m47A

0.19

0.96

1.39

wdPPAS

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVTRSEVIVAEPNRCFGWSVTDG-NVKWIYSMEPLEEGTVLTESWEFTPKGQRFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV-HHHHHH---

2m47A

0.18

0.17

0.96

1.33

wMUSTER

PKSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEGPVVGFGWSVTDG-NVKWIYSMEPLEEGTVLTESWEFTPKGQRFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV-HHHHHH---

2m47A

0.20

0.19

0.96

1.29

wPPAS

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVEKCWWDEDEGPVGFGWSVTDG-NVKWIYSMEPLEEGTVLTESWEFTPKGQRFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV-HHHHHH---

2m47A

0.16

0.98

2.14

dPPAS2

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVCEKCWWDEDEGPERTWETRTDGNVKWIYSMEPLEEGTVLTESWEFTPKGQRFGDKSIEEIEKRRLAAITGIPETLVAIQRILEVEHHHHHH---

2m47A

0.18

0.17

0.97

1.39

PPAS

MPSLTFEDSINIAAPINQVYALVSDITRTGEWSPVEKCWWDEDEGPVERTWETRTDGNVKWIYSMEPLEEGTVLTESWEFTPKGQRFGDKSIEEIEKRRLAAITGIPETLVAIQRILEV-HHHHHH---

2m89A

0.17

0.14

0.84

1.18

Env-PPAS

M--VNINHRIGIKASPEKIYQALTTDDGLKKWWTGPDFKVTKLIPNKTVCWQHAGNMPEEISFQLETVENQTFVRFTHSNWHETT-----------DFMAHCNTKWAVFLLSLKDALEIGK--G-----

1xn5A

0.15

0.14

0.91

1.16

MUSTER

MTLPDIKKEVRFNAPIEKVWEAVSTSEGLAFWFMESPCQVTDVERPIKLSFTW-DTDGWSVTFHLKEEENGTIFTIVHSGWKQGDTKVEKAGAESAVVHERMDRGWHDLVERLRQIVE-----------

1xn5A

0.13

0.12

0.91

1.32

dPPAS

TRLPDIKKEVRFNAPIEKVWEAVSTSEGLAFWFMESPCQVTDVERPIKLSFTW-DTDGWSVTFHLKEEENGTIFTIVHSGKQGDTKVEKAGAESAVVHERMDRGWHDLVNERLRQIVE-----------

(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=-1.01

Estimated TM-score = 0.59±0.14

Estimated RMSD = 6.5±3.9Å

Download Model 2

C-score=-2.57

Download Model 3

C-score=-1.15

Download Model 4

C-score=-1.34

Download Model 5

C-score=-1.24

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	2m47A	0.785	2.82	0.142	0.985
2	3tfzA	0.762	2.65	0.143	0.938
3	4xrwA	0.747	2.25	0.139	0.899
4	2rezA	0.747	2.78	0.133	0.922
5	4xrtA2	0.736	2.57	0.125	0.930
6	3oquA	0.736	2.64	0.094	0.907
7	3qtjA	0.733	2.48	0.099	0.899
8	3ie5B	0.728	2.49	0.118	0.899
9	3kdhA	0.722	2.41	0.059	0.884
10	4oicA	0.720	2.54	0.114	0.884

(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	0.18	10	4n3eD	2AN	Rep, Mult	8,10,19,23,63,65,76,106,107,110
2	0.08	5	3fxjA	MN	Rep, Mult	70,71
3	0.06	3	4a81A	2AN	Rep, Mult	8,10,22,51,63,76,78,103,106,107,110,111
4	0.05	3	3gtsB	D3M	Rep, Mult	38,51,53,61,63,102,105,109
5	0.05	3	3gb4A	FES	Rep, Mult	50,61,63,76
6	0.02	1	3s7bA	BU3	Rep, Mult	44,51
7	0.02	1	3c0vC	TBR	Rep, Mult	43,46,48,62
8	0.02	1	2anuA	ZN	Rep, Mult	66,75
9	0.02	1	2qx6A	ML1	Rep, Mult	29,55
10	0.02	1	4dz4A	UNK	Rep, Mult	43,55
11	0.02	1	1gqcA	MG	Rep, Mult	5,8,9
12	0.02	1	4ryvA	ZEA	Rep, Mult	6,8,78,80,99,100,103

	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	0.166	1ul7A	0.488	3.28	0.087	0.682	2.7.11.1	10,62,110
2	0.060	2ewnA	0.559	3.30	0.034	0.760	6.3.4.15	NA
3	0.060	1umfC	0.509	3.95	0.046	0.783	4.2.3.5	NA
4	0.060	2v8qA	0.526	3.13	0.093	0.713	2.7.11.1	65,74
5	0.060	1ciaA	0.520	3.87	0.029	0.744	2.3.1.28	NA
6	0.060	2pmgB	0.418	4.19	0.060	0.659	5.4.2.2	46
7	0.060	1wqlA	0.611	3.36	0.034	0.853	1.14.12.-	15
8	0.060	2cghB	0.552	3.56	0.094	0.775	6.3.4.15	NA
9	0.060	3en1A	0.549	3.77	0.059	0.853	1.14.12.11	15
10	0.060	1wnlA	0.533	3.77	0.060	0.767	6.3.4.15	NA
11	0.060	2ej9A	0.534	4.07	0.078	0.806	6.3.4.15	47
12	0.060	2zfdB	0.538	2.92	0.110	0.698	2.7.11.1	12,113
13	0.060	2vq5A	0.663	2.84	0.115	0.868	4.2.1.78	48,65
14	0.060	1kfqB	0.569	3.64	0.092	0.845	5.4.2.2	68,70
15	0.060	1cf3A	0.517	4.13	0.061	0.767	1.1.3.4	NA
16	0.060	1crkA	0.532	3.47	0.091	0.767	2.7.3.2	NA
17	0.060	2ii4A	0.550	4.32	0.054	0.806	2.3.1.168	NA
18	0.060	1q23B	0.528	3.76	0.048	0.744	2.3.1.28	NA
19	0.060	1uliC	0.617	3.29	0.026	0.853	1.14.12.18	25
20	0.060	1galA	0.509	3.98	0.043	0.752	1.1.3.4	40,113

(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	0.20	0.750	2.67	0.13	0.91	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
1	0.10	0.667	2.99	0.08	0.87	2kewA	GO:0006950
2	0.07	0.426	4.10	0.01	0.66	1z05A	GO:0003700 GO:0006355 GO:0046872
3	0.07	0.438	4.69	0.05	0.75	3l2nA	GO:0004180 GO:0004181 GO:0006508 GO:0008270 GO:0046872
4	0.06	0.370	4.43	0.03	0.57	3rd7B	GO:0006637 GO:0047617
5	0.06	0.359	4.94	0.06	0.61	1lldA	GO:0003824 GO:0004459 GO:0005737 GO:0005975 GO:0006096 GO:0016491 GO:0016616 GO:0019752 GO:0055114
6	0.06	0.371	5.13	0.10	0.71	4iilA	GO:0005886 GO:0016020
7	0.06	0.348	4.92	0.08	0.65	2qk4B	GO:0000166 GO:0003360 GO:0003824 GO:0004637 GO:0004641 GO:0004644 GO:0005524 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006544 GO:0008152 GO:0009058 GO:0009113 GO:0009156 GO:0009168 GO:0010033 GO:0010035 GO:0016740 GO:0016742 GO:0016874 GO:0021549 GO:0021987 GO:0046654 GO:0046872 GO:0070062
8	0.06	0.396	4.38	0.02	0.64	5bsmA	GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0009698 GO:0016207 GO:0016874
9	0.06	0.307	5.27	0.02	0.58	4v6wAI	GO:0000462 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022008 GO:0022627 GO:0030529 GO:0035167
10	0.06	0.295	5.50	0.06	0.60	4d4zB	GO:0004497 GO:0005829 GO:0008612 GO:0016491 GO:0019135 GO:0046872 GO:0055114
11	0.06	0.302	2.68	0.11	0.37	4iylA	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
12	0.06	0.296	4.52	0.09	0.49	1fneA	GO:0002376 GO:0002504 GO:0006955 GO:0016020 GO:0016021 GO:0019882 GO:0042613
13	0.06	0.682	2.53	0.15	0.83	4xrtA
14	0.06	0.785	2.82	0.14	0.98	2m47A
15	0.06	0.365	4.49	0.11	0.60	3bt5A
16	0.06	0.272	4.12	0.03	0.42	3hg9B
17	0.06	0.762	2.65	0.14	0.94	3tfzA
18	0.06	0.689	2.60	0.10	0.88	2le1A

Consensus prediction of GO terms

Molecular Function	GO:0008168
GO-Score	0.40
Biological Processes	GO:0044249	GO:0016999
GO-Score	0.40	0.40
Cellular Component
GO-Score

(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.