I-TASSER results

I-TASSER results for job id Rv2683

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

Input Sequence in FASTA format

>protein (165 residues)
MKVNIDPTAPTFATYRRDMRAEQMAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGK
QYAVLPASQVVRFIVPRYVQDDPLLAGVLNESTADRCAERLSGKKVRDVLPDHLVEVPPA
NADDTIIEVAAVMARLRSPLLAVVKDGSLLGVVTASRLLAAALKT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKVNIDPTAPTFATYRRDMRAEQMAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGKQYAVLPASQVVRFIVPRYVQDDPLLAGVLNESTADRCAERLSGKKVRDVLPDHLVEVPPANADDTIIEVAAVMARLRSPLLAVVKDGSLLGVVTASRLLAAALKT
Prediction	CCCCCCCCCCCCCCCCCCCEEEEHCCCCEEHCCCCCHHHHHHHHHHHCCCEEEEHCCCCCEEEEEEHHHHHHHHCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCHHHHCCCCCEEEHCCCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHC
Conf.Score	987877666676544677478885699878689999999999999979997999869995999985888889875655556654455468688999999875997566358998787658999999999999999899868887699899998777999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKVNIDPTAPTFATYRRDMRAEQMAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGKQYAVLPASQVVRFIVPRYVQDDPLLAGVLNESTADRCAERLSGKKVRDVLPDHLVEVPPANADDTIIEVAAVMARLRSPLLAVVKDGSLLGVVTASRLLAAALKT
Prediction	753635444744553455030430266233044723043004103646031001137742000001342003312443144342323234453144115415724055163661340431447230340051236460512331766210102033443311177
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCEEEEHCCCCEEHCCCCCHHHHHHHHHHHCCCEEEEHCCCCCEEEEEEHHHHHHHHCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCHHHHCCCCCEEEHCCCCCCCHHHHHHHHHHHCCCEEEEEHCCEEEEEEEHHHHHHHHHHC
MKVNIDPTAPTFATYRRDMRAEQMAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGKQYAVLPASQVVRFIVPRYVQDDPLLAGVLNESTADRCAERLSGKKVRDVLPDHLVEVPPANADDTIIEVAAVMARLRSPLLAVVKDGSLLGVVTASRLLAAALKT

4esyA

0.16

0.96

2.84

MUSTER

-RVAEQARRRAIARAIRQVPIDILTSPVVTVREDDTLDAVAKTLEHQ-IGCAPVVDQNGHLVGIITESDFLRGSIPFWIYEASEILSRAIPAPEVEHLFETGRKLTASAVTQPVVTAA---PEDSVGSIADQRRHG-IHRIPVVQDGVPVGIVTRRDLLKLLLLE

4nocA

0.50

0.43

0.86

3.80

dPPAS

--------------------HGEQAEQFPVVGLDSDAREAVELLASRRLPGLIVVDEKGSPHSVLPASQVVRFLVPSYVQD--SLARVIDESLADQVADKLAGVTVRKLLPSQPAELPVVKHDDTVLEVAAIARLR-CPLVAVVKNKEIIGAITASRLLELVVSP

4nocA

0.49

0.42

0.86

3.81

wdPPAS

--------------------HGEQAEQFPVVGLDSDAREAVELLASRRLPGLIVVDEKGSPHSVLPASQVVRFLVPSYVQ--DSLARVIDESLADQVADKLAGVTVRKLLPSQPAELPVVKHDDTVLEVAAIARLR-CPLVAVVKNKEIIGAITASRLLELVVSP

4esyA

0.16

0.15

0.96

3.17

wMUSTER

V--AEQARRRAIARAIRQVPIDILTSPVVTVREDDTLDAVAKTLEHQ-IGCAPVVDQNGHLVGIITESDFLRGSIPFWIYEASEILSRAIPAPEVEHLFETGRKLTASAVTQPVVTAA---PEDSVGSIADQRRHG-IHRIPVVQDGVPVGIVTRRDLLKLLLLE

4esyA

0.16

0.96

3.32

wPPAS

-RVAEQARRRAIARAIRQVPIDILTSPVVTVREDDTLDAVAKTLEHQ-IGCAPVVDQNGHLVGIITESDFLRGSIPFWIYEASEILSRAIPAPEVEHLFETGRKLTASAVTQPVVTAA---PEDSVGSIADQRRHG-IHRIPVVQDGVPVGIVTRRDLLKLLLLE

3kh5A2

0.12

0.10

0.87

4.21

dPPAS2

VIRALLDKIDENEVIDDY-----ITRDVIVATPGERLKDVARTMVRNGFRRLPVVS-EGRLVGIITSTDFIKLLGS----------DWAFNHMQTGNVREITNVRMEEIMKRDVITAK---EGDKLKKIAEIMVTNDIGALPVVDNLRIKGIITEKDVLKYFA--

4esyA

0.16

0.96

3.21

PPAS

-RVAEQARRRAIARAIRQVPIRDLTSPVVTVREDDTLDAVAKTLEHQ-IGCAPVVDQNGHLVGIITESDFLRGSIPFWIYEASEILSRAIPAPEVEHLFETGRKLTASAVTQPVVTAA---PEDSVGSIADQRRHG-IHRIPVVQDGVPVGIVTRRDLLKLLLLE

5ks7A

0.18

0.13

0.73

3.60

Env-PPAS

----------------DVTQVAQMNTNPVSITADKSLQAAITVMKEKRVDTLLVVDEGNVLKGFIDVEQIDLNRRT--------------------------ATSVMDIIEKNVFYVY---EDTLLRDTVQRILKRGYKYIPVVDDKRLVGIVTRASLVDIVYDS

3kh5A2

0.12

0.10

0.89

2.79

MUSTER

TERDV--IRALLDKIDENEVIDYITRDVIVATPGERLKDVARTMVRNGFRRLPVVS-EGRLVGIITSTDFIKLLGS----------DWAFNHMQTGNVREITNVRMEEIMKRDVITAK---EGDKLKKIAEIMVTNDIGALPVVDNLRIKGIITEKDVLKYFA--

4esyA

0.17

0.16

0.96

3.76

dPPAS

-RVAEQARRRAIARAIRQVPIRDLTSPVVTVREDDTLDAVAKTLEHQ-IGCAPVVDQNGHLVGIITESDFLRGSIPFWIYEASEILSRAIPAPEVEHLFETGRKLTASAVTQPVVTAAPEDS----VGSIADQRRHGIHRIPVVQDGVPVGIVTRRDLLKLLLLE

(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=0.60

Estimated TM-score = 0.79±0.09

Estimated RMSD = 3.8±2.6Å

Download Model 2

C-score=-1.07

Download Model 3

C-score=-2.79

Download Model 4

C-score=-3.29

Download Model 5

C-score=-3.65

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	4esyA	0.871	1.66	0.176	0.952
2	2v9jE	0.680	2.74	0.161	0.818
3	3fwrB	0.676	2.75	0.146	0.824
4	2ooxE	0.671	3.14	0.120	0.861
5	2qlvC1	0.666	3.23	0.095	0.867
6	3lqnA	0.654	2.70	0.144	0.794
7	3kh5A	0.648	2.37	0.138	0.764
8	4nocA	0.645	2.50	0.419	0.770
9	3ddjA2	0.636	2.79	0.121	0.782
10	2p9mC	0.635	2.27	0.121	0.746

(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	65	2uv6A	AMP	Rep, Mult	24,27,28,29,49,50,51,52,53,152,153,154,156,157
2	0.18	34	3kpbA	SAM	Rep, Mult	64,66,68,69,111,113,114,115,137,138,139,140
3	0.04	9	2rc3A	NAD	Rep, Mult	133,134,137,138,139,155
4	0.01	3	1yav0	III	Rep, Mult	17,42,44,45,50,102,127,130,155,156,158,159,162,163
5	0.01	2	2j9l3	III	Rep, Mult	60,61,62,112,113,115,118,124,132,135,136,146,147
6	0.01	2	2v92E	ATP	Rep, Mult	50,67
7	0.01	2	2nyc0	III	Rep, Mult	38,42,45,48,50,66,67,68,71,72,74,133,134,138,139,155,159,160,162,163
8	0.01	3	3k2vA	CMK	Rep, Mult	48,49,50,67,154,156
9	0.00	1	3fnaA	AMP	Rep, Mult	64,66,68,69,72,111,138
10	0.00	1	3kh5A	AMP	Rep, Mult	85,88,89,92,93,108
11	0.00	1	2y94E	III	Rep, Mult	55,60,116,144,146,147,148
12	0.00	1	2j9l0	III	Rep, Mult	126,130,131,133,134

	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	3ljkA	0.421	4.94	0.056	0.709	5.3.1.9	NA
2	0.060	2vz8A	0.351	5.19	0.043	0.618	2.3.1.85	NA
3	0.060	2djiA	0.425	5.33	0.020	0.776	1.2.3.3	NA
4	0.060	2o2dB	0.425	5.09	0.090	0.715	5.3.1.9	NA
5	0.060	1onxA	0.400	5.21	0.041	0.697	3.4.19.-	NA
6	0.060	2z8kC	0.349	5.15	0.053	0.618	2.3.2.2	73
7	0.060	2hb6B	0.414	4.74	0.047	0.667	3.4.11.1	36
8	0.060	2vz9B	0.392	5.71	0.081	0.727	2.3.1.85	NA
9	0.060	1ynyB	0.413	4.92	0.045	0.685	3.5.2.2	146
10	0.060	2hb6A	0.414	4.74	0.047	0.667	3.4.11.1	NA
11	0.060	2wu8A	0.447	5.23	0.058	0.812	5.3.1.9	NA
12	0.060	2e1rA	0.436	4.68	0.078	0.685	3.6.5.3	NA
13	0.060	1k1dA	0.415	4.89	0.052	0.685	3.5.2.-	NA
14	0.060	2z8yD	0.422	5.61	0.071	0.812	1.2.7.4,1.2.99.2	122,130,143
15	0.060	2e0wB	0.439	5.06	0.077	0.764	2.3.2.2	NA
16	0.060	1a5lC	0.416	5.17	0.063	0.685	3.5.1.5	34
17	0.060	2q8nB	0.459	5.14	0.066	0.800	5.3.1.9	NA
18	0.060	3ifsE	0.422	5.09	0.036	0.727	5.3.1.9	72
19	0.060	2v3eA	0.426	5.12	0.043	0.727	3.2.1.45	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	0.39	0.886	1.61	0.19	0.96	4esyA	GO:0006950
1	0.30	0.641	2.18	0.25	0.75	5aweA	GO:0003824
2	0.28	0.623	2.57	0.20	0.76	4gqwA	GO:0009507 GO:0009536 GO:0045454
3	0.27	0.601	2.60	0.19	0.74	4fryB	GO:0000166
4	0.27	0.620	2.50	0.21	0.76	4o9kA	GO:0005975 GO:0016853 GO:0019146 GO:0030246
5	0.26	0.622	2.51	0.20	0.74	4gqyA	GO:0009507 GO:0009536 GO:0009570 GO:0045454
6	0.26	0.654	2.70	0.14	0.79	3lqnA
7	0.24	0.608	2.55	0.14	0.75	2o16B
8	0.24	0.620	2.45	0.11	0.75	2p9mB
9	0.22	0.672	2.99	0.07	0.86	3tdhC	GO:0000166 GO:0001302 GO:0003824 GO:0004679 GO:0005524 GO:0005634 GO:0005641 GO:0005737 GO:0005886 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0006468 GO:0007031 GO:0031588 GO:0043539 GO:0045722 GO:0071902
10	0.22	0.614	2.87	0.22	0.78	3ocoA	GO:0003824 GO:0016020 GO:0016021 GO:0016614 GO:0050660 GO:0055114
11	0.22	0.628	2.40	0.15	0.75	3lv9A	GO:0003824 GO:0016020 GO:0016021 GO:0016614 GO:0050660 GO:0055114
12	0.22	0.547	3.00	0.18	0.72	2yziB
13	0.22	0.590	2.50	0.17	0.72	2ef7A
14	0.21	0.616	2.47	0.19	0.73	2rifA	GO:0000166
15	0.20	0.659	2.84	0.11	0.81	4qfsC	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
16	0.20	0.681	2.68	0.16	0.82	2v8qE	GO:0000166 GO:0004679 GO:0005524 GO:0005654 GO:0006468 GO:0006629 GO:0006631 GO:0006633 GO:0016208 GO:0019901 GO:0031588 GO:0042304 GO:0043234 GO:0043531 GO:0050790 GO:0051291
17	0.20	0.617	3.06	0.16	0.79	3fhmA	GO:0000166
18	0.20	0.654	2.74	0.15	0.79	3ddjA	GO:0000166 GO:0003824
19	0.20	0.671	2.78	0.15	0.82	3fv6B	GO:0003677 GO:0006351 GO:0006355 GO:0045013
20	0.18	0.567	2.47	0.17	0.69	1vr9A	GO:0008152 GO:0016597
21	0.18	0.583	2.64	0.20	0.71	1xkfB	GO:0001666 GO:0005576 GO:0005618 GO:0005829 GO:0005886 GO:0046872 GO:0052553 GO:0052572
22	0.17	0.628	2.31	0.14	0.73	3kpcA	GO:0003824
23	0.17	0.591	2.84	0.13	0.75	2emqA
24	0.17	0.523	3.12	0.16	0.69	1pbjA
25	0.17	0.671	3.14	0.12	0.86	2ooxE	GO:0000166 GO:0003824 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005975 GO:0006351 GO:0006355 GO:0006357 GO:0007165 GO:0016208 GO:0030295 GO:0031588 GO:0032147
26	0.16	0.612	2.44	0.13	0.73	3lfrB	GO:0000166 GO:0003824 GO:0016614 GO:0050660 GO:0055114
27	0.16	0.653	2.44	0.14	0.78	3lfzA
28	0.16	0.635	2.73	0.10	0.79	3oi8A	GO:0003824 GO:0016614 GO:0046872 GO:0050660 GO:0055114
29	0.15	0.609	2.38	0.16	0.73	2rc3C	GO:0000166
30	0.14	0.589	3.07	0.15	0.74	1o50A	GO:0003824
31	0.07	0.631	2.75	0.12	0.77	3pc3A	GO:0004122 GO:0004124 GO:0005737 GO:0006535 GO:0008340 GO:0008652 GO:0016829 GO:0019343 GO:0019344 GO:0030170 GO:0034976 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0016861
GO-Score	0.55	0.55	0.54
Biological Processes	GO:0050794	GO:0019725	GO:0044238	GO:0071704	GO:0006950
GO-Score	0.57	0.57	0.47	0.44	0.39
Cellular Component	GO:0044444	GO:0043231
GO-Score	0.57	0.57

(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.