I-TASSER results

I-TASSER results for job id Rv2147c

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

Input Sequence in FASTA format

>protein (241 residues)
MNSHCSHTFITDNRSPRARRGHAMSTLHKVKAYFGMAPMEDYDDEYYDDRAPSRGYARPR
FDDDYGRYDGRDYDDARSDSRGDLRGEPADYPPPGYRGGYADEPRFRPREFDRAEMTRPR
FGSWLRNSTRGALAMDPRRMAMMFEDGHPLSKITTLRPKDYSEARTIGERFRDGSPVIMD
LVSMDNADAKRLVDFAAGLAFALRGSFDKVATKVFLLSPADVDVSPEERRRIAETGFYAY
Q

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MNSHCSHTFITDNRSPRARRGHAMSTLHKVKAYFGMAPMEDYDDEYYDDRAPSRGYARPRFDDDYGRYDGRDYDDARSDSRGDLRGEPADYPPPGYRGGYADEPRFRPREFDRAEMTRPRFGSWLRNSTRGALAMDPRRMAMMFEDGHPLSKITTLRPKDYSEARTIGERFRDGSPVIMDLVSMDNADAKRLVDFAAGLAFALRGSFDKVATKVFLLSPADVDVSPEERRRIAETGFYAYQ
Prediction	CCCCCCCCEHCCCCCCCHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCHHHHHHHHHHHCCCCCEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCEEEEHCCCCCCCCHHHHHHHHHHCCCCCC
Conf.Score	9887776465689986456555555899999998899988888888899988888888887777777787777877777777777888788888878887788877877677777788877777776666665557666666667778875678758999789999887765897589865678857888899998889998757557654457875789887898999988766777689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MNSHCSHTFITDNRSPRARRGHAMSTLHKVKAYFGMAPMEDYDDEYYDDRAPSRGYARPRFDDDYGRYDGRDYDDARSDSRGDLRGEPADYPPPGYRGGYADEPRFRPREFDRAEMTRPRFGSWLRNSTRGALAMDPRRMAMMFEDGHPLSKITTLRPKDYSEARTIGERFRDGSPVIMDLVSMDNADAKRLVDFAAGLAFALRGSFDKVATKVFLLSPADVDVSPEERRRIAETGFYAYQ
Prediction	8554143210266544552445302001221000100335626463224644544564554456456456663556445665554554464555445664455654434646445544444444445444543344444444446665522301103065163034104414522000000141466303200000001100032314400420000004615135644542375222448
	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                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEHCCCCCCCHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCHHHHHHHHHHHCCCCCEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCEEEEHCCCCCCCCHHHHHHHHHHCCCCCC
MNSHCSHTFITDNRSPRARRGHAMSTLHKVKAYFGMAPMEDYDDEYYDDRAPSRGYARPRFDDDYGRYDGRDYDDARSDSRGDLRGEPADYPPPGYRGGYADEPRFRPREFDRAEMTRPRFGSWLRNSTRGALAMDPRRMAMMFEDGHPLSKITTLRPKDYSEARTIGERFRDGSPVIMDLVSMDNADAKRLVDFAAGLAFALRGSFDKVATKVFLLSPADVDVSPEERRRIAETGFYAYQ

3zihA

0.32

0.10

0.33

1.92

dPPAS

-----------------------------------------------------------------------------------------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPDNVDVSGTI-------------

2nbiA2

0.10

0.04

0.43

1.06

dPPAS

-----------------------------------------------QPSSQPTGPQPSSQPSECADVLELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMPSPLPSPTE------------------------------------------------------------------------------------------

3zihA

0.32

0.10

0.33

2.44

wdPPAS

-----------------------------------------------------------------------------------------------------------------------------------------------------SSKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPDNVDVSGTI-------------

2nbiA2

0.10

0.04

0.43

1.67

dPPAS2

-----------------------------------------------QPSSQPTGPQPSSQPSECADVLELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSPDGSPPVCSPTMMPSPLPSPTE------------------------------------------------------------------------------------------

3zihA

0.33

0.11

0.32

0.98

wMUSTER

------------------------------------------------------------------------------------------------------------------------------------------------------SKVVLSEPRVYAEAQEIADHLKNRRAVVVNLQRIQHDQAKRIVDFLSGTVYAIGGDIQRIGSDIFLCTPDNVDVSGT----I---------

1mv3A

0.08

0.07

0.80

1.02

dPPAS

RVNHEPEPAGGATPGATL------------------PKSPSQLRKGPPVPPPPKHTPSKEVKQEQILSLFEDTFVPEISVTTPSQPAEASEVAGGTQPAAGAQEPGETAASEAASSSLPAVVVETFPATVNGTVEGGSGAGRLDLPPGFMFKVQAQHDYTATDTDEL--QLKAGD-VVLVIPFQNPEEQKESDWNQHKKLEKCRGVFENFTERVP--------------------------

3p04A

0.36

0.11

0.31

2.28

wPPAS

--------------------------------------------------------------------------------------------------------------------------------------------------SYQ-STIVPVELHSFEDAQVIGGAFRDGDAVVFDS-LLSREEARRIVDFAAGLCFALHGK-QKIDSVTFAVVPELSNI-----------------

4nl6A

0.10

0.06

0.59

1.17

dPPAS2

KRETCVVVYLSDLLSPICE------------------VANNIEQNAQENENESQVSTDESENSRSPGNKSDNIKPKSAPWNSFLPPPPPMPGPRLGPGKPGLKFNGPPPPPPPPPPHLLSCWLPPFPSGPPIIPPPPPICPDSLDDADALGEGRCSHSLN---------------------------------------------------------------------------------

3p04A

0.36

0.11

0.31

4.88

dPPAS2

---------------------------------------------------------------------------------------------------------------------------------------------------SYQSTIVPVELHSFEDAQVIGGAFRDGDAVVFD-SLLSREEARRIVDFAAGLCFALHGK-QKIDSVTFAVVPELSNI-----------------

3p04A

0.36

0.11

0.31

0.90

MUSTER

--------------------------------------------------------------------------------------------------------------------------------------------------SYQ-STIVPVELHSFEDAQVIGGAFRDGDAVVFDS-LLSREEARRIVDFAAGLCFALHGK-QKIDSVTFAVVPELSNI-----------------

(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=-3.90

Estimated TM-score = 0.29±0.09

Estimated RMSD = 15.2±3.4Å

Download Model 2

C-score=-4.38

Download Model 3

C-score=-4.33

Download Model 4

C-score=-4.56

Download Model 5

C-score=-3.74

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	3i39X	0.435	4.88	0.031	0.651
2	1jqkA	0.433	5.05	0.015	0.656
3	2jg0A	0.432	5.48	0.050	0.705
4	2xryA	0.431	5.63	0.036	0.714
5	3i04A2	0.430	4.82	0.031	0.643
6	2cqtA2	0.429	6.00	0.061	0.755
7	2vzvA	0.426	5.40	0.097	0.668
8	2eabA	0.424	5.80	0.043	0.714
9	3w5mA4	0.423	5.75	0.041	0.710
10	3m1cA	0.423	6.11	0.057	0.734

(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	0.08	4	3uilB	DAO	Rep, Mult	202,203
2	0.08	4	3jcuH	CLA	Rep, Mult	192,195,199
3	0.04	2	2zc2A	ZN	Rep, Mult	188,191
4	0.04	2	3qvyA	ZN	Rep, Mult	185,188
5	0.02	1	2z8yD	SF4	Rep, Mult	208,210,211,214,216,234
6	0.02	1	3t1gA	ZN	Rep, Mult	41,45
7	0.02	1	2xquB	CVM	Rep, Mult	196,200
8	0.02	1	2z8yC	SF4	Rep, Mult	165,168,172,203
9	0.02	1	3lxvN	CO3	Rep, Mult	172,174
10	0.02	1	4f8hD	LMD	Rep, Mult	193,197
11	0.02	1	3cmvE	ANP	Rep, Mult	161,163,166,167,168,196,199
12	0.02	1	1cq1A	CA	Rep, Mult	14,35,38
13	0.02	1	1q9xC	CA	Rep, Mult	64,223
14	0.02	1	2v01A	CA	Rep, Mult	190,194
15	0.02	1	3nc3A	MG	Rep, Mult	226,229
16	0.02	1	1cq1B	CA	Rep, Mult	35,38
17	0.02	1	3fbyA	CA	Rep, Mult	185,194,208,210,220,223,226
18	0.02	1	2b0qA	MG	Rep, Mult	136,160

	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	2vz8A	0.404	5.81	0.044	0.693	2.3.1.85	207,215
2	0.060	2vz9B	0.406	5.90	0.044	0.701	2.3.1.85	207,215
3	0.060	2je8B	0.411	5.44	0.017	0.660	3.2.1.25	227
4	0.060	2z8yD	0.435	5.03	0.026	0.656	1.2.7.4,1.2.99.2	164
5	0.060	2gp6A	0.408	5.72	0.047	0.676	2.3.1.41	195
6	0.060	1w6jA	0.408	5.55	0.045	0.664	5.4.99.7	195,198
7	0.060	1dd8A	0.395	5.98	0.045	0.680	2.3.1.41	207,215
8	0.060	1ut9A	0.398	6.24	0.055	0.701	3.2.1.4	NA
9	0.060	2gqdA	0.400	5.79	0.034	0.685	2.3.1.179	215
10	0.060	1jqkF	0.432	5.05	0.015	0.656	1.2.99.2	184
11	0.060	2vn7A	0.406	5.93	0.015	0.689	3.2.1.3	168
12	0.060	3gzkA	0.398	6.36	0.049	0.705	3.2.1.4	NA
13	0.060	3i39X	0.435	4.88	0.031	0.651	1.2.99.2	216
14	0.060	2eabA	0.424	5.80	0.043	0.714	3.2.1.63	NA
15	0.060	1gaiA	0.403	5.87	0.034	0.689	3.2.1.3	NA
16	0.060	2ix4A	0.409	5.97	0.043	0.701	2.3.1.41	98
17	0.060	2jfdA	0.296	6.91	0.015	0.577	2.3.1.85	207
18	0.060	1kasA	0.403	6.12	0.050	0.714	2.3.1.179	162
19	0.060	2pflA	0.406	5.32	0.048	0.635	2.3.1.54	179

(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	0.06	0.433	5.05	0.01	0.66	1jqkA	GO:0003824 GO:0005737 GO:0005886 GO:0006091 GO:0016020 GO:0016151 GO:0016491 GO:0018492 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
1	0.06	0.357	6.20	0.04	0.63	4wvbB	GO:0003824 GO:0004555 GO:0004573 GO:0005991 GO:0009311
2	0.06	0.435	4.88	0.03	0.65	3i39X	GO:0003824 GO:0005737 GO:0005886 GO:0006091 GO:0016020 GO:0016151 GO:0016491 GO:0018492 GO:0019415 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
3	0.06	0.409	6.07	0.04	0.72	1v7vA	GO:0003824 GO:0005975 GO:0016740 GO:0030246 GO:0046872
4	0.06	0.379	5.36	0.06	0.59	3cf4A	GO:0003824 GO:0005506 GO:0006084 GO:0015948 GO:0016151 GO:0016491 GO:0018492 GO:0019385 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
5	0.06	0.348	6.18	0.04	0.62	1oj7A	GO:0000302 GO:0005829 GO:0008106 GO:0008270 GO:0016491 GO:0018455 GO:0033721 GO:0046872 GO:0055114 GO:1990002
6	0.06	0.331	5.77	0.04	0.56	1y8pA	GO:0000166 GO:0004672 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035357 GO:0071333 GO:0071398 GO:0097411 GO:2000377
7	0.06	0.432	5.48	0.05	0.71	2jg0A	GO:0003824 GO:0004555 GO:0005991 GO:0005993 GO:0006974 GO:0008152 GO:0016787 GO:0016798 GO:0030288 GO:0042597 GO:0071474
8	0.06	0.311	6.61	0.04	0.61	4xdbA	GO:0016491 GO:0055114
9	0.06	0.303	5.30	0.04	0.47	3j0cC	GO:0004252 GO:0005198 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0019012 GO:0019028 GO:0019031 GO:0019062 GO:0020002 GO:0030430 GO:0033644 GO:0039619 GO:0039654 GO:0039663 GO:0046718 GO:0046983 GO:0055036 GO:0075509 GO:0075512
10	0.06	0.303	6.86	0.06	0.59	2taaA	GO:0003824 GO:0004556 GO:0005509 GO:0005576 GO:0005975 GO:0008152 GO:0009277 GO:0016052 GO:0016787 GO:0016798 GO:0030287 GO:0030428 GO:0031521 GO:0032163 GO:0043169 GO:0046872
11	0.06	0.288	6.00	0.04	0.49	3pb6X	GO:0000139 GO:0005794 GO:0008270 GO:0016020 GO:0016021 GO:0016603 GO:0016740 GO:0016746 GO:0017186 GO:0046872
12	0.06	0.434	5.06	0.03	0.66	3i01A	GO:0003824 GO:0006091 GO:0015977 GO:0016151 GO:0016491 GO:0018492 GO:0043885 GO:0046872 GO:0051536 GO:0051539 GO:0055114
13	0.06	0.297	5.70	0.04	0.49	2j289	GO:0000166 GO:0003723 GO:0003924 GO:0005525 GO:0005737 GO:0005829 GO:0006612 GO:0006614 GO:0008312 GO:0030529 GO:0048500
14	0.06	0.297	6.89	0.04	0.59	3vm7A	GO:0003824 GO:0004556 GO:0005509 GO:0005975 GO:0008152 GO:0016052 GO:0016787 GO:0016798 GO:0046872
15	0.06	0.264	6.93	0.03	0.53	3q6dA	GO:0006508 GO:0016787 GO:0016805 GO:0046872 GO:0102009
16	0.06	0.290	6.05	0.05	0.51	1nosA	GO:0001542 GO:0001666 GO:0004517 GO:0005102 GO:0005516 GO:0005622 GO:0005737 GO:0005777 GO:0005829 GO:0006527 GO:0006801 GO:0006809 GO:0006954 GO:0007263 GO:0007623 GO:0010181 GO:0010629 GO:0016491 GO:0018119 GO:0020037 GO:0030863 GO:0031284 GO:0032310 GO:0032496 GO:0034617 GO:0034618 GO:0035690 GO:0042127 GO:0042177 GO:0042742 GO:0042803 GO:0045776 GO:0045909 GO:0046872 GO:0048471 GO:0050660 GO:0050796 GO:0051712 GO:0055114 GO:0071222 GO:0071345 GO:0071346 GO:0071407 GO:0072604 GO:0072606 GO:1900015
17	0.06	0.295	5.94	0.07	0.49	2pnrB	GO:0000166 GO:0004672 GO:0004674 GO:0004740 GO:0005524 GO:0005739 GO:0005759 GO:0005975 GO:0006006 GO:0010510 GO:0010906 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0035357 GO:0071333 GO:0071398 GO:0097411 GO:2000377
18	0.06	0.304	6.22	0.05	0.56	1e1dA	GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0051540	GO:0016625	GO:0046914
GO-Score	0.36	0.36	0.36
Biological Processes	GO:0044710
GO-Score	0.36
Cellular Component	GO:0005886	GO:0005737
GO-Score	0.12	0.12

(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.