I-TASSER results

I-TASSER results for job id Rv2086

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

Input Sequence in FASTA format

>protein (201 residues)
MRPATPLICAFGDKHKHTYGVTPICRALAVHGVQIASRTYFADRAAAPSKRALWDTTITE
ILAGYYEPDAEGKRPPECLYGSLKMWAHLQRQGFRWPSATVKTIMRANGWRGVPLAAHIT
HHRTRPGRGPGPRPGGSAMAGFSNEPAGSGRLHLRADDVEFRLHRVRGRRLRRCDRGLGM
LADQRRSVRRTRITPRPSRLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRPATPLICAFGDKHKHTYGVTPICRALAVHGVQIASRTYFADRAAAPSKRALWDTTITEILAGYYEPDAEGKRPPECLYGSLKMWAHLQRQGFRWPSATVKTIMRANGWRGVPLAAHITHHRTRPGRGPGPRPGGSAMAGFSNEPAGSGRLHLRADDVEFRLHRVRGRRLRRCDRGLGMLADQRRSVRRTRITPRPSRLT
Prediction	CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCEEEHCCEEEEEEEEEEEHCCCEEEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	999767899999999976686899999986577777889999975898767888899999999999998766556766555558999999989745568999999998986776688766788998888999998588865567888687999998898746775766663446657899999999999979899988899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRPATPLICAFGDKHKHTYGVTPICRALAVHGVQIASRTYFADRAAAPSKRALWDTTITEILAGYYEPDAEGKRPPECLYGSLKMWAHLQRQGFRWPSATVKTIMRANGWRGVPLAAHITHHRTRPGRGPGPRPGGSAMAGFSNEPAGSGRLHLRADDVEFRLHRVRGRRLRRCDRGLGMLADQRRSVRRTRITPRPSRLT
Prediction	855546201300461276140420030044443412321033135354353433444035213301442453344343213123013203421141244102101433403023444443444555643324324101000011130453200000000002012000220443433211232234315545456536638
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCEEEHCCEEEEEEEEEEEHCCCEEEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCC
MRPATPLICAFGDKHKHTYGVTPICRALAVHGVQIASRTYFADRAAAPSKRALWDTTITEILAGYYEPDAEGKRPPECLYGSLKMWAHLQRQGFRWPSATVKTIMRANGWRGVPLAAHITHHRTRPGRGPGPRPGGSAMAGFSNEPAGSGRLHLRADDVEFRLHRVRGRRLRRCDRGLGMLADQRRSVRRTRITPRPSRLT

4fcyA

0.10

0.09

0.97

1.20

dPPAS2

QRRLAEKWLPAVQAADEMLSTKTAFATVAGH-YQVSASTLRDKYYQQKFAKPDWAAALVEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSISRATAFRRIQQLDEAMVVACRE-----GEHALMEHLDAMQWINGDGYFVRWFNGDVIKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITI

1b4aA1

0.15

0.05

0.32

1.06

dPPAS2

-------------------------------------------------------GQRHIKIREIIMSN--------DIETQDELVDRLREAGFNVTQATVSRDIKEMQLVKVPMANRYKYSLPSDQR-------------------------------------------------------------------------

2zozB

0.10

0.09

0.87

0.69

MUSTER

MRTSKEMILRTAIDYIGEYSLESYDSLAEA--TGLSKSGLIYH----PSRHALLLGMHELLADDWDKELRDITRDPED--PLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNARTVNHQWIPDTDDLENDAHKRAVY-------------LVQLAADLFVHDY----IHDDVLSKSKRQAMLETILELIPSELHHHH-

4cj9A1

0.04

0.02

0.51

0.56

dPPAS

LNLSPLERSKIEKQYGGATTLAFISNKQNELAQILSRADILKIASYDCAAHALQAVLDCGPLGKRQSDIVKIAGNIGGAQALQAVLDLESLGKRGFSRDDIAK--------------------------------------------------------------------------------------------------

4fcyA

0.11

0.10

0.95

0.79

wdPPAS

QRRLAEKWLPAVQAADEM-STKTAFATVAGH-YQVSASTLRDKYYQQKFAKPDWAAALVSEFEDAWQFLIADYLRPEKCY--ERLELAAREHGWSISRATAFRRIQQLDEAMVVACRE-----GEHALMEHLDAMQWINGDGYFVRWFNGDVIKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYG--PEDFHIT

3k1zA

0.11

0.10

0.93

0.75

wMUSTER

LRHPLGEAYATKARAHGEVEPSALEQGFRQAYRAQSHSFPNYGLSHGLTSRQWWLDVVLQTFHLAAQAVAPIAESHPCTWGAEDTLRECRTRGLRLFDRRLEGILGGLGLRFVLTSEAAGWPKPDPRIFQE-EPVAAHVGD-NYLCDYQG---HSFLVVG---PQALDPVVRDSVPKEHILAHLLPALDCLEGS-------

4fcyA

0.10

0.09

0.93

0.83

wPPAS

QRRLAEKWLPAVQAADEM-AFATVAGHY-----QVSASTLRDKYYQQKFAKPDWAAALVSEFEDAWQFLIADYLRPEKCY--ERLELAAREHGWSISRATAFRRIQQLDEAMVVACRE-----GEHALMEHLDAMQWINGDGYFVRWFNGDVIKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYG--PEDFHIT

1f9nB1

0.12

0.04

0.34

1.06

dPPAS2

----------------------------------------------------MNKGQRHIKIREIITSN--------EIETQDELVDMLKQDGYKVTQATVSRDIKELHLVKVPTNNSYKYSLPADQRF------------------------------------------------------------------------

4ixjA

0.10

0.09

0.94

0.77

PPAS

RENIKTQIVIAMAEESSKDKNEVIKEVLENKEPKCKSGGIYSATFDKPDGIEMARDIHQSMKDLIASFAQDPSIIPGASKGNDDFRKYLLDNKYKNGWPTIDEFKAKYGLYIQPYAYNPTKSDATVVVFANNKTGGNWYTSLVYDY-DEGRWYKGKNGISVAGRS---WDVDTDSVKSVKTEIHS------KEGWGPLN--

4fcyA

0.11

0.10

0.97

0.71

Env-PPAS

QRRLAEKWLPAVQAADEMLSTKTAFATVAGH-YQVSASTLRDKYYQQKFAKPDWAAALVEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSISRATAFRRIQQLDEAMVVACRE-----GEHALMEHLDAMQWINGDGYFVRWFNGDVIKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGI-PEDFHIT

(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=-3.77

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.4±3.7Å

Download Model 2

C-score=-4.23

Download Model 3

C-score=-4.35

Download Model 4

C-score=-4.71

Download Model 5

C-score=-4.81

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	2zozB	0.552	4.03	0.050	0.776
2	1t33A	0.535	4.56	0.089	0.811
3	4ichA	0.529	4.48	0.043	0.771
4	3qbmA	0.520	4.42	0.080	0.761
5	2hyjA	0.520	4.67	0.075	0.786
6	5d1rA	0.517	5.03	0.059	0.826
7	2g3bB	0.516	4.50	0.050	0.771
8	2nx4A	0.515	4.63	0.086	0.766
9	3ih4A	0.514	4.72	0.072	0.766
10	2genA	0.512	4.71	0.042	0.786

(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	0.07	4	4rkuL	CLA	Rep, Mult	58,62
2	0.07	4	3jcuL	CLA	Rep, Mult	62,66
3	0.06	3	1jt0C	QNA	Rep, Mult	20,21,41,49,50
4	0.06	3	4qvpK	MG	Rep, Mult	101,105
5	0.04	2	1jt0A	QNA	Rep, Mult	24,38,41,49,50
6	0.04	2	3fhzC	ARG	Rep, Mult	153,156,157,160,169,171
7	0.02	1	1shkA	MG	Rep, Mult	106,107,109
8	0.02	1	1jt0D	QNA	Rep, Mult	10,11,25,50,55
9	0.02	1	5fmiA	ZN	Rep, Mult	67,71
10	0.02	1	1i9dA	SO3	Rep, Mult	133,169
11	0.02	1	4ej7A	CA	Rep, Mult	143,160
12	0.02	1	1yzxA	GSF	Rep, Mult	16,176
13	0.02	1	3ke6B	MN	Rep, Mult	160,166,168
14	0.02	1	2icpA	MG	Rep, Mult	35,36,39
15	0.02	1	1sl0A	MG	Rep, Mult	13,100

	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	3gpbA	0.452	5.29	0.049	0.746	2.4.1.1	84
2	0.060	2zf5Y	0.466	5.15	0.049	0.746	2.7.1.30	39
3	0.060	1e1yA	0.446	5.62	0.022	0.791	2.4.1.1	NA
4	0.060	1cwyA	0.436	5.33	0.062	0.721	2.4.1.25	NA
5	0.060	1cygA	0.435	5.78	0.059	0.786	2.4.1.19	NA
6	0.060	3ezwG	0.444	5.45	0.062	0.746	2.7.1.30	154,156
7	0.060	1cevA	0.441	5.37	0.048	0.721	3.5.3.1	NA
8	0.060	2je8B	0.445	5.99	0.071	0.831	3.2.1.25	NA
9	0.060	2qllA	0.438	5.72	0.071	0.781	2.4.1.1	NA
10	0.060	2olsA	0.437	5.42	0.058	0.731	2.7.9.2	NA
11	0.060	1oqzB	0.452	5.13	0.037	0.726	3.5.1.93	82,88,159
12	0.060	1bglA	0.364	5.95	0.023	0.672	3.2.1.23	NA
13	0.060	2i7pB	0.449	5.22	0.069	0.736	2.7.1.33	59
14	0.060	3ig5A	0.440	5.24	0.040	0.736	6.3.2.2	123
15	0.060	2qaeA	0.435	5.91	0.065	0.766	1.8.1.4	9
16	0.060	1bvnP	0.458	5.49	0.080	0.796	3.2.1.1	55
17	0.060	3l76A	0.464	5.73	0.032	0.816	2.7.2.4	51
18	0.060	1bsiA	0.454	5.77	0.069	0.811	3.2.1.1	NA
19	0.060	3hxxA	0.459	5.70	0.101	0.826	6.1.1.7	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	0.16	0.552	4.03	0.05	0.78	2zozB	GO:0003677 GO:0006351 GO:0006355
1	0.15	0.534	4.49	0.05	0.78	4ichA	GO:0003677 GO:0006351 GO:0006355
2	0.07	0.523	4.87	0.07	0.80	3vibC	GO:0003677 GO:0006351 GO:0006355
3	0.07	0.520	4.94	0.09	0.83	3pasB	GO:0003677 GO:0006351 GO:0006355
4	0.07	0.535	4.56	0.09	0.81	1t33A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
5	0.07	0.527	4.90	0.09	0.81	4jykA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892 GO:0045893
6	0.07	0.509	4.87	0.06	0.79	2g3bA	GO:0003677 GO:0006351 GO:0006355
7	0.07	0.511	4.68	0.07	0.75	2o7tA	GO:0003677 GO:0006351 GO:0006355
8	0.07	0.492	5.12	0.08	0.79	3vprA	GO:0003677 GO:0006351 GO:0006355 GO:0042802
9	0.07	0.513	4.50	0.09	0.75	3on4A	GO:0003677 GO:0006351 GO:0006355
10	0.07	0.520	4.67	0.07	0.79	2hyjA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
11	0.07	0.530	4.73	0.08	0.79	2id6A	GO:0003677 GO:0006351 GO:0006355
12	0.07	0.506	5.01	0.05	0.81	3lhqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
13	0.07	0.499	5.27	0.08	0.81	3bcgA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
14	0.07	0.497	4.86	0.06	0.76	4nn1A	GO:0003677 GO:0003700 GO:0006351 GO:0006355
15	0.07	0.474	5.37	0.07	0.79	3bqyA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
16	0.07	0.487	4.67	0.09	0.74	4aciB	GO:0000287 GO:0003677 GO:0006351 GO:0006355 GO:0046872
17	0.07	0.493	5.03	0.09	0.77	4gctC	GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
18	0.07	0.486	5.05	0.09	0.77	5f1jA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.42
Biological Processes	GO:0006355
GO-Score	0.42
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.