I-TASSER results

I-TASSER results for job id Rv0012

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

Input Sequence in FASTA format

>protein (262 residues)
MRLTHPTPCPENGETMIDRRRSAWRFSVPLVCLLAGLLLAATHGVSGGTEIRRSDAPRLV
DLVRRAQASVNRLATEREALTTRIDSVHGRSVDTALAAMQRRSAKLAGVAAMNPVHGPGL
VVTLQDAQRDANGRFPRDASPDDLVVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIAR
CVGNTLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRFGLGYCEEVHPDL
QIVGYADPVRMHFAQPAGPLDY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MRLTHPTPCPENGETMIDRRRSAWRFSVPLVCLLAGLLLAATHGVSGGTEIRRSDAPRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDTALAAMQRRSAKLAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRDASPDDLVVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGNTLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRFGLGYCEEVHPDLQIVGYADPVRMHFAQPAGPLDY
Prediction	CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEHCCEEEEEEHCCCCCCCCCCCCCCCCCCEEHCHHHHHHHHHHHHHHCCCEEEHCCEEEHCCEEEEEHCCEEEHCCEEHCCCEEEEEHCCHHHHHHHHHCCHHHHHHHHHHHHHCCEEEEEEEEEEEHCCCCCCCCCCCEEHCCCCCC
Conf.Score	9988888888888777777765457899999999999999877645897765454999999999999999999999999999999999986668999999999999999797555757599999589876677788888887645579999999999999888589988999867868998499799988886898899998699999999866758999999999869789999966799857888887654566688999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MRLTHPTPCPENGETMIDRRRSAWRFSVPLVCLLAGLLLAATHGVSGGTEIRRSDAPRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDTALAAMQRRSAKLAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRDASPDDLVVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGNTLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRFGLGYCEEVHPDLQIVGYADPVRMHFAQPAGPLDY
Prediction	7534534544554743463444301000122233323221201113557534554254035205635643550463355146405514754556425414531551433142340533303010313555454534655444322022510230031035110201104611010301021223202034441322020301143740360052451243034106436040414547504032255525251043236678
	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                 260

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

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEHCCEEEEEEHCCCCCCCCCCCCCCCCCCEEHCHHHHHHHHHHHHHHCCCEEEHCCEEEHCCEEEEEHCCEEEHCCEEHCCCEEEEEHCCHHHHHHHHHCCHHHHHHHHHHHHHCCEEEEEEEEEEEHCCCCCCCCCCCEEHCCCCCC
MRLTHPTPCPENGETMIDRRRSAWRFSVPLVCLLAGLLLAATHGVSGGTEIRRSDAPRLVDLVRRAQASVNRLATEREALTTRIDSVHGRSVDTALAAMQRRSAKLAGVAAMNPVHGPGLVVTLQDAQRDANGRFPRDASPDDLVVHQQDIEAVLNALWNAGAEAIQMQDQRIIAMSIARCVGNTLLLNGRTYSPPYTIAAIGDAAAMQAALAAAPLVTLYKQYVVRFGLGYCEEVHPDLQIVGYADPVRMHFAQPAGPLDY

3gmgA

0.29

0.16

0.53

1.84

MUSTER

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

5cwqA2

0.12

0.05

0.43

1.10

dPPAS2

EKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKESAEEQGD-----SEVKRLAEEAEQLAREARRHVQECRGGWLEHHH-------------------------------------------------------------------------------------------------------------------------------------------------

3gmgA

0.29

0.16

0.53

2.47

dPPAS

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

4tqlA2

0.08

0.02

0.29

1.04

dPPAS2

------------------------MKKLYDEAKKKIEQMIQQIKQGGDKQKMEELLKRAKEEMKKVKDKMEKAKQVAEELIKKILQLIEKAKEIAEKVLKG-----------------------------------------------------------------------------------------------------------------------------------------------------------------

3gmgA

0.29

0.16

0.53

3.90

wdPPAS

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

4tkoB3

0.08

0.03

0.41

1.01

dPPAS2

LHISLSAKKLKVESLKKKREALREKLLQVEEKIKLVKLDWERYKSLFQKGLIP------RRKFEEVDTNLKVLLHEREYLEKSIQEINTEIKRAKKGIENARNEFKTIEELKK-----------------------------------------------------------------------------------------------------------------------------------------------------

3gmgA

0.29

0.16

0.53

2.47

wMUSTER

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

3gmgA

0.29

0.16

0.53

3.81

wPPAS

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

3gmgA

0.29

0.16

0.53

7.26

dPPAS2

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

3gmgA

0.29

0.16

0.53

3.01

PPAS

----------------------------------------------------------------------------------------------------ARLAALSILVGAVGATGPGVMITIDDPGPG---------------VAPEVMIDVINELRAAGAEAIQINDVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGG---AQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV-----

(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=-3.15

Estimated TM-score = 0.36±0.12

Estimated RMSD = 13.4±4.0Å

Download Model 2

C-score=-3.23

Download Model 3

C-score=-3.48

Download Model 4

C-score=-3.84

Download Model 5

C-score=-3.80

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	3gmgA	0.511	1.27	0.288	0.530
2	2y8nA	0.456	6.15	0.042	0.786
3	3ikmD1	0.451	4.60	0.064	0.637
4	4pkcA1	0.448	6.09	0.066	0.771
5	5a0uA	0.438	5.84	0.044	0.744
6	5i2aA1	0.436	5.92	0.069	0.748
7	1r8wA	0.435	5.94	0.061	0.756
8	5fauA	0.431	6.24	0.052	0.759
9	4ybqA	0.426	5.92	0.043	0.714
10	5c65A	0.426	5.67	0.035	0.687

(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	0.13	7	3pg9A	TYR	Rep, Mult	120,121,200,201,202,203,204,237,238
2	0.04	2	1lgbB	UUU	Rep, Mult	162,163,164
3	0.04	2	1wc1A	MG	Rep, Mult	126,204
4	0.04	2	3hi7A	UUU	Rep, Mult	155,188,191,193
5	0.04	2	3khhB	AF	Rep, Mult	115,172
6	0.02	1	3prqX	CLA	Rep, Mult	30,37
7	0.02	1	1yklG	DHB	Rep, Mult	117,118
8	0.02	1	3d5aC	MG	Rep, Mult	34,68
9	0.02	1	2azcA	3TL	Rep, Mult	126,196,199
10	0.02	1	1fa0A	3AD	Rep, Mult	122,161,200,210
11	0.02	1	1fa0A	3AT	Rep, Mult	177,178,180
12	0.02	1	2wo0B	NA	Rep, Mult	124,171,193,197
13	0.02	1	1fa0A	POP	Rep, Mult	34,38,46,59,60
14	0.02	1	2v8vD	URP	Rep, Mult	133,184
15	0.02	1	3ehfA	MG	Rep, Mult	152,156
16	0.02	1	1fa0B	3AD	Rep, Mult	161,200,202

	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	1vncA	0.390	6.12	0.063	0.668	1.11.1.10	163
2	0.060	3kzuA	0.378	6.11	0.073	0.645	2.3.1.41	NA
3	0.060	2fqfA	0.376	5.37	0.056	0.588	1.-.-.-	NA
4	0.060	3ikmD	0.407	6.60	0.065	0.737	2.7.7.7	205
5	0.060	3eifA	0.373	5.98	0.040	0.630	3.4.21.110	NA
6	0.060	1w7cA	0.401	5.94	0.051	0.672	1.4.3.13	NA
7	0.060	1bglA	0.307	6.86	0.038	0.588	3.2.1.23	NA
8	0.060	2g8eA	0.331	5.69	0.029	0.523	3.4.22.52	NA
9	0.060	1qxpB	0.369	6.63	0.059	0.676	3.4.22.53,3.4.22.52	NA
10	0.060	1h2rL	0.378	6.22	0.052	0.641	1.12.2.1	NA
11	0.060	2wpnB	0.370	6.24	0.054	0.641	1.12.7.2	NA
12	0.060	2wgqB	0.400	5.70	0.051	0.645	1.4.3.21	166
13	0.060	3fy4A	0.369	6.35	0.030	0.664	4.1.99.13	NA
14	0.060	2g49A	0.395	5.98	0.060	0.664	3.4.24.56	NA
15	0.060	1h2aL	0.375	6.32	0.044	0.653	1.12.2.1	181
16	0.060	1iduA	0.395	6.37	0.054	0.695	1.11.1.10	NA
17	0.060	2aryA	0.312	6.11	0.056	0.542	3.4.22.52	NA
18	0.060	1occA	0.354	6.31	0.055	0.622	1.9.3.1	NA
19	0.060	1xmeA	0.379	5.68	0.061	0.622	1.9.3.1	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	0.26	0.511	1.27	0.29	0.53	3gmgA	GO:0005576 GO:0005886 GO:0005887 GO:0016020 GO:0016021
1	0.07	0.425	6.07	0.07	0.73	2yajC	GO:0003824 GO:0008152 GO:0016829 GO:0043722
2	0.07	0.442	5.90	0.06	0.76	5i2aB	GO:0003824 GO:0008152
3	0.07	0.431	6.13	0.07	0.76	5i2gA	GO:0003824 GO:0008152
4	0.06	0.407	6.60	0.07	0.74	3ikmD	GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
5	0.06	0.292	6.86	0.06	0.54	1cm5A	GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
6	0.06	0.436	5.96	0.06	0.74	4mtjA	GO:0003824 GO:0008152
7	0.06	0.289	6.36	0.08	0.51	4dleA	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
8	0.06	0.359	5.95	0.04	0.59	1kfdA	GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
9	0.06	0.298	6.63	0.04	0.55	3pw3A	GO:0004177 GO:0004197 GO:0006508 GO:0046872
10	0.06	0.395	6.11	0.07	0.69	4lgyA	GO:0000166 GO:0004642 GO:0005524 GO:0005737 GO:0006164 GO:0006189 GO:0006541 GO:0009156 GO:0016874 GO:0046872
11	0.06	0.295	6.92	0.07	0.57	5bweA	GO:0003824 GO:0008152
12	0.06	0.447	4.63	0.07	0.64	5c51A	GO:0002020 GO:0003676 GO:0003677 GO:0003682 GO:0003887 GO:0005739 GO:0005760 GO:0006259 GO:0006260 GO:0006261 GO:0006264 GO:0006287 GO:0007568 GO:0008408 GO:0009416 GO:0010332 GO:0016740 GO:0016779 GO:0042645 GO:0043195 GO:0043234 GO:0055093 GO:0070062 GO:0071333 GO:0071897 GO:0090305
13	0.06	0.390	6.22	0.05	0.68	2f3oA	GO:0003824 GO:0008152 GO:0016829
14	0.06	0.328	5.96	0.03	0.57	3r0xA	GO:0003941 GO:0005737 GO:0006520 GO:0006563 GO:0008721 GO:0016829 GO:0016836 GO:0030170 GO:0030378 GO:0036088 GO:0046416 GO:0070179
15	0.06	0.289	6.59	0.04	0.52	3pw3D	GO:0004177 GO:0004197 GO:0006508 GO:0046872
16	0.06	0.339	6.27	0.04	0.58	5btoB	GO:0000463 GO:0000466 GO:0000956 GO:0005634 GO:0005829 GO:0030234 GO:0030846 GO:0031087 GO:0034353 GO:0050790 GO:0071035 GO:0090502 GO:1990174
17	0.06	0.294	6.63	0.01	0.55	3hjzA	GO:0003824 GO:0004801 GO:0005737 GO:0005975 GO:0006098 GO:0016740
18	0.06	0.292	6.13	0.04	0.48	5jc7A	GO:0003677 GO:0005524 GO:0016787 GO:0016817

Consensus prediction of GO terms

Molecular Function	GO:0008408	GO:0043722	GO:0003887	GO:0003677	GO:0003682	GO:0002020
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0010332	GO:0071333	GO:0071897	GO:0090305	GO:0007568	GO:0055093	GO:0009416	GO:0006287	GO:0006264
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0031226
GO-Score	0.52

(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.