I-TASSER results

I-TASSER results for job id Rv2203

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

Input Sequence in FASTA format

>protein (230 residues)
MPGPHSPNPGVGTNGPAPYPEPSSHEPQALDYPHDLGAAEPAFAPGPADDAALPPAAYPG
VPPQVSYPKRRHKRLLIGIVVALALVSAMTAAIIYGVRTNGANTAGTFSEGPAKTAIQGY
LNALENRDVDTIVRNALCGIHDGVRDKRSDQALAKLSSDAFRKQFSQVEVTSIDKIVYWS
QYQAQVLFTMQVTPAAGGPPRGQVQGIAQLLFQRGQVLVCSYVLRTAGSY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPGPHSPNPGVGTNGPAPYPEPSSHEPQALDYPHDLGAAEPAFAPGPADDAALPPAAYPGVPPQVSYPKRRHKRLLIGIVVALALVSAMTAAIIYGVRTNGANTAGTFSEGPAKTAIQGYLNALENRDVDTIVRNALCGIHDGVRDKRSDQALAKLSSDAFRKQFSQVEVTSIDKIVYWSQYQAQVLFTMQVTPAAGGPPRGQVQGIAQLLFQRGQVLVCSYVLRTAGSY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHHHHHHHHHHHHHHHHHHEEEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCEEEEEEEEEEHCCCCCCCCHHHHHHHHHHHHCCEEEEEEEEHCCCCCC
Conf.Score	99999999999999999999999999999999999999999999999999999999999999999999999875356889999999999876457766899887888776899999999999999888888898764565444444456899999999999998795478775688876876678999998756889987546788888876489799998875688889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPGPHSPNPGVGTNGPAPYPEPSSHEPQALDYPHDLGAAEPAFAPGPADDAALPPAAYPGVPPQVSYPKRRHKRLLIGIVVALALVSAMTAAIIYGVRTNGANTAGTFSEGPAKTAIQGYLNALENRDVDTIVRNALCGIHDGVRDKRSDQALAKLSSDAFRKQFSQVEVTSIDKIVYWSQYQAQVLFTMQVTPAAGGPPRGQVQGIAQLLFQRGQVLVCSYVLRTAGSY
Prediction	87554436444467435444534545354352245264373434343443444444534444442424745332000000111011111100000013374454434244440342045015214635343123301001023145443441134134520464155240320230032363301010103134456444544342203112554301000001434668
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHHHHHHHHHHHHHHHHHHEEEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEHCCCCEEEEEEEEEEHCCCCCCCCHHHHHHHHHHHHCCEEEEEEEEHCCCCCC
MPGPHSPNPGVGTNGPAPYPEPSSHEPQALDYPHDLGAAEPAFAPGPADDAALPPAAYPGVPPQVSYPKRRHKRLLIGIVVALALVSAMTAAIIYGVRTNGANTAGTFSEGPAKTAIQGYLNALENRDVDTIVRNALCGIHDGVRDKRSDQALAKLSSDAFRKQFSQVEVTSIDKIVYWSQYQAQVLFTMQVTPAAGGPPRGQVQGIAQLLFQRGQVLVCSYVLRTAGSY

2miiA

0.17

0.14

0.83

1.00

wMUSTER

MVGQREP-------APVEEVKPAPEQPAE---PQQPVPTVPSVPTIPQQ-PGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGADGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNKFTLVSAQQLSMAKQQLGLSPQDSLGTRSKAIGIARNVG-AHYVLYSSASGNVN---APTLQMQLM---------LVQG--EIIWS-GKGAV-----S---Q-

2miiA

0.18

0.15

0.82

1.21

wPPAS

--GSHMVGQR--EPAPVEEVKPAPEQPAE---PQQPVPTVPSVPTIP-QQPGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGADGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNG---VSAQQL----SMAKQQLGLSPQDSLGTRSKAIGIA--RNVGAH-YVLYSSASGNVTLQMQLM---------LVQG--EIIWS-GKGAV-----S---Q-

2miiA

0.17

0.13

0.74

1.20

dPPAS2

---------GSHMVGQREP-APVEEVKPAPEQPAEPQQPVPTVPSVPTIPQQPGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNGKFTLV--------------------SAQQLSMAKQQ-------------------------LGLSPQDSLGTRSKAIGIARNV--GAHYVLYSSASGNVNAP

2miiA

0.19

0.14

0.73

1.06

PPAS

MVGQREP-------APVEEVKPAPEQPAE---PQQPVPTVPSVPTIP-QQPGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGADGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNGKFTLV--------------------SAQQLSMAKQQ-------------------------LGLSPQDSLGTRSKAIGIARNV--GAHYVLYSSASGNVNAP

2miiA

0.17

0.14

0.83

1.12

Env-PPAS

MVGQREP-------APVEEVKPAPEQPAE---PQQPVPTVPSVPTIP-QQPGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGADGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNKFTLVSAQQLSMAKQQLGLSPQDSLGTRSKAIGIARNVG-AHYVLYSSASGNVNA---PTLQMQLM---------LVQG--EIIWS-GKGAV---SQQ-----

4i4kA

0.15

0.08

0.54

0.97

wPPAS

-------------------------------------------------------------------------------------------------STDSITSAPDAALAAVAALPARIVAAWADHDADRFADVFA-GLF------RKGRENIRTHAAAFAGPYKGTVIGSPIDARLLGDGIALLITEGGILAPGETEASGDGAVRASWLAQDGQWRLAAYQN-SGND-

2miiA

0.16

0.13

0.83

0.88

MUSTER

MVGQREPAP----------VEEVKPAPEQPAEPQQPVPTVPSVPTIPQQPGPIEHED-QTAPPAPHIRHYDWNGAMQPMVSKMLGADGVTAGSVLLVDSVNNRTNGSLN---AAEATETLRNALANNKFTLVSAQQLSMAKQQLGLSPQDSLGTRSKAIGIARNVG-AHYVLYSSASGNVN---APTLQMQLM----LVQTGEISGKGAVSQQ-----------------

2miiA

0.08

0.07

0.84

0.89

dPPAS

------------GSHMVGQREPAPVEEVKPAPEQPAEPQQPVPTVPSVPTIPQQPGPIEHEDQTAPPAPHIRHYDWNGAMQPMVSKMLGADGVVLLVDSVNNRTNGSLNAAEATETLRNALANNGKFTLVSAQQLSM--AKQQLGLSPQDSLGTRSKAIGIARNVGAH---YVLYSSASGNVNAPTLQMQLMLVQTGEIIWSGKGAVSQQ--------------------

2miiA

0.13

0.10

0.78

0.93

wdPPAS

--GSHMVGQR--EPAPVEEVKPAPEQPAE---PQQPVPTVPSVPTIPQQPGPIEHEDQTAPPAPHIRH---------WNGAMQPMVSKMLGAVLLVDSVNNRTNGSLNAAEATETLRNALANNVSAQQLSMAKQQL--GLS-------PQDSLGTRSKAIGIARNVGAHYVLYSSASGNVN---APTLQMQLMLVQTGE-----SGKGAVSQQ-----------------

4i4kA

0.14

0.08

0.54

0.77

wMUSTER

--------------------------------------------------------------------------------------------------TDSITSAPDAALAAVAALPARIVAAWADHDADRFADVFA-GTI----LFRKGRENIRTHAAAFAGPYKGTVIGSPIDARLLGDGIALLITEGGILAPGETEASGDGAVRASWLAQDGQWRLAAYQN-RGND-

(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=-2.84

Estimated TM-score = 0.39±0.13

Estimated RMSD = 12.3±4.4Å

Download Model 2

C-score=-3.86

Download Model 3

C-score=-3.98

Download Model 4

C-score=-4.55

Download Model 5

C-score=-3.48

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	2miiA	0.719	2.73	0.144	0.839
2	4q6lA	0.484	2.75	0.135	0.574
3	4zhjA	0.456	5.46	0.063	0.735
4	5a22A	0.451	5.29	0.053	0.722
5	4xqkA3	0.421	4.96	0.062	0.639
6	4ihqA	0.418	5.31	0.029	0.656
7	4eu3A	0.416	4.58	0.043	0.604
8	3jvvA	0.415	5.23	0.073	0.643
9	1p9wA	0.413	5.28	0.037	0.648
10	2fuvA	0.412	4.63	0.067	0.609

(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	0.08	4	4eneA	DMU	Rep, Mult	117,121
2	0.06	3	2axtH	CLA	Rep, Mult	120,121,124
3	0.04	2	2ewwA	ATP	Rep, Mult	75,108,113,114,115,177,185
4	0.04	2	2qveA	247	Rep, Mult	64,67,70
5	0.04	2	1iuqA	GOL	Rep, Mult	99,100,102,110,113,114,117
6	0.02	1	3s23A	XE	Rep, Mult	84,95,128,130,172,192
7	0.02	1	1e4mM	SO4	Rep, Mult	70,75,126
8	0.02	1	4fevD	KAN	Rep, Mult	24,25
9	0.02	1	1foaA	MN	Rep, Mult	98,174
10	0.02	1	2z51A	MG	Rep, Mult	135,169
11	0.02	1	3thrB	C2F	Rep, Mult	175,177,187,189
12	0.02	1	3k7tA	GP7	Rep, Mult	59,60
13	0.02	1	1aiyB	III	Rep, Mult	85,86
14	0.02	1	2gyqA	ZN	Rep, Mult	72,175
15	0.02	1	3g0kA	CA	Rep, Mult	105,110
16	0.02	1	1bk5B	CO	Rep, Mult	139,159
17	0.02	1	3f8hA	CA	Rep, Mult	128,130
18	0.02	1	2rlfB	RIM	Rep, Mult	124,128

	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	2p0uA	0.389	5.10	0.034	0.600	2.3.1.74	NA
2	0.060	2ffvA	0.396	5.21	0.053	0.609	2.4.1.41	NA
3	0.060	1kfqB	0.384	4.36	0.053	0.539	5.4.2.2	NA
4	0.060	1wznA	0.383	4.90	0.094	0.565	2.1.1.-	NA
5	0.060	2pffA	0.384	5.23	0.051	0.604	2.3.1.41,2.3.1.86	NA
6	0.060	1bi5A	0.387	5.01	0.034	0.587	2.3.1.74	NA
7	0.060	1z1eA	0.387	5.03	0.038	0.587	2.3.1.95	NA
8	0.060	3e1hB	0.362	4.27	0.068	0.509	2.3.1.74	115
9	0.060	1k30A	0.407	5.39	0.047	0.661	2.3.1.15	NA
10	0.060	1afwB	0.382	5.07	0.047	0.570	2.3.1.16	NA
11	0.060	2pmgB	0.395	5.09	0.059	0.600	5.4.2.2	NA
12	0.060	1gz3A	0.380	5.37	0.047	0.635	1.1.1.38	NA
13	0.060	1skaA	0.383	4.94	0.019	0.574	3.1.3.8	112,139
14	0.060	2yxnA	0.378	5.23	0.043	0.596	6.1.1.1	109,139
15	0.060	2e1pA	0.382	5.19	0.094	0.604	3.4.21.62	NA
16	0.060	2pffD	0.382	5.09	0.046	0.596	2.3.1.86	101,124,173
17	0.060	1qlvA	0.384	4.99	0.034	0.583	2.3.1.74	NA
18	0.060	2dvmA	0.381	4.99	0.078	0.587	1.1.1.38	NA
19	0.060	1qwoA	0.381	5.03	0.019	0.578	3.1.3.8	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	0.22	0.719	2.73	0.14	0.84	2miiA	GO:0008360 GO:0009252 GO:0009279 GO:0016020 GO:0030234 GO:0031241 GO:0050790
1	0.06	0.318	4.50	0.02	0.45	4r0mA	GO:0003824 GO:0008152 GO:0016740 GO:0031177
2	0.06	0.376	5.09	0.04	0.58	3h9uC	GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
3	0.06	0.312	5.57	0.06	0.51	4zhjB	GO:0009058 GO:0015995 GO:0016851
4	0.06	0.276	6.25	0.05	0.50	4yjdA	GO:0003884 GO:0005102 GO:0005741 GO:0005777 GO:0005778 GO:0005829 GO:0006562 GO:0016491 GO:0036088 GO:0042416 GO:0046416 GO:0046983 GO:0048037 GO:0055114 GO:0055130 GO:0070178 GO:0071949
5	0.06	0.311	5.20	0.05	0.49	1cvrA	GO:0004197 GO:0004198 GO:0005509 GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0009405 GO:0016787
6	0.06	0.335	4.64	0.10	0.48	1so8A	GO:0001540 GO:0003857 GO:0004303 GO:0005496 GO:0005737 GO:0005739 GO:0005759 GO:0005886 GO:0006629 GO:0007569 GO:0008033 GO:0008709 GO:0009083 GO:0016491 GO:0018454 GO:0030283 GO:0030331 GO:0033327 GO:0042802 GO:0044822 GO:0047015 GO:0051287 GO:0051289 GO:0055114 GO:0070901 GO:0090646
7	0.06	0.324	5.22	0.04	0.51	4hktB	GO:0008152 GO:0016491 GO:0050112 GO:0055114
8	0.06	0.282	6.03	0.06	0.50	4rkcA	GO:0003824 GO:0006520 GO:0008483 GO:0008793 GO:0009058 GO:0016740 GO:0030170 GO:0080130
9	0.06	0.321	5.42	0.04	0.53	1f75A	GO:0000287 GO:0004659 GO:0008834 GO:0016740 GO:0016765 GO:0046872
10	0.06	0.307	5.64	0.06	0.52	4itrA	GO:0000166 GO:0003824 GO:0004197 GO:0005524 GO:0005576 GO:0006464 GO:0006508 GO:0008152 GO:0008233 GO:0008234 GO:0009279 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0016787 GO:0018117 GO:0034260 GO:0070733
11	0.06	0.292	5.64	0.05	0.48	2f6uA	GO:0000287 GO:0002094 GO:0005737 GO:0006629 GO:0006650 GO:0008654 GO:0016740 GO:0016765 GO:0046474 GO:0046872 GO:0047294
12	0.06	0.456	5.46	0.06	0.73	4zhjA	GO:0009058 GO:0015995 GO:0016851
13	0.06	0.280	6.31	0.02	0.53	4yuub1	GO:0009507 GO:0009521 GO:0009523 GO:0009535 GO:0009536 GO:0009579 GO:0009767 GO:0009772 GO:0015979 GO:0016020 GO:0016021 GO:0016168 GO:0018298 GO:0019684 GO:0045156
14	0.06	0.260	5.06	0.02	0.40	1byeA	GO:0004364 GO:0016740
15	0.06	0.266	6.25	0.02	0.48	1izlB	GO:0009521 GO:0009523 GO:0009579 GO:0009767 GO:0009772 GO:0015979 GO:0016020 GO:0016021 GO:0016168 GO:0018298 GO:0019684 GO:0042651 GO:0045156
16	0.06	0.263	5.23	0.05	0.41	3esvF
17	0.06	0.254	5.19	0.03	0.39	1zjrA	GO:0000049 GO:0002938 GO:0003723 GO:0006396 GO:0008033 GO:0008168 GO:0008173 GO:0009020 GO:0016740 GO:0032259
18	0.06	0.227	4.45	0.03	0.33	2ybrH

Consensus prediction of GO terms

Molecular Function	GO:0098772
GO-Score	0.43
Biological Processes	GO:0009273	GO:0000270	GO:0065008	GO:0006024	GO:0044038	GO:0022604	GO:0065009
GO-Score	0.43	0.43	0.43	0.43	0.43	0.43	0.43
Cellular Component	GO:0009279	GO:0098552
GO-Score	0.43	0.43

(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.