I-TASSER results

I-TASSER results for job id Rv2401

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

Input Sequence in FASTA format

>protein (109 residues)
MRDFGQRSRSGGKAIAEHCRTHELHIRPRTGGESATTVQVGRSAANERADIAPRKTRCCV
HVAKPNRIRLADQLARSSMGEKPGHDHQRNQRDQNQRDVRPRHPGYLGA

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MRDFGQRSRSGGKAIAEHCRTHELHIRPRTGGESATTVQVGRSAANERADIAPRKTRCCVHVAKPNRIRLADQLARSSMGEKPGHDHQRNQRDQNQRDVRPRHPGYLGA
Prediction	CCHHHHHCCCHHHHHHHHHHHCEEEEHCCCCCCCCEEEEHCCHHHHHHHCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Conf.Score	9656654555568899987653567766889877656664444555665568765556887679864458899998765789997555667776765578899998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MRDFGQRSRSGGKAIAEHCRTHELHIRPRTGGESATTVQVGRSAANERADIAPRKTRCCVHVAKPNRIRLADQLARSSMGEKPGHDHQRNQRDQNQRDVRPRHPGYLGA
Prediction	7553465445324301630543514133444464333242345335642523454230023124453141244136553475444645555556645534453453458
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHCCCHHHHHHHHHHHCEEEEHCCCCCCCCEEEEHCCHHHHHHHCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
MRDFGQRSRSGGKAIAEHCRTHELHIRPRTGGESATTVQVGRSAANERADIAPRKTRCCVHVAKPNRIRLADQLARSSMGEKPGHDHQRNQRDQNQRDVRPRHPGYLGA

5fvmA

0.17

1.00

0.74

MUSTER

ASRQFFGEHNTEKMFATLEPLHEMLKRPETLREISFQNSFGRDAYEWVLNYKRTKDINNLNQAWDIYYNVFRRISRKLPQLQTLDLQHVSPKLSAAKDLELAVPGYHAG

2wtzB4

0.19

0.12

0.64

0.69

dPPAS

----------------------------SAADRPATDVAPTDAGGQQFTAIDPAGVGHHIGIRLPGRYNVANCLVALAILDTVGVS--PEQAVPGLREIR---------

2jvzA1

0.15

0.10

0.67

0.59

wdPPAS

AGKAGLVIGKGGETIKQLQER--------AG----VKMILIQDG-----SQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDGGFGDRN-------------------

5cwjA2

0.36

0.25

0.69

0.63

wMUSTER

-----QDSEVLEEAIRVILRIAK-----ESGSEEAL-----RQAIRAVAEIA--KE------AQDPRIRVIRQIAEESGSE-----EARRQAERAEEEIRRR------A

3m8wA1

0.36

0.25

0.70

0.56

wPPAS

LDELEEKTRSGTEILDELGQEQ------ETGS-SASVLQI---AAHE--EVVPE--KIC-KIAEKYMVRV---IARPFVGE-PGN-----TRTPNRHD-------YL--

2jvzA1

0.15

0.10

0.67

0.75

dPPAS2

AGKAGLVIGKGGETIKQLQER--------AG----VKMILIQ-----DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDGGFGDRN-------------------

3iujA3

0.20

0.16

0.77

0.61

PPAS

-RYVGTVTEDD--SAANSTSGNRLYVKDLSQENAPLLTVQGD----LDADVDNKGSTLYLLTNRPNRLVTVD--------ANPG--------PAHWRDLIPERQQVL--

3iujA3

0.18

0.15

0.82

0.90

Env-PPAS

-RYVGTVTED-DRSAANSTSGNRLYVKDLSQENAPLLTVQGDLDADV-SLVDNKGSTLYLLTNRPNRLVTVD-A------ANPG--------PAHWRDLIPERQQVL--

4cgkA

0.07

0.06

0.94

0.71

MUSTER

NQQKLADDAQALTTKQAELKAAELSLAAEKATAEGEKASLLEQKAAAEAEARAAAVAEAAY------KEKRASQQQSVLASANTNLTAQVQAVSESAAAPVRAKVRPTY

2jvzA1

0.14

0.09

0.67

0.68

dPPAS

AGKAGLVIGKGGETIKQLQER------------AGVKMILIQ-----DGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDGGFGDRN-------------------

(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=-4.00

Estimated TM-score = 0.29±0.09

Estimated RMSD = 13.4±4.1Å

Download Model 2

C-score=-4.12

Download Model 3

C-score=-4.31

Download Model 4

C-score=-4.30

Download Model 5

C-score=-4.84

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	4quwA	0.575	3.61	0.092	0.881
2	1syyA	0.563	4.01	0.065	0.899
3	2oc5A	0.551	3.68	0.047	0.862
4	3ee4A	0.549	3.42	0.083	0.817
5	1h0nA	0.542	4.12	0.046	0.881
6	1mhyB	0.536	3.83	0.048	0.899
7	1xmgC	0.530	4.01	0.076	0.890
8	3ixzA4	0.525	3.94	0.058	0.789
9	2inpD	0.523	4.10	0.087	0.862
10	3cvnA	0.523	3.86	0.044	0.835

(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	0.09	3	3ebbA	III	Rep, Mult	14,15,18,44,45,48,62
2	0.09	3	3m4bA	ZN	Rep, Mult	63,103
3	0.06	2	4cojA	MG	Rep, Mult	91,94
4	0.03	1	2icsA	ZN	Rep, Mult	55,85,103
5	0.03	1	2i0mA	ZN	Rep, Mult	68,72,96,100
6	0.03	1	3g4fB	MG	Rep, Mult	69,72,76
7	0.03	1	1oczB	HEA	Rep, Mult	15,74
8	0.03	1	2wsrA	AZI	Rep, Mult	8,88
9	0.03	1	3q72A	CA	Rep, Mult	97,100
10	0.03	1	1xvbD	3BR	Rep, Mult	7,10,11,14
11	0.03	1	1iw7F	MG	Rep, Mult	100,102

	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	3d66A	0.486	3.85	0.094	0.743	3.4.17.20	NA
2	0.060	2vuxB	0.458	4.65	0.019	0.826	1.17.4.1	NA
3	0.060	2uw1B	0.469	3.66	0.071	0.743	1.14.99.6	NA
4	0.060	3hf1B	0.510	4.32	0.028	0.890	1.17.4.1	NA
5	0.060	1lpsA	0.490	4.40	0.064	0.826	3.1.1.3	12
6	0.060	1eulA	0.505	3.70	0.040	0.771	3.6.3.8	NA
7	0.060	3g4dA	0.508	3.73	0.049	0.771	4.2.3.13	NA
8	0.060	1gz7C	0.473	4.54	0.041	0.844	3.1.1.3	NA
9	0.060	3b8eC	0.525	3.96	0.048	0.789	3.6.3.9	7,14
10	0.060	3b8eA	0.522	3.97	0.058	0.789	3.6.3.9	NA
11	0.060	1syyA	0.563	4.01	0.065	0.899	1.17.4.1	NA
12	0.060	1mo7A	0.320	4.46	0.040	0.550	3.6.3.9	8
13	0.060	2dqmA	0.496	3.87	0.032	0.780	3.4.11.2	NA
14	0.060	1h0nA	0.542	4.12	0.046	0.881	1.17.4.1	NA
15	0.060	3ee4A	0.549	3.42	0.083	0.817	1.17.4.1	NA
16	0.060	1mhyB	0.536	3.83	0.048	0.899	1.14.13.25	50,52
17	0.060	2j2fA	0.496	3.59	0.056	0.780	1.14.19.2,1.14.99.6	NA
18	0.060	1crlA	0.491	4.41	0.064	0.826	3.1.1.3	NA
19	0.060	3l76A	0.491	4.21	0.053	0.835	2.7.2.4	7

(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	0.07	0.574	3.40	0.06	0.85	4kvqA	GO:0009924 GO:0016829 GO:0046872 GO:0046914 GO:0071771 GO:1990465
1	0.07	0.575	3.61	0.09	0.88	4quwA	GO:0009924 GO:0016829 GO:0046872 GO:0046914 GO:0071771 GO:1990465
2	0.07	0.569	3.58	0.06	0.87	4z5sA	GO:0009924 GO:0016829 GO:0046872 GO:0046914 GO:0071771 GO:1990465
3	0.07	0.460	3.66	0.06	0.71	1smsA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0051188 GO:0055114
4	0.07	0.495	4.73	0.03	0.90	1jk0A	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
5	0.07	0.461	3.83	0.07	0.75	4bmqA	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
6	0.07	0.502	4.33	0.07	0.88	4m1fA	GO:0004748 GO:0005506 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
7	0.07	0.566	3.95	0.06	0.89	4m1hB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
8	0.07	0.521	3.56	0.09	0.82	5dcsA	GO:0004748 GO:0009186 GO:0016491 GO:0046872 GO:0055114
9	0.07	0.522	3.97	0.06	0.79	3b8eA	GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
10	0.07	0.548	3.58	0.11	0.83	4ac8A	GO:0004748 GO:0005506 GO:0005829 GO:0005971 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
11	0.07	0.458	4.65	0.02	0.83	2vuxB	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
12	0.07	0.518	3.51	0.06	0.76	2rccA	GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
13	0.07	0.572	3.58	0.03	0.87	5cnvH	GO:0004748 GO:0005506 GO:0005737 GO:0005829 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0015949 GO:0016491 GO:0042802 GO:0046872 GO:0055114
14	0.06	0.425	4.15	0.02	0.69	3wccC	GO:0004310 GO:0008610 GO:0009058 GO:0016021 GO:0016740 GO:0016765 GO:0046872 GO:0051996
15	0.06	0.514	4.61	0.03	0.93	4djnA	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
16	0.06	0.407	3.89	0.04	0.66	4cgvB	GO:0097255
17	0.06	0.401	4.04	0.08	0.67	1t0tV	GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
18	0.06	0.394	4.88	0.02	0.72	1o20A	GO:0004350 GO:0005737 GO:0006561 GO:0008152 GO:0008652 GO:0016491 GO:0016620 GO:0050661 GO:0055114 GO:0055129

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0016830
GO-Score	0.48	0.37
Biological Processes	GO:0009263	GO:0055114	GO:0009186	GO:0006260	GO:0051188
GO-Score	0.13	0.13	0.13	0.13	0.07
Cellular Component	GO:0005971	GO:0005634
GO-Score	0.13	0.13

(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.