I-TASSER results

I-TASSER results for job id Rv0274

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

Input Sequence in FASTA format

>protein (193 residues)
MIKPHNTNTEFELGGINHVALVCSDMARTVDFYSNILGMPLIKALDLPGGQGQHFFFDAG
NGDCVAFFWFADAPDRVPGLSSPVAIPGIGDITSAVSTMNHLAFHVPAERFDAYRQRLKD
KGVRVGPVLNHDDSETQVSAVVHPGVYVRSFYFQDPDGITLEFACWTKEFTTSDAQAVPK
TAADRRPPVAADR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MIKPHNTNTEFELGGINHVALVCSDMARTVDFYSNILGMPLIKALDLPGGQGQHFFFDAGNGDCVAFFWFADAPDRVPGLSSPVAIPGIGDITSAVSTMNHLAFHVPAERFDAYRQRLKDKGVRVGPVLNHDDSETQVSAVVHPGVYVRSFYFQDPDGITLEFACWTKEFTTSDAQAVPKTAADRRPPVAADR
Prediction	CCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHHHCCEEEEEHCCCCCCCEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHHHHHHHHHHHHHHCCCEHCEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCHHHHHCCHHHCCCC
Conf.Score	9999999987655686589999799999999999987995788765899985799986799978999977898777788777777778888888888656899986878999999999999995765565688776555555677656899998899989999978999888766567656765565555689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MIKPHNTNTEFELGGINHVALVCSDMARTVDFYSNILGMPLIKALDLPGGQGQHFFFDAGNGDCVAFFWFADAPDRVPGLSSPVAIPGIGDITSAVSTMNHLAFHVPAERFDAYRQRLKDKGVRVGPVLNHDDSETQVSAVVHPGVYVRSFYFQDPDGITLEFACWTKEFTTSDAQAVPKTAADRRPPVAADR
Prediction	7454874735140421120002143053025225717425214424255361210001046311000021343464344343444344445356542101000010346104301510573606244234254544444434444431200001234433312014447044454562362157444634678
	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

CCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHHHCCEEEEEHCCCCCCCEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCHHHHHHHHHHHHHHCCCEHCEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCHHHHHCCHHHCCCC
MIKPHNTNTEFELGGINHVALVCSDMARTVDFYSNILGMPLIKALDLPGGQGQHFFFDAGNGDCVAFFWFADAPDRVPGLSSPVAIPGIGDITSAVSTMNHLAFHVPAERFDAYRQRLKDKGVRVGPVLNHDDSETQVSAVVHPGVYVRSFYFQDPDGITLEFACWTKEFTTSDAQAVPKTAADRRPPVAADR

3l7tA

0.29

0.20

0.69

2.09

MUSTER

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCGD-IELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYV--EDVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.29

0.20

0.69

3.17

dPPAS

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCG-DIELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYVE--DVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.29

0.20

0.69

3.48

wdPPAS

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCGD-IELEIFGNKLTDSNYCAPPER------ISWPREACGLRHLAFYV--EDVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.30

0.20

0.68

2.55

wMUSTER

------------LKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCGD-IELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYV--EDVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.29

0.20

0.69

3.23

wPPAS

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCG-DIELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYV--EDVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.29

0.20

0.69

4.75

dPPAS2

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCG-DIELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYVE--DVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

3l7tA

0.29

0.20

0.69

2.81

PPAS

-----------KLKAVHHVALIVSDYDKSYEFYVNQLGFEVIRENHRPKRHDYKLDLKCG-DIELEIFGNKLTDSNYCAPPERISWP------REACGLRHLAFYV--EDVEASRQELIALGIRVEEVRYDDYTGK------------KMAFFFDPDGLPLELHE----------------------------

4jh1A

0.30

0.20

0.68

3.08

Env-PPAS

M-----------LNGINHLCFSVSNLEDSIEFYEKVLEGELLVRGRK------LAYFNIC-GVWVALNEEIHIP-----------------RNEIYQSYTHIAFSVEQKDFESLLQRLEENDVHILKGRERDVRDC------------ESIYFVDPDGHKFEFHSGT--------------LQDRLNYYREDK

2rk0A

0.20

0.14

0.69

1.93

MUSTER

-----------SLSGVSHVSLTVRDLDISCRWYTEILDWKELVRG--RGDTTSFAHGVLPGGLSIVLREHDGGGTDLFDETRP--------------GLDHLSFSVESTDLDVLEERLAKAGAAFTPTQELP--------------FGWILAFRDADNIALEALGREGHHHHHH-------------------

2rk0A

0.20

0.13

0.69

3.02

dPPAS

-----------SLSGVSHVSLTVRDLDISCRWYTEILDWKELVRG--RGDTTSFAHGVLPGGLSIVLREHDGGGT--------------DLFDETRPGLDHLSFSVESTDLDVLEERLAKAGAAFTPTQELP--------------FGWILAFRDADNIALEALGREGHHHHHH-------------------

(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=-1.37

Estimated TM-score = 0.55±0.15

Estimated RMSD = 8.2±4.5Å

Download Model 2

C-score=-1.37

Download Model 3

C-score=-1.64

Download Model 4

C-score=-1.68

Download Model 5

C-score=-2.86

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	3l7tA	0.612	2.03	0.278	0.689
2	2rk0A	0.598	2.13	0.197	0.684
3	3zi1A	0.595	3.15	0.156	0.720
4	4ro6A	0.583	3.12	0.143	0.715
5	4huzA	0.583	2.71	0.123	0.684
6	1zswA	0.582	2.58	0.154	0.684
7	3oajA	0.577	2.67	0.171	0.694
8	1mpyA	0.576	2.73	0.144	0.674
9	3hpvA	0.575	2.84	0.131	0.674
10	2zi8A	0.572	3.36	0.146	0.694

(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	0.49	46	2p7pA	MN	Rep, Mult	101,152,162
2	0.03	3	2p7qC	GG6	Rep, Mult	99,101,152,162,193
3	0.02	2	2p7qF	GG6	Rep, Mult	99,101,129,135,152,162
4	0.02	2	3oa4A	ZN	Rep, Mult	18,66,101,162
5	0.01	1	2ei3A	BPY	Rep, Mult	28,32,36,123,155,156
6	0.01	1	1lqkB	PO4	Rep, Mult	101,131,152,162,185
7	0.01	1	3l7tA	ZN	Rep, Mult	18,66

	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	0.409	1lqkA	0.530	2.09	0.265	0.601	2.5.1.18	162
2	0.361	1fa7B	0.551	2.50	0.202	0.642	4.4.1.5	21,37,39,156,158,162
3	0.236	1npbA	0.527	2.78	0.248	0.622	2.5.1.18	38,104,123,156
4	0.123	2c21A	0.541	2.89	0.156	0.642	4.1.1.-	NA
5	0.093	1qipB	0.557	4.02	0.188	0.731	4.4.1.5	NA
6	0.060	3ivtB	0.414	5.35	0.055	0.705	2.3.3.14	NA
7	0.060	2j62A	0.411	5.93	0.058	0.762	3.2.1.52	NA
8	0.060	2zi8A	0.572	3.36	0.146	0.694	1.13.11.39	NA
9	0.060	3hpvA	0.575	2.84	0.131	0.674	1.13.11.2	NA
10	0.060	3ecjA	0.565	3.17	0.113	0.674	1.13.11.15	NA
11	0.060	1pj6A	0.411	5.50	0.074	0.710	1.5.3.10	NA
12	0.060	1vrqB	0.414	5.26	0.049	0.705	1.5.3.1	NA
13	0.060	3lm4D	0.565	2.90	0.112	0.663	1.13.11.2	20,102,122,124
14	0.060	3c46B	0.337	6.00	0.030	0.637	2.7.7.6	NA
15	0.060	1y56B	0.417	5.43	0.068	0.710	1.5.99.8	NA
16	0.060	1x31B	0.413	5.23	0.054	0.705	1.5.3.1	59,65
17	0.060	2p25A	0.556	2.25	0.234	0.642	4.4.1.5	NA
18	0.060	1f9zA	0.542	2.49	0.194	0.632	4.4.1.5	NA
19	0.060	1f1uA	0.565	2.93	0.119	0.663	1.13.11.15	NA
20	0.060	1lqoB	0.526	2.15	0.265	0.601	2.5.1.18	38,104,124,156,158
21	0.060	1ikpA	0.414	5.30	0.054	0.684	2.4.2.-	NA
22	0.060	1mpyA	0.576	2.73	0.144	0.674	1.13.11.2	NA
23	0.060	2uzzB	0.415	5.40	0.045	0.710	1.5.3.-	NA
24	0.060	1eilA	0.566	3.56	0.123	0.705	1.13.11.39	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	0.49	0.612	2.03	0.28	0.69	3l7tA	GO:0004462 GO:0046872
1	0.42	0.528	2.47	0.25	0.61	1r9cA	GO:0005737 GO:0046677 GO:0046872
2	0.40	0.542	2.49	0.19	0.63	1f9zA	GO:0004462 GO:0005829 GO:0016151 GO:0016829 GO:0019243 GO:0046872
3	0.36	0.508	2.84	0.18	0.61	3ey7A	GO:0003824 GO:0051213 GO:0055114
4	0.34	0.541	2.89	0.16	0.64	2c21A	GO:0004462 GO:0016829 GO:0046872
5	0.33	0.557	4.02	0.19	0.73	1qipB	GO:0004462 GO:0005737 GO:0005829 GO:0005975 GO:0006090 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0030316 GO:0043066 GO:0046872 GO:0070062
6	0.32	0.527	2.78	0.25	0.62	1npbA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
7	0.32	0.568	2.51	0.23	0.66	3kolA	GO:0004462 GO:0046872 GO:0051213 GO:0055114
8	0.29	0.556	2.25	0.23	0.64	2p25A
9	0.28	0.531	2.81	0.25	0.63	4jd1B	GO:0000287 GO:0004364 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
10	0.26	0.557	2.53	0.22	0.65	4mtsA	GO:0004462 GO:0016829 GO:0046872
11	0.26	0.498	3.05	0.17	0.61	3hnqA	GO:0009405
12	0.25	0.527	2.86	0.23	0.63	4jh1A	GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
13	0.25	0.604	2.11	0.20	0.69	2rk0A	GO:0051213 GO:0055114
14	0.24	0.510	2.90	0.18	0.62	4hc5D	GO:0051213 GO:0055114
15	0.22	0.509	2.95	0.15	0.62	3rriA	GO:0051213 GO:0055114
16	0.20	0.538	2.73	0.18	0.64	3ct8A	GO:0046872
17	0.19	0.465	2.82	0.17	0.58	3g12B	GO:0016829
18	0.18	0.558	4.02	0.18	0.73	4kykA	GO:0004462 GO:0005975 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0019243 GO:0030316 GO:0043066 GO:0046872 GO:0070062
19	0.18	0.584	3.12	0.14	0.71	5d7zA	GO:0004462 GO:0016829 GO:0046872
20	0.14	0.475	3.10	0.14	0.60	3bt3A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0043565
21	0.12	0.484	2.95	0.14	0.60	1jieA	GO:0008144 GO:0046677
22	0.07	0.577	2.67	0.17	0.69	3oajA	GO:0005737 GO:0009636 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
23	0.07	0.576	2.73	0.14	0.67	1mpyA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0042203 GO:0046872 GO:0051213 GO:0055114
24	0.07	0.544	2.51	0.26	0.64	2p7pA	GO:0005737 GO:0046677 GO:0046872
25	0.07	0.582	2.58	0.15	0.68	1zswA	GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0004462	GO:0016151	GO:0051213
GO-Score	0.80	0.40	0.36
Biological Processes	GO:0046677	GO:0019243	GO:0055114
GO-Score	0.41	0.40	0.36
Cellular Component	GO:0005829
GO-Score	0.40

(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.