I-TASSER results

I-TASSER results for job id Rv1147

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

Input Sequence in FASTA format

>protein (216 residues)
MTSGAAASASRVDHPLFARIWPVVAAHEAEAIRALRRENLAGLSGRVLEVGAGVGTNFAY
YPVAVEQVIAMEPEPRLAAKARIAAADAPVPIVVTDKTVEEFRDTETFDAVVCSLVLCSV
SDPGAVLAHLRSLLRRGGELRYLEHVASAGARGRVQRFVDATFWPRLAGNCHTHRHTERA
ILDAGFVVDSSRREWAFPAWVPLPVSELALGRAHRT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTSGAAASASRVDHPLFARIWPVVAAHEAEAIRALRRENLAGLSGRVLEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARIAAADAPVPIVVTDKTVEEFRDTETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEHVASAGARGRVQRFVDATFWPRLAGNCHTHRHTERAILDAGFVVDSSRREWAFPAWVPLPVSELALGRAHRT
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCHHHHHCCCCCCEEEEEHCCHHHHHHHHHHHHHCCCCEEEHCCCCCCCCCCCCCEEEEEHCCHHHCCCHHHHHHHHHHHCCCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCEEEEEEEEHCCCCCCCCCEEEEEEEEEEHC
Conf.Score	998878885787777777888877666788999999999866899689985899857876776688799986999999999999886899899975766899999975478876554456899999999999859996899995789998689999999878888766799888889999999899799998765577877654456899999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTSGAAASASRVDHPLFARIWPVVAAHEAEAIRALRRENLAGLSGRVLEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARIAAADAPVPIVVTDKTVEEFRDTETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEHVASAGARGRVQRFVDATFWPRLAGNCHTHRHTERAILDAGFVVDSSRREWAFPAWVPLPVSELALGRAHRT
Prediction	456644242441334100200210142245203500440066162302400430230042026312210001103400530363077371402213053261347410000000100110320430030014103450200000001244212201320142013110110202230351276043403424432324431131012102020337
	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

CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHCCCCCHHHHHCCCCCCEEEEEHCCHHHHHHHHHHHHHCCCCEEEHCCCCCCCCCCCCCEEEEEHCCHHHCCCHHHHHHHHHHHCCCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCEEEEEEEEHCCCCCCCCCEEEEEEEEEEHC
MTSGAAASASRVDHPLFARIWPVVAAHEAEAIRALRRENLAGLSGRVLEVGAGVGTNFAYYPVAVEQVIAMEPEPRLAAKARIAAADAPVPIVVTDKTVEEFRDTETFDAVVCSLVLCSVSDPGAVLAHLRSLLRRGGELRYLEHVASAGARGRVQRFVDATFWPRLAGNCHTHRHTERAILDAGFVVDSSRREWAFPAWVPLPVSELALGRAHRT

2yqzA

0.20

0.19

0.93

1.55

MUSTER

----------SSALLRAAYAYDRLRAHPPEVAGQIATAASAGEEPVFLELGVGTGRIALPLIARGYRYIALDADA-ALEVFRQKIAGVDVQVVQADARAIPLP-DESVHGVIVVHLWHLVPDWPKVLAEAIRVLKPGGALLEGWDQAEASPEWTLQERWRAFAAEEVERGLHAKREVEEALRRLGLKPRTREVARWREERTP---REALEALSERL

3dh0B

0.15

0.12

0.85

2.10

dPPAS

---------AHKFDPSKIKKLDDPSRLELFDPEKVLKEFGLKEGMTVLDVGTGAGFYLPYLSGEKGKVYAIDVQEEMVNYAWEKVNKLGLKVLKSEENKIPLPD-NTVDFIFMAFTFHELSEPLKFLEELKRVAKPFAYLAIIDWKKEERDKGPPPEEV------------YSEWEVGLILEDAGIRVGRVVEVGKY--------CFGVYAMIV--

3ou2A

0.17

0.15

0.90

2.16

wdPPAS

-TSHGLIESQLSYYRARASEYDATFVPYMDAAPAALERLRANIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGL-DNVEFRQQDLFDWTP--DRQWDAVFFAHWLAHVPDFEAFWESVRSAVAPGGVVEFVDVTDHEVAVRRTLQD-------RIVKVFRSPAELTERLTALGWSCSVDEVHPG-----------FLYATCRPG

3dh0B

0.15

0.12

0.85

2.17

wMUSTER

---------AHKFDPSKIKKLDDPSRLELFDPEKVLKEFGLKEGMTVLDVGTGAGFYLPYLSKMVGKVYAIDVQEEMVNYAWEKVNKLGLKVLKSEENKIPLPDN-TVDFIFMAFTFHELSEPLKFLEELKRVAKPFAYLAIIDWKKEERDKG-------PPPEEVYSE-----WEVGLILEDAGIRVGRVVEVG---KY-----CFGVYAMIV--

3dh0B

0.15

0.13

0.85

2.43

wPPAS

---------AHKFDPSKIKKLDDPSRLELFDPEKVLKEFGLKEGMTVLDVGTGAGFYLPYLSKMVGKVYAIDVQEEMVNYAWEKVNKLGLKVLKSEENKIPLPDN-TVDFIFMAFTFHELSEPLKFLEELKRVAKPFAYLAIIDWKKEERDKG-------PPPEEVYSE-----WEVGLILEDAGIRVGRVVEVG-----------KYCFGVYAMI

3hnrA

0.17

0.14

0.84

2.90

dPPAS2

---------------------DIQYKEVFAHYEDILEDVVNKSFGNVLEFGVGTGNLTNKLLLAGRTVYGIEPSREMRMIAKEKL-PKEFSITEGDFLSFEV--PTSIDTIVSTYAFHHLTDKNVAIAKYSQLLNKGGKIVFADTIFADQTVEAAKQRGFHQLANDLQTEYYTRIVMQTIFENNGFHVTFTRLNHF-----------VWVMEATKQ

3ou2A

0.17

0.15

0.92

2.19

PPAS

-TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAGRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGL-DNVEFRQQDLFDWTP--DRQWDAVFFAHWLAHVPDFEAFWESVRSAVAPGGVVEFVDVTDHEVA---VRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPG-----------FLYATCRPG

3dh0B

0.16

0.13

0.85

2.44

Env-PPAS

---------AHKFDPSKIKKLDDPSRLELFDPEKVLKEFGLKEGMTVLDVGTGAGFYLPYLSKMVGKVYAIDVQEEMVNYAWEKVNKLGLKVLKSEENKIPLPD-NTVDFIFMAFTFHELSEPLKFLEELKRVAKPFAYLAIIDWKKEERDKGPPPEEV------------YSEWEVGLILEDAGIRVGRVVEVG-----------KYCFGVYAMI

3ou2A

0.17

0.16

0.92

1.43

MUSTER

-TSHGLIESQLSYYRARASEYDATFVPYMDSAAPAALERLRAIRGDVLELASGTGYWTRHLSGLADRVTALDGSAEMIAEAGRHGLD-NVEFRQQDLFDWTP--DRQWDAVFFAHWLAHVPDFEAFWESVRSAVAPGGVVEFVDVTDHEVA---VRRTLQDGRSFRIVKVFRSPAELTERLTALGWSCSVDEVHPG-----------FLYATCRPG

3hnrA

0.17

0.14

0.84

2.08

dPPAS

---------------------DIQYKEVFAHYEDILEDVVNKSFGNVLEFGVGTGNLTNKLLLAGRTVYGIEPSREMRMIAKEKL---PKEFSITEGDFLSFEVPTSIDTIVSTYAFHHLTDKNVAIAKYSQLLNKGGKIVFADTIFADQTVEAAKQRGFHQLANDLQTEYYTRIVMQTIFENNGFHVTFTRLNHF-----------VWVMEATKQ

(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=0.10

Estimated TM-score = 0.73±0.11

Estimated RMSD = 5.3±3.4Å

Download Model 2

C-score=-2.15

Download Model 3

C-score=-4.76

Download Model 4

C-score=-4.81

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	4pneA	0.807	2.49	0.175	0.921
2	3vc1A	0.802	2.53	0.133	0.931
3	4iv0A	0.793	2.85	0.132	0.944
4	4krgA1	0.792	2.96	0.150	0.954
5	3ou2A	0.790	2.71	0.167	0.912
6	4ineA	0.787	3.12	0.125	0.949
7	1m6eX	0.785	2.98	0.130	0.958
8	3ggdA	0.782	3.34	0.099	0.982
9	2ex4A	0.782	2.56	0.126	0.917
10	5f2kA	0.781	3.07	0.121	0.954

(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	0.55	47	3ou7A	SAM	Rep, Mult	11,14,21,25,51,52,53,72,73,74,77,95,96,97,98,114,115,116,119
2	0.02	2	3rodD	NCA	Rep, Mult	21,24,115,118,119,144,155

	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	2qyoA	0.660	3.49	0.141	0.819	2.1.1.46	NA
2	0.060	1tw2B	0.756	3.27	0.209	0.926	2.1.1.-	NA
3	0.060	1kphC	0.770	3.00	0.127	0.940	2.1.1.79	155
4	0.060	1p91A	0.682	3.27	0.130	0.829	2.1.1.51	31
5	0.060	1fp1D	0.685	3.09	0.126	0.819	2.1.1.-	NA
6	0.060	1kpgA	0.755	3.04	0.124	0.921	2.1.1.79	125
7	0.060	3i58A	0.733	3.24	0.159	0.893	2.1.1.-	NA
8	0.060	2i62C	0.768	3.05	0.109	0.921	2.1.1.1	51,53,96,98
9	0.060	1wznA	0.760	2.83	0.131	0.880	2.1.1.-	NA
10	0.060	2o06A	0.671	3.58	0.111	0.857	2.5.1.16	51,53,114
11	0.060	3bgdA	0.723	3.30	0.097	0.903	2.1.1.67	NA
12	0.060	3eppB	0.711	3.16	0.099	0.880	2.1.1.56	116,155
13	0.060	1kpiA	0.762	3.27	0.111	0.944	2.1.1.79	NA
14	0.060	2e5wA	0.664	3.26	0.101	0.829	2.5.1.16	51,114,120,127
15	0.060	3g5tA	0.730	3.20	0.095	0.898	2.1.1.145	56,69
16	0.060	1mjfA	0.656	3.33	0.112	0.824	2.5.1.16	51
17	0.060	2ip2A	0.714	2.98	0.141	0.852	2.1.1.-	NA
18	0.060	2h11B	0.728	3.22	0.103	0.903	2.1.1.67	NA
19	0.060	2aovA	0.716	3.66	0.133	0.912	2.1.1.8	73,80

(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	0.34	0.760	2.83	0.13	0.88	1wznA
1	0.34	0.769	2.71	0.18	0.89	1vlmA	GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0032259
2	0.33	0.766	3.34	0.15	0.93	4necB	GO:0008168 GO:0016740 GO:0032259
3	0.32	0.774	2.91	0.15	0.92	2avnA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
4	0.30	0.755	2.79	0.20	0.89	3busA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
5	0.30	0.777	3.11	0.12	0.95	4krhA	GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
6	0.29	0.737	3.42	0.17	0.90	2yqzA	GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
7	0.26	0.747	2.76	0.16	0.88	4oqdC	GO:0008168 GO:0008757 GO:0016740 GO:0017000 GO:0032259 GO:0042803
8	0.26	0.808	2.44	0.17	0.92	4pneB	GO:0008152 GO:0008168 GO:0016740 GO:0032259
9	0.25	0.787	3.12	0.12	0.95	4ineA	GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
10	0.25	0.768	3.20	0.14	0.94	5je1A	GO:0008168 GO:0016740 GO:0032259
11	0.24	0.789	2.90	0.15	0.94	4f86A	GO:0008168 GO:0008169 GO:0008757 GO:0016740 GO:0032259 GO:0042214
12	0.23	0.802	2.52	0.13	0.93	3vc1D	GO:0008152 GO:0008168 GO:0008169 GO:0008757 GO:0016740 GO:0032259 GO:0042214
13	0.23	0.762	3.25	0.11	0.94	3hemA	GO:0001666 GO:0005737 GO:0005829 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0046500 GO:0052167 GO:0071766 GO:0071768 GO:0071769
14	0.22	0.748	3.08	0.13	0.91	2fk8A	GO:0005618 GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008757 GO:0016740 GO:0032259 GO:0071768
15	0.21	0.771	3.12	0.13	0.94	1tpyA	GO:0005618 GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0071768
16	0.16	0.730	3.61	0.14	0.91	4kdcA	GO:0005829 GO:0006744 GO:0008168 GO:0008425 GO:0008689 GO:0008757 GO:0016740 GO:0032259 GO:0043431 GO:0061542 GO:0102004
17	0.15	0.771	3.03	0.12	0.94	1kpgA	GO:0005737 GO:0005886 GO:0006629 GO:0008168 GO:0008610 GO:0008825 GO:0016740 GO:0032259 GO:0046500 GO:0071768
18	0.14	0.792	2.84	0.13	0.94	4mwzB	GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539

Consensus prediction of GO terms

Molecular Function	GO:0008757
GO-Score	0.34
Biological Processes	GO:0032259
GO-Score	0.79
Cellular Component	GO:0005737
GO-Score	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.