I-TASSER results

I-TASSER results for job id Rv0177

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

Input Sequence in FASTA format

>protein (184 residues)
MSPRRKFEPGEGALLAPQSIEPSRRWGLPLALTASAVVMAAAISACALMRISHESHQRAA
HKDIVMLSDVRSFMTMFTSPDPFHANEYAERVLSHATGDFAKQYHERANDILIRISGVEP
TTGTVLDAGVQRWNEDGSANVLVVTQITSKSADGKRVVSNANRWLVTAKQEGNEWKISSL
LPVI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSPRRKFEPGEGALLAPQSIEPSRRWGLPLALTASAVVMAAAISACALMRISHESHQRAAHKDIVMLSDVRSFMTMFTSPDPFHANEYAERVLSHATGDFAKQYHERANDILIRISGVEPTTGTVLDAGVQRWNEDGSANVLVVTQITSKSADGKRVVSNANRWLVTAKQEGNEWKISSLLPVI
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEHCCCCEEEEEEEEEEEEHCCCCCCCCCCEEEEEEEEEEHCCEEEEHCCEHCC
Conf.Score	9987778888887667888888876456999999999999999999999876557788999999999999999999977897758999999998599899999999999999999985747899987899998699869999999999975899887655579999999989989986465589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSPRRKFEPGEGALLAPQSIEPSRRWGLPLALTASAVVMAAAISACALMRISHESHQRAAHKDIVMLSDVRSFMTMFTSPDPFHANEYAERVLSHATGDFAKQYHERANDILIRISGVEPTTGTVLDAGVQRWNEDGSANVLVVTQITSKSADGKRVVSNANRWLVTAKQEGNEWKISSLLPVI
Prediction	7555564546656555665454533211100000000001022222011112234444445424402510351023011233730451053027322460264147325402520464542434134100443366330100000113143475574544321030203537440204514436
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEHCCCCEEEEEEEEEEEEHCCCCCCCCCCEEEEEEEEEEHCCEEEEHCCEHCC
MSPRRKFEPGEGALLAPQSIEPSRRWGLPLALTASAVVMAAAISACALMRISHESHQRAAHKDIVMLSDVRSFMTMFTSPDPFHANEYAERVLSHATGDFAKQYHERANDILIRISGVEPTTGTVLDAGVQRWNEDGSANVLVVTQITSKSADGKRVVSNANRWLVTAKQEGNEWKISSLLPVI

5d9rA

0.15

0.10

0.69

0.88

MUSTER

---------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITEGSVL-

5d9rA

0.15

0.10

0.69

0.68

dPPAS

---------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITEGSVL-

5d9rA

0.15

0.10

0.65

1.22

wdPPAS

-------------------------------------------------------SEADARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQL----DYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITEGSVL-

4v1ai

0.12

0.11

0.97

0.85

wMUSTER

LVIPHERLERPIHLACTAGIPPEGDARISSLSKEGLAQRAERLKKNVASQLSIRKIRESDPKIKDFPEKAKDIFIEAHLC----NNSDHDRLHTLVTENCFPDMVWDIRYKTVRWSFVELEPPQVVQVRCSSLMNQGNIYGQVTVRMHTRQRFGREDVPRDVLEYVVFEKHYGSWRMH--GKII

5d9rA

0.16

0.10

0.65

1.41

wPPAS

-------------------------------------------------------SEADARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQL----DYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITE-GSVL

5cwmA1

0.09

0.05

0.62

1.02

dPPAS2

-----------------------DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQG-----------------------------------------------

5d9rA

0.15

0.10

0.69

1.16

PPAS

---------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITEGSVL-

5d9rA

0.15

0.10

0.69

1.20

Env-PPAS

---------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPENNTYTTRYEVFWSKSGWKITEGSVL-

5ig5A

0.10

0.07

0.74

0.84

MUSTER

-----------------------------------------------HTIIEEDTESTKTQREQEIIRLTQQLITSITAKDFDSYSKLVDPKITAFEPEALGNQVEGLEFHKFYFDNLPTTVNTTILAPHVQMLGEEGACISYVRLTQGIGPDG-LPRTTQSEETRVWQKKKGVWLNVHFHRSV

5cwmA1

0.09

0.05

0.62

0.67

dPPAS

-----------------------DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQG-----------------------------------------------

(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=-3.56

Estimated TM-score = 0.32±0.11

Estimated RMSD = 13.6±4.0Å

Download Model 2

C-score=-3.76

Download Model 3

C-score=-3.60

Download Model 4

C-score=-4.06

Download Model 5

C-score=-4.23

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	5d9rA	0.562	2.76	0.134	0.674
2	4v1ai	0.552	3.27	0.062	0.723
3	2fxtA	0.544	3.70	0.060	0.734
4	4xzzA	0.537	3.66	0.069	0.707
5	2cw9A	0.537	3.73	0.032	0.707
6	4l8oA	0.522	2.94	0.031	0.647
7	3a76A	0.518	2.98	0.108	0.652
8	4gb5A	0.517	2.80	0.070	0.625
9	3soyA	0.516	2.81	0.069	0.630
10	2bmqB	0.513	3.99	0.064	0.707

(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	0.10	6	5stdB	UNN	Rep, Mult	74,106,107,111,145,147,149,161,180,182,184
2	0.07	4	1a2k0	III	Rep, Mult	99,100,125,126,128,129,131,132,133,134,140,142,144,145,146,163,165,167,169,178,179,180,181
3	0.07	4	4fcmA	III	Rep, Mult	61,62,65,66,69,94,95,174,175,176
4	0.03	2	3biwE	CA	Rep, Mult	109,110
5	0.03	2	3hx8D	IMD	Rep, Mult	70,141,166,177
6	0.03	2	1gybB	III	Rep, Mult	130,131,132,135
7	0.03	2	2vt5H	ROK	Rep, Mult	97,98
8	0.02	1	2bngB	CA	Rep, Mult	59,170
9	0.02	1	4jolA	III	Rep, Mult	35,38
10	0.02	1	2z77C	HE7	Rep, Mult	66,73,77
11	0.02	1	1nr5B	CO	Rep, Mult	91,98
12	0.02	1	1wraA	FE	Rep, Mult	53,56,162,179
13	0.02	1	3i8hT	MG	Rep, Mult	177,178
14	0.02	1	1ia5A	MAN	Rep, Mult	122,124

	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	0.096	1hkxA	0.487	3.28	0.116	0.630	2.7.11.17	138
2	0.066	2ux0A	0.496	3.29	0.092	0.641	2.7.11.17	98,105
3	0.066	8choA	0.450	2.77	0.098	0.554	5.3.3.1	176
4	0.060	1hcuB	0.423	4.87	0.046	0.679	3.2.1.113	71
5	0.060	2d0vA	0.434	5.04	0.043	0.701	1.1.99.8	NA
6	0.060	2v7oA	0.301	5.50	0.055	0.522	2.7.11.17	NA
7	0.060	3gzxB	0.513	3.55	0.068	0.679	1.14.12.18	NA
8	0.060	1kb0A	0.436	4.75	0.057	0.674	1.1.99.-	NA
9	0.060	3cxhN	0.338	5.47	0.050	0.620	1.10.2.2	NA
10	0.060	1oygA	0.421	5.77	0.050	0.766	2.4.1.10	NA
11	0.060	1lrwC	0.435	5.03	0.038	0.690	1.1.99.8	167
12	0.060	1nu3B	0.448	3.84	0.076	0.609	3.3.2.8	142
13	0.060	1kitA	0.420	5.66	0.053	0.788	3.2.1.18	NA
14	0.060	1kv9A	0.442	4.72	0.069	0.679	1.1.99.-	NA
15	0.060	1g72A	0.432	5.02	0.031	0.685	1.1.99.8	73
16	0.060	4stdA	0.510	2.76	0.094	0.625	4.2.1.94	NA
17	0.060	2epoB	0.431	4.29	0.063	0.636	3.2.1.52	63
18	0.060	1sa3A	0.441	4.00	0.022	0.636	3.1.21.4	127
19	0.060	3hmjA	0.416	5.48	0.052	0.734	2.3.1.86	88
20	0.060	1e3vB	0.438	3.35	0.047	0.576	5.3.3.1	104
21	0.060	1w6sC	0.433	5.06	0.038	0.690	1.1.99.8	NA
22	0.060	1o7hB	0.520	4.06	0.071	0.717	1.14.12.12	85,93,95,121

(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	0.17	0.562	2.76	0.13	0.67	5d9rA	GO:0009507 GO:0009528 GO:0009536 GO:0009658 GO:0009706 GO:0009941 GO:0010020 GO:0016020 GO:0016021 GO:0031357 GO:0043621
1	0.15	0.520	3.07	0.12	0.66	3a76B	GO:0009636 GO:0016829 GO:0042597
2	0.11	0.548	3.59	0.04	0.71	2cw9A	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0005759 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0051087
3	0.09	0.485	2.99	0.10	0.61	5ig4E	GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
4	0.09	0.489	3.43	0.06	0.65	3j7yd	GO:0005739 GO:0005743 GO:0005840 GO:0030529 GO:0044822 GO:0070125 GO:0070126
5	0.08	0.489	2.67	0.06	0.60	5ig0A	GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0006468 GO:0016301 GO:0016310 GO:0016740
6	0.07	0.544	3.70	0.06	0.73	2fxtA	GO:0000166 GO:0001405 GO:0005524 GO:0005739 GO:0005743 GO:0006626 GO:0006810 GO:0015031 GO:0016020 GO:0030150 GO:0030674 GO:0051087
7	0.07	0.537	3.66	0.07	0.71	4xzzA	GO:0016740
8	0.07	0.518	2.97	0.03	0.65	4lehA	GO:0016829 GO:0033988
9	0.07	0.522	2.94	0.03	0.65	4l8oA	GO:0016829 GO:0033988
10	0.07	0.517	2.98	0.06	0.65	4l8pA	GO:0016829 GO:0033988
11	0.07	0.496	3.29	0.09	0.64	2ux0A	GO:0000082 GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0004723 GO:0005088 GO:0005516 GO:0005524 GO:0005654 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006816 GO:0007275 GO:0007399 GO:0014733 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0030073 GO:0030154 GO:0030666 GO:0033017 GO:0042803 GO:0043547 GO:0046777 GO:0051259 GO:0051924 GO:0060333 GO:0097481 GO:1900034 GO:1901897
12	0.07	0.477	3.33	0.09	0.61	2w2cH	GO:0000082 GO:0000165 GO:0000166 GO:0001558 GO:0001666 GO:0002026 GO:0002028 GO:0003254 GO:0004672 GO:0004674 GO:0004683 GO:0005088 GO:0005516 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006357 GO:0006468 GO:0006816 GO:0008016 GO:0010389 GO:0010613 GO:0010649 GO:0010666 GO:0010880 GO:0010881 GO:0014704 GO:0014911 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0018105 GO:0018107 GO:0019871 GO:0030007 GO:0030315 GO:0030666 GO:0031432 GO:0031594 GO:0032469 GO:0033017 GO:0034704 GO:0035022 GO:0042383 GO:0042803 GO:0043025 GO:0043194 GO:0043234 GO:0043547 GO:0044325 GO:0046777 GO:0048471 GO:0048661 GO:0050998 GO:0051259 GO:0055119 GO:0060048 GO:0060314 GO:0060333 GO:0060341 GO:0061049 GO:0070374 GO:0071277 GO:0086003 GO:0086091 GO:0098901 GO:0098909 GO:1900034 GO:1901725 GO:1901844 GO:1901897 GO:1902306 GO:1902514 GO:2000650
13	0.07	0.479	3.18	0.06	0.61	2f86B	GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0005516 GO:0005524 GO:0005737 GO:0006468 GO:0010628 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0018107 GO:0030424 GO:0042995 GO:0043005 GO:0043204 GO:0044325 GO:0046872 GO:0072375 GO:1904115
14	0.07	0.458	2.90	0.05	0.58	3b7cA	GO:0004067 GO:0016787
15	0.06	0.326	6.00	0.06	0.64	2nn6E	GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0004532 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006364 GO:0006401 GO:0017091 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0043488 GO:0043928 GO:0071028 GO:0071035 GO:0071038 GO:0071042
16	0.06	0.308	5.25	0.05	0.51	4pc9A	GO:0006810 GO:0008643 GO:0030288 GO:0042597
17	0.06	0.332	5.54	0.03	0.61	4l5cC	GO:0003824 GO:0005634 GO:0005737 GO:0006166 GO:0009116 GO:0016740 GO:0016757 GO:0016763 GO:0017061 GO:0019509
18	0.06	0.311	5.47	0.05	0.53	3rscA	GO:0008152 GO:0016758 GO:0016999

Consensus prediction of GO terms

Molecular Function	GO:0032559	GO:0032550	GO:0035639	GO:0005515
GO-Score	0.39	0.39	0.39	0.34
Biological Processes	GO:0043572	GO:0009657
GO-Score	0.34	0.34
Cellular Component	GO:0031966	GO:0031356	GO:0031353
GO-Score	0.38	0.34	0.34

(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.