I-TASSER results

I-TASSER results for job id Rv2254c

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

Input Sequence in FASTA format

>protein (151 residues)
MRYRDLETVAAPTINVLRVWPEIVGAIVLLVIAAMGIGHGLRPSPEPVPAPQKQLGCVRF
ALIFGLTAINPATFVYFTAVAVTLARALRATTAIAVVVGVALASLLWQLLLVSAGAFLRS
RATARVRRMTVLAGNAVIAAFGAVLVVHAFA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRYRDLETVAAPTINVLRVWPEIVGAIVLLVIAAMGIGHGLRPSPEPVPAPQKQLGCVRFALIFGLTAINPATFVYFTAVAVTLARALRATTAIAVVVGVALASLLWQLLLVSAGAFLRSRATARVRRMTVLAGNAVIAAFGAVLVVHAFA
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	9875577888988888788999999999999999999997567766555666665688999999999976789999999999864678876467899999999999999999999999997578899999999999999999999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRYRDLETVAAPTINVLRVWPEIVGAIVLLVIAAMGIGHGLRPSPEPVPAPQKQLGCVRFALIFGLTAINPATFVYFTAVAVTLARALRATTAIAVVVGVALASLLWQLLLVSAGAFLRSRATARVRRMTVLAGNAVIAAFGAVLVVHAFA
Prediction	7635514220143046341212031122113113310232355465555447544113212210102333333333221221122343443311101211331133113321302220343144312301221121001311231223327
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MRYRDLETVAAPTINVLRVWPEIVGAIVLLVIAAMGIGHGLRPSPEPVPAPQKQLGCVRFALIFGLTAINPATFVYFTAVAVTLARALRATTAIAVVVGVALASLLWQLLLVSAGAFLRSRATARVRRMTVLAGNAVIAAFGAVLVVHAFA

2n4xA

0.12

0.11

0.91

1.43

wPPAS

L-MLILGSLFFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR--TSGLSWKIQTLPSFFFGMLLAFL-PLPFAGIAISQTLLSEN------PLVMLSYGLGMAVTIAAVFKMGEK----FVKANFQLIRKVTGAIVLLYLAYFALTEVL

4bwzA2

0.09

0.96

1.17

dPPAS2

----RLKDILAV--GKEAFLVAVLGVALPFLGGYLYGLEIGFETLPQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGRGEVGLIVAALGLKAGAV

2n4xA

0.12

0.11

0.91

1.17

PPAS

L-MLILGYTASGFFRVVAMLFLLIFALILLSDELDEKVSIFASRMTSGLS-WKIQTLPSFFFGMLLAFL-PLPFAGIAISQTLLS----ENPLVMLSYGLGMAVTIAAVFKMGE-------FVKANFQLIRKVTGAIVLLYLAYFALTEVL

4o6yA

0.11

0.10

0.91

1.00

wPPAS

VHYRGLSSDNKDHIFNVHPVMMVIGLILFNGEAMLAYKS------------QGTKNLKKLVHLTLQLTAFILSLIGVWAALKFH-KGIENFYSLHSWLGLACLFLFAFQWAAGFVTYWYPGGSRASLMPWHVFLGISIYALALVTATTGIL

2n4xA

0.10

0.09

0.92

1.16

dPPAS2

LGYTA--SLFFGFFRVVAMLFLLIFALILLSDELDEKVSIFASRMTSGLSWKIQTLPSFFFGMLLAFLWLPLPFAGIAISQTLL----SENPLVMLSYGLGMAVTIAAVFKMGEK------FVKANFQLIRKVTGAIVLLYLAYFALTEVL

5a43A

0.15

0.10

0.68

0.96

wPPAS

LRWL-LSTKFNSLLPPGTLVVNLLAGLIIGTLAYFLRQ------------PHLDPFWKLITTGLCGGLS---TFSTFSVEVFALLQAGNYIWALTSVLVHVIGSLITALGFFIITILF---------------------------------

3jbrE

0.08

0.07

0.91

1.14

dPPAS2

--------------MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSEFTTQKEYSISAAAISVFSLGFLIMGTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIYYYSWSFACACAAFVLLFLGGISLLLFSLP

4o6yA

0.10

0.09

0.93

1.14

dPPAS2

RGGLALSSDNKDHIFNVHPVMMVIGLILFNGEAMLAYKSVQ-----------GTKNLKKLVHLTLQLTAFILSLIGVWAALKFHIENFYSLHSWLGLACLFLFAFQWAAGFVTYWYPGGSRNSRASLMPWHVFLGISIYALALVTATTGIL

4ke2A

0.15

0.99

1.12

dPPAS2

AAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAA-ASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAA

3jbrA

0.10

1.00

0.86

MUSTER

KYWTSLSNLVASLLNSIRSIASLLLLLFLFIIIFALLGMQLDFEDTEVRRSNFDNFPQALISVFQVLTGEDWNSVMYNGIMAYGGPSYPGVLVCIYFIILFVCGNYILLNVFLAIAVDNLAEAFTNFILLFILLSSAALAAEDPIRAESVR

(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=-2.80

Estimated TM-score = 0.39±0.13

Estimated RMSD = 11.1±4.6Å

Download Model 2

C-score=-3.23

Download Model 3

C-score=-3.57

Download Model 4

C-score=-3.77

Download Model 5

C-score=-4.83

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	4ui9I	0.726	3.14	0.107	0.974
2	1sj8A	0.714	2.76	0.104	0.894
3	2j0oA	0.707	2.31	0.047	0.854
4	2yevA	0.705	2.81	0.083	0.881
5	1oczC2	0.703	2.80	0.070	0.874
6	1j3uA	0.701	3.58	0.068	0.967
7	3oceA	0.695	3.43	0.068	0.940
8	3no9A	0.694	3.65	0.061	0.980
9	5doqA	0.694	3.28	0.047	0.967
10	1qleC	0.692	3.00	0.056	0.887

(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	0.15	10	2qjyG	HEM	Rep, Mult	26,27,30,31,33,34,37,69,70,73,102,103,106,107,109,110,138,139,142
2	0.10	6	2dyrC	CDL	Rep, Mult	20,24,27,35,143,146,147
3	0.05	3	1zrtC	HEM	Rep, Mult	18,22,23,25,26,73,76,77,79,99,100,102,106,142,145,149
4	0.05	3	1v54P	CDL	Rep, Mult	24,28,32,35,139,142,143,146
5	0.03	2	2o01H	CLA	Rep, Mult	25,29
6	0.03	2	2xqtD	CVM	Rep, Mult	142,145,149
7	0.02	1	1m57D	PEH	Rep, Mult	129,133
8	0.02	1	2jstB	HLT	Rep, Mult	107,110,136
9	0.02	1	2einC	CDL	Rep, Mult	60,64,67
10	0.02	1	4ezcC	BGC	Rep, Mult	67,70
11	0.02	1	3pyrI	MG	Rep, Mult	29,32
12	0.02	1	4o79A	HEC	Rep, Mult	34,39,59,62,63,66,106,109,110,113,114,117,128,131,132,135
13	0.02	1	2at9A	2DP	Rep, Mult	135,138,139,146

	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	0.209	1tqgA	0.560	2.54	0.086	0.695	2.7.13.3	103,105,134
2	0.189	2ksfA	0.504	3.14	0.078	0.669	2.7.13.3	23,97
3	0.165	3eziA	0.491	3.52	0.098	0.675	2.7.13.3	23,29,140,146
4	0.150	3g4xA	0.605	2.48	0.044	0.729	1.15.1.1	110,132
5	0.094	2npuA	0.482	2.85	0.050	0.629	2.7.11.1	58,62
6	0.060	3bhgA	0.633	3.86	0.059	0.894	4.3.2.2	NA
7	0.060	1jtnA	0.295	5.01	0.016	0.483	3.2.1.17	NA
8	0.060	1dofA	0.655	3.79	0.083	0.960	4.3.2.2	NA
9	0.060	3cxhN	0.673	3.16	0.110	0.874	1.10.2.2	109
10	0.060	1yisA	0.658	3.54	0.113	0.940	4.3.2.2	NA
11	0.060	3i9wA	0.619	2.65	0.042	0.781	2.7.13.3	34,68
12	0.060	1cc1L	0.591	3.69	0.035	0.801	1.12.99.6	62
13	0.060	1f1oA	0.678	3.58	0.069	0.960	4.3.2.2	NA
14	0.060	1syyA	0.596	3.20	0.040	0.762	1.17.4.1	NA
15	0.060	1k04A	0.493	3.17	0.091	0.669	2.7.10.2	NA
16	0.060	2pfdB	0.581	3.00	0.041	0.735	2.1.2.5,4.3.1.4	61
17	0.060	3gm1B	0.612	2.64	0.062	0.788	2.7.10.2	31,139
18	0.060	3e04D	0.669	3.50	0.099	0.940	4.2.1.2	NA
19	0.060	3bvlF	0.589	3.14	0.051	0.775	1.16.3.1	133
20	0.060	1q0mD	0.610	2.44	0.044	0.729	1.15.1.1	132,136
21	0.060	1q5nA	0.640	4.05	0.089	0.954	5.5.1.2	NA
22	0.060	1yfmA	0.629	3.86	0.108	0.934	4.2.1.2	NA
23	0.060	3ee4A	0.593	2.93	0.056	0.735	1.17.4.1	NA
24	0.060	1k62B	0.628	3.94	0.049	0.947	4.3.2.1	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	0.20	0.707	2.31	0.05	0.85	2j0oA	GO:0005576 GO:0009405
1	0.17	0.714	2.76	0.10	0.89	1sj8A	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
2	0.16	0.604	3.68	0.10	0.83	2izpA	GO:0005576 GO:0009405
3	0.13	0.454	5.08	0.08	0.80	2jk6A	GO:0000166 GO:0005623 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
4	0.13	0.707	3.42	0.05	0.96	5bptA	GO:0005680 GO:0030071 GO:0031145
5	0.12	0.723	3.38	0.05	0.95	5bpwA	GO:0004842 GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
6	0.08	0.624	3.58	0.07	0.87	2p7nA	GO:0009405
7	0.08	0.562	4.29	0.08	0.86	3zqbA	GO:0005576 GO:0006810 GO:0008565 GO:0009405 GO:0015031
8	0.08	0.642	2.90	0.08	0.82	1st6A	GO:0001725 GO:0002009 GO:0002162 GO:0003779 GO:0005198 GO:0005623 GO:0005737 GO:0005743 GO:0005856 GO:0005886 GO:0005903 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005916 GO:0005925 GO:0005927 GO:0007155 GO:0008013 GO:0015629 GO:0016020 GO:0017166 GO:0030018 GO:0030032 GO:0030054 GO:0030334 GO:0030486 GO:0031594 GO:0031625 GO:0034333 GO:0034394 GO:0042383 GO:0042803 GO:0043034 GO:0043234 GO:0043297 GO:0045121 GO:0045294 GO:0045296 GO:0048675 GO:0051015 GO:0051371 GO:0051393 GO:0070062 GO:0070527 GO:0090136 GO:0090636 GO:0090637 GO:0097110 GO:0098723 GO:1903561 GO:1990357
9	0.07	0.552	4.19	0.06	0.81	2jaaA	GO:0005576 GO:0009405
10	0.07	0.726	3.14	0.11	0.97	5a31I	GO:0004842 GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
11	0.07	0.543	4.57	0.06	0.87	3zqeB	GO:0005576 GO:0006810 GO:0008565 GO:0009405 GO:0015031
12	0.07	0.555	4.42	0.09	0.87	2ym9A	GO:0005576 GO:0009405
13	0.07	0.502	3.61	0.08	0.70	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
14	0.07	0.461	5.35	0.07	0.83	1feaA	GO:0005737 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
15	0.07	0.485	2.57	0.09	0.59	1u89A	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
16	0.07	0.458	2.78	0.04	0.56	1fxkB	GO:0005737 GO:0006457 GO:0016272 GO:0051082
17	0.06	0.403	4.45	0.01	0.63	2yv9A	GO:0002064 GO:0004364 GO:0005244 GO:0005254 GO:0005634 GO:0005737 GO:0005764 GO:0005887 GO:0006749 GO:0006810 GO:0006811 GO:0006821 GO:0016020 GO:0016021 GO:0016324 GO:0034707 GO:0034765 GO:0035150 GO:0043296 GO:1902476
18	0.06	0.385	3.73	0.03	0.56	1pmtA	GO:0004364 GO:0005737 GO:0016740

Consensus prediction of GO terms

Molecular Function	GO:0019904	GO:0008092	GO:0005198	GO:0050839	GO:0005102	GO:0032403
GO-Score	0.34	0.34	0.34	0.34	0.34	0.34
Biological Processes	GO:0030168	GO:0034329	GO:0030865	GO:0030036	GO:0034109	GO:0032507	GO:0009405
GO-Score	0.34	0.34	0.34	0.34	0.34	0.34	0.33
Cellular Component	GO:0044430	GO:0001726	GO:0031988	GO:1903561	GO:0031253	GO:0005924	GO:0031256	GO:0015630
GO-Score	0.34	0.34	0.34	0.34	0.34	0.34	0.34	0.34

(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.