I-TASSER results

I-TASSER results for job id Rv1234

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

Input Sequence in FASTA format

>protein (175 residues)
MTSPFQPRQVPGSTPAAAGAGRRGVPALPTPPKGWPVGSYPTYAEAQRAVDYLSEQQFPV
QQVTIVGVDLMQVERVTGRLTWPKVLGGGVLSGAWLGLFIGLVLGFFSPNPWSALVTGLV
AGVFFGLITSAVPYAMARGTRDFSSTMQLVAGRYDVLCDPQNAEKARDLLARLAI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSPFQPRQVPGSTPAAAGAGRRGVPALPTPPKGWPVGSYPTYAEAQRAVDYLSEQQFPVQQVTIVGVDLMQVERVTGRLTWPKVLGGGVLSGAWLGLFIGLVLGFFSPNPWSALVTGLVAGVFFGLITSAVPYAMARGTRDFSSTMQLVAGRYDVLCDPQNAEKARDLLARLAI
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCEEEEEHCHHHHHHHHHHHHHCCC
Conf.Score	9998888888888988888888788878889998579998899999999999999899964689996687678887577889999999999999999999999997468758999999999999999999999999789888755678877778999865889999999998599
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSPFQPRQVPGSTPAAAGAGRRGVPALPTPPKGWPVGSYPTYAEAQRAVDYLSEQQFPVQQVTIVGVDLMQVERVTGRLTWPKVLGGGVLSGAWLGLFIGLVLGFFSPNPWSALVTGLVAGVFFGLITSAVPYAMARGTRDFSSTMQLVAGRYDVLCDPQNAEKARDLLARLAI
Prediction	7544553574444444444444444463453454220030642740350053037570416300000442432430333232340023103313331333133223334333332333333223323332321312444444242344343530201023730740251057278
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEHCCEEEEEHCHHHHHHHHHHHHHCCC
MTSPFQPRQVPGSTPAAAGAGRRGVPALPTPPKGWPVGSYPTYAEAQRAVDYLSEQQFPVQQVTIVGVDLMQVERVTGRLTWPKVLGGGVLSGAWLGLFIGLVLGFFSPNPWSALVTGLVAGVFFGLITSAVPYAMARGTRDFSSTMQLVAGRYDVLCDPQNAEKARDLLARLAI

3jd8A

0.11

0.10

0.97

0.67

MUSTER

LSDNPNPKCGKGGHAAYSSAVNILLGHGTRVGATYFMTYHTVLKKARLIASNVTETGINGSAYRVFPYSVFYV-----FYEQYLTIIDDTIFNLGVSLGAIFLVTMVLLGCELWSAVIMCATIAMVLVNMFGVMWLWGISLNAVSLVNLVTRAFTVSMKGSRVERAEEALAHMGS

2m5yA

0.15

0.10

0.67

0.69

dPPAS

GSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEVRVYNTEGAAARTADRLKAAGFTVTDVGNLSLPDVAATTVYYTEVEGERATADAVGRTLAAVELRLPELSDQPPGVIVVVTG---------------------------------------------------------

2m5yA

0.17

0.11

0.65

0.71

wdPPAS

GSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEVRVYNI-GAAARTADRLKAAGFTVTDVGNLSLPDVAATTVY-YTEVEGERATADAVGRTLGA----LPELSDQPPGVIVV---VTG-----------------------------------------------------

3jd8A

0.11

0.96

0.78

wMUSTER

LSDNPNPKCGKGGHAAYSSAVNILLGHGTRVGATYFMTYHTVLKKARLIASNVTETGINGSAYRVFPYSVFYV-----FYEQYLTIIDDTIFNLGVSLGAIFLVTLLGCELWSAVIMCATIAMVLVNMFGVMWL--WGISLNAVSLVNLVTRAFTVSMKGSRVERAEEALAHMGS

1susA1

0.18

0.11

0.60

0.75

wPPAS

----------------------------------------KSLLQSDALYQYILETSVFPREHEAM----KELREVTAKHPWNIMT-----TSADEGQFLSMLLKLINAK----TM----IGVYTG--YSLLATALA--PED---------GKILAMDNKENYELGLPVIKKAGV

2m5yA

0.18

0.12

0.67

1.05

dPPAS2

GSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEVRVYNTEGAAARTADRLKAAGFTVTDVGNLSLPDVAATTVY-YTEVEGERATADAVGRTLGAAVRLPELSDQPPGVIVVVTG---------------------------------------------------------

2m5yA

0.14

0.10

0.67

0.80

PPAS

GSSPNSEDDSSAISTMTTTTAAPTSTSVKPAAPRAEVRVY-TEGAAARTADRLKAAGFTVTDVGNLSLPDVAATTVYYTEVEGERATADAVGRTLGAAVELRLPELSDQPPGVIVV---VTG-----------------------------------------------------

4pqgA2

0.11

0.09

0.86

0.72

Env-PPAS

-------------------SIDSLTDSSQGRKPFSLITALAKIDWLVKAVIEAHKE-LPELTFDIYGSLLREIDYIQGHAELSQIYSQYEVLTLMEAIGSGLLIGFDVPYGNQTFIEDHVEDQIKQAYAAKICQLYQENREAMRAYSYQIAEGFLT---KEILEKWKKTVEEV-L

3jd8A3

0.10

0.97

0.67

MUSTER

LSDNPNPKCGKGGHAAYSSAVNILLGHGTRVGATYFMTYHTVLKKARLIASNVTETGINGSAYRVFPYSV-----FYVFYEQYLTIIDDTIFNLGVSLGAIFLVTMVLLGCELWSAVIMCATIAMVLVNMFGVMWLWGISLNAVSLVNLVTRAFTVSMKGSRVERAEEALAHMGS

4tshA

0.08

0.05

0.68

0.65

dPPAS

TQTGNPATNLPEAQGSASKEAEQSQNQAGETNGSIPVEV--PKTDLDQAAKDAKSAGVNVVQDADVNKGT--------VKTAEEAVQKETEIKEDYTKQAEDIKKTTDQYKSDVAAHEAEVAKIKAKNQ----------------------------------------------

(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=-2.73

Estimated TM-score = 0.40±0.13

Estimated RMSD = 11.3±4.5Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.88

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	3jd8A3	0.731	3.28	0.071	0.960
2	2j8sA	0.567	4.44	0.058	0.846
3	4mt1A	0.559	4.41	0.058	0.851
4	3k07A	0.552	4.58	0.065	0.857
5	4k0eA	0.528	4.90	0.084	0.851
6	3kdpA	0.487	4.82	0.084	0.794
7	3aqpA	0.483	4.40	0.094	0.714
8	3ba6A	0.470	5.30	0.081	0.800
9	3b8cA	0.466	4.80	0.074	0.749
10	3j9tA	0.460	5.32	0.029	0.789

(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	0.06	3	1gzmA	C8E	Rep, Mult	100,103
2	0.06	3	3wmmO	CRT	Rep, Mult	86,103
3	0.05	2	2voyK	III	Rep, Mult	119,123,126,127,134
4	0.04	2	2eauA	PTY	Rep, Mult	94,127,131,135
5	0.04	2	3arcx	CLA	Rep, Mult	118,119,122
6	0.04	2	2xqtD	CVM	Rep, Mult	87,90,94
7	0.04	2	3ze3C	78N	Rep, Mult	100,104,107,108
8	0.04	2	2zfeA	XE	Rep, Mult	101,102,105,116,119,120
9	0.02	1	3ar3A	PTY	Rep, Mult	118,121,125,129
10	0.02	1	1dq8B	COA	Rep, Mult	40,74
11	0.02	1	2fbvA	MN	Rep, Mult	69,70
12	0.02	1	2e75G	OPC	Rep, Mult	115,119
13	0.02	1	2h1iC	CA	Rep, Mult	155,158
14	0.02	1	4dz4A	UNK	Rep, Mult	69,97
15	0.02	1	1s5lT	CLA	Rep, Mult	96,99

	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	1yj8A	0.421	4.76	0.024	0.640	1.1.1.8	NA
2	0.060	2fhbA	0.355	5.49	0.030	0.651	3.2.1.41	NA
3	0.060	1yqyA	0.374	5.85	0.029	0.703	3.4.24.83	NA
4	0.060	3b8cB	0.466	4.80	0.074	0.749	3.6.3.6	94
5	0.060	3b8cA	0.466	4.80	0.074	0.749	3.6.3.6	NA
6	0.060	3c46B	0.423	4.92	0.036	0.714	2.7.7.6	98,123
7	0.060	1q5nA	0.413	5.29	0.063	0.686	5.5.1.2	NA
8	0.060	1y0vD	0.416	5.46	0.013	0.743	4.6.1.1	91
9	0.060	1v6yA	0.251	4.91	0.009	0.400	3.2.1.8	69
10	0.060	2zxqA	0.422	5.57	0.025	0.754	3.2.1.97	NA
11	0.060	2f43B	0.364	5.65	0.071	0.651	3.6.3.14	153
12	0.060	2uv8G	0.428	4.55	0.072	0.663	2.3.1.86	NA
13	0.060	1isvA	0.322	5.71	0.034	0.606	3.2.1.8	NA
14	0.060	3iydC	0.417	5.29	0.059	0.749	2.7.7.6	90,94,125
15	0.060	1sk6C	0.356	6.03	0.038	0.703	4.6.1.1	NA
16	0.060	1on3E	0.418	5.06	0.070	0.691	2.1.3.1	NA
17	0.060	3b8eC	0.478	5.01	0.087	0.806	3.6.3.9	NA
18	0.060	1vdzA	0.400	6.01	0.030	0.749	3.6.3.14	127
19	0.060	3kvnX	0.417	5.54	0.083	0.709	3.1.1.1	120,127

(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	0.13	0.731	3.28	0.07	0.96	3jd8A	GO:0001618 GO:0004872 GO:0004888 GO:0005319 GO:0005576 GO:0005635 GO:0005764 GO:0005765 GO:0005768 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0006486 GO:0006629 GO:0006897 GO:0006914 GO:0007041 GO:0007165 GO:0007628 GO:0008202 GO:0008203 GO:0008206 GO:0015248 GO:0015485 GO:0016020 GO:0016021 GO:0016032 GO:0016242 GO:0030301 GO:0031579 GO:0031902 GO:0031982 GO:0033344 GO:0042493 GO:0042632 GO:0045121 GO:0046686 GO:0046718 GO:0048471 GO:0060548 GO:0070062 GO:0071383 GO:0071404 GO:0090150 GO:2000189
1	0.07	0.557	4.54	0.06	0.85	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
2	0.07	0.557	4.74	0.07	0.87	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
3	0.07	0.544	4.67	0.07	0.86	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
4	0.07	0.559	4.41	0.06	0.85	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
5	0.07	0.572	4.52	0.06	0.86	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
6	0.07	0.534	4.76	0.07	0.87	4dnrA	GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
7	0.07	0.524	4.94	0.07	0.86	4k0eC	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
8	0.07	0.528	4.90	0.08	0.85	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
9	0.07	0.503	4.82	0.09	0.80	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
10	0.06	0.397	4.03	0.09	0.58	3wxvA	GO:0004872 GO:0005886 GO:0006629 GO:0006631 GO:0007186 GO:0009755 GO:0010633 GO:0010719 GO:0010906 GO:0016020 GO:0016021 GO:0019216 GO:0019395 GO:0019901 GO:0030308 GO:0031226 GO:0033210 GO:0033211 GO:0042593 GO:0042802 GO:0046426 GO:0046427 GO:0046628 GO:0046872 GO:0046982 GO:0055100 GO:0097003 GO:1901223
11	0.06	0.286	5.18	0.07	0.49	1vknA	GO:0003942 GO:0005737 GO:0006526 GO:0008652 GO:0016491 GO:0016620 GO:0046983 GO:0051287 GO:0055114
12	0.06	0.287	5.01	0.07	0.46	3qntA	GO:0005886 GO:0006629 GO:0006695 GO:0008144 GO:0008202 GO:0008203 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0017137 GO:0030299 GO:0030301 GO:0030659 GO:0031410 GO:0031489 GO:0031526 GO:0042157 GO:0042493
13	0.06	0.305	4.73	0.04	0.49	4r86B	GO:0005215 GO:0006810 GO:0016020 GO:0016021
14	0.06	0.290	5.07	0.05	0.48	5en5C	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
15	0.06	0.253	5.27	0.04	0.44	3ge6A	GO:0000166 GO:0016491 GO:0055114
16	0.06	0.272	5.73	0.04	0.50	2fi7A	GO:0009297 GO:0043683 GO:0046903
17	0.06	0.327	6.36	0.05	0.67	4i0wD	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
18	0.06	0.250	5.11	0.05	0.41	1h6eA	GO:0005048 GO:0005215 GO:0005739 GO:0005765 GO:0005829 GO:0005886 GO:0005905 GO:0006810 GO:0006886 GO:0006897 GO:0007018 GO:0008289 GO:0015031 GO:0016020 GO:0016192 GO:0019886 GO:0030122 GO:0030131 GO:0030666 GO:0030669 GO:0035615 GO:0036020 GO:0042059 GO:0043195 GO:0044325 GO:0048013 GO:0050690 GO:0050750 GO:0060071 GO:0070062 GO:0072583 GO:1903077

Consensus prediction of GO terms

Molecular Function	GO:0022857	GO:0090484
GO-Score	0.37	0.37
Biological Processes	GO:0015893	GO:0055085
GO-Score	0.37	0.37
Cellular Component	GO:0031226	GO:0016021
GO-Score	0.37	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.