I-TASSER results

I-TASSER results for job id Rv2327

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

Input Sequence in FASTA format

>protein (163 residues)
MSPSPAAANRSEVGGPLPGLGADLLAVVARLNRLATQRIQMPLPAAQARLLATIEAQGEA
RIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEGIRTLTAVRADR
AAAIEPQLALLPPADRRVLADAVDVLRRLLDHAATTPGRATRQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSPSPAAANRSEVGGPLPGLGADLLAVVARLNRLATQRIQMPLPAAQARLLATIEAQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEGIRTLTAVRADRAAAIEPQLALLPPADRRVLADAVDVLRRLLDHAATTPGRATRQ
Prediction	CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Conf.Score	9999888877666655789999999999999999999768899999999999999969999999999988985679999999999899788579888968999989999999999999999999999858999999999999999999999657888765679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MSPSPAAANRSEVGGPLPGLGADLLAVVARLNRLATQRIQMPLPAAQARLLATIEAQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEGIRTLTAVRADRAAAIEPQLALLPPADRRVLADAVDVLRRLLDHAATTPGRATRQ
Prediction	8656455654753554145004302410230332244347370430003001103744623133005426144430242043017432141342473312220301650351055026404520451276046601520350052035016535756546668
	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

CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
MSPSPAAANRSEVGGPLPGLGADLLAVVARLNRLATQRIQMPLPAAQARLLATIEAQGEARIGDLAAVDHCSQPTMTTQVRRLEDAGLVTRTADPGDARAVRIRITPEGIRTLTAVRADRAAAIEPQLALLPPADRRVLADAVDVLRRLLDHAATTPGRATRQ

4yifA

0.29

0.25

0.85

2.29

MUSTER

---------------SDARLASDLSLAVMRLSRQLRFRPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

2.75

dPPAS

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

2.94

wdPPAS

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

2.65

wMUSTER

---------------SDARLASDLSLAVMRLSRQLRFRPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

3.13

wPPAS

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

4.11

dPPAS2

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

2.80

PPAS

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4yifA

0.29

0.25

0.85

3.62

Env-PPAS

---------------SDARLASDLSLAVMRLSRQLRFNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP---------

4xrfA

0.21

0.18

0.87

2.21

MUSTER

MTH-------------IDKIQALAFSIGKKMQTELLEQMQTGLTPPQFYILKILDHYGASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ---------

4xrfA

0.20

0.17

0.87

2.60

dPPAS

-------------MTHIDKIQALAFSIGKKMQTELLEQMATGLTPPQFYILKILDHYGASRATTLAKKMYVKPSAITVMIDRLIDQELVERYHDKDDRRVVIIELTKKGKARVEEAMTARNEHIAKYFSHLELQEREDLLRLFEKLETIICGTQ---------

(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=-0.48

Estimated TM-score = 0.65±0.13

Estimated RMSD = 5.9±3.7Å

Download Model 2

C-score=-1.95

Download Model 3

C-score=-2.81

Download Model 4

C-score=-1.22

Download Model 5

C-score=-1.24

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	4yifA	0.811	1.17	0.295	0.853
2	2hr3D	0.716	2.45	0.279	0.828
3	2nyxB	0.696	2.72	0.190	0.822
4	2rdpA	0.678	2.49	0.224	0.804
5	4em0B	0.664	2.97	0.122	0.841
6	2a61A	0.657	3.30	0.209	0.834
7	2qwwA	0.645	3.09	0.147	0.816
8	1jgsA	0.642	2.80	0.176	0.791
9	3gfiA	0.631	3.31	0.179	0.822
10	3kp2A	0.630	2.95	0.136	0.797

(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	9	1z9cF	QNA	Rep, Mult	61,62,63,73,74,77,81,91,100,101
2	0.09	7	1z9cF	NUC	Rep, Mult	29,33,61,62,63,73,74,77,81,91,93,99,100,101
3	0.09	7	4ejwA	SRY	Rep, Mult	32,39,41,45,46,48,49,52,53,69,116
4	0.05	4	1z9cD	QNA	Rep, Mult	44,46,47,74,75,79,82
5	0.05	4	3echB	III	Rep, Mult	21,22,23,25,26,28,29,31,32,35,36,39,49,50,53,120,124
6	0.05	4	4fx4B	NUC	Rep, Mult	44,46,47,71,72,74,75,79,85,97,98,99
7	0.03	2	4aikA	NUC	Rep, Mult	46,72,74,75,97,98,99
8	0.02	2	3bpv0	III	Rep, Mult	45,68,69,70,71,138,141,142,143,145,146,148,149,150
9	0.02	2	3bpxA	SAL	Rep, Mult	49,52,56,68,69
10	0.01	1	3bpxA	NA	Rep, Mult	47,78,82
11	0.01	1	3bpxB	NA	Rep, Mult	44,46,47,82
12	0.01	1	3fm5C	MG	Rep, Mult	141,144
13	0.01	1	2fbhA	ZN	Rep, Mult	38,39,40
14	0.01	1	2yr2B	ZN	Rep, Mult	94,96
15	0.01	1	3hsrD	BT6	Rep, Mult	24,25,146
16	0.01	1	3gezA	CA	Rep, Mult	152,155
17	0.01	1	1z910	III	Rep, Mult	45,48,49,52,53,56,69,70,116,118,146,147,150
18	0.01	1	3bpxB	SAL	Rep, Mult	22,25,26,29,33

	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	1prhA	0.464	5.41	0.053	0.810	1.14.99.1	NA
2	0.060	1pgjA	0.457	4.65	0.047	0.718	1.1.1.44	NA
3	0.060	1h16A	0.453	4.83	0.055	0.730	2.3.1.54	NA
4	0.060	1e1hC	0.307	4.51	0.066	0.472	3.4.24.69	77,90
5	0.060	2ewgA	0.459	5.43	0.092	0.828	2.5.1.10	NA
6	0.060	2rnpC	0.320	5.76	0.042	0.626	2.7.7.6	NA
7	0.060	1uwkA	0.452	5.16	0.125	0.791	4.2.1.49	NA
8	0.060	2imcB	0.374	5.26	0.049	0.632	3.4.24.69	NA
9	0.060	2pflA	0.452	4.91	0.055	0.742	2.3.1.54	114
10	0.060	1ob2A	0.317	5.28	0.047	0.583	3.6.1.48	NA
11	0.060	1rqxC	0.445	5.35	0.080	0.767	3.5.99.7	NA
12	0.060	1kizA	0.455	4.75	0.073	0.736	4.2.3.6	NA
13	0.060	2vkzG	0.446	5.60	0.088	0.822	2.3.1.38,3.1.2.14	NA
14	0.060	1veoA	0.470	4.68	0.036	0.761	3.2.1.2	45
15	0.060	1mswD	0.388	5.17	0.085	0.663	2.7.7.6	NA
16	0.060	1cxpC	0.485	5.49	0.068	0.841	1.11.1.7	NA
17	0.060	1b90A	0.476	4.84	0.036	0.779	3.2.1.2	NA
18	0.060	2v6kA	0.446	4.29	0.102	0.656	5.2.1.2	NA
19	0.060	1cvuA	0.467	5.26	0.052	0.804	1.14.99.1	83

(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	0.40	0.621	3.36	0.17	0.80	3bpxA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
1	0.34	0.657	3.30	0.21	0.83	2a61A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.33	0.575	3.41	0.18	0.72	4l9tA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
3	0.31	0.750	2.14	0.28	0.84	4yifB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
4	0.31	0.653	3.13	0.19	0.81	1s3jA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0006367 GO:0044212
5	0.29	0.726	2.39	0.27	0.83	2hr3D	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0006367
6	0.29	0.604	3.42	0.20	0.78	5aipA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010124 GO:0045892
7	0.25	0.571	3.82	0.17	0.79	4hblD	GO:0003677 GO:0003700 GO:0006351 GO:0006355
8	0.24	0.538	3.59	0.14	0.75	1z9cC	GO:0003677 GO:0003700 GO:0005737 GO:0006351 GO:0006355 GO:0044212
9	0.24	0.590	3.41	0.13	0.77	2ethA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
10	0.23	0.709	2.70	0.19	0.83	2nyxB	GO:0003677 GO:0003700 GO:0005886 GO:0006351 GO:0006355 GO:0044212
11	0.23	0.603	3.74	0.21	0.84	3e6mD	GO:0003677 GO:0003700 GO:0006351 GO:0006355
12	0.22	0.574	3.73	0.17	0.83	4b8xA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
13	0.22	0.572	3.38	0.18	0.79	3f3xA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
14	0.21	0.564	3.69	0.17	0.81	3bjaA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
15	0.21	0.587	3.67	0.12	0.81	4rguB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
16	0.19	0.642	2.80	0.18	0.79	1jgsA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009408 GO:0044212 GO:0045892 GO:0046677 GO:0071236
17	0.18	0.618	3.29	0.21	0.79	2fbiA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0010124 GO:0044212 GO:0045892
18	0.17	0.489	3.76	0.12	0.68	3bddA
19	0.16	0.525	3.79	0.21	0.77	2nnnA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
20	0.15	0.581	3.75	0.20	0.81	5cyvB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
21	0.15	0.513	3.79	0.20	0.74	4xrfA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
22	0.14	0.520	3.99	0.12	0.77	3g3zA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
23	0.12	0.695	2.57	0.22	0.83	2rdpA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
24	0.10	0.522	3.89	0.10	0.75	4rbrA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405 GO:0016020 GO:0016021

Consensus prediction of GO terms

Molecular Function	GO:0003700	GO:0044212
GO-Score	0.87	0.31
Biological Processes	GO:0006355	GO:0006367
GO-Score	0.87	0.31
Cellular Component
GO-Score

(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.