I-TASSER results

I-TASSER results for job id Rv1341

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

Input Sequence in FASTA format

>protein (204 residues)
MALVTKLLVASRNRKKLAELRRVLDGAGLSGLTLLSLGDVSPLPETPETGVTFEDNALAK
ARDAFSATGLASVADDSGLEVAALGGMPGVLSARWSGRYGDDAANTALLLAQLCDVPDER
RGAAFVSACALVSGSGEVVVRGEWPGTIAREPRGDGGFGYDPVFVPYGDDRTAAQLSPAE
KDAVSHRGRALALLLPALRSLATG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MALVTKLLVASRNRKKLAELRRVLDGAGLSGLTLLSLGDVSPLPETPETGVTFEDNALAKARDAFSATGLASVADDSGLEVAALGGMPGVLSARWSGRYGDDAANTALLLAQLCDVPDERRGAAFVSACALVSGSGEVVVRGEWPGTIAREPRGDGGFGYDPVFVPYGDDRTAAQLSPAEKDAVSHRGRALALLLPALRSLATG
Prediction	CCCCCEEEEHCCCCHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEHCCCCEEHCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEHCCCEEEEEEEEEEEEEHCCCCCCCCCCCEEEEHCCCCCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHC
Conf.Score	999978999969975899999999765996799764556788889888999899999999999999989988997678666456999974334453899999999999999986999766679999999999699669999999899985788999999865688689998744499899987569999999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MALVTKLLVASRNRKKLAELRRVLDGAGLSGLTLLSLGDVSPLPETPETGVTFEDNALAKARDAFSATGLASVADDSGLEVAALGGMPGVLSARWSGRYGDDAANTALLLAQLCDVPDERRGAAFVSACALVSGSGEVVVRGEWPGTIAREPRGDGGFGYDPVFVPYGDDRTAAQLSPAEKDAVSHRGRALALLLPALRSLATG
Prediction	762445404034453104103510672716314134164265334162456203300230032006317100000000000302662300100211464352641043015206735364020100000000247431102132404003224264411000002057362121104672144212114005301620561378
	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

CCCCCEEEEHCCCCHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEHCCCCEEHCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEHCCCEEEEEEEEEEEEEHCCCCCCCCCCCEEEEHCCCCCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHC
MALVTKLLVASRNRKKLAELRRVLDGAGLSGLTLLSLGDVSPLPETPETGVTFEDNALAKARDAFSATGLASVADDSGLEVAALGGMPGVLSARWSGRYGDDAANTALLLAQLCDVPDERRGAAFVSACALVSGSGEVVVRGEWPGTIAREPRGDGGFGYDPVFVPYGDDRTAAQLSPAEKDAVSHRGRALALLLPALRSLATG

3tquA

0.43

0.40

0.94

4.26

MUSTER

L----EIVLASQNSSKLAEQEL-LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

7.77

dPPAS

----LEIVLASQNSSKLAEQEL-LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

6.63

wdPPAS

----LEIVLASQNSSKLAEQE--LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

5.10

wMUSTER

-----EIVLASQNSSKLAEQEL-LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

5.61

wPPAS

L----EIVLASQNSSKLAEQE--LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

10.23

dPPAS2

----LEIVLASQNSSKLAEQEL-LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

5.13

PPAS

L----EIVLASQNSSKLAEQE--LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

3tquA

0.43

0.40

0.94

6.49

Env-PPAS

L----EIVLASQNSSKLAEQEL-LRDLEIKFIPQTEFS----VPDIEETGSTFVENAIIKARHAAKQTGLPALADDSGLTIAALNSAPGVFSSRYAGKNATDAERIQKVLEALEAADDSDRSASFHCVIALENENDPLICHGVWEGEIAREPRGKNGFGYDPIFYVPSHQRTAAELDPQEKNAISHRGQALEQLSTVLTEA---

4bnqA

0.37

0.35

0.94

4.03

MUSTER

----KEIVIASNNQGKINDFKVIFPDY-----HVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTD--RRAQFVCVISMSGPDMTKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEK-N

4bnqA

0.37

0.35

0.95

7.39

dPPAS

----KEIVIASNNQGKINDFKVIFPDY-----HVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTD--RRAQFVCVISMSGPDMTKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEKNV

(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 2 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=1.74

Estimated TM-score = 0.96±0.05

Estimated RMSD = 2.0±1.6Å

Download Model 2

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	3tquA	0.918	0.96	0.427	0.941
2	2pyuA	0.906	1.33	0.441	0.956
3	1vp2A	0.837	1.77	0.326	0.917
4	2mjpA	0.830	1.59	0.264	0.892
5	4bnqA	0.828	2.33	0.363	0.946
6	2carA	0.807	2.23	0.305	0.912
7	1v7rA	0.783	2.40	0.270	0.907
8	2p5xA	0.637	3.35	0.149	0.789
9	4p0eA	0.625	3.29	0.169	0.779
10	1excA	0.624	3.34	0.125	0.774

(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	0.85	41	2q16A	ITT	Rep, Mult	11,12,13,16,48,60,76,77,78,92,93,125,158,159,160,161,181,186,187
2	0.19	8	3tquB	CA	Rep, Mult	48,76,93
3	0.07	5	2j4eD	POP	Rep, Mult	11,12,13,16,48,60,93
4	0.03	2	2j4eC	MG	Rep, Mult	46,48
5	0.01	1	2dvp0	III	Rep, Mult	52,54,82,83,85,86,122,124,126,145,167
6	0.01	1	2pyu0	III	Rep, Mult	51,52,53,54,55,58,62,85,86,124,126,134,137,139
7	0.01	1	2car0	III	Rep, Mult	48,49,50,51,59,84,85,87,91,94,95,111,112,114,117,118
8	0.01	1	1b780	III	Rep, Mult	48,49,50,59,63,84,85,87,88,91,94,111,112

	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	0.460	2pyuA	0.906	1.33	0.441	0.956	3.6.1.15	53,78,89,93,158,160,187
2	0.389	2carA	0.807	2.23	0.305	0.912	3.6.1.19	16,19,76,159,161,174,184,186
3	0.060	2vroB	0.462	5.22	0.091	0.745	1.2.1.3	NA
4	0.060	2gzmA	0.475	4.84	0.091	0.730	5.1.1.3	11
5	0.060	1b78A	0.831	1.59	0.264	0.892	3.6.1.15	16,77,92,157,161,187
6	0.060	1vp2A	0.837	1.77	0.326	0.917	3.6.1.15	13,16,53,78,89,93,125,157,160,162
7	0.060	1o9jA	0.315	6.13	0.038	0.593	1.2.1.3	13
8	0.060	1bxsA	0.460	5.21	0.067	0.730	1.2.1.36	13
9	0.060	1cddA	0.369	4.96	0.040	0.578	2.1.2.2	NA
10	0.060	1a4sA	0.464	4.95	0.071	0.711	1.2.1.8,1.2.1.3	NA
11	0.060	1escA	0.469	4.80	0.063	0.716	3.1.1.-	NA
12	0.060	1zuwC	0.463	4.94	0.090	0.726	5.1.1.3	11
13	0.060	3cmmC	0.479	5.44	0.062	0.838	6.3.2.19	NA
14	0.060	2cfiA	0.463	4.53	0.038	0.681	1.5.1.6	NA
15	0.060	1up7A	0.469	4.53	0.084	0.686	3.2.1.86	NA
16	0.060	1ortI	0.467	5.11	0.049	0.735	2.1.3.3	NA
17	0.060	1a1sA	0.468	5.00	0.088	0.745	2.1.3.3	187
18	0.060	1c2tA	0.465	4.28	0.075	0.652	2.1.2.2	NA
19	0.060	3hfsB	0.463	5.14	0.088	0.740	1.3.1.77	NA
20	0.060	2o2pA	0.466	5.00	0.088	0.726	1.5.1.6	16
21	0.060	2ve5H	0.464	4.96	0.069	0.711	1.2.1.8	60

(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	0.62	0.929	0.92	0.42	0.95	3tquA	GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
1	0.62	0.906	1.33	0.44	0.96	2pyuA	GO:0000166 GO:0000287 GO:0005829 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
2	0.50	0.831	1.59	0.26	0.89	1b78A	GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
3	0.50	0.828	2.33	0.36	0.95	4bnqA	GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
4	0.50	0.836	1.76	0.33	0.92	3s86A	GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
5	0.41	0.807	2.23	0.30	0.91	2carA	GO:0000166 GO:0005737 GO:0005829 GO:0006193 GO:0009117 GO:0009143 GO:0009204 GO:0016787 GO:0035870 GO:0036220 GO:0036222 GO:0046872 GO:0047429 GO:0051276 GO:0055086
6	0.41	0.780	2.33	0.30	0.90	2dvnA	GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
7	0.07	0.437	4.94	0.12	0.70	4bkqA	GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0051287 GO:0055114
8	0.07	0.419	5.32	0.10	0.71	4f2pB	GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
9	0.06	0.431	5.29	0.09	0.71	4gmgA	GO:0000166 GO:0016491 GO:0055114
10	0.06	0.426	5.23	0.06	0.70	2fn8A	GO:0005886 GO:0015145 GO:0015749 GO:0016021
11	0.06	0.336	6.10	0.06	0.63	5bxpA	GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0047403
12	0.06	0.372	5.39	0.05	0.63	3b50A	GO:0006810 GO:0008643 GO:0030288 GO:0042597
13	0.06	0.370	5.63	0.05	0.64	4mnpA	GO:0006810 GO:0030288
14	0.06	0.332	6.07	0.09	0.62	4qqaA	GO:0009405 GO:0015485
15	0.06	0.396	6.18	0.04	0.76	4c20B	GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
16	0.06	0.413	4.62	0.09	0.64	2gvqD	GO:0000162 GO:0000287 GO:0003824 GO:0004048 GO:0005829 GO:0008152 GO:0008652 GO:0009073 GO:0016740 GO:0016757 GO:0046872
17	0.06	0.347	6.37	0.06	0.65	3gh4A	GO:0004553 GO:0004563 GO:0005975
18	0.06	0.336	5.64	0.05	0.60	2a5jA	GO:0000139 GO:0000166 GO:0005525 GO:0005783 GO:0005789 GO:0005794 GO:0005886 GO:0006810 GO:0007264 GO:0015031 GO:0016020 GO:0016192 GO:0045921 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0017111	GO:0047429	GO:0000166	GO:0000287
GO-Score	0.98	0.98	0.98	0.62
Biological Processes	GO:0006163	GO:0009143
GO-Score	0.98	0.98
Cellular Component	GO:0005829
GO-Score	0.62

(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.