I-TASSER results

I-TASSER results for job id Rv1957

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

Input Sequence in FASTA format

>protein (181 residues)
MTDRTDADDLDLQRVGARLAARAQIRDIRLLRTQAAVHRAPKPAQGLTYDLEFEPAVDAD
PATISAFVVRISCHLRIQNQAADDDVKEGDTKDETQDVATADFEFAALFDYHLQEGEDDP
TEEELTAYAATTGRFALYPYIREYVYDLTGRLALPPLTLEILSRPMPVSPGAQWPATRGT
P

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTDRTDADDLDLQRVGARLAARAQIRDIRLLRTQAAVHRAPKPAQGLTYDLEFEPAVDADPATISAFVVRISCHLRIQNQAADDDVKEGDTKDETQDVATADFEFAALFDYHLQEGEDDPTEEELTAYAATTGRFALYPYIREYVYDLTGRLALPPLTLEILSRPMPVSPGAQWPATRGTP
Prediction	CCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEHCCCCCCCCCCCEEEEEHCCCCCCCCCCEEEEEEEEEEEEEEEEHCCCEHCCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9875555688999999999998543347998777764778888766657999857766776655456777666667787655544445666565545677768999999985577766689899999998687533648999999999999899987667655677788987666666899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTDRTDADDLDLQRVGARLAARAQIRDIRLLRTQAAVHRAPKPAQGLTYDLEFEPAVDADPATISAFVVRISCHLRIQNQAADDDVKEGDTKDETQDVATADFEFAALFDYHLQEGEDDPTEEELTAYAATTGRFALYPYIREYVYDLTGRLALPPLTLEILSRPMPVSPGAQWPATRGTP
Prediction	8554554443405400540163150450233314354444264654241313144516344542432313441313133453544156355764443244241302021214343557313561043027440301010202320441144361340313314431634456745556668
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEHCCCCCCCCCCCEEEEEHCCCCCCCCCCEEEEEEEEEEEEEEEEHCCCEHCCCCCCCCCCEEEEEEEEEEEEEEEHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MTDRTDADDLDLQRVGARLAARAQIRDIRLLRTQAAVHRAPKPAQGLTYDLEFEPAVDADPATISAFVVRISCHLRIQNQAADDDVKEGDTKDETQDVATADFEFAALFDYHLQEGEDDPTEEELTAYAATTGRFALYPYIREYVYDLTGRLALPPLTLEILSRPMPVSPGAQWPATRGTP

1fx3B

0.15

0.12

0.80

1.43

MUSTER

-------------------QPVLQIQRIYVKDVSFEAPNLPHFQQEWKPKLGFDLSTETTQVGDDLYEVVLNISVETTLE------------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.15

0.12

0.80

0.98

dPPAS

-------------------QPVLQIQRIYVKDVSFEAPNLPHFQQEWKPKLGFDLSTETTQVGDDLYEVVLNISVETTLE------------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.13

0.10

0.78

1.87

wdPPAS

-------------------QPVLQIQRIYVKDVSFEAPNLPHQEWKPKLGFDLSTETTQVGDD----LYEVVLNISVETTLE----------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.15

0.12

0.79

1.70

wMUSTER

-------------------QPVLQIQRIYVKDVSFEAPNLPH-QQEWKPKLGFD--LSTETTQVGDDLYEVVLNISVETTLE----------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.12

0.09

0.76

2.04

wPPAS

--------------------QVLQIQRIYVKDVSFE----FQQEWKPKLGFDLSTETTQVGDD----LYEVVLNISVETTLE----------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.14

0.11

0.78

2.04

dPPAS2

-------------------QPVLQIQRIYVKDVSFEAPNLFQQEWKPKLGFDLSTETTQVGDDLYEVVLNISVETTLE--------------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1fx3B

0.14

0.11

0.78

1.60

PPAS

-------------------QPVLQIQRIYVKDVSFEAPNLFQQEWKPKLGFDLSTETTQVGDDLYEVVLNISVETTLE--------------DSGDVAFICEVKQAGVFTIS------GLEDVQMAHCLTSQCPNMLFPYARELVSNLVNRGTFPALNLSPVNFDALFVEYMNRQQAENAE

1qynD

0.14

0.10

0.73

1.81

Env-PPAS

--------------------MTFQIQRIYTKDISFEAPNAFQKDWQPEVKLDLDTASSQLADDVYEVVLRVTVTASLG----------------EETAFLCEVQQGGIFSIA------GIEGTQMAHCLGAYCPNILFPYARECITSMVSRGTFPQLNLAPVNFDALF---MNYLQQQ---

1qynD

0.14

0.10

0.73

1.33

MUSTER

--------------------MTFQIQRIYTKDISFEAPNAPHKDWQPEVKLDLDTASSQLADD----VYEVVLRVTVTASLGE------------ETAFLCEVQQGGIFSIA------GIEGTQMAHCLGAYCPNILFPYARECITSMVSRGTFPQLNLAPVNFDALFMNYLQQQ------

1qynD

0.15

0.11

0.73

0.96

dPPAS

--------------------MTFQIQRIYTKDISFEAPNAPHKDWQPEVKLDLDTASSQLADDVYEVVLRVTVTASLG----------------EETAFLCEVQQGGIFSIA------GIEGTQMAHCLGAYCPNILFPYARECITSMVSRGTFPQLNLAPVNFDALFMNYLQQQ------

(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=-1.14

Estimated TM-score = 0.57±0.15

Estimated RMSD = 7.6±4.3Å

Download Model 2

C-score=-3.43

Download Model 3

C-score=-2.17

Download Model 4

C-score=-3.36

Download Model 5

C-score=-4.05

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	1fx3B	0.719	1.78	0.120	0.784
2	1qynD	0.682	1.51	0.143	0.735
3	2o2aB	0.494	3.05	0.084	0.608
4	2hngA	0.489	2.97	0.060	0.591
5	4wwxB	0.464	5.16	0.086	0.779
6	4r1iA	0.460	5.56	0.062	0.818
7	1f31A	0.453	4.95	0.033	0.735
8	3b4tA	0.452	4.57	0.087	0.685
9	3vuoA4	0.449	4.02	0.023	0.635
10	3tijA	0.447	4.62	0.056	0.691

(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	4	2ckjA	FES	Rep, Mult	132,133,135,163,164,165
2	0.07	3	2a4xB	BLM	Rep, Mult	143,151,158
3	0.07	3	3mflB	DHY	Rep, Mult	139,140
4	0.05	2	1i1eA	DM2	Rep, Mult	28,29,104,106,137,138
5	0.05	2	3eubS	FES	Rep, Mult	146,149,150,156,157,158
6	0.02	1	1ozbD	III	Rep, Mult	31,32,33,35,38,77,97,98,101,103
7	0.02	1	1i72B	PUT	Rep, Mult	157,160
8	0.02	1	2ow9B	CA	Rep, Mult	6,102,104
9	0.02	1	1fiqA	FAD	Rep, Mult	142,143,144,159
10	0.02	1	1d8mA	CA	Rep, Mult	6,102,104,114
11	0.02	1	2o01G	CLA	Rep, Mult	142,181
12	0.02	1	5jtpD	III	Rep, Mult	46,47,48,49,50,51,53,54,55,59,67,69,120,121,122,125,126,129,130,157,158,159,162,164,166,167

	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	3fvrA	0.424	4.95	0.049	0.668	3.1.1.6	NA
2	0.060	1fo4A	0.423	5.73	0.048	0.779	1.17.1.4	NA
3	0.060	2pywA	0.421	4.39	0.067	0.630	2.7.1.100	NA
4	0.060	1oyrD	0.442	4.54	0.052	0.668	2.7.7.56	NA
5	0.060	3dd6A	0.442	4.64	0.066	0.674	2.7.7.56	NA
6	0.060	1vlqA	0.436	5.06	0.056	0.702	3.1.1.41	NA
7	0.060	1maaD	0.325	5.46	0.060	0.575	3.1.1.7	NA
8	0.060	3b9jI	0.240	5.23	0.040	0.381	1.17.1.4,1.17.3.2	79
9	0.060	3ffzA	0.405	5.36	0.033	0.713	3.4.24.69	NA
10	0.060	1h7aA	0.401	4.53	0.093	0.619	1.17.4.2	NA
11	0.060	3btaA	0.425	4.91	0.068	0.680	3.4.24.69	NA
12	0.060	1lpaB	0.401	5.06	0.035	0.674	3.1.1.3	NA
13	0.060	1jrpB	0.412	5.22	0.036	0.702	1.17.1.4	137
14	0.060	2pplA	0.405	4.94	0.042	0.668	3.1.1.3	NA
15	0.060	1r6lA	0.430	4.55	0.096	0.652	2.7.7.56	63,110
16	0.060	1m0wA	0.406	5.67	0.058	0.757	6.3.2.3	NA
17	0.060	2oz5A	0.403	5.41	0.069	0.685	3.1.3.48	145,162
18	0.060	2vuaA	0.325	5.53	0.050	0.575	3.4.24.69	143,148
19	0.060	1clqA	0.430	4.04	0.048	0.608	2.7.7.7	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	0.30	0.682	1.51	0.14	0.73	1qynD	GO:0005737 GO:0005829 GO:0006457 GO:0006605 GO:0006810 GO:0008104 GO:0015031 GO:0043952 GO:0051082 GO:0051262 GO:0072321
1	0.25	0.719	1.78	0.12	0.78	1fx3B	GO:0005737 GO:0006457 GO:0006810 GO:0015031 GO:0051082 GO:0051262
2	0.11	0.502	2.95	0.06	0.61	2hngA	GO:0015031 GO:0051082 GO:0051262
3	0.07	0.503	3.04	0.08	0.62	2o2aB	GO:0015031 GO:0051082 GO:0051262
4	0.07	0.460	5.56	0.06	0.82	4r1iA	GO:0015558 GO:0016020 GO:0016021 GO:1902604
5	0.07	0.464	5.16	0.09	0.78	4wwxB	GO:0002250 GO:0002331 GO:0003676 GO:0003677 GO:0003824 GO:0004518 GO:0004519 GO:0004842 GO:0005634 GO:0006310 GO:0008152 GO:0008270 GO:0010390 GO:0016568 GO:0016787 GO:0016874 GO:0030183 GO:0033077 GO:0033151 GO:0042393 GO:0042803 GO:0043029 GO:0043154 GO:0043565 GO:0045580 GO:0045582 GO:0046872 GO:0048538 GO:0051865 GO:0061630 GO:0070233 GO:0070244 GO:0090305
6	0.07	0.497	5.09	0.07	0.82	3jbwA	GO:0003677 GO:0003824 GO:0004518 GO:0004519 GO:0004842 GO:0005634 GO:0006310 GO:0008152 GO:0008270 GO:0010390 GO:0016568 GO:0016787 GO:0016874 GO:0030183 GO:0033077 GO:0033151 GO:0042393 GO:0042803 GO:0043565 GO:0046872 GO:0061630 GO:0090305
7	0.07	0.470	4.69	0.05	0.73	2np0A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
8	0.07	0.427	4.19	0.02	0.63	3v0aB	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
9	0.06	0.397	5.36	0.05	0.67	3v0aA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
10	0.06	0.405	5.36	0.03	0.71	3ffzA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
11	0.06	0.435	3.70	0.02	0.61	3vuoA	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
12	0.06	0.335	5.08	0.05	0.53	4gpaA	GO:0004872 GO:0004970 GO:0004971 GO:0005216 GO:0005234 GO:0005886 GO:0006810 GO:0006811 GO:0007268 GO:0008328 GO:0014069 GO:0016020 GO:0016021 GO:0030054 GO:0030425 GO:0032281 GO:0032983 GO:0034220 GO:0035235 GO:0042995 GO:0043025 GO:0043195 GO:0045202 GO:0045211 GO:0050803 GO:0050804 GO:0051968 GO:0060992
13	0.06	0.320	5.69	0.03	0.59	3rsjA	GO:0004222 GO:0005576 GO:0006508 GO:0008270 GO:0009405 GO:0050827 GO:0051609
14	0.06	0.433	5.28	0.06	0.72	4r0cD	GO:0015558 GO:0016020 GO:0016021 GO:1902604
15	0.06	0.329	5.73	0.05	0.57	1a8dA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
16	0.06	0.299	5.61	0.06	0.54	1xtfA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
17	0.06	0.321	5.05	0.05	0.52	3npkA	GO:0004337 GO:0008299 GO:0016740
18	0.06	0.320	5.30	0.04	0.55	4xx6B	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031176

Consensus prediction of GO terms

Molecular Function	GO:0051082
GO-Score	0.56
Biological Processes	GO:0051262	GO:0006457	GO:0043952	GO:0006605	GO:0072321
GO-Score	0.56	0.48	0.30	0.30	0.30
Cellular Component	GO:0005829
GO-Score	0.30

(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.