I-TASSER results

I-TASSER results for job id Rv2060

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

Input Sequence in FASTA format

>protein (133 residues)
MLTVVCLLVVTVLAICYRPLLFATVDPEVAAARGVPVRALGIVFAALMGVVAAQAVQIVG
ALLVMSLLITPAAAAARVVVAPVAAIATSVVFAEVSAVGGILLSLAPGVPVSVFVATISF
VIYLICWLLRRRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLTVVCLLVVTVLAICYRPLLFATVDPEVAAARGVPVRALGIVFAALMGVVAAQAVQIVGALLVMSLLITPAAAAARVVVAPVAAIATSVVFAEVSAVGGILLSLAPGVPVSVFVATISFVIYLICWLLRRRR
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Conf.Score	7679999999999999757778745999888888986999999999999999999999999999999999999999997588899999999999999999999998699865699999999999999974589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLTVVCLLVVTVLAICYRPLLFATVDPEVAAARGVPVRALGIVFAALMGVVAAQAVQIVGALLVMSLLITPAAAAARVVVAPVAAIATSVVFAEVSAVGGILLSLAPGVPVSVFVATISFVIYLICWLLRRRR
Prediction	3110113322222333334110100145204034132431311003213322033133333331313332222002210542330002113313331331233133343332231133133323202223558
	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

CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
MLTVVCLLVVTVLAICYRPLLFATVDPEVAAARGVPVRALGIVFAALMGVVAAQAVQIVGALLVMSLLITPAAAAARVVVAPVAAIATSVVFAEVSAVGGILLSLAPGVPVSVFVATISFVIYLICWLLRRRR

2nq2A

0.21

0.20

0.93

1.02

MUSTER

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSI-----LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYL----

1l7vA1

0.10

0.98

1.11

dPPAS

WLLCLSVLLLALLLSLCAGEQWISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVQALFENLVIPHILRLCGLTDHRVLLPGCALAGASALLLADIVARLAELPIGVVTATLGAPVFIWLLLKA---

2nq2A1

0.21

0.20

0.93

1.56

wdPPAS

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSI-----LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYL----

2nq2A

0.22

0.20

0.94

1.22

wMUSTER

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSI-V---LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYL----

1l7vA1

0.11

0.95

1.43

wPPAS

WLLCLSVLLLALLLSLCAGEQWISPGDWFTPRGEIRLPRTLAVLLVGAALAISGAVQALPLAFI---LVIPHILRLCGLTDHRVLLPGCALAGASALLLADIVARLAELPIGVVTATLGAPVFIWLLLKA---

2nq2A1

0.21

0.20

0.93

2.54

dPPAS2

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSI-----LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYL----

1l7vA1

0.11

0.98

1.24

PPAS

WLLCLSVLLLALLLSLCAGEQWISPGDWELFVWQIRLPRTLAVLLVGAALAISGAVQALFENPLAGFLVIPHILRLCGLTDHRVLLPGCALAGASALLLADIVARLAELPIGVVTATLGAPVFIWLLLKA---

1l7vA1

0.11

0.98

1.12

Env-PPAS

WLLCLSVLLLALLLSLCAGEQWISPGDWELFVWQIRLPRTLAVLLVGAALAISGAVQALFENPLAGFLVIPHILRLCGLTDHRVLLPGCALAGASALLLADIVARLAELPIGVVTATLGAPVFIWLLLKA---

2nq2A1

0.21

0.20

0.93

1.00

MUSTER

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSI-----LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYL----

2nq2A1

0.19

0.97

1.06

dPPAS

FFFVPFLLCSSILLSLSWRLNLLSLDEKEAKALGVKMAPLRWLVIFLSGSLVACQVAISGSIGWVG-LIIPHLSRMLVGANHQSLLPCTMLVGATYMLLVDNVARSLEIPISILTALIGAPLFGVLVYKL---

(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=0.00

Estimated TM-score = 0.71±0.11

Estimated RMSD = 4.5±3.0Å

Download Model 2

C-score=-2.47

Download Model 3

C-score=-3.37

Download Model 4

C-score=-3.95

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	2nq2A1	0.898	1.27	0.194	0.970
2	5b57A	0.854	2.04	0.144	0.993
3	4g1uA	0.845	1.80	0.157	0.955
4	1l7vA	0.818	2.03	0.151	0.947
5	4k0eA	0.570	4.16	0.102	0.865
6	3rkoN	0.556	3.89	0.112	0.865
7	4he8N	0.552	3.74	0.096	0.850
8	5c65A	0.547	4.69	0.076	0.947
9	4rp8A	0.543	3.91	0.083	0.827
10	3fvyA2	0.539	3.98	0.041	0.804

(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	0.05	3	1m56D	PEH	Rep, Mult	55,62
2	0.05	3	2h2pA	SEK	Rep, Mult	64,68
3	0.03	2	1hmoB	OXY	Rep, Mult	10,13,47,48,86,89,90,94
4	0.03	2	1m57D	PEH	Rep, Mult	44,51,55,56
5	0.03	2	2x2vH	DPV	Rep, Mult	90,98
6	0.03	2	2xquB	CVM	Rep, Mult	93,97
7	0.03	2	2nq24	III	Rep, Mult	14,15,16,17,18,19,21,25,28,29,31,32,33,35,75,80,82,83
8	0.03	2	3wmoP	BCL	Rep, Mult	105,106
9	0.02	1	1sqpC	CDL	Rep, Mult	40,43,44,47
10	0.02	1	3h1jC	CDL	Rep, Mult	60,61,62
11	0.02	1	4i9oA	KI1	Rep, Mult	69,72,89,92,93,96,122,125,126
12	0.02	1	3h1jC	CDL	Rep, Mult	96,100,103,104
13	0.02	1	2pg0B	FAD	Rep, Mult	69,74,93,117,118,121
14	0.02	1	3rkoN	LFA	Rep, Mult	44,47,48,51
15	0.02	1	3wmnU	CRT	Rep, Mult	92,103
16	0.02	1	3s8gA	OLC	Rep, Mult	68,72,123,127
17	0.02	1	2nr9A	PA6	Rep, Mult	98,102
18	0.02	1	3ojcA	CA	Rep, Mult	104,110,111
19	0.02	1	3ug6A	MG	Rep, Mult	3,26
20	0.02	1	3s8gA	OLC	Rep, Mult	119,120,123

	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	1xmeA	0.501	5.14	0.089	0.872	1.9.3.1	NA
2	0.060	1q50A	0.470	4.74	0.068	0.789	5.3.1.9	NA
3	0.060	1ta9B	0.490	3.96	0.042	0.767	1.1.1.6	NA
4	0.060	1e5eA	0.482	4.94	0.064	0.857	4.4.1.11	NA
5	0.060	1g4wR	0.425	3.71	0.054	0.647	3.1.3.48	NA
6	0.060	3fvyA	0.536	3.80	0.033	0.804	3.4.14.4	50,52,60
7	0.060	1qleA	0.492	4.66	0.087	0.865	1.9.3.1	NA
8	0.060	3cskA	0.521	4.14	0.024	0.804	3.4.14.4	NA
9	0.060	2o8rA	0.484	4.48	0.032	0.759	2.7.4.1	45
10	0.060	2wu8A	0.486	4.63	0.060	0.797	5.3.1.9	NA
11	0.060	1occA	0.485	4.74	0.059	0.850	1.9.3.1	NA
12	0.060	1m56A	0.493	4.67	0.059	0.850	1.9.3.1	NA
13	0.060	1h4sA	0.486	4.51	0.037	0.804	6.1.1.15	NA
14	0.060	3nztA	0.478	4.63	0.033	0.812	6.3.2.2	NA
15	0.060	1n8pC	0.485	4.65	0.048	0.835	4.4.1.1	NA
16	0.060	1n1zA	0.484	4.49	0.081	0.812	5.5.1.8	NA
17	0.060	3lomA	0.486	3.74	0.049	0.714	2.5.1.10	33,47
18	0.060	3g4dA	0.480	4.43	0.063	0.789	4.2.3.13	NA
19	0.060	1g4uS	0.491	4.26	0.031	0.782	3.1.3.48	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	0.27	0.898	1.27	0.19	0.97	2nq2A	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021
1	0.20	0.835	1.90	0.15	0.97	4dblA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0015235 GO:0015420 GO:0015889 GO:0016020 GO:0016021 GO:0035461 GO:0043190
2	0.07	0.845	1.80	0.16	0.95	4g1uA	GO:0005215 GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0055072
3	0.07	0.577	4.07	0.09	0.86	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
4	0.07	0.576	4.15	0.09	0.88	4k0eC	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
5	0.07	0.570	4.16	0.10	0.86	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
6	0.07	0.427	5.11	0.07	0.79	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
7	0.07	0.474	4.34	0.07	0.76	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
8	0.07	0.465	4.95	0.07	0.81	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
9	0.07	0.478	4.71	0.13	0.86	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
10	0.07	0.465	4.25	0.05	0.71	3i6sA	GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
11	0.07	0.444	4.56	0.07	0.72	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
12	0.06	0.507	4.44	0.08	0.83	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
13	0.06	0.538	4.25	0.06	0.79	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
14	0.06	0.340	4.66	0.05	0.61	3qvjA	GO:0006807 GO:0036361
15	0.06	0.365	4.97	0.04	0.65	5fsrA	GO:0004175 GO:0004180 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0008360 GO:0008658 GO:0009002 GO:0009252 GO:0016020 GO:0016787 GO:0071555
16	0.06	0.552	3.82	0.10	0.86	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
17	0.06	0.350	4.49	0.01	0.56	3gbsA	GO:0005576 GO:0008152 GO:0016042 GO:0016787 GO:0050525 GO:0052689
18	0.06	0.361	2.98	0.02	0.46	3n00A	GO:0000122 GO:0000790 GO:0000977 GO:0000978 GO:0001046 GO:0001078 GO:0001222 GO:0003677 GO:0003700 GO:0003707 GO:0003714 GO:0004879 GO:0005634 GO:0005654 GO:0005737 GO:0005978 GO:0006351 GO:0006355 GO:0006367 GO:0007623 GO:0008270 GO:0010498 GO:0010871 GO:0019216 GO:0020037 GO:0030154 GO:0030425 GO:0030522 GO:0032922 GO:0034144 GO:0035947 GO:0042752 GO:0042995 GO:0043197 GO:0043401 GO:0043565 GO:0044212 GO:0044321 GO:0045598 GO:0045892 GO:0045893 GO:0046872 GO:0048511 GO:0060086 GO:0061178 GO:0061469 GO:0070859 GO:0071222 GO:2000188 GO:2000189

Consensus prediction of GO terms

Molecular Function	GO:0042626	GO:0015235	GO:0090482
GO-Score	0.39	0.39	0.39
Biological Processes	GO:0055085	GO:0071702	GO:0051180	GO:0071705
GO-Score	0.39	0.39	0.39	0.39
Cellular Component	GO:0098533	GO:0098797	GO:0031226
GO-Score	0.39	0.39	0.39

(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.