I-TASSER results

I-TASSER results for job id Rv1829

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

Input Sequence in FASTA format

>protein (164 residues)
MGEVRVVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDL
IRDLIAALGHSLKEVRIVDLQEGTFYADLIFDRNIKVSARPSDSVAIALRVGVPIYVEEA
VLAQAGLLIPDESDEEATTAVREDEVEKFKEFLDSVSPDDFKAT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGEVRVVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDLIRDLIAALGHSLKEVRIVDLQEGTFYADLIFDRNIKVSARPSDSVAIALRVGVPIYVEEAVLAQAGLLIPDESDEEATTAVREDEVEKFKEFLDSVSPDDFKAT
Prediction	CEEEEEEEEEHCCCCCCEEEEEEHCCCCEEEEEEHCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCEEEEEEEEEEHCCEEEEEEEHCCCEEEHCCHCHHHHHHHHHCCCEEHCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHCCC
Conf.Score	97899999998578996799998579986899985999999999999899999986899999999998998999999998788999999988988997555589999999899888769999987987776666555555556789999999997998886579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGEVRVVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDLIRDLIAALGHSLKEVRIVDLQEGTFYADLIFDRNIKVSARPSDSVAIALRVGVPIYVEEAVLAQAGLLIPDESDEEATTAVREDEVEKFKEFLDSVSPDDFKAT
Prediction	74404044022344552100001267562100010234103301321574754432213002300641624044020342552101020205571403010000000013170102025500661424156555664554446632640461067045732678
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CEEEEEEEEEHCCCCCCEEEEEEHCCCCEEEEEEHCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCEEEEEEEEEEHCCEEEEEEEHCCCEEEHCCHCHHHHHHHHHCCCEEHCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHCCC
MGEVRVVGIRVEQPQNQPVLLLREANGDRYLPIWIGQSEAAAIALEQQGVEPPRPLTHDLIRDLIAALGHSLKEVRIVDLQEGTFYADLIFDRNIKVSARPSDSVAIALRVGVPIYVEEAVLAQAGLLIPDESDEEATTAVREDEVEKFKEFLDSVSPDDFKAT

1sj5A

0.33

0.27

0.84

3.17

MUSTER

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

7.25

dPPAS

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

6.31

wdPPAS

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

3.82

wMUSTER

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

4.67

wPPAS

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

18.10

dPPAS2

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

4.20

PPAS

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

1sj5A

0.33

0.27

0.84

4.46

Env-PPAS

MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNERDLIN--------------------------

2mr6A

0.16

0.12

0.76

0.72

MUSTER

---------------MGVVILVLTGD----------ERIAEELRKEVQKHDPNVTKDKEKVKEEIEKA-----------RKQGRPIVVFVRGGDDE---RAKDIAEYAQKEGLRVIVIEEALRKGYEDKKKKGYDVYTSRNEDEAKKKLKEALEKSGSLEHHHH

2mr6A

0.15

0.12

0.76

0.91

dPPAS

-------------------------MGVVILVLTGDERIAEELRKEVQKHDPNVTKDKEKVKEEIEKARKQGRPIVVFVRGGD--------------DERAKDIAEYAQKEGLRVIVIEEALRKGYEDKKKKGYDVYTSRNEDEAKKKLKEALEKSGSLEHHHH

(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=0.12

Estimated TM-score = 0.73±0.11

Estimated RMSD = 4.7±3.1Å

Download Model 2

C-score=-1.49

Download Model 3

C-score=-0.06

Download Model 4

C-score=-1.40

Download Model 5

C-score=-1.63

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	1sj5A	0.825	0.77	0.326	0.842
2	4zdaA	0.448	5.72	0.031	0.848
3	1itwA	0.447	5.68	0.032	0.835
4	4mruA	0.441	4.69	0.050	0.707
5	3n0qA	0.436	5.17	0.052	0.744
6	2j0kB	0.436	4.46	0.033	0.652
7	3zdtA	0.436	4.23	0.041	0.646
8	4ekuA	0.433	3.90	0.078	0.616
9	2gahA1	0.433	5.80	0.046	0.835
10	1cjyA	0.431	5.72	0.045	0.829

(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	0.06	3	4oz1A	LYS	Rep, Mult	58,106
2	0.04	2	1knyB	KAN	Rep, Mult	102,103,147,151
3	0.04	2	1t68X	NO	Rep, Mult	20,22,33
4	0.04	2	3wixC	LC3	Rep, Mult	58,61,62,65,90,97,100,103,104,107,108,115
5	0.04	2	4kahA	BYZ	Rep, Mult	59,60
6	0.04	2	4r7cC	GLY	Rep, Mult	100,101,102
7	0.04	2	1cjyA	CA	Rep, Mult	79,86,88,99
8	0.03	1	1sj50	III	Rep, Mult	54,55,56,57,58,60,61,63,64,67,68,86,95,97,98,99,100,103
9	0.02	1	2ih9A	UUU	Rep, Mult	86,88,90,97,99
10	0.02	1	1zxyD	MG	Rep, Mult	83,102
11	0.02	1	1iw7P	MG	Rep, Mult	105,109
12	0.02	1	4dwzB	ZN	Rep, Mult	143,147
13	0.02	1	4fc5F	ZN	Rep, Mult	147,150
14	0.02	1	1bjpA	OXP	Rep, Mult	85,100
15	0.02	1	1a1cB	III	Rep, Mult	35,39
16	0.02	1	2x5rA	ZN	Rep, Mult	58,92
17	0.02	1	1wuuB	MG	Rep, Mult	38,59

	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	1l9mB	0.393	5.27	0.061	0.695	2.3.2.13	NA
2	0.060	2j0kB	0.436	4.46	0.033	0.652	2.7.10.2	NA
3	0.060	2h6jH	0.400	5.32	0.092	0.707	3.4.25.1	NA
4	0.060	2j0mA	0.322	4.88	0.025	0.543	2.7.10.2	9,51
5	0.060	1cjyA	0.431	5.72	0.045	0.829	3.1.1.4,3.1.1.5	NA
6	0.060	1aorB	0.402	5.39	0.026	0.744	1.2.7.5	NA
7	0.060	2j0lA	0.323	5.14	0.063	0.555	2.7.10.2	NA
8	0.060	2e7zA	0.412	5.43	0.085	0.744	4.2.1.71	NA
9	0.060	1qdbA	0.405	5.54	0.055	0.750	1.7.2.2	111
10	0.060	1tnzL	0.400	4.98	0.022	0.665	2.5.1.59	36,86
11	0.060	2zxcA	0.397	5.57	0.021	0.720	3.5.1.23	NA
12	0.060	2vn7A	0.400	5.06	0.088	0.652	3.2.1.3	24
13	0.060	3hfaV	0.406	5.18	0.115	0.707	3.4.25.1	NA
14	0.060	2e8iA	0.406	5.35	0.030	0.726	3.5.1.46	18
15	0.060	2fp0B	0.400	5.33	0.043	0.713	3.2.1.143	126
16	0.060	2hfuA	0.399	5.37	0.052	0.707	2.7.1.36	NA
17	0.060	1gpeB	0.400	5.34	0.076	0.701	1.1.3.4	152
18	0.060	3f93A	0.414	5.71	0.065	0.793	3.2.1.-	103
19	0.060	1f13A	0.393	5.50	0.027	0.707	2.3.2.13	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	0.47	0.825	0.77	0.33	0.84	1sj5A	GO:0004518 GO:0090305
1	0.08	0.341	6.25	0.06	0.73	2bneB	GO:0000166 GO:0003824 GO:0005524 GO:0005737 GO:0005829 GO:0006221 GO:0008152 GO:0009041 GO:0016301 GO:0016310 GO:0016740 GO:0033862 GO:0042802 GO:0044210 GO:0046939
2	0.07	0.438	5.20	0.08	0.76	4qurA	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
3	0.06	0.327	5.53	0.04	0.60	4l9oA	GO:0005634 GO:0005643 GO:0005783 GO:0005789 GO:0006810 GO:0012507 GO:0015031 GO:0016020 GO:0016192 GO:0031410 GO:0051028
4	0.06	0.306	6.03	0.03	0.63	3mx3A	GO:0046872
5	0.06	0.330	5.78	0.02	0.65	1uliC	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018687 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
6	0.06	0.346	5.82	0.07	0.67	3gkqA	GO:0016491 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
7	0.06	0.301	5.96	0.05	0.60	3gl0C	GO:0005506 GO:0016491 GO:0016708 GO:0019439 GO:0046872 GO:0051536 GO:0051537 GO:0055114
8	0.06	0.447	5.68	0.03	0.84	1itwA	GO:0004450 GO:0005737 GO:0006097 GO:0006099 GO:0016491 GO:0016616 GO:0046872 GO:0055114
9	0.06	0.329	5.70	0.05	0.63	5aeuA	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018687 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
10	0.06	0.317	5.63	0.04	0.59	1l1lA	GO:0000166 GO:0003824 GO:0004748 GO:0006260 GO:0008152 GO:0008998 GO:0016491 GO:0031419 GO:0055114
11	0.06	0.343	5.83	0.05	0.66	1eg9A	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018625 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
12	0.06	0.332	5.15	0.07	0.59	2zylA	GO:0005506 GO:0006629 GO:0006694 GO:0006707 GO:0008198 GO:0008202 GO:0009405 GO:0016042 GO:0016491 GO:0036200 GO:0046872 GO:0047086 GO:0050292 GO:0051536 GO:0051537 GO:0055114 GO:0070207 GO:0070723
13	0.06	0.360	5.81	0.03	0.67	4pucB	GO:0046872
14	0.06	0.339	5.70	0.06	0.65	3en1A	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0018619 GO:0018624 GO:0019439 GO:0042184 GO:0042203 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
15	0.06	0.355	5.63	0.05	0.66	3gcfA	GO:0016491 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
16	0.06	0.447	5.01	0.07	0.75	3n0qA	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051536 GO:0051537 GO:0055114
17	0.06	0.359	6.06	0.08	0.73	2b1xA	GO:0005506 GO:0006725 GO:0016491 GO:0016705 GO:0016708 GO:0019439 GO:0046872 GO:0051213 GO:0051536 GO:0051537 GO:0055114
18	0.06	0.313	5.08	0.05	0.54	4qdfB	GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0004518
GO-Score	0.47
Biological Processes	GO:0090305
GO-Score	0.47
Cellular Component	GO:0005829	GO:0005643	GO:0005789	GO:0012507
GO-Score	0.08	0.06	0.06	0.06

(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.