I-TASSER results

I-TASSER results for job id Rv3284

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

Input Sequence in FASTA format

>protein (143 residues)
MTAPASLPAPLAEVVSDFAEVQGQDKLRLLLEFANELPALPSHLAESAMEPVPECQSPLF
LHVDASDPNRVRLHFSAPAEAPTTRGFASILAAGLDEQPAADILAVPEDFYTELGLAALI
SPLRLRGMSAMLARIKRRLREAD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTAPASLPAPLAEVVSDFAEVQGQDKLRLLLEFANELPALPSHLAESAMEPVPECQSPLFLHVDASDPNRVRLHFSAPAEAPTTRGFASILAAGLDEQPAADILAVPEDFYTELGLAALISPLRLRGMSAMLARIKRRLREAD
Prediction	CCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHCHHHCCCCCCCEEEEEEEEHCCCCEEEEEEHCCCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	99988887899999999997998999999999999799999888657554688866558999999589867999997677789999999999999599999998699999999898554895789999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTAPASLPAPLAEVVSDFAEVQGQDKLRLLLEFANELPALPSHLAESAMEPVPECQSPLFLHVDASDPNRVRLHFSAPAEAPTTRGFASILAAGLDEQPAADILAVPEDFYTELGLAALISPLRLRGMSAMLARIKRRLREAD
Prediction	86556725640550263066154640141013106614613762553554405503230102032567542202020444041021001000211473306303723351054141553034313400420052036205738
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCHHHHHCHHHCCCCCCCEEEEEEEEHCCCCEEEEEEHCCCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHC
MTAPASLPAPLAEVVSDFAEVQGQDKLRLLLEFANELPALPSHLAESAMEPVPECQSPLFLHVDASDPNRVRLHFSAPAEAPTTRGFASILAAGLDEQPAADILAVPEDFYTELGLAALISPLRLRGMSAMLARIKRRLREAD

1wloA

0.38

0.36

0.94

3.43

MUSTER

M-----VPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGGK-VRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.37

0.35

0.94

5.28

dPPAS

-----MVPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPG---VELERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.37

0.35

0.94

5.47

wdPPAS

-----MVPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.38

0.35

0.93

4.07

wMUSTER

------VPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGGK-VRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.38

0.36

0.94

4.96

wPPAS

M-----VPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.37

0.35

0.94

12.09

dPPAS2

-----MVPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.38

0.36

0.94

4.11

PPAS

M-----VPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1wloA

0.38

0.36

0.94

5.92

Env-PPAS

M-----VPPKLKQALELFKSLPKELRSQVLLEYAAKVPPPPPGVE---LERVHECQTPFFVHADVEGG-KVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVLEVPPGFYRGYGLEEFFTPLRLRGLEAALLRLQAQVRKAL

1ni7A

0.26

0.98

3.24

MUSTER

MTHPFGTTVTAETLRNTFAPLQWEDKYRQLIMLGKQLPALPDELKA-QAKEIAGCENRVWLGYTVAENG--KMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVL

1ni7A

0.25

0.24

0.98

5.09

dPPAS

AGHPFGTTVTAETLRNTFAPLQWEDKYRQLIMLGKQLPALPDELKA-QAKEIAGCENRVWLGYTVAENG--KMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVL

(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 3 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=0.86

Estimated TM-score = 0.83±0.08

Estimated RMSD = 3.0±2.1Å

Download Model 2

C-score=-0.16

Download Model 3

C-score=0.88

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	1wloA	0.902	0.92	0.373	0.937
2	1mzgA	0.734	2.59	0.176	0.909
3	1ni7A	0.678	3.19	0.226	0.930
4	2qq4A	0.626	3.31	0.116	0.839
5	1su0B	0.622	2.85	0.103	0.818
6	1xjsA	0.593	3.62	0.105	0.818
7	4eb5C	0.591	3.22	0.103	0.804
8	2z7eB	0.591	3.23	0.095	0.804
9	1e6yA	0.539	4.31	0.070	0.839
10	3sqgA	0.529	4.61	0.078	0.874

(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	3jz0A	APC	Rep, Mult	118,124
2	0.06	3	1n38A	CH1	Rep, Mult	95,96,104,132
3	0.06	3	4bo4B	36G	Rep, Mult	84,87,88,91,127,130,131,134
4	0.04	2	4il6x	CLA	Rep, Mult	127,128
5	0.02	1	2nr9A	PA6	Rep, Mult	135,139
6	0.02	1	2h6bA	3C4	Rep, Mult	132,135
7	0.02	1	3rkoC	LFA	Rep, Mult	83,86,90,95
8	0.02	1	3zvwC	MG	Rep, Mult	51,52
9	0.02	1	3t1gA	ZN	Rep, Mult	97,102
10	0.02	1	2z51A	MG	Rep, Mult	69,97
11	0.02	1	1iw7F	MG	Rep, Mult	124,126
12	0.02	1	2bq8X	ZN	Rep, Mult	13,17
13	0.02	1	3jskD	AHZ	Rep, Mult	100,102
14	0.02	1	1e6yA	F43	Rep, Mult	35,36,37,38,86,89
15	0.02	1	4g1vA	NO2	Rep, Mult	111,132
16	0.02	1	3rl3A	MN	Rep, Mult	94,96
17	0.02	1	3s5yA	FUC	Rep, Mult	87,124

	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	3gh4A	0.491	4.70	0.055	0.846	3.2.1.52	108
2	0.060	1w07B	0.460	4.80	0.106	0.762	1.3.3.6	NA
3	0.060	1e6yA	0.539	4.31	0.070	0.839	2.8.4.1	NA
4	0.060	2ckpA	0.451	4.37	0.060	0.734	2.7.1.32	NA
5	0.060	1n1hA	0.511	4.73	0.044	0.874	2.7.7.48	NA
6	0.060	2np0A	0.399	4.92	0.039	0.699	3.4.24.69	NA
7	0.060	2fonB	0.459	4.56	0.101	0.741	1.3.3.6	NA
8	0.060	2ckpB	0.447	4.48	0.060	0.734	2.7.1.32	NA
9	0.060	1hp4A	0.498	4.71	0.061	0.860	3.2.1.52	96,97
10	0.060	1fo4A	0.468	4.16	0.057	0.727	1.17.1.4	NA
11	0.060	2pulA	0.461	4.91	0.049	0.846	2.7.1.100	NA
12	0.060	2qcxB	0.459	4.74	0.114	0.776	3.5.99.2	31,37,77,79,111
13	0.060	1p2yA	0.446	5.04	0.058	0.776	1.14.15.1	NA
14	0.060	2npxA	0.461	3.74	0.023	0.664	1.11.1.1	19,92,117
15	0.060	3b9jC	0.341	5.06	0.049	0.636	1.17.3.2,1.17.1.4	NA
16	0.060	2e1qA	0.471	4.17	0.057	0.727	1.17.3.2,1.17.1.4	NA
17	0.060	2pywA	0.469	4.66	0.076	0.804	2.7.1.100	NA
18	0.060	3bpwA	0.478	3.97	0.055	0.727	4.1.1.23	114
19	0.060	1f7uA	0.465	3.71	0.039	0.671	6.1.1.19	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	0.37	0.678	3.19	0.23	0.93	1ni7A	GO:0016226
1	0.35	0.767	2.46	0.17	0.93	3g0mA	GO:0005737 GO:0006790 GO:0016226
2	0.33	0.754	2.55	0.16	0.93	1mzgA	GO:0005737 GO:0006790 GO:0006810 GO:0006979 GO:0008047 GO:0016226 GO:0031162 GO:0043085 GO:0097163
3	0.17	0.626	3.31	0.12	0.84	2qq4A	GO:0005506 GO:0016226 GO:0046872 GO:0051536
4	0.13	0.591	3.22	0.10	0.80	4eb5C	GO:0005506 GO:0016226 GO:0046872 GO:0051536 GO:0051537
5	0.12	0.591	3.23	0.10	0.80	2z7eB	GO:0005506 GO:0005737 GO:0006879 GO:0008198 GO:0016226 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
6	0.09	0.622	2.85	0.10	0.82	1su0B	GO:0005506 GO:0016226 GO:0046872 GO:0051536
7	0.07	0.514	3.20	0.09	0.70	2kqkA	GO:0005506 GO:0005829 GO:0006879 GO:0008198 GO:0016226 GO:0036455 GO:0042802 GO:0044571 GO:0051536 GO:0051537 GO:0051539 GO:0097428
8	0.07	0.563	3.51	0.08	0.79	2azhA	GO:0005506 GO:0005737 GO:0006879 GO:0008198 GO:0016226 GO:0016740 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
9	0.07	0.522	3.56	0.07	0.76	1wfzA	GO:0005506 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006879 GO:0008198 GO:0016226 GO:0032947 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
10	0.07	0.493	3.78	0.06	0.71	1q48A	GO:0005506 GO:0005737 GO:0006879 GO:0008198 GO:0016226 GO:0036455 GO:0044571 GO:0046872 GO:0051536 GO:0051537 GO:0051539 GO:0097428
11	0.06	0.412	3.32	0.10	0.58	3r07C	GO:0000166 GO:0005524 GO:0009249 GO:0016874 GO:0016979 GO:0017118
12	0.06	0.362	5.30	0.08	0.64	2hytA	GO:0003677 GO:0006351 GO:0006355
13	0.06	0.320	5.35	0.07	0.62	2i5bA	GO:0000166 GO:0005524 GO:0008478 GO:0008972 GO:0009228 GO:0016301 GO:0016310 GO:0016740 GO:0046872
14	0.06	0.373	5.19	0.07	0.70	1zorA	GO:0004450 GO:0006099 GO:0006102 GO:0016491 GO:0016616 GO:0046872 GO:0055114
15	0.06	0.315	5.31	0.06	0.58	1ub0A	GO:0000166 GO:0005524 GO:0008972 GO:0009228 GO:0016301 GO:0016310 GO:0016740
16	0.06	0.370	4.48	0.04	0.62	1j6wA	GO:0003824 GO:0005506 GO:0009372 GO:0016829 GO:0043768 GO:0046872
17	0.06	0.299	5.92	0.06	0.62	4fxkC	GO:0001849 GO:0002376 GO:0004252 GO:0004866 GO:0005576 GO:0005615 GO:0005886 GO:0006508 GO:0006954 GO:0006956 GO:0006958 GO:0010951 GO:0030449 GO:0045087 GO:0070062 GO:0072562 GO:2000427
18	0.06	0.227	4.19	0.01	0.36	1k0vA	GO:0005507 GO:0005737 GO:0006825 GO:0030001 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0051540	GO:0046914	GO:0008047	GO:0097163
GO-Score	0.56	0.56	0.33	0.33
Biological Processes	GO:0016226	GO:0031162	GO:0006979	GO:0006810	GO:0043085
GO-Score	0.81	0.33	0.33	0.33	0.33
Cellular Component	GO:0005737
GO-Score	0.57

(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.