I-TASSER results

I-TASSER results for job id Rv3831

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

Input Sequence in FASTA format

>protein (160 residues)
MVSLLVHAALGVVVIGWIVSSNPKVFTRPAGGSWFSLPECVYYVVGIASIALGWYFNIRF
VQQYAHGAANPLWGPGSWAEYVRLMFTNPAASSAGQDYTIANVILLPLFSTTDGYRRGLR
RPWLYFVSSLFTSFAFAFAFYFATIERQHRHERSRATVGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVSLLVHAALGVVVIGWIVSSNPKVFTRPAGGSWFSLPECVYYVVGIASIALGWYFNIRFVQQYAHGAANPLWGPGSWAEYVRLMFTNPAASSAGQDYTIANVILLPLFSTTDGYRRGLRRPWLYFVSSLFTSFAFAFAFYFATIERQHRHERSRATVGA
Prediction	CCHHHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	9458999999999999999758445346888888777899999999999999989999999997677767667777599999998668566666666899999999999987444347886456555889999999999999999999998655778899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVSLLVHAALGVVVIGWIVSSNPKVFTRPAGGSWFSLPECVYYVVGIASIALGWYFNIRFVQQYAHGAANPLWGPGSWAEYVRLMFTNPAASSAGQDYTIANVILLPLFSTTDGYRRGLRRPWLYFVSSLFTSFAFAFAFYFATIERQHRHERSRATVGA
Prediction	6120303313131111100333452144347333132132011011321133123201210342354344333344313400422354322331333121122333311111203434143010121223322333230100012333354674566468
	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

CCHHHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MVSLLVHAALGVVVIGWIVSSNPKVFTRPAGGSWFSLPECVYYVVGIASIALGWYFNIRFVQQYAHGAANPLWGPGSWAEYVRLMFTNPAASSAGQDYTIANVILLPLFSTTDGYRRGLRRPWLYFVSSLFTSFAFAFAFYFATIERQHRHERSRATVGA

2mgyA

0.17

0.16

0.93

1.05

wPPAS

MVGLTLVPSLGGFMGAYFVRGELRWYAKP---SWHPPRWTLAPIWGTLYSAMGYGSYIVWKELGGFTEDAMVP----LGLYTGQLALNWAPPIFFGGWALADLLLVSGVATATTLA-RVSPPRLLYPYLAWLAFATVLNYYVWRDNSGRRGGSRLAE---

2mgyA

0.14

0.98

1.06

dPPAS2

AVGLTLVPSLGGFMGAYFVRGELRWYAGLQKPSWHPPRWTLAPIWGTLYSAMGYGSYIVWKELGGFTEDAMVPLGLYTGQLALNWAWPPIFFGAWALADLLLVSGVATATTLAWHRVSPPAARLLYPYLAWLAFATVLNYYVWRDNSGRRGGSRLAE---

2mgyA

0.15

0.14

0.98

1.06

PPAS

MVGLTLVPSLGGFMGAYFVRGELRWYAGLQKPSWHPPRWTLAPIWGTLYSAMGYGSYIVWKELGGFTEDAMVPLGLYTGQLALNWAWPPIFFGAWALADLLLVSGVATATTLAWHRVSPPAARLLYPYLAWLAFATVLNYYVWRDNSGRRGGSRLAE---

5kk2E

0.16

0.14

0.86

1.00

wPPAS

MLLTTVGAFAAFSLMTIAVGTD--LYSREDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASE-----------------HNIILSAGIFFVSAGLSNIIGIIVYISANAGYSYGWFGALSFIIAEMVGVLAVHMFIDRHKQLRATARAT---

4ryiA

0.09

0.08

0.91

1.02

dPPAS2

MIIVFFLTYGLFYVSSVLFPIDRTWYDALEKPSWTPPGMTIGMIWAVLFGLIALSVAIIYNNYGFKPKTFWFLFLLNYIFNQAFSYFQFSQNLFLATVDCLLVAITTLLLIMFSSNLSKVSAWLLIPYFLWSAFATYLSWTIYSIN--------------

4ryiA

0.16

0.13

0.82

0.96

wPPAS

MKIIVFFLTYGLFYVSSVLFPIRTWYDKP---SWTPPGMTIGMIWAVLFGLIALSVAIIYNNYGFKPKT--------WFLFLLNYIFNQAFSYFQFSLFLATVDCLLVAITTLLSNLS----WLLIPYFLWSAFATYLSWTIYSIN--------------

4bwzA2

0.10

0.09

0.97

1.01

dPPAS2

LYGLEIETLPALFLGTALVATSVGITARQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGMAGAVNEEEYLFMVVFTTLFAPFALKPLIAWTERERAAKE-----

5tj5D

0.10

0.09

0.88

1.00

dPPAS2

CAAAMVLSCLGAAIGTAKSG--IGIAGIGTFKPELIM--KSLIPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLC--VGFACLSSGYAIGMVGDVGVRKYMHQPR-------LFVGIVLILIFSEVLGLYGMIVALILNTRGS------

5kk2E

0.15

0.13

0.88

1.00

dPPAS2

MLLTTVGAFAAFSLMTIAVGTDYWLYSREDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASE-------------RHNIILSAGIFFVSAGLSNIIGIIVYISANA---GYSYGWFGALSFIIAEMVGVLAVHMFIDRHKQLRATARAT---

2mgyA

0.11

0.99

0.93

MUSTER

MVGLTLVPSLGGFMGAYFVRGEGLRWYAGLQKPSWHPPRWTLAPIWGTLYSAMGYGSYIVWKELGGFTEDAMVPLGLYTGQLALNWAWPPIFFGQMGWALADLLLVSGVATATTLAWHRVSPPAARLLYYLAWLAFATVLNYYVWRDNSGRRGGSRLAE-

(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=-1.39

Estimated TM-score = 0.54±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-3.09

Download Model 3

C-score=-3.75

Download Model 4

C-score=-4.47

Download Model 5

C-score=-5.00

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	2mgyA	0.810	2.53	0.135	0.975
2	2jswA	0.651	3.78	0.074	0.931
3	1r0dA	0.639	3.73	0.055	0.912
4	4ryiA	0.627	3.22	0.080	0.863
5	4uc1A	0.620	3.51	0.048	0.875
6	3ge8B	0.620	3.84	0.065	0.881
7	2vzbA	0.620	3.54	0.028	0.838
8	1t0sB	0.616	3.87	0.039	0.869
9	3ee4A	0.608	3.85	0.054	0.856
10	1oquC	0.605	3.97	0.074	0.869

(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	3	3a0hK	CLA	Rep, Mult	56,60
2	0.06	2	4ryrA	MPG	Rep, Mult	34,44,47,48,130,131,134,137
3	0.06	2	2n02A	PKA	Rep, Mult	12,15,16,19,31,38,41,44,45,96,99,100,131,134,135,139
4	0.05	2	3dhhB	BML	Rep, Mult	49,53,56,109,110,113
5	0.03	1	3a0hK	CLA	Rep, Mult	60,63
6	0.03	1	1diiA	HEM	Rep, Mult	106,109
7	0.03	1	2r2fB	FEO	Rep, Mult	49,52,106,109,129,132
8	0.03	1	1dlmB	LIO	Rep, Mult	100,133
9	0.03	1	4amjA	2CV	Rep, Mult	116,121
10	0.03	1	1xvgC	BRJ	Rep, Mult	42,45,49
11	0.03	1	2v9jE	MG	Rep, Mult	47,121
12	0.03	1	3g5nD	PB2	Rep, Mult	109,119
13	0.03	1	1jkuA	CA	Rep, Mult	88,93,95,101
14	0.03	1	2o9dA	HSG	Rep, Mult	123,126,127

	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	0.074	2htnG	0.562	3.99	0.022	0.794	1.16.3.1	5,47,105
2	0.066	3e6sF	0.545	3.86	0.036	0.794	1.16.3.1	130
3	0.060	1uzrB	0.599	3.87	0.068	0.856	1.17.4.1	NA
4	0.060	2j2fA	0.560	4.29	0.040	0.819	1.14.19.2,1.14.99.6	NA
5	0.060	3no6A	0.510	3.97	0.043	0.744	3.5.99.2	NA
6	0.060	1mhyB	0.603	4.11	0.039	0.875	1.14.13.25	128
7	0.060	1rsrB	0.573	4.11	0.041	0.844	1.17.4.1	NA
8	0.060	2vuxB	0.530	3.93	0.074	0.744	1.17.4.1	NA
9	0.060	1smsA	0.560	3.80	0.068	0.800	1.17.4.1	NA
10	0.060	3a68R	0.523	4.13	0.065	0.769	1.16.3.1	106
11	0.060	1biqB	0.535	4.04	0.047	0.806	1.17.4.1	NA
12	0.060	1otwA	0.547	4.19	0.034	0.806	1.3.3.11	15,126,133
13	0.060	2uw1B	0.559	4.46	0.047	0.825	1.14.99.6	NA
14	0.060	2wlaA	0.547	4.01	0.060	0.781	1.16.3.1	15,39,84
15	0.060	1r03A	0.535	4.07	0.022	0.794	1.16.3.1	NA
16	0.060	3bvlF	0.545	3.92	0.044	0.762	1.16.3.1	131,137
17	0.060	1bg7A	0.485	3.82	0.047	0.719	1.16.3.1	NA
18	0.060	1xvgC	0.600	3.97	0.045	0.856	1.14.13.25	5
19	0.060	1o9iA	0.592	3.99	0.039	0.875	1.11.1.6	17,51,78
20	0.060	2rd3D	0.527	4.19	0.034	0.794	3.5.99.2	5
21	0.060	1mfrW	0.530	4.32	0.058	0.812	1.16.3.1	39,105

(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	0.25	0.810	2.53	0.14	0.97	2mgyA	GO:0005497 GO:0005737 GO:0005739 GO:0005741 GO:0006694 GO:0006810 GO:0006811 GO:0006821 GO:0006869 GO:0007268 GO:0007568 GO:0008347 GO:0008503 GO:0010042 GO:0010266 GO:0010823 GO:0010940 GO:0014012 GO:0016020 GO:0016021 GO:0030325 GO:0031397 GO:0031965 GO:0031966 GO:0032570 GO:0032720 GO:0033574 GO:0042493 GO:0043065 GO:0043231 GO:0044325 GO:0045019 GO:0048265 GO:0048266 GO:0048678 GO:0050810 GO:0051901 GO:0051928 GO:0060242 GO:0060252 GO:0060253 GO:0070062 GO:0071222 GO:0071294 GO:0071476 GO:0072655 GO:0072656 GO:0098794 GO:0099565 GO:1903147 GO:1903579 GO:2000379
1	0.14	0.537	3.99	0.04	0.78	3r2hA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0016491 GO:0046872 GO:0055114
2	0.14	0.620	3.91	0.07	0.88	3dhiB	GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
3	0.13	0.613	3.45	0.09	0.86	4rymA	GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0033013 GO:0046906
4	0.13	0.616	3.88	0.04	0.87	3n1xB	GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0055114
5	0.11	0.577	4.45	0.05	0.89	1mhyD	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
6	0.09	0.620	3.54	0.03	0.84	2vzbA	GO:0005623 GO:0006879 GO:0008199 GO:0046872
7	0.09	0.674	3.73	0.04	0.96	1r0dA	GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
8	0.08	0.553	4.14	0.04	0.84	1fziA	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
9	0.08	0.651	3.78	0.07	0.93	2jswA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
10	0.07	0.620	3.50	0.05	0.88	5duoA	GO:0005886 GO:0006810 GO:0008289 GO:0016020 GO:0016021 GO:0033013 GO:0046906
11	0.07	0.545	4.08	0.05	0.82	2inpD	GO:0006725 GO:0016491 GO:0016709 GO:0055114
12	0.07	0.561	3.84	0.03	0.79	4e6kA	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0006880 GO:0008199 GO:0046872 GO:0055114
13	0.07	0.551	3.72	0.10	0.78	2vxxB	GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0046872 GO:0055114
14	0.07	0.579	3.95	0.10	0.81	2c41C	GO:0003677 GO:0005623 GO:0006879 GO:0006950 GO:0008199 GO:0016722 GO:0055114
15	0.07	0.542	4.13	0.05	0.79	4am2A	GO:0004322 GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0016491 GO:0046872 GO:0055114
16	0.07	0.546	4.00	0.08	0.79	2clbA	GO:0005737 GO:0006879 GO:0008199 GO:0009295 GO:0016491 GO:0046872 GO:0055114
17	0.07	0.565	4.24	0.05	0.86	2innA	GO:0006725 GO:0016491 GO:0046872 GO:0055114
18	0.07	0.547	3.66	0.03	0.75	2qqyA	GO:0005623 GO:0006879 GO:0008199

Consensus prediction of GO terms

Molecular Function	GO:0016705	GO:0004497	GO:0030594	GO:0042562	GO:0005515
GO-Score	0.50	0.50	0.50	0.50	0.50
Biological Processes	GO:1903556	GO:0071470	GO:0031325	GO:0042981	GO:0070585	GO:1903321	GO:0072595	GO:1905114	GO:0060251	GO:0044708	GO:0071219	GO:0051924	GO:0046890	GO:0043068	GO:1903146	GO:0071248	GO:0033555	GO:1903578	GO:0033273	GO:0010243	GO:0006971	GO:0010043	GO:0007268	GO:0008284	GO:0016477	GO:1904181	GO:0051900	GO:0048732	GO:0019218	GO:0031396	GO:0045978	GO:0048545	GO:0035270	GO:1904406	GO:0010876	GO:1901362	GO:1901701	GO:0010939	GO:0032496	GO:0014014	GO:0032680	GO:0071702	GO:0031103	GO:0051220	GO:0031327	GO:1903427	GO:0072594	GO:0014015	GO:0071396	GO:0010639	GO:1900543	GO:0043270	GO:0015698	GO:1901654	GO:0045428	GO:0010507	GO:0008285	GO:0055114
GO-Score	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.36
Cellular Component	GO:1903561	GO:0044456	GO:0031968	GO:0005635	GO:0031988	GO:0005740	GO:0016021
GO-Score	0.50	0.50	0.50	0.50	0.50	0.50	0.35

(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.