I-TASSER results

I-TASSER results for job id Rv1117

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

Input Sequence in FASTA format

>protein (107 residues)
MIFIVVKFETKPEWTERWPDLVASFTAATRAEEGNLWFEWSRSLDDPAEYVLVESFRDGE
AGGVHVNSDHFRQAMRELPKALASTPKIISQTIDATGWSAMGEMTVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MIFIVVKFETKPEWTERWPDLVASFTAATRAEEGNLWFEWSRSLDDPAEYVLVESFRDGEAGGVHVNSDHFRQAMRELPKALASTPKIISQTIDATGWSAMGEMTVG
Prediction	CEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEHCCCCCCEEEEEEEHCCHHHHHHHHHCHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCC
Conf.Score	98999999979988999999999999999879995799999869999889999998899999999969999999999999986798799998588876555565569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MIFIVVKFETKPEWTERWPDLVASFTAATRAEEGNLWFEWSRSLDDPAEYVLVESFRDGEAGGVHVNSDHFRQAMRELPKALASTPKIISQTIDATGWSAMGEMTVG
Prediction	40301030304663154025105611640463631230312424745320000011324601640371620440164046105551512334254741541353538
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEHCCCCCCEEEEEEEHCCHHHHHHHHHCHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCC
MIFIVVKFETKPEWTERWPDLVASFTAATRAEEGNLWFEWSRSLDDPAEYVLVESFRDGEAGGVHVNSDHFRQAMRELPKALASTPKIISQTIDATGWSAMGEMTVG

4zosA

0.25

0.22

0.90

2.48

MUSTER

ERHIICELRCEPENRERVKELVLKFVEPARLETGCLYYDLYQKIDEPDTFYIIDGWVNQEAVTSHAENPHVAEVMSDLQPLLTFGPSISLITRVSD-----------

3qmqC

0.16

0.14

0.90

5.67

dPPAS

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

3qmqC

0.16

0.14

0.90

5.08

wdPPAS

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

4zosA

0.25

0.22

0.90

3.02

wMUSTER

ERHIICELRCEPENRERVKELVLKFVEPARLETGCLYYDLYQKIDEPDTFYIIDGWVNQEAVTSHAENPHVAEVMSDLQPLLTFGPSISLITRVSD-----------

3qmqC

0.16

0.14

0.90

4.32

wPPAS

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

3qmqC

0.16

0.14

0.90

6.61

dPPAS2

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

3qmqC

0.16

0.14

0.90

4.13

PPAS

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

3qmqC

0.16

0.14

0.90

3.92

Env-PPAS

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

3qmqC

0.16

0.14

0.90

2.41

MUSTER

MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP-----------

4zosA

0.25

0.22

0.90

5.35

dPPAS

ERHIICELRCEPENRERVKELVLKFVEPARLETGCLYYDLYQKIDEPDTFYIIDGWVNQEAVTSHAENPHVAEVMSDLQPLLTFGPSISLITRVSD-----------

(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=0.32

Estimated TM-score = 0.76±0.10

Estimated RMSD = 3.5±2.4Å

Download Model 2

C-score=-0.99

Download Model 3

C-score=-0.34

Download Model 4

C-score=-0.77

Download Model 5

C-score=-4.86

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	4zosA	0.863	0.78	0.250	0.897
2	3qmqC	0.852	0.93	0.156	0.897
3	3mcsA	0.846	2.04	0.150	0.991
4	1y0hA	0.834	1.24	0.206	0.906
5	2omoA	0.833	1.32	0.200	0.888
6	3e8oA	0.810	1.75	0.192	0.916
7	1x7vC	0.803	1.20	0.237	0.869
8	3f44A	0.800	2.27	0.163	0.972
9	4dpoA	0.800	1.10	0.261	0.860
10	2gffB	0.796	1.50	0.179	0.888

(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	0.39	17	1n5vA	NOM	Rep, Mult	4,6,38,52,54,56,62,65,74,75,86,88
2	0.16	14	4fvcA	HEM	Rep, Mult	6,8,21,22,24,27,28,29,38,52,65,71,82,86,88
3	0.06	5	3fgvB	UNL	Rep, Mult	25,26,29,65,75
4	0.04	4	2od6C	OHA	Rep, Mult	4,6,54,56,66,88,90
5	0.04	4	1xbw1	III	Rep, Mult	2,3,23,30,32,35,36,37,38,39,40,41,42,43,44,51,89,90,91,92,93,94,95,100
6	0.03	3	1r6y0	III	Rep, Mult	2,3,5,7,19,40,41,42,43,44,46,49,51,53,59,66,87,88,89,90,91,92,93
7	0.01	1	3kkfA	CA	Rep, Mult	1,57
8	0.01	1	3fgvB	UNL	Rep, Mult	6,52,86
9	0.01	1	3hdsC	III	Rep, Mult	26,29,35,36,37,38,39,40
10	0.01	1	3kkfA	CA	Rep, Mult	11,13
11	0.01	1	1iujB	ZN	Rep, Mult	60,63

	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	0.225	2zdoD	0.674	2.72	0.124	0.906	1.14.99.3	61,74
2	0.180	1v3zA	0.555	3.36	0.069	0.785	3.6.1.7	30
3	0.138	1w2iA	0.554	3.28	0.081	0.785	3.6.1.7	35,37
4	0.107	2ko1A	0.522	2.76	0.063	0.729	2.7.6.5	26,72,85
5	0.091	1ulrA	0.565	3.15	0.070	0.766	3.6.1.7	NA
6	0.074	1gxtA	0.535	3.05	0.049	0.729	2.1.3.-	NA
7	0.067	2gv1A	0.568	3.24	0.078	0.804	3.6.1.7	NA
8	0.067	2fhmA	0.556	3.13	0.047	0.766	3.6.1.7	NA
9	0.067	1apsA	0.578	3.16	0.046	0.785	3.6.1.7	NA
10	0.067	1mliA	0.542	3.44	0.129	0.794	5.3.3.4	NA
11	0.066	1urrA	0.562	3.43	0.000	0.813	3.6.1.7	NA
12	0.066	1fvqA	0.498	2.88	0.085	0.664	3.6.3.4	NA
13	0.066	2acyA	0.556	3.68	0.044	0.832	3.6.1.7	NA
14	0.066	1fwpA	0.457	2.72	0.045	0.626	2.7.13.3	NA
15	0.066	2k7jA	0.549	3.37	0.056	0.804	3.6.1.7	NA
16	0.066	1aw0A	0.473	2.74	0.087	0.645	3.6.3.4	22,24,41
17	0.060	2g49A	0.589	3.86	0.084	0.925	3.4.24.56	NA
18	0.060	1z2lA	0.647	3.28	0.039	0.906	3.5.3.-	NA
19	0.060	2w01A	0.605	3.15	0.104	0.878	4.6.1.2	NA
20	0.060	1q2lA	0.584	3.37	0.040	0.916	3.4.24.55	NA
21	0.060	1yk9A	0.607	3.22	0.062	0.869	4.6.1.1	NA
22	0.060	3bxvA	0.781	2.26	0.123	0.944	1.13.11.55	38
23	0.060	2zofA	0.572	3.74	0.087	0.897	3.4.13.18	NA
24	0.060	2d3aA	0.571	3.80	0.087	0.916	6.3.1.2	NA
25	0.060	2zdpA	0.669	2.78	0.144	0.906	1.14.99.3	74
26	0.060	3nn1A	0.590	4.01	0.102	0.906	1.13.11.49	44,46
27	0.060	1vgyA	0.608	2.99	0.092	0.841	3.5.1.18	NA
28	0.060	1m5hC	0.630	3.36	0.082	0.916	2.3.1.101	49,51
29	0.060	2fgeA	0.599	3.71	0.106	0.944	3.4.24.-	NA
30	0.060	3eoqB	0.588	3.11	0.105	0.869	3.4.24.56	NA
31	0.060	1x8dA	0.611	3.35	0.083	0.888	5.1.3.-	NA
32	0.060	1fnoA	0.592	3.64	0.089	0.860	3.4.11.4	NA
33	0.060	2pfdB	0.627	3.08	0.092	0.878	2.1.2.5,4.3.1.4	NA
34	0.060	2wz1A	0.607	3.07	0.063	0.869	4.6.1.2	NA
35	0.060	1qd1B	0.613	3.39	0.081	0.888	2.1.2.5,4.3.1.4	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	0.37	0.825	1.25	0.26	0.89	2bbeA	GO:0004497 GO:0055114
1	0.37	0.816	1.74	0.19	0.92	2gffB	GO:0005737 GO:0016853
2	0.36	0.769	1.57	0.14	0.87	1r6yA	GO:0005829 GO:0010447 GO:0016491 GO:0055114
3	0.32	0.803	1.21	0.19	0.87	4hl9A	GO:0004497 GO:0055114
4	0.30	0.834	1.24	0.21	0.91	1y0hA	GO:0004497 GO:0016491 GO:0055114
5	0.30	0.833	1.32	0.20	0.89	2omoA
6	0.28	0.852	0.93	0.16	0.90	3qmqC
7	0.27	0.795	1.21	0.22	0.86	3bm7A
8	0.27	0.803	1.20	0.24	0.87	1x7vC
9	0.26	0.811	1.57	0.16	0.93	3kkfA	GO:0046872
10	0.25	0.762	2.00	0.12	0.90	4dn9A	GO:0004497 GO:0055114
11	0.24	0.750	2.32	0.12	0.93	1iujB
12	0.21	0.778	1.07	0.18	0.83	2fb0A
13	0.19	0.847	2.03	0.15	0.99	3mcsB
14	0.17	0.681	2.20	0.14	0.82	1q8bA
15	0.16	0.800	2.27	0.16	0.97	3f44A
16	0.06	0.426	4.78	0.06	0.82	3r64A	GO:0008152 GO:0016491 GO:0016620 GO:0018479 GO:0055114
17	0.06	0.420	4.24	0.06	0.72	5k8bA	GO:0000271 GO:0003824 GO:0008483 GO:0009103 GO:0016740
18	0.06	0.389	4.29	0.08	0.66	2eryB	GO:0000166 GO:0001649 GO:0003924 GO:0005525 GO:0005622 GO:0005783 GO:0005886 GO:0005925 GO:0007165 GO:0007264 GO:0007265 GO:0009987 GO:0016020 GO:0030335 GO:0070062 GO:1901214

Consensus prediction of GO terms

Molecular Function	GO:0004497	GO:0016853
GO-Score	0.70	0.37
Biological Processes	GO:0055114	GO:0010447
GO-Score	0.81	0.36
Cellular Component	GO:0005829
GO-Score	0.36

(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.