I-TASSER results

I-TASSER results for job id Rv1972

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

Input Sequence in FASTA format

>protein (191 residues)
MSVAVDSDAEDDAVSEIAEAAGVSPAPAKPSMSAPRRMLLFGLVVVVALAVLLCCWGFRV
QRARHAQDQRGHFLQAARQCALNLTTIDWRNAEADVRRILDGATGEFYNDFAQRSQPFVE
VLRHAKASTVGTITEAGLQTQTADTAQALVAVSVQTSNAGEADPVPRAWRMRITVQRVGD
RVKVSDVGFVP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSVAVDSDAEDDAVSEIAEAAGVSPAPAKPSMSAPRRMLLFGLVVVVALAVLLCCWGFRVQRARHAQDQRGHFLQAARQCALNLTTIDWRNAEADVRRILDGATGEFYNDFAQRSQPFVEVLRHAKASTVGTITEAGLQTQTADTAQALVAVSVQTSNAGEADPVPRAWRMRITVQRVGDRVKVSDVGFVP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEEHCCCCC
Conf.Score	99888888888888888888888888888877645799999999999999999999998877778999999999999999999986897658999999998599899999999999999999986978999999899999869989999999999985899887555689999999989989986555689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSVAVDSDAEDDAVSEIAEAAGVSPAPAKPSMSAPRRMLLFGLVVVVALAVLLCCWGFRVQRARHAQDQRGHFLQAARQCALNLTTIDWRNAEADVRRILDGATGEFYNDFAQRSQPFVEVLRHAKASTVGTITEAGLQTQTADTAQALVAVSVQTSNAGEADPVPRAWRMRITVQRVGDRVKVSDVGFVP
Prediction	75445556567566666566666656556454432211000000000011121011012224445445324402510340032021133730552154037322460263046316503520574634140413300033237530200000113143575674544311020203447340204525537
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEEEEEHCCEEEEEEEEEEEEEHCCCCCCCEEEEEEEEEEEEHCCEEEEEHCCCCC
MSVAVDSDAEDDAVSEIAEAAGVSPAPAKPSMSAPRRMLLFGLVVVVALAVLLCCWGFRVQRARHAQDQRGHFLQAARQCALNLTTIDWRNAEADVRRILDGATGEFYNDFAQRSQPFVEVLRHAKASTVGTITEAGLQTQTADTAQALVAVSVQTSNAGEADPVPRAWRMRITVQRVGDRVKVSDVGFVP

4ke2A

0.12

0.97

MUSTER

AAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAAT---AAAVAAATLEAAAAKAAATAVSAAAAAAAAA---IAFAAAP

2nd4A

0.09

0.08

0.86

0.70

dPPAS

LIQKKYVSWRDAADEANTQVAAHEAEIKEETLRQPGVVAAQQALDKANAIVGHDHEQAVKRAQEDYNTAYNEAYNTVRNRYIQVLQQKYIEAAKAQGNYYDETAVEANRTNEQRIADDIKAQTGKDVTVTKDENGNYVVKDEKGNVVATVDKDGKTVKADAKAG---------------------------

5cnlA

0.12

0.08

0.64

1.27

wdPPAS

-----------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKYFSADGWIAYSKALNQSLPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQY---QKQNLKVVLGFTVASRGFSVTSLQSTP

3wz4A

0.17

0.11

0.63

1.15

wMUSTER

------------------------------------------------------------------HQSDSAVLQWANQAAIAAFTYNFVNYRDELQASSGFFTDQFLGALEQS--NNLDAVKAKKLVVSAVATRAPIILQKGRYSWRVQPILVTYQSASE---FTQQNNVVTLITRVSRGIGISQFVVGP

5cnlA

0.12

0.07

0.62

1.41

wPPAS

-----------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKY--SIAYSKALNQS---LPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQ--YEQKQNLKVVLGFTVASGSLQSTPISP-P

5cwqA2

0.08

0.05

0.63

1.15

dPPAS2

-----SEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKE------SAEEQGDSEVKRLAEEAEQLAREARRHVQECRGGWLEHHH------------------------------------------------------------

5cnlA

0.12

0.08

0.65

1.19

PPAS

-----------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKYFSADGWIAYSKALNQSLPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQYE--QKQNLKVVLGFTVASRGFSVTSLQSTP

5d9rA

0.09

0.06

0.66

1.10

Env-PPAS

----------------------------------------------------------SEALPRMDARTAENIVSKWQKIKSLAFGPDHR-----IEMLPEVLDGRMLKIWTDRAAETAQLGLVYDYTLLKLSVDSVTVSADGTRALVEATLEESACLSDLVHPEVRTYTTRYEVFWSKSGWKITEGSVL-

5cnlA

0.12

0.08

0.65

0.86

MUSTER

-----------------------------------------------------------------GGPDRAQLAVWANEAIIATYTFDYKNYQQQKEIAKYFSADGWIAYSKALNQSLPEVVQKNAYFVNAVATEPPKLITLDPTHWQAIPILVVYKNPQYE--QKQNLKVVLGFTVASRGFSVTSLQSTP

5cwqA2

0.07

0.04

0.63

0.67

dPPAS

---SEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKESAEEQGDSEVKRLAEEAEQLAREARRHVQECRGGWLEHHH--------------------------------------------------------------------

(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=-3.47

Estimated TM-score = 0.33±0.11

Estimated RMSD = 13.4±4.0Å

Download Model 2

C-score=-3.77

Download Model 3

C-score=-3.71

Download Model 4

C-score=-4.19

Download Model 5

C-score=-4.46

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	4xzzA	0.562	3.65	0.063	0.770
2	4o3vA	0.560	2.13	0.116	0.633
3	2cc3A	0.559	2.30	0.073	0.644
4	5cnlA	0.556	2.32	0.148	0.639
5	3wz4A	0.550	2.17	0.165	0.628
6	3soaA	0.541	4.42	0.072	0.764
7	4lsoA	0.532	2.66	0.133	0.628
8	4jf8A	0.525	2.74	0.179	0.633
9	3wz3A	0.523	2.44	0.136	0.618
10	4akyA	0.522	2.69	0.153	0.618

(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	0.17	9	3ov4B	EQU	Rep, Mult	80,86,113,152,154,156,167,171,187,191
2	0.06	3	1jn5B	III	Rep, Mult	141,142,143,145,146,147,175,176,177,182
3	0.04	2	3fkaC	UNL	Rep, Mult	80,84,152,169,171,187
4	0.04	2	1a2k0	III	Rep, Mult	134,136,138,139,140,141,142,143,147,149,151,152,153,168,170,172,174,176,185,186,187,188,190
5	0.04	2	4fcmA	III	Rep, Mult	71,72,75,76,79,100,102,180,181,182,183
6	0.04	2	2fhyA	A37	Rep, Mult	104,105
7	0.02	1	1bt0A	ZN	Rep, Mult	171,186
8	0.02	1	1nr5B	CO	Rep, Mult	98,105
9	0.02	1	3oa0B	HP7	Rep, Mult	137,138
10	0.02	1	2vn9A	GVD	Rep, Mult	136,137,138,150,170,172,190
11	0.02	1	2wlzA	PEG	Rep, Mult	86,87,89,187
12	0.02	1	1nh2C	NUC	Rep, Mult	181,183

	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	0.112	1hkxA	0.504	3.11	0.066	0.639	2.7.11.17	79
2	0.066	2ux0A	0.496	3.39	0.089	0.644	2.7.11.17	NA
3	0.060	4stdA	0.487	3.06	0.076	0.623	4.2.1.94	88
4	0.060	1yiqA	0.436	4.90	0.056	0.665	1.1.99.-	NA
5	0.060	1jrpB	0.444	4.78	0.040	0.723	1.17.1.4	116
6	0.060	3e99A	0.459	3.32	0.104	0.592	1.14.12.10	88
7	0.060	1rsrB	0.458	5.14	0.030	0.754	1.17.4.1	NA
8	0.060	1e3vB	0.447	3.10	0.066	0.550	5.3.3.1	NA
9	0.060	1jroB	0.451	5.08	0.040	0.749	1.1.1.204	NA
10	0.060	8choA	0.446	2.80	0.107	0.539	5.3.3.1	103,183
11	0.060	1biqB	0.461	5.25	0.030	0.759	1.17.4.1	118
12	0.060	1kb0A	0.438	4.25	0.048	0.628	1.1.99.-	NA
13	0.060	1nu3B	0.433	3.47	0.068	0.565	3.3.2.8	148
14	0.060	1lrwC	0.438	4.42	0.057	0.649	1.1.99.8	88,157
15	0.060	2vuxB	0.376	5.08	0.062	0.628	1.17.4.1	NA
16	0.060	3czoB	0.413	5.50	0.054	0.717	4.3.1.3	111
17	0.060	3b9jI	0.315	5.48	0.053	0.539	1.17.1.4,1.17.3.2	145
18	0.060	1t3qB	0.454	5.06	0.063	0.764	1.3.99.17	NA
19	0.060	1h0nA	0.439	4.93	0.056	0.707	1.17.4.1	NA
20	0.060	3b9jJ	0.476	4.49	0.030	0.702	1.17.1.4,1.17.3.2	131,133
21	0.060	1buqA	0.441	2.70	0.098	0.534	5.3.3.1	111

(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	0.561	2.12	0.11	0.63	4o3vB	GO:0016020 GO:0016021
1	0.13	0.525	2.74	0.18	0.63	4jf8A	GO:0016020 GO:0016021 GO:0030255
2	0.12	0.532	2.69	0.17	0.63	4akzA	GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0030255 GO:0042802
3	0.11	0.529	2.26	0.14	0.61	4meiA	GO:0016020 GO:0030255
4	0.10	0.561	2.27	0.16	0.64	3wz4G	GO:0016020 GO:0016021
5	0.09	0.532	2.66	0.13	0.63	4lsoA	GO:0005886 GO:0006810 GO:0009405 GO:0016020 GO:0016021 GO:0030255
6	0.09	0.559	2.30	0.07	0.64	2cc3A	GO:0005886 GO:0016020 GO:0016021 GO:0030255 GO:0042802 GO:0043684
7	0.09	0.526	2.63	0.14	0.63	4nhfA	GO:0016020 GO:0016021 GO:0030255
8	0.08	0.496	3.39	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
9	0.07	0.562	3.65	0.06	0.77	4xzzA	GO:0016740
10	0.07	0.478	3.05	0.08	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
11	0.06	0.442	2.91	0.07	0.55	3b7cA	GO:0004067 GO:0016787
12	0.06	0.270	5.99	0.07	0.49	4xhrA	GO:0005739 GO:0005743 GO:0005758 GO:0006810 GO:0006869 GO:0008289 GO:0015914 GO:0016020 GO:0031314 GO:0032048 GO:1990050 GO:2001247
13	0.06	0.294	5.01	0.06	0.46	2ws2A	GO:0016740
14	0.06	0.321	5.00	0.05	0.52	1x9qA
15	0.06	0.215	5.89	0.04	0.40	3cxdH
16	0.06	0.235	5.47	0.08	0.41	1ck0H
17	0.06	0.243	5.74	0.08	0.45	1lo0H	GO:0001788 GO:0001798 GO:0001812 GO:0002455 GO:0003823 GO:0005771 GO:0005829 GO:0005886 GO:0006910 GO:0006911 GO:0006958 GO:0008333 GO:0009897 GO:0016020 GO:0016021 GO:0016064 GO:0019882 GO:0030162 GO:0034987 GO:0042571 GO:0042742 GO:0045022 GO:0045087 GO:0045807 GO:0050766 GO:0050778 GO:0050853 GO:0050871 GO:0072562
18	0.06	0.244	5.39	0.02	0.41	2ojzH

Consensus prediction of GO terms

Molecular Function	GO:0042802
GO-Score	0.12
Biological Processes	GO:0030255
GO-Score	0.31
Cellular Component	GO:0016021
GO-Score	0.43

(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.