I-TASSER results

I-TASSER results for job id Rv2698

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

Input Sequence in FASTA format

>protein (161 residues)
MSGTRLAPHSVRYRERLWVPWWWWPLAFALAALIAFEVNLGVAALPDWVPFATLFTVAAG
TLLWLGRVEIRVTAGSADGAGVKLWAGPAHLPVAVIARSAEIPATAKSAALGRQLDPAAY
VLHRAWVGPMVLVVLDDPNDPTPYWLVSCRHPERVLSALRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSGTRLAPHSVRYRERLWVPWWWWPLAFALAALIAFEVNLGVAALPDWVPFATLFTVAAGTLLWLGRVEIRVTAGSADGAGVKLWAGPAHLPVAVIARSAEIPATAKSAALGRQLDPAAYVLHRAWVGPMVLVVLDDPNDPTPYWLVSCRHPERVLSALRS
Prediction	CCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCCCCCEEEEHCEEHCHHHEEEEEHCCHHHHHHHHCCCCCCCEEEEHCCCCCCEEEEEHCCCCCCCCEEEEEHCCHHHHHHHHHC
Conf.Score	99999998887578775788589999999999999999857856889999999999999999997885899985876667878999657855444555566698999998788888434666547767679999779999997789985999999999969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSGTRLAPHSVRYRERLWVPWWWWPLAFALAALIAFEVNLGVAALPDWVPFATLFTVAAGTLLWLGRVEIRVTAGSADGAGVKLWAGPAHLPVAVIARSAEIPATAKSAALGRQLDPAAYVLHRAWVGPMVLVVLDDPNDPTPYWLVSCRHPERVLSALRS
Prediction	85666467651314120313333133123313331222323333333321311121232022213433303034444545443030240402241124045144742343234703120000002304400203042573221000000340630161178
	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

CCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCCCCCEEEEHCEEHCHHHEEEEEHCCHHHHHHHHCCCCCCCEEEEHCCCCCCEEEEEHCCCCCCCCEEEEEHCCHHHHHHHHHC
MSGTRLAPHSVRYRERLWVPWWWWPLAFALAALIAFEVNLGVAALPDWVPFATLFTVAAGTLLWLGRVEIRVTAGSADGAGVKLWAGPAHLPVAVIARSAEIPATAKSAALGRQLDPAAYVLHRAWVGPMVLVVLDDPNDPTPYWLVSCRHPERVLSALRS

4kl0A2

0.16

0.94

0.67

MUSTER

LHRPQLPLDTLLFTDPNKDPVVTYTIAKQLQADGFLRLTDVVVTLGDADMRSQRAQLAKGVFDRLALPDVRVARGQDYPMTST----QAREHSKFLAEGAALRAA--PDAVHTDGVRAMCERLATSPHKLGMVVIAGMTDAS---ALLAEAGDLVREKVAS

4eunA

0.10

0.09

0.94

0.58

dPPAS

VSGSGKTTIAHGVADETGLEFAEADAFHSPENIATMQRGIPLT-DEDRWPWLRSLAEWMDARADAGVSTIITCSALKRTYRDVLREGPPSV---DFLHLDGPAEVIKGRMSKREGHFMPASLLQSQLAT-----LEALEPDESGIVLDLQPPEQLIERALT

3nvoA1

0.17

0.12

0.68

0.57

wdPPAS

------------------------------------------GHMEAIKGSDVNVPDAVFAWLLDGRGGVKPLEDNDVIDSQWLHLNYTH--ARWLASTPLLPNNVRDALAGESSRPRTLITLRC-ILVAMRLYMDE-------FIVSTRQLDDVVSDLQE

3jacA

0.12

0.97

0.67

wMUSTER

WTDTTLSLSNWMCVEDIY--ANIFIIKCSRETEKKYPQPKGQKYGMGGLIILFLIAIIWFPLLFMSLIRSVVVVNQPIDVTVTLKLGGYE-PLFTMSAIVPFTPQAYEELSQQDPYPLAMQFISQYSPEIVTAQI--EGSSGALWRISPPSRAQMKQELYN

4di7A2

0.15

0.12

0.80

0.65

wPPAS

VTKLPQRTLD-------------WLLDTDVAEALETGRRLVLDESCT-------RAVLRERLTDADGLTGIVSVLAGAERTG---VPGTGLVLGVAL------VALVQALGDAGIDTPLWALTRG----AVSTGRSDKTAPAQVTTAALECPARAGQRLAA

2mmuA

0.18

0.06

0.31

0.93

dPPAS2

---------------------SVWFVSLFIGLMLIGLIWLMVFQLLGPWNYAIAFAFMITGLLLTMRWHLE------------------------------------------------------------------------------------------

4eunA

0.10

0.09

0.94

0.74

PPAS

VSGSGKTTIAHGVADETGLEFAEADAFHSPENIATMQRGIPLT-DEDRWPWLRSLAEWMDARADAGVSTIITCSALKRTYRDVLREGPPSV---DFLHLDGPAEVIKGRMSKREGHFMPASLLQSQLAT-----LEALEPDESGIVLDLQPPEQLIERALT

1wscA1

0.14

0.12

0.88

0.70

Env-PPAS

------QEQLVAV-NELNENLGKVLIKIARDSIANKLGILKINLEDYLSSLN--------DPILNKKGLAFVTLETYYGNSTSLRGC-IGYVEAVAPLKEIVSKAAIAAAFS---DPRFPPLSKGEFDNIIEVTVLGIEKPKSEKILIIK-PSEVKCKKEE

3zt9A

0.09

1.00

0.66

MUSTER

IYTRAREGEIACCLVKRVEGVIFLAVGDGIGPEAARAAEIAIASMESSMNTGLVNIFQLCHRELRGTRGAVAALCRVDRRQGLWQAAIVNIHVKILSAKGIITPLATPGILGYNYPHQLLIAKGSYQEGDLFLIHSDQEGAVPLALLANLTAEELVRLIGE

4yzfA2

0.11

0.05

0.46

0.53

dPPAS

KPPKYHPDVPYVKRVKTWRMHLFTGIQIICLAVLWVVKSTPASLALPFVLILTVPLRRVLLPLIFRNVELQCLD---------------------------------------------------------------------------------------

(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=-3.14

Estimated TM-score = 0.36±0.12

Estimated RMSD = 12.1±4.4Å

Download Model 2

C-score=-4.89

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.58

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	4eunA	0.649	3.71	0.081	0.907
2	1ko5A	0.606	3.92	0.096	0.857
3	1qhxA	0.603	4.29	0.087	0.907
4	3tlxA	0.601	4.19	0.053	0.913
5	3hjnA	0.601	3.86	0.083	0.857
6	3dl0A	0.599	4.11	0.079	0.913
7	1m7gC	0.598	3.84	0.072	0.845
8	3akyA	0.595	4.20	0.059	0.925
9	2rgxA	0.595	3.97	0.068	0.876
10	2pbrA	0.594	4.01	0.074	0.882

(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	0.12	6	2bo6B	MN	Rep, Mult	137,140
2	0.08	4	1ko5B	ATP	Rep, Mult	5,109,113,149,150,152,155
3	0.04	2	2ly0A	A2Y	Rep, Mult	49,52
4	0.04	2	3wmnU	CRT	Rep, Mult	51,62
5	0.04	2	1zgnB	FE	Rep, Mult	144,150
6	0.02	1	2wsf1	CLA	Rep, Mult	141,145,151
7	0.02	1	3wmmO	CRT	Rep, Mult	45,62
8	0.02	1	3unxA	CA	Rep, Mult	143,144
9	0.02	1	4il6R	HEM	Rep, Mult	58,62
10	0.02	1	2ofxA	PO4	Rep, Mult	62,63,69,91,92
11	0.02	1	3l39A	PO4	Rep, Mult	16,69,71
12	0.02	1	4h13D	TDS	Rep, Mult	51,54
13	0.02	1	1qhsA	CLM	Rep, Mult	27,29,32,47
14	0.02	1	1q90M	BCR	Rep, Mult	53,57

	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	0.067	1kofA	0.609	3.95	0.095	0.870	2.7.1.12	10
2	0.066	2yvuA	0.580	3.81	0.099	0.826	2.7.1.25	19
3	0.066	1zuiA	0.553	4.22	0.070	0.839	2.7.1.71	10
4	0.066	3hjnA	0.601	3.86	0.083	0.857	2.7.4.9	10,73
5	0.066	2ax4C	0.588	3.84	0.079	0.845	2.7.1.25,2.7.7.4	NA
6	0.066	2cdnA	0.573	4.31	0.060	0.901	2.7.4.3	113,116
7	0.066	1viaA	0.539	4.09	0.051	0.814	2.7.1.71	41
8	0.066	1qf9A	0.577	4.32	0.080	0.907	2.7.4.14	113,124
9	0.066	1kagA	0.496	4.80	0.058	0.839	2.7.1.71	10,14
10	0.066	2peyB	0.544	3.48	0.056	0.745	2.7.1.25,2.7.7.4	3
11	0.060	2gksB	0.591	3.78	0.077	0.851	2.7.7.4,2.7.1.25	14
12	0.060	2pbrB	0.603	3.93	0.074	0.882	2.7.4.9	NA
13	0.060	1z83A	0.583	4.46	0.072	0.919	2.7.4.3	NA
14	0.060	1bifA	0.585	4.31	0.079	0.901	3.1.3.46,2.7.1.105	109,114
15	0.060	1m8pA	0.588	4.01	0.071	0.851	2.7.7.4	14
16	0.060	3dkvA	0.600	3.93	0.060	0.894	2.7.4.3	113
17	0.060	1ukyA	0.581	4.30	0.059	0.919	2.7.4.-	113
18	0.060	1x6vA	0.495	3.84	0.069	0.702	2.7.1.25,2.7.7.4	14
19	0.060	2ofxA	0.598	3.71	0.074	0.832	2.7.7.4	NA
20	0.060	1xnjB	0.594	3.86	0.065	0.845	2.7.1.25,2.7.7.4	NA
21	0.060	1akyA	0.591	4.23	0.059	0.925	2.7.4.3	113
22	0.060	2rgxA	0.595	3.97	0.068	0.876	2.7.4.3	NA
23	0.060	1akeA	0.577	4.22	0.060	0.901	2.7.4.3	113
24	0.060	1m7hC	0.580	4.11	0.065	0.845	2.7.1.25	NA
25	0.060	2ccgA	0.574	4.27	0.033	0.876	2.7.4.9	NA
26	0.060	1zakA	0.588	4.33	0.060	0.913	2.7.4.3	113
27	0.060	4tmkA	0.593	4.41	0.065	0.919	2.7.4.9	NA
28	0.060	1ki9B	0.516	4.58	0.063	0.801	2.7.4.3	60
29	0.060	1zinA	0.608	4.08	0.072	0.919	2.7.4.3	113

(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	0.09	0.649	3.71	0.08	0.91	4eunA	GO:0000166 GO:0005524 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0046316
1	0.07	0.620	3.99	0.10	0.89	3t61A	GO:0000166 GO:0005524 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0046316
2	0.07	0.606	3.91	0.07	0.90	4mkhA	GO:0000166 GO:0004017 GO:0005524 GO:0005737 GO:0006139 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0016776 GO:0019205 GO:0044209 GO:0046872 GO:0046939
3	0.07	0.598	3.84	0.07	0.84	1m7gC	GO:0000103 GO:0000166 GO:0004020 GO:0005524 GO:0005829 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019344 GO:0070814 GO:0098617
4	0.07	0.606	3.92	0.10	0.86	1ko5A	GO:0000166 GO:0005524 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0046177 GO:0046316
5	0.07	0.580	3.81	0.10	0.83	2yvuA	GO:0000103 GO:0000166 GO:0004020 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0070814
6	0.07	0.588	3.83	0.08	0.84	2ax4A	GO:0000103 GO:0000166 GO:0001501 GO:0003824 GO:0004020 GO:0004781 GO:0005524 GO:0005829 GO:0007596 GO:0008152 GO:0016301 GO:0016310 GO:0016740 GO:0016779 GO:0050428 GO:0060348
7	0.07	0.584	3.69	0.07	0.82	4fxpB	GO:0000103 GO:0000166 GO:0004020 GO:0005524 GO:0008652 GO:0009507 GO:0009536 GO:0016301 GO:0016310 GO:0016740 GO:0019344 GO:0070814
8	0.07	0.586	3.91	0.07	0.84	4bzpA	GO:0000103 GO:0000166 GO:0003924 GO:0004020 GO:0005524 GO:0005525 GO:0006790 GO:0016301 GO:0016310 GO:0016740 GO:0016779
9	0.07	0.581	3.99	0.07	0.84	5cb8B	GO:0000103 GO:0000166 GO:0004020 GO:0004781 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0070814
10	0.07	0.583	3.81	0.07	0.84	1xjqB	GO:0000103 GO:0000166 GO:0001501 GO:0003824 GO:0004020 GO:0004781 GO:0005524 GO:0005829 GO:0008152 GO:0016301 GO:0016310 GO:0016740 GO:0016779 GO:0050428
11	0.07	0.534	4.23	0.08	0.81	3n2eA	GO:0000166 GO:0000287 GO:0004765 GO:0005524 GO:0005737 GO:0008652 GO:0009073 GO:0009423 GO:0016301 GO:0016310 GO:0016740 GO:0046872
12	0.07	0.537	4.55	0.06	0.86	2f6rA	GO:0000166 GO:0003824 GO:0004140 GO:0004595 GO:0005524 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0008152 GO:0009058 GO:0015937 GO:0016301 GO:0016310 GO:0016740 GO:0016779 GO:0070062
13	0.07	0.557	4.49	0.08	0.85	3r20A	GO:0000166 GO:0004127 GO:0005524 GO:0005737 GO:0006139 GO:0006220 GO:0016301 GO:0016310 GO:0016740 GO:0046939
14	0.07	0.571	4.43	0.03	0.88	4dwjB	GO:0000166 GO:0004798 GO:0005524 GO:0006233 GO:0006235 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046939
15	0.07	0.510	4.52	0.12	0.81	2iyvA	GO:0000166 GO:0000287 GO:0004765 GO:0005524 GO:0005737 GO:0005829 GO:0008652 GO:0009073 GO:0009423 GO:0016301 GO:0016310 GO:0016740 GO:0019632 GO:0040007 GO:0046872
16	0.07	0.545	4.58	0.06	0.84	4dieC	GO:0000166 GO:0004127 GO:0005524 GO:0005737 GO:0006139 GO:0006220 GO:0016301 GO:0016310 GO:0016740 GO:0046939
17	0.07	0.503	4.57	0.07	0.78	4cw7A	GO:0000166 GO:0004017 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0046939
18	0.07	0.519	4.52	0.06	0.81	3nwjA	GO:0000166 GO:0000287 GO:0004765 GO:0005524 GO:0008652 GO:0009073 GO:0009423 GO:0009507 GO:0009536 GO:0016301 GO:0016310 GO:0016740 GO:0019632 GO:0046872
19	0.07	0.531	3.55	0.08	0.74	1d6jB	GO:0000103 GO:0000166 GO:0004020 GO:0005524 GO:0005829 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019344 GO:0070814 GO:0098617

Consensus prediction of GO terms

Molecular Function	GO:0016773	GO:0005524	GO:0016301
GO-Score	0.43	0.32	0.32
Biological Processes	GO:0044238	GO:0071704	GO:0016310
GO-Score	0.37	0.35	0.32
Cellular Component	GO:0005829
GO-Score	0.07

(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.