I-TASSER results

I-TASSER results for job id Rv1830

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

Input Sequence in FASTA format

>protein (225 residues)
MTQLVTRARSARGSTLGEQPRQDQLDFADHTGTAGDGNDGAAAASGPVQPGLFPDDSVPD
ELVGYRGPSACQIAGITYRQLDYWARTSLVVPSIRSAAGSGSQRLYSFKDILVLKIVKRL
LDTGISLHNIRVAVDHLRQRGVQDLANITLFSDGTTVYECTSAEEVVDLLQGGQGVFGIA
VSGAMRELTGVIADFHGERADGGESIAAPEDELASRRKHRDRKIG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTQLVTRARSARGSTLGEQPRQDQLDFADHTGTAGDGNDGAAAASGPVQPGLFPDDSVPDELVGYRGPSACQIAGITYRQLDYWARTSLVVPSIRSAAGSGSQRLYSFKDILVLKIVKRLLDTGISLHNIRVAVDHLRQRGVQDLANITLFSDGTTVYECTSAEEVVDLLQGGQGVFGIAVSGAMRELTGVIADFHGERADGGESIAAPEDELASRRKHRDRKIG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCC
Conf.Score	998877777777877788887666777667788887777777787766556678888887777668999999989999999999987887786657888887666899999999999999998999999999999999867899998455665576787669999999999766466666478999999999975555677665556765589999999987659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTQLVTRARSARGSTLGEQPRQDQLDFADHTGTAGDGNDGAAAASGPVQPGLFPDDSVPDELVGYRGPSACQIAGITYRQLDYWARTSLVVPSIRSAAGSGSQRLYSFKDILVLKIVKRLLDTGISLHNIRVAVDHLRQRGVQDLANITLFSDGTTVYECTSAEEVVDLLQGGQGVFGIAVSGAMRELTGVIADFHGERADGGESIAAPEDELASRRKHRDRKIG
Prediction	754435545535545445534644251445545545555544544663464125375256753403033004317034400110264310404334764444311024600420330330273614073035005304743364045231344444134244463024015544421212154115403530561455426456445444431352354446758
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCEHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCC
MTQLVTRARSARGSTLGEQPRQDQLDFADHTGTAGDGNDGAAAASGPVQPGLFPDDSVPDELVGYRGPSACQIAGITYRQLDYWARTSLVVPSIRSAAGSGSQRLYSFKDILVLKIVKRLLDTGISLHNIRVAVDHLRQRGVQDLANITLFSDGTTVYECTSAEEVVDLLQGGQGVFGIAVSGAMRELTGVIADFHGERADGGESIAAPEDELASRRKHRDRKIG

3hh0A

0.18

0.11

0.58

1.40

MUSTER

--------------------------------------------------------------LAWLISEFASVGDVTVRALRYYDKINLLKPSDYTEGG---HRLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQ--RDIETEVFLRQHFQREVLLAEQERIAKVLSHDETKK--FQKEERVNVALFSSFLQTFIWEKE-------------------------

3hh0A

0.15

0.09

0.58

1.55

dPPAS

--------------------------------------------------------------LAWLISEFASVGDVTVRALRYYDKINLLKPSDYTEGGH---RLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQ-RDIETEVFLRQHFQREVLLAEQERIAKVLSHDETKKFQKEERVNVALFSSFLQTFIWEKE----------------------------

3hh0A

0.18

0.11

0.58

2.64

wdPPAS

--------------------------------------------------------------LAWLISEFASVGDVTVRALRYYDKINLLKPSDYTEGGH---RLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQ--RDIETEVFLRQHFQREVLLAEQERIAKVLSHDETKKFQKEERVN--VALFSSFLQTFIWEKE-------------------------

3hh0A

0.18

0.11

0.58

1.80

wMUSTER

---------------------------------------------------------------AWLISEFASVGDVTVRALRYYDKINLLKPSDYTEGG---HRLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQ--RDIETEVFLRQHFQREVLLAEQERIAKVLSHDETKKFQKEERVN--VALFSSFLQTFIWEKE-------------------------

3hh0A

0.18

0.11

0.58

2.99

wPPAS

--------------------------------------------------------------LAWLISEFASVGDVTVRALRYYDKINLLKPSDYTEGGH---RLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQRDIE--TEVFLRQHFQREVLLAEQERIAKVLSHDETKKFQKEERVN--VALFSSFLQTFIWEKE-------------------------

1r8dA

0.21

0.10

0.48

3.54

dPPAS2

--------------------------------------------------------------MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGY---RLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVD---------------------------------------------------

3qaoA

0.20

0.12

0.59

2.00

PPAS

--------------------------------------------------------------SNAQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNGY---RIYSEKDVDKLQQILFFKELDFPLKKIQQILDDPLFDKNVALDQRHLLIEKKQRIET-TLDLTIKNEKGEI-------------------TTNKEKFTGFDFSSNPYEEEARKL-------G

3qaoA

0.19

0.12

0.60

2.36

Env-PPAS

--------------------------------------------------------------SNAQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNGY---RIYSEKDVDKLQQILFFKELDFPLKKIQQILDDPLFDKNVALDQRHLLIEKKQRIET--LATLDLTIKNEKGEI----------------TTNKEKFTGFDFSSNPYEEEARKLW------G

3qaoA

0.19

0.11

0.58

1.34

MUSTER

--------------------------------------------------------------SNAQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNG---YRIYSEKDVDKLQQILFFKELDFPLKKIQQILDD-FDKNVALDQRHLLIEKKQRIETLATLDLTIKNEKGEI---------------------NKEKFTGFDFSSNPYEEEARKL-------G

1r8dA

0.21

0.10

0.48

1.52

dPPAS

--------------------------------------------------------------MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGY---RLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVD---------------------------------------------------

(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=-2.88

Estimated TM-score = 0.39±0.13

Estimated RMSD = 12.3±4.4Å

Download Model 2

C-score=-3.16

Download Model 3

C-score=-3.54

Download Model 4

C-score=-3.33

Download Model 5

C-score=-4.35

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	3hh0A	0.515	2.05	0.202	0.573
2	3dl8A	0.469	5.63	0.024	0.787
3	3dinA	0.469	5.75	0.033	0.791
4	3qaoA	0.457	3.32	0.135	0.582
5	1q05B	0.454	2.88	0.163	0.542
6	2cseW	0.453	5.11	0.031	0.693
7	4bedA	0.451	5.98	0.082	0.787
8	3rkoL	0.450	5.00	0.036	0.680
9	3eqxA	0.447	5.43	0.063	0.702
10	3ayfA2	0.446	4.70	0.029	0.671

(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	0.16	7	1r8dA	QNA	Rep, Mult	66,67,68,79,82,103,104
2	0.15	7	1r8dA	NUC	Rep, Mult	77,79,80,83,84,98,103,121,126,127,128
3	0.04	2	1vf5S	III	Rep, Mult	169,170
4	0.04	2	2fkwD	BCL	Rep, Mult	154,157
5	0.02	1	3n1vF	3N1	Rep, Mult	114,117,118,121,130
6	0.02	1	1r8eA	IMD	Rep, Mult	171,175
7	0.02	1	1q060	III	Rep, Mult	115,116,119,122,123,133,137,140,141,142,143,145,146,149,150,153,156,157,159,160,163,164,166,170,188,189,190
8	0.02	1	1r8d0	III	Rep, Mult	122,123,124,149,153,156,157,159,160,163,164,166,167,170,171
9	0.02	1	1r8eA	IMD	Rep, Mult	196,198,209,212
10	0.02	1	1exjA	P4P	Rep, Mult	64,94,105
11	0.02	1	2q6qA	CO	Rep, Mult	164,168
12	0.02	1	2oa6D	MG	Rep, Mult	129,133,137

	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	1fpsA	0.426	5.32	0.059	0.684	2.5.1.1,2.5.1.10	7
2	0.060	1gph1	0.409	5.38	0.055	0.658	2.4.2.14	124
3	0.060	2vn0A	0.412	5.53	0.076	0.689	1.14.14.1	NA
4	0.060	2w90B	0.414	5.06	0.068	0.622	1.1.1.44	NA
5	0.060	1og2A	0.367	5.96	0.051	0.649	1.14.14.1	NA
6	0.060	3c46B	0.419	5.60	0.033	0.671	2.7.7.6	NA
7	0.060	1n6bA	0.379	5.76	0.104	0.649	1.14.14.1	NA
8	0.060	1hm7A	0.390	5.81	0.041	0.689	4.2.3.7,4.6.1.5	NA
9	0.060	1i1iP	0.412	4.24	0.024	0.573	3.4.24.16	NA
10	0.060	3cf4A	0.441	5.86	0.072	0.782	1.2.99.2	NA
11	0.060	1kqfA	0.403	5.96	0.033	0.716	1.2.1.2	NA
12	0.060	2z8kC	0.368	5.88	0.064	0.644	2.3.2.2	NA
13	0.060	1qmgA	0.423	5.43	0.059	0.680	1.1.1.86	165
14	0.060	2f89F	0.436	5.32	0.053	0.702	2.5.1.1,2.5.1.10	NA
15	0.060	1yrlA	0.410	5.22	0.054	0.649	1.1.1.86	NA
16	0.060	3jvpD	0.414	5.78	0.056	0.724	2.7.1.16	NA
17	0.060	2e0wB	0.416	5.93	0.062	0.716	2.3.2.2	NA
18	0.060	2h1nA	0.413	5.04	0.032	0.627	3.4.24.-	NA
19	0.060	1yrlC	0.385	5.59	0.064	0.644	1.1.1.86	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	0.18	0.523	2.01	0.20	0.58	3hh0A	GO:0003677 GO:0006355
1	0.14	0.377	3.22	0.10	0.48	3gp4A	GO:0003677 GO:0006355
2	0.14	0.471	3.45	0.14	0.61	3qaoA	GO:0003677 GO:0006355
3	0.11	0.472	2.56	0.18	0.55	4wlwA	GO:0000986 GO:0001131 GO:0001204 GO:0003677 GO:0003700 GO:0005507 GO:0005737 GO:0006351 GO:0006355 GO:0045893 GO:0046872 GO:0071248
4	0.11	0.436	1.95	0.19	0.48	1r8dA	GO:0003677 GO:0005737 GO:0006351 GO:0006355
5	0.10	0.428	3.11	0.13	0.52	4ua1B	GO:0003677 GO:0006355 GO:0045340 GO:0046689
6	0.09	0.364	2.69	0.25	0.44	2vz4A	GO:0003677 GO:0006351 GO:0006355
7	0.09	0.428	3.64	0.11	0.56	3d6yA	GO:0003677 GO:0006351 GO:0006355
8	0.08	0.318	2.14	0.20	0.35	4r4eB	GO:0003677 GO:0006351 GO:0006355
9	0.06	0.412	5.74	0.03	0.69	3iqmA	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0043952 GO:0046872 GO:0065002
10	0.06	0.388	3.02	0.11	0.48	3gpvB	GO:0003677 GO:0006355
11	0.06	0.368	5.94	0.03	0.63	2fsfB	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
12	0.06	0.281	6.32	0.04	0.51	3enoA	GO:0000166 GO:0002949 GO:0003824 GO:0004222 GO:0004674 GO:0004712 GO:0005506 GO:0005524 GO:0005737 GO:0006468 GO:0006508 GO:0008033 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016746 GO:0016747 GO:0046872 GO:0061711
13	0.06	0.378	5.72	0.04	0.63	2fshA	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
14	0.06	0.379	5.67	0.01	0.64	2vdaA	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0017038 GO:0031522 GO:0042802 GO:0043952 GO:0046872 GO:0061077 GO:0065002
15	0.06	0.306	6.27	0.06	0.55	2zskA	GO:0006520 GO:0006807 GO:0008152 GO:0016855 GO:0036361
16	0.06	0.338	5.38	0.06	0.55	3b6uB	GO:0000166 GO:0003777 GO:0005524 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005873 GO:0005874 GO:0005876 GO:0005929 GO:0006890 GO:0007018 GO:0007052 GO:0007100 GO:0007368 GO:0008017 GO:0008089 GO:0008574 GO:0015630 GO:0016020 GO:0016939 GO:0017048 GO:0019886 GO:0030496 GO:0030990 GO:0032467 GO:0070062 GO:0072372 GO:0072383 GO:0090307 GO:0097542 GO:1904115
17	0.06	0.297	5.13	0.05	0.47	2gqkA	GO:0005507 GO:0005739 GO:0005743 GO:0006091 GO:0006825 GO:0006878 GO:0008535 GO:0030016 GO:0046872 GO:0072492
18	0.06	0.317	2.17	0.20	0.35	4r24B	GO:0003677 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.52
Biological Processes	GO:0006355
GO-Score	0.52
Cellular Component	GO:0044424
GO-Score	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.