I-TASSER results

I-TASSER results for job id Rv3766

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

Input Sequence in FASTA format

>protein (229 residues)
MRSAFDSGRLTFGIVYTYARPNWWANANTVRSMIDAAGGLHPRVALMLDVESGGNPPGDG
SSWINRLYWNLADYAGSPVRIIGYANAYDFFNMWRVRPAGLRVIGAGYGSNPNLPGQVAH
QYTDGSGYSPNLPQGAPPFGRCDMNSANGLTPQQFAAACGVTTTGGPLMALTDEEQTELL
TKVREIWDQLRGPNGAGWPQLGQNEQGQDLTPVDAIAVIKNDVAAMLAE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRSAFDSGRLTFGIVYTYARPNWWANANTVRSMIDAAGGLHPRVALMLDVESGGNPPGDGSSWINRLYWNLADYAGSPVRIIGYANAYDFFNMWRVRPAGLRVIGAGYGSNPNLPGQVAHQYTDGSGYSPNLPQGAPPFGRCDMNSANGLTPQQFAAACGVTTTGGPLMALTDEEQTELLTKVREIWDQLRGPNGAGWPQLGQNEQGQDLTPVDAIAVIKNDVAAMLAE
Prediction	CHHHHHHHHHHEEEEEEEEHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC
Conf.Score	8778898764356899999789975799999999997898888579999857999887668999999999999985776578756766676657678888765665799999999887787778887778888888888665544556899899988757788888887777666665467899999999799999977678888888888899999999999999879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRSAFDSGRLTFGIVYTYARPNWWANANTVRSMIDAAGGLHPRVALMLDVESGGNPPGDGSSWINRLYWNLADYAGSPVRIIGYANAYDFFNMWRVRPAGLRVIGAGYGSNPNLPGQVAHQYTDGSGYSPNLPQGAPPFGRCDMNSANGLTPQQFAAACGVTTTGGPLMALTDEEQTELLTKVREIWDQLRGPNGAGWPQLGQNEQGQDLTPVDAIAVIKNDVAAMLAE
Prediction	6452144041300000000003355305203400464454333000000001444244631530340044035124442301010012203321443244231001222242523342324133433343413443232130110203234342242223443555424444454335445224201420324745304411645634412012002303641550478
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CHHHHHHHHHHEEEEEEEEHCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC
MRSAFDSGRLTFGIVYTYARPNWWANANTVRSMIDAAGGLHPRVALMLDVESGGNPPGDGSSWINRLYWNLADYAGSPVRIIGYANAYDFFNMWRVRPAGLRVIGAGYGSNPNLPGQVAHQYTDGSGYSPNLPQGAPPFGRCDMNSANGLTPQQFAAACGVTTTGGPLMALTDEEQTELLTKVREIWDQLRGPNGAGWPQLGQNEQGQDLTPVDAIAVIKNDVAAMLAE

2nw0A

0.17

0.11

0.65

1.20

wPPAS

YKDYVAAMKARNIPFGSYAFCRFVSVEDAKVEARDFW-GDKDSLFWVADVEVTTM--SDMRAGTQAFIDELYRLGA--KKVGLYVGHHKYEEFGAAQIKCDFTWIPRYGAKPAYPCDL-WQYDE-YGQVPGI-------GKCDLNRLNGDKSLDWFTGKGEE-------------------------------------------------------------------

2wagA

0.14

0.10

0.67

1.67

dPPAS2

FSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKALPPVIDVEFYANKREDVTKELSVMIEMLEKHYG--KKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWTYTN----RGKLSGYNGKEKYIDLNVFYGNEEEFENYGM----------------------------------------------------------------------

5a6sA

0.12

0.10

0.89

1.23

PPAS

YKQNYTNTKAQGKITGAYHFANFSTKAQQEANFFLNCIAGTTPDFVVLDLEQQCT--GDITDACLAFLNIVAKK----FKCVVYCNSSFIKEHLNSKICAYPLWIANYGVATP-------AFTLWTKYA----KGQVS-GYIDFSYITD--EFIKYIKGEDEVENLVVYNDGADQRAAEYLADRLACPTINNARKFDYSNVGGNKEQYTSYTMQAVLDYIKNL------

2nw0A

0.15

0.10

0.65

1.34

Env-PPAS

YKDYVAAMKARNIPFGSYAFCRFVSVEDAKVEARDFWNGDKDSLFWVADVEVTTM--SDMRAGTQAFIDELYRLGA--KKVGLYVGHHKYEEFGAAQIKCDFTWIPRYGAKPAYPCDL-WQYDEYGQVPG--------IGKCDLNRLNGDKS--LDWFTGKGEE-----------------------------------------------------------------

2wagA

0.16

0.10

0.67

1.16

wPPAS

FSKNWTNANKTSMRVGAYHFFSFDKGETQAEQFIRNVPKYKQALPPVIDVEFYANKREDVTKELSVMIEMLEKHYG--KKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWQYTN-RGKLSGY-NG--KEKYIDLNVFYGNEEEFENYGM----------------------------------------------------------------------

1jfxA

0.17

0.12

0.68

1.62

dPPAS2

FSANYTNAYNAGIIRGAYHFPNASSGTAQADYFASNGGGWSRDLPGVLDIESGAMCYGLSTTQMRTWINDFHARYKATRDVVIYTTASTCTGSWNGMAAKSPFWVAHWGVSAPTVPSGFPTWTSATGRVGGVS------GDVDRNKFNGSAARLLALANNTA-------------------------------------------------------------------

2wagA

0.14

0.10

0.67

1.17

PPAS

FSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKALPPVIDVEFYANKKDNVTKELSVMIEMLEKHYG--KKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWQYTN----RGKLSGYNGKEKYIDLNVFYGNEEEFENYGM----------------------------------------------------------------------

2wagA

0.15

0.10

0.67

1.31

Env-PPAS

FSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKALPPVIDVEFYANKREDVTKELSVMIEMLEKHYG--KKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWQYTN----RGKLSGYNGKEKYIDLNVFYGNEEEFENYGM----------------------------------------------------------------------

5a6sA

0.15

0.13

0.88

1.15

wPPAS

YKQNYTNTKAQGKITGAYHFANFSAKAQQEANFFLNCIAGTTPDFVVLDLEQQCT--GDITDACLAFLNIVAK-----FKCVVYCNSSFIKEHLNSKICAYPLWIANYGVAPAFTLWTKYQFTE-KGQVSGIS------GYIDFSYITDEFIKYIKG-------EDEVENLVVYNDGADQRAAEYLADRLACPNARKFD-VGGNKEQYTSYTMQAVLDYIKNL------

4krtA1

0.18

0.11

0.62

1.57

dPPAS2

AKQNYEGAKEQGLSVGFYHFFRANKQANFFIDYLNEIGAVNYDCKLALDIETTEGVGRDLTSMCIEFLEEVKRLTG--KEVVVYTYTSFANNNLDSRLGNYPVWIAHYGVNTPGANNIWSSWVSENGSVAGVN------GGCDMNEFTEI-------------------------------------------------------------------------------

(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=-2.25

Estimated TM-score = 0.45±0.14

Estimated RMSD = 10.8±4.6Å

Download Model 2

C-score=-3.74

Download Model 3

C-score=-4.21

Download Model 4

C-score=-4.32

Download Model 5

C-score=-4.60

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	5a6sA	0.732	3.25	0.130	0.904
2	4krtA	0.631	3.46	0.112	0.760
3	5jipA	0.602	3.20	0.093	0.725
4	1h09A	0.597	4.09	0.103	0.795
5	2wagA	0.592	2.33	0.116	0.677
6	1jfxA	0.590	2.41	0.155	0.677
7	4jz5A	0.567	2.57	0.141	0.651
8	4ff5A	0.564	2.55	0.146	0.659
9	5f0eA	0.563	4.51	0.063	0.821
10	4kmqA	0.561	5.07	0.049	0.852

(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	0.20	12	2zadA	MN	Rep, Mult	18,49,51,84,106,122
2	0.15	9	2wwdA	UUU	Rep, Mult	51,84,86,87,88,106,107,108,109
3	0.03	2	3hneB	TTP	Rep, Mult	35,70,74,75,76
4	0.03	2	1zzdA	III	Rep, Mult	31,62,63,66,67,70
5	0.02	1	3ke6B	MN	Rep, Mult	49,50,53
6	0.02	1	3zvwC	MG	Rep, Mult	203,207
7	0.02	1	3au6A	ZN	Rep, Mult	51,120
8	0.02	1	3hncA	TTP	Rep, Mult	41,74,75,77,78
9	0.02	1	3k7tA	GP7	Rep, Mult	57,58

	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	0.067	1jfxA	0.590	2.41	0.155	0.677	3.2.1.17	18,84,106,143
2	0.060	1cgtA	0.503	5.07	0.070	0.751	2.4.1.19	49,90
3	0.060	1ynyB	0.501	4.03	0.033	0.668	3.5.2.2	124
4	0.060	2e28A	0.508	4.73	0.080	0.716	2.7.1.40	NA
5	0.060	1a47A	0.504	5.12	0.066	0.764	2.4.1.19	49,124
6	0.060	1b90A	0.517	4.71	0.078	0.747	3.2.1.2	NA
7	0.060	3gg8C	0.503	4.91	0.046	0.742	2.7.1.40	NA
8	0.060	3ff6A	0.510	5.00	0.050	0.799	6.4.1.2,6.3.4.14	NA
9	0.060	1h09A	0.597	4.09	0.103	0.795	3.2.1.17	49,51,143
10	0.060	1uyvA	0.483	5.14	0.089	0.760	6.3.4.14,6.4.1.2	NA
11	0.060	1qhoA	0.502	5.02	0.058	0.742	3.2.1.133	49,143
12	0.060	1kfwA	0.506	3.82	0.087	0.664	3.2.1.14	49,51,108
13	0.060	2ftyA	0.520	3.84	0.035	0.690	3.5.2.2	NA
14	0.060	2cvtA	0.520	4.89	0.104	0.782	1.17.4.1	NA
15	0.060	2oykB	0.509	4.57	0.053	0.729	3.2.1.123	108
16	0.060	1iq8A	0.506	5.30	0.059	0.786	2.4.2.29	NA
17	0.060	2wghB	0.537	4.97	0.062	0.812	1.17.4.1	NA
18	0.060	3icgA	0.506	4.75	0.036	0.734	3.2.1.4	73
19	0.060	9cgtA	0.500	4.97	0.074	0.742	2.4.1.19	25,52,55,62,65
20	0.060	1on3E	0.508	4.80	0.103	0.773	2.1.3.1	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	0.31	0.597	4.09	0.10	0.79	1h09A	GO:0003796 GO:0003824 GO:0005975 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998 GO:0019835 GO:0042742 GO:0044659
1	0.30	0.732	3.25	0.13	0.90	5a6sA	GO:0003796 GO:0005975 GO:0009253 GO:0016998
2	0.24	0.564	2.55	0.15	0.66	4ff5A	GO:0003796 GO:0005975 GO:0009253 GO:0016020 GO:0016021 GO:0016998
3	0.10	0.631	3.46	0.11	0.76	4krtA	GO:0003796 GO:0005975 GO:0009253 GO:0016998
4	0.09	0.592	2.33	0.12	0.68	2wagA	GO:0003796 GO:0005975 GO:0009253 GO:0016020 GO:0016021 GO:0016787 GO:0016998 GO:0046872
5	0.07	0.590	2.41	0.15	0.68	1jfxA	GO:0003796 GO:0005576 GO:0005615 GO:0005975 GO:0008152 GO:0009253 GO:0016787 GO:0016798 GO:0016998
6	0.07	0.567	2.57	0.14	0.65	4jz5A	GO:0003796 GO:0005975 GO:0009253 GO:0016998
7	0.07	0.555	2.62	0.13	0.65	2nw0A
8	0.07	0.556	2.53	0.16	0.65	2x8rB	GO:0003796 GO:0005975 GO:0009253 GO:0016787 GO:0016998
9	0.07	0.545	2.48	0.14	0.63	3hmcA	GO:0003796 GO:0005975 GO:0009253 GO:0016787 GO:0016998
10	0.07	0.431	4.06	0.05	0.61	2i5gA	GO:0006508 GO:0016805 GO:0031457 GO:0042426
11	0.06	0.425	4.08	0.03	0.57	3dxiA	GO:0003824 GO:0008701 GO:0019439
12	0.06	0.338	5.43	0.04	0.53	2b69A	GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
13	0.06	0.322	4.67	0.06	0.47	4m55E	GO:0005739 GO:0005794 GO:0016020 GO:0016021 GO:0016829 GO:0016831 GO:0032580 GO:0033320 GO:0042803 GO:0048040 GO:0051262 GO:0070062 GO:0070403
14	0.06	0.303	4.42	0.04	0.43	3c65A	GO:0003677 GO:0004518 GO:0005737 GO:0006281 GO:0006289 GO:0006974 GO:0009380 GO:0009381 GO:0009432 GO:0090305
15	0.06	0.287	5.70	0.06	0.48	5cw3A	GO:0000922 GO:0005634 GO:0005737 GO:0005856 GO:0006508 GO:0007049 GO:0007067 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0051301
16	0.06	0.249	4.43	0.02	0.34	5cw5A	GO:0000922 GO:0005634 GO:0005737 GO:0005856 GO:0006508 GO:0007049 GO:0007067 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0051301
17	0.06	0.267	4.45	0.04	0.37	5enuA	GO:0016209 GO:0016491 GO:0055114 GO:0098869
18	0.06	0.189	5.37	0.05	0.31	1s28A	GO:0005737 GO:0050708

Consensus prediction of GO terms

Molecular Function	GO:0003796
GO-Score	0.70
Biological Processes	GO:0016998	GO:0009253	GO:0005975	GO:0042742	GO:0044659
GO-Score	0.70	0.70	0.70	0.30	0.30
Cellular Component	GO:0016021
GO-Score	0.32

(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.