I-TASSER results

I-TASSER results for job id Rv1717

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

Input Sequence in FASTA format

>protein (116 residues)
MKLTRASQAPRYVAPAHHEVSTMRLQGREAGRTERFWVGLSVYRPGGTAEPAPTREETVY
VVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVTVAHPVAEVA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MKLTRASQAPRYVAPAHHEVSTMRLQGREAGRTERFWVGLSVYRPGGTAEPAPTREETVYVVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVTVAHPVAEVA
Prediction	CCCHCHHHCCCCCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCEEEEEEEEEEEEEHCCEEEEHCCCEEEEHCCCCCEEEEHCCCCCEEEEEEHCCCCCCCC
Conf.Score	98655666654568886566899865777788775899999988999998777899689999987999999998999879889998899868999789985999999958998889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MKLTRASQAPRYVAPAHHEVSTMRLQGREAGRTERFWVGLSVYRPGGTAEPAPTREETVYVVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVTVAHPVAEVA
Prediction	66435376154242442441222303447635244022211203225536425264131000131302030575523044310020137341314043643020000012356658
	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

CCCHCHHHCCCCCCCCCCCEEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCEEEEEEEEEEEEEHCCEEEEHCCCEEEEHCCCCCEEEEHCCCCCEEEEEEHCCCCCCCC
MKLTRASQAPRYVAPAHHEVSTMRLQGREAGRTERFWVGLSVYRPGGTAEPAPTREETVYVVLDGELVVTVDGAETVLGWLDSVHLAKGELRSIHNRTDRQALLLVTVAHPVAEVA

1vj2A

0.22

0.97

2.74

MUSTER

MILKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.19

0.98

3.76

dPPAS

MILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.97

3.60

wdPPAS

MILKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.21

0.96

3.17

wMUSTER

I-LKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.97

3.73

wPPAS

MILKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.97

5.34

dPPAS2

MILKRAYDVTPISTDKVRGVRKRVLIGLKD--APNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.97

3.59

PPAS

MILKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1vj2A

0.22

0.97

3.61

Env-PPAS

MILKRAYDVTPISTDKVRGVRKRVLIGLK--DAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE--

1v70A

0.25

0.22

0.90

2.59

MUSTER

MEIKDLKRLARYN---PEKMAKIPVF-----QSERMLYDLYALLPGQAQKVHVHEGSKVYYALEGEVVVRVGEEEALLAPGMAAFAPAGAPHGVRNESASPALLLVVTAPRP----

1v70A

0.25

0.22

0.90

3.41

dPPAS

MEIKDLKRLARYNPEKMAKIPVFQS--------ERMLYDLYALLPGQAQKVHVHEGSKVYYALEGEVVVRVGEEEALLAPGMAAFAPAGAPHGVRNESASPALLLVVTAPRP----

(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 4 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=1.08

Estimated TM-score = 0.86±0.07

Estimated RMSD = 2.2±1.7Å

Download Model 2

C-score=-2.43

Download Model 3

C-score=1.15

Download Model 4

C-score=-3.42

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	1vj2A	0.924	1.00	0.223	0.966
2	3ht1A	0.877	1.78	0.174	0.974
3	5flhA	0.849	1.56	0.145	0.948
4	1lr5A	0.838	2.14	0.174	0.991
5	1sfnA	0.829	2.05	0.124	0.948
6	4la2A	0.828	2.09	0.139	0.983
7	1o4tA	0.827	1.75	0.204	0.931
8	4e2qA	0.825	1.86	0.098	0.940
9	1h1iB	0.822	2.12	0.124	0.974
10	2h0vA1	0.820	1.66	0.185	0.931

(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	0.43	67	3elnA	2CO	Rep, Mult	20,22,41,52,54,58,60,92,94,106,108,116
2	0.14	20	1o4tB	OXL	Rep, Mult	52,54,58,60,92,108
3	0.02	3	4nplA	AKG	Rep, Mult	41,43,49,52,92,94,102,104,106
4	0.02	4	3ht10	III	Rep, Mult	2,3,4,5,6,25,26,31,32,33,34,35,36,37,38,40,57,59,61,63,69,71,80,81,82,83,84,85,87,88,105,107,109
5	0.01	1	1sfn0	III	Rep, Mult	17,19,45,46,68,75,93,97,98,99
6	0.01	1	1lr5A	BMA	Rep, Mult	42,101
7	0.01	2	1lr5A	UUU	Rep, Mult	7,11,12,13,18,19,20,21,23,40,42,101,103
8	0.00	1	3h7jA	FE	Rep, Mult	57,87
9	0.00	1	3h7jA	FE	Rep, Mult	45,99
10	0.00	1	3aclA	3F1	Rep, Mult	37,39,41,49,52,54,60,61,67,78,105,106,108
11	0.00	1	3o14A	NIO	Rep, Mult	22,27,39,41,106,108

	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	0.158	3balD	0.744	2.63	0.101	0.940	1.13.11.50	25
2	0.155	1fi2A	0.768	2.53	0.144	0.948	1.2.3.4	55
3	0.104	1zvfA	0.698	2.58	0.108	0.853	1.13.11.6	38
4	0.071	1yfxA	0.708	2.51	0.125	0.888	1.13.11.6	NA
5	0.060	1pmiA	0.706	2.67	0.103	0.922	5.3.1.8	NA
6	0.060	1uw8A	0.801	2.01	0.156	0.940	4.1.1.2	NA
7	0.060	1ey2A	0.666	2.85	0.085	0.862	1.13.11.5	17,85
8	0.060	2yu1A	0.722	2.88	0.079	0.905	1.14.11.27	6,64
9	0.060	1uofA	0.582	3.56	0.107	0.871	1.14.20.1	NA
10	0.060	3bu7B	0.773	2.83	0.130	0.974	1.13.11.4	NA
11	0.060	2eteA	0.768	2.54	0.144	0.948	1.2.3.4	55
12	0.060	1gp6A	0.703	3.21	0.070	0.948	1.14.11.19	NA
13	0.060	3elnA	0.759	2.51	0.119	0.905	1.13.11.20	111
14	0.060	2ilmA	0.725	2.62	0.103	0.879	1.14.11.16	50
15	0.060	1x8eA	0.769	2.52	0.133	0.948	5.3.1.9	45,59,61,84,105
16	0.060	3eqeA	0.744	2.31	0.114	0.879	1.13.11.20	62,105
17	0.060	2og6A	0.584	3.61	0.112	0.819	1.14.11.-	NA
18	0.060	1upiA	0.415	3.54	0.093	0.629	5.1.3.13	NA
19	0.060	1w9yA	0.595	3.85	0.123	0.879	1.14.17.4	NA
20	0.060	1ywkA	0.700	2.43	0.058	0.888	5.3.1.17	55,57,60,93
21	0.060	1yjlA	0.599	3.49	0.071	0.888	1.14.17.3,4.3.2.5	NA
22	0.060	3kv4A	0.722	2.91	0.079	0.905	1.14.11.27	60
23	0.060	2qnkA	0.673	2.69	0.196	0.836	1.13.11.6	63,77,105

(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	0.47	0.924	1.00	0.22	0.97	1vj2A	GO:0046872
1	0.41	0.801	2.35	0.13	0.97	4bifA	GO:0046872
2	0.36	0.874	1.81	0.17	0.97	3ht2A	GO:0016301 GO:0016310 GO:0046872
3	0.31	0.777	1.92	0.18	0.92	2pytA	GO:0046336
4	0.28	0.770	2.51	0.14	0.95	2et1A	GO:0005576 GO:0005618 GO:0016491 GO:0030145 GO:0045735 GO:0046872 GO:0048046 GO:0050162 GO:0055114 GO:0071555
5	0.26	0.734	1.82	0.20	0.81	3ibmB	GO:0046872
6	0.22	0.838	2.14	0.17	0.99	1lr5A	GO:0004872 GO:0005783 GO:0005788 GO:0008270 GO:0009734 GO:0010011 GO:0046872
7	0.21	0.771	2.64	0.12	0.97	1ipkC	GO:0005773 GO:0033095 GO:0045735
8	0.20	0.845	1.64	0.18	0.96	2h0vA	GO:0008127 GO:0016491 GO:0046872 GO:0051213 GO:0055114
9	0.19	0.815	2.03	0.13	0.96	2vqaA	GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
10	0.17	0.827	1.75	0.20	0.93	1o4tA	GO:0030145 GO:0033609 GO:0042802 GO:0042803 GO:0046564 GO:0046872
11	0.16	0.811	2.12	0.12	0.95	3kgzA	GO:0046872
12	0.16	0.782	2.37	0.12	0.92	3h9aA	GO:0005506 GO:0005737 GO:0016853 GO:0016863 GO:0017000 GO:0046872 GO:0050897
13	0.16	0.793	2.21	0.13	0.92	3jzvA	GO:0046872
14	0.16	0.718	2.12	0.17	0.84	3cewA	GO:0046872
15	0.15	0.744	2.65	0.10	0.94	3balA	GO:0016491 GO:0033752 GO:0046872 GO:0051213 GO:0055114
16	0.15	0.795	2.04	0.16	0.94	4metA	GO:0005737 GO:0016829 GO:0016831 GO:0030288 GO:0033609 GO:0045735 GO:0046564 GO:0046872
17	0.15	0.759	2.77	0.12	0.97	1uikA	GO:0045735
18	0.15	0.771	2.58	0.14	0.97	2cavA	GO:0045735
19	0.15	0.765	2.64	0.12	0.97	1uijC	GO:0005773 GO:0033095 GO:0045735
20	0.12	0.742	2.65	0.12	0.93	5bpxA	GO:0016491 GO:0046872 GO:0047073 GO:0051213 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016623	GO:0046914	GO:0016301
GO-Score	0.56	0.56	0.36
Biological Processes	GO:0045229	GO:0071554	GO:0016310	GO:0046336
GO-Score	0.56	0.56	0.36	0.30
Cellular Component	GO:0030312
GO-Score	0.56

(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.