I-TASSER results

I-TASSER results for job id Rv2405

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

Input Sequence in FASTA format

>protein (189 residues)
MQRFAENLVFTEAPKLVRHLQNTQETLRTIRQAVKITANIMTTAVPSPPAEIAAGRPVTS
TSCPTAARARRLVYAPDLDGRADPGEIVWTWVAYEQDPTRGKDRPVLVVGRDRSVLLGLL
VSSQERHAADRDWVGIGSGAWDYEGRESWVRLDRVLDVPEESIRREGAILEREVFDVVAA
RLRADYAWR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MQRFAENLVFTEAPKLVRHLQNTQETLRTIRQAVKITANIMTTAVPSPPAEIAAGRPVTSTSCPTAARARRLVYAPDLDGRADPGEIVWTWVAYEQDPTRGKDRPVLVVGRDRSVLLGLLVSSQERHAADRDWVGIGSGAWDYEGRESWVRLDRVLDVPEESIRREGAILEREVFDVVAARLRADYAWR
Prediction	CCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCEEEEEEEHCCCCCCCCCCEEEEEEEEHCCEEEEEEHCCCCCCCCCCCEEHCCCCCCCCCCCCCEEEEEEEEEHCHHHCEEHCCCCCHHHHHHHHHHHHHHHCCC
Conf.Score	986555544455657777657765444544556667788888888988888899998765567877776557876788999999779999976678999987547999986699899999658876789998787789999998897478866678868777555444589999999999999998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MQRFAENLVFTEAPKLVRHLQNTQETLRTIRQAVKITANIMTTAVPSPPAEIAAGRPVTSTSCPTAARARRLVYAPDLDGRADPGEIVWTWVAYEQDPTRGKDRPVLVVGRDRSVLLGLLVSSQERHAADRDWVGIGSGAWDYEGRESWVRLDRVLDVPEESIRREGAILEREVFDVVAARLRADYAWR
Prediction	655335511154004303425547524532454353445444444455556456445344454245633241311253645240000000100125776534300000002444200000001454267453106024162167335010303301504474033300314562053005203742638
	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

CCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCEEEEEEEHCCCCCCCCCCEEEEEEEEHCCEEEEEEHCCCCCCCCCCCEEHCCCCCCCCCCCCCEEEEEEEEEHCHHHCEEHCCCCCHHHHHHHHHHHHHHHCCC
MQRFAENLVFTEAPKLVRHLQNTQETLRTIRQAVKITANIMTTAVPSPPAEIAAGRPVTSTSCPTAARARRLVYAPDLDGRADPGEIVWTWVAYEQDPTRGKDRPVLVVGRDRSVLLGLLVSSQERHAADRDWVGIGSGAWDYEGRESWVRLDRVLDVPEESIRREGAILEREVFDVVAARLRADYAWR

1ne8A

0.19

0.11

0.58

1.24

MUSTER

-------------------------------------------------------------------------------LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEIDAKR-YGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.19

0.11

0.58

1.41

dPPAS

-------------------------------------------------------------------------------LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQRFSPTAIVAAITAQIQKAKLPTHVEIDAKR-YGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.20

0.12

0.58

2.29

wdPPAS

-----------------------------------------------------------------------------L--IVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEIDAKR-YGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.19

0.11

0.57

1.52

wMUSTER

--------------------------------------------------------------------------------IVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEIDAKR-YGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.22

0.12

0.56

1.75

wPPAS

-----------------------------------------------------------------------------L---VKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEI---DAKRYGRDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLAF-

1ne8A

0.21

0.12

0.57

2.89

dPPAS2

-------------------------------------------------------------------------------LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQRFSPTAIVAAITAQIQKAKLPTHVEI---DAKRYGRDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.19

0.11

0.58

1.31

PPAS

-------------------------------------------------------------------------------LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEIDAKR-YGFERDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

1ne8A

0.21

0.12

0.57

1.52

Env-PPAS

-------------------------------------------------------------------------------LIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDSPTAIVAAITAQIQKAKLPTHVEI---DAKRYGRDSVILLEQIRTIDKQRLTDKITHLDDEMMDKVDEALQISLALI

2mf2A

0.13

0.08

0.63

1.21

MUSTER

---------------------------------------------------GSSHHHHHHSQDP-----------------IRRGDVYLADLSPVQGSEQGGVRPVVIIQNDSPTVIVAAITGRINKAKIPTHVEI-EKKKYKLDKDSVILLEQIRTLDKKRLKEKLTYLSDDKMKEVDNALMISLGNA

2mf2A

0.12

0.08

0.63

1.32

dPPAS

---------------------------------------------------------GSSHHHHHHSQD-----------PIRRGDVYLADLSPVQGSEQGGVRPVVIIQKYSPTVIVAAITGRINKAKIPTHVEI-EKKKYKLDKDSVILLEQIRTLDKKRLKEKLTYLSDDKMKEVDNALMISLGLN

(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=-3.26

Estimated TM-score = 0.35±0.12

Estimated RMSD = 12.9±4.2Å

Download Model 2

C-score=-3.61

Download Model 3

C-score=-3.84

Download Model 4

C-score=-3.75

Download Model 5

C-score=-3.89

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	2mf2A	0.539	2.49	0.134	0.619
2	1ne8A	0.527	1.58	0.183	0.571
3	5ikjA	0.480	4.85	0.028	0.741
4	2c06A	0.460	2.36	0.186	0.540
5	4rmoA	0.458	2.42	0.139	0.534
6	4atoA	0.443	3.10	0.135	0.545
7	1ub4A	0.439	2.44	0.144	0.508
8	1bagA	0.432	5.30	0.057	0.730
9	5exiA	0.430	5.63	0.042	0.762
10	3hpaA	0.430	4.92	0.058	0.698

(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	2	3vub0	III	Rep, Mult	84,109,110,113,117,132,154,156,157,179,182,183,184,185,186,187
2	0.06	2	2c06A	RQA	Rep, Mult	93,95,98,100,101,102,103,104,122,131,132,148,151,153,154
3	0.06	2	3g7zB	III	Rep, Mult	83,84,87,89
4	0.06	2	1xu25	III	Rep, Mult	116,118,120,162,163,165,166
5	0.03	1	1fzfE	CA	Rep, Mult	83,85
6	0.03	1	3slpA	CA	Rep, Mult	79,86
7	0.03	1	2dsdB	MG	Rep, Mult	165,166
8	0.03	1	2xg4A	XC2	Rep, Mult	87,106,136
9	0.03	1	5cr2B	NUC	Rep, Mult	89,104,105,122,123,124,145,146,167
10	0.03	1	3attA	MG	Rep, Mult	142,144
11	0.03	1	3huzF	MG	Rep, Mult	142,151
12	0.03	1	2vk6A	MG	Rep, Mult	79,133
13	0.03	1	2pwaA	B2A	Rep, Mult	120,121,133,135,136,178
14	0.03	1	2c06B	RQA	Rep, Mult	103,104,105,123

	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	1ea0A	0.418	5.43	0.065	0.720	1.4.1.13	177
2	0.060	1k6wA	0.427	5.40	0.029	0.741	3.5.4.1	24,171
3	0.060	1jdaA	0.408	5.50	0.063	0.730	3.2.1.60	89
4	0.060	2e1pA	0.415	6.07	0.057	0.799	3.4.21.62	NA
5	0.060	1vi1A	0.413	5.74	0.070	0.757	2.3.1.-	NA
6	0.060	2vncB	0.412	5.62	0.088	0.725	3.2.1.-	NA
7	0.060	1amyA	0.419	5.60	0.075	0.746	3.2.1.1	NA
8	0.060	1bjrE	0.419	5.85	0.065	0.788	3.4.21.64	NA
9	0.060	1bh6A	0.420	5.72	0.026	0.772	3.4.21.62	NA
10	0.060	2gokA	0.422	5.58	0.089	0.762	3.5.2.7	NA
11	0.060	2puzA	0.421	5.53	0.083	0.757	3.5.2.7	NA
12	0.060	3lggA	0.427	5.59	0.059	0.751	3.5.4.4	NA
13	0.060	1meeA	0.417	5.78	0.026	0.772	3.4.21.62,3.4.21.14	NA
14	0.060	1scaA	0.416	5.75	0.047	0.767	3.4.21.62	NA
15	0.060	2vdcF	0.416	5.42	0.084	0.725	1.4.1.13	NA
16	0.060	2oodA	0.414	5.37	0.031	0.720	3.5.4.3	NA
17	0.060	3f7oA	0.414	5.77	0.073	0.751	3.4.21.-	NA
18	0.060	2vk6A	0.417	5.29	0.045	0.698	3.2.1.18	NA
19	0.060	1bagA	0.432	5.30	0.057	0.730	3.2.1.1	176

(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	0.21	0.539	2.49	0.13	0.62	2mf2A	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0090305
1	0.17	0.527	1.79	0.16	0.58	4hkeA	GO:0003677 GO:0004518 GO:0004519 GO:0016787 GO:0090305
2	0.10	0.445	2.71	0.14	0.52	5cqxB	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006402 GO:0006417 GO:0009372 GO:0016075 GO:0016787 GO:0030308 GO:0051607 GO:0090305 GO:0090502
3	0.09	0.409	2.13	0.15	0.47	3nfcA	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006351 GO:0006355 GO:0006402 GO:0006417 GO:0009372 GO:0016075 GO:0016787 GO:0030308 GO:0051607 GO:0090305 GO:0090502
4	0.09	0.460	2.36	0.19	0.54	2c06A	GO:0003677 GO:0003723 GO:0004518 GO:0004519 GO:0016787 GO:0090305
5	0.06	0.350	5.78	0.06	0.64	3p0bA	GO:0003824 GO:0003844 GO:0005975 GO:0005977 GO:0005978 GO:0016740 GO:0016757
6	0.06	0.342	6.03	0.08	0.65	2oekA	GO:0000287 GO:0008652 GO:0009086 GO:0015977 GO:0016853 GO:0016984 GO:0019284 GO:0019509 GO:0043715 GO:0046872
7	0.06	0.333	5.95	0.06	0.59	2gjlA	GO:0003824 GO:0004497 GO:0016491 GO:0018580 GO:0055114
8	0.06	0.295	6.38	0.05	0.60	2p0yA	GO:0005737 GO:0008360
9	0.06	0.336	6.27	0.04	0.66	1up6E	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0008706 GO:0016616 GO:0016787 GO:0016798 GO:0046872 GO:0055114
10	0.06	0.318	5.22	0.03	0.52	1xxpA	GO:0004721 GO:0004725 GO:0005576 GO:0006470 GO:0009405 GO:0016311 GO:0016787 GO:0016791 GO:0035335
11	0.06	0.283	5.69	0.06	0.49	2z63A	GO:0000187 GO:0001530 GO:0001875 GO:0002218 GO:0002224 GO:0002322 GO:0002376 GO:0002537 GO:0002730 GO:0002755 GO:0002756 GO:0004872 GO:0004888 GO:0005737 GO:0005886 GO:0005887 GO:0006954 GO:0006955 GO:0007165 GO:0007249 GO:0007252 GO:0009617 GO:0009897 GO:0009986 GO:0010008 GO:0010572 GO:0010628 GO:0014002 GO:0016020 GO:0016021 GO:0016046 GO:0030890 GO:0031226 GO:0031663 GO:0032496 GO:0032497 GO:0032609 GO:0032689 GO:0032700 GO:0032707 GO:0032715 GO:0032720 GO:0032722 GO:0032727 GO:0032728 GO:0032729 GO:0032732 GO:0032733 GO:0032735 GO:0032755 GO:0032757 GO:0032760 GO:0032874 GO:0034128 GO:0034142 GO:0035666 GO:0042088 GO:0042116 GO:0042346 GO:0042535 GO:0042742 GO:0043123 GO:0045084 GO:0045087 GO:0045348 GO:0045359 GO:0045416 GO:0045429 GO:0045671 GO:0045944 GO:0046330 GO:0046696 GO:0048471 GO:0050671 GO:0050702 GO:0050707 GO:0050727 GO:0050729 GO:0050829 GO:0051092 GO:0051770 GO:0060729 GO:0060907 GO:0070266 GO:0070373 GO:0070374 GO:0070430 GO:0070434 GO:0071222 GO:0071223 GO:0071260 GO:0097190 GO:1900227
12	0.06	0.339	5.52	0.06	0.58	3w8wB	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
13	0.06	0.480	4.85	0.03	0.74	5ikjA	GO:0000122 GO:0000183 GO:0000775 GO:0000781 GO:0005634 GO:0005694 GO:0006342 GO:0006351 GO:0006355 GO:0016568 GO:0016575 GO:0030466 GO:0030702 GO:0031618 GO:0031934 GO:0033553 GO:0070824 GO:1990707
14	0.06	0.300	5.24	0.06	0.51	4pdeA	GO:0003824 GO:0005737 GO:0005829 GO:0006777 GO:0006810 GO:0016783 GO:0043546 GO:0097163
15	0.06	0.349	5.90	0.08	0.65	5i6hB	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0006633 GO:0016874 GO:0046872
16	0.06	0.405	3.55	0.08	0.53	2xd0A	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0006276 GO:0006351 GO:0006355 GO:0016787 GO:0045892 GO:0051607 GO:0090305 GO:0090502
17	0.06	0.237	5.48	0.04	0.41	1dd5A	GO:0002184 GO:0005737 GO:0005829 GO:0006412 GO:0006415 GO:0043023
18	0.06	0.421	3.15	0.06	0.53	4glkA	GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005737 GO:0016787 GO:0051607 GO:0090305 GO:0090502

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0004519	GO:0003723	GO:0004540
GO-Score	0.51	0.51	0.41	0.36
Biological Processes	GO:0048523	GO:0006412	GO:0009615	GO:0016071	GO:0010608	GO:0001558	GO:0045926	GO:0006351	GO:0034248	GO:0098542	GO:0034661	GO:1903506	GO:0032268	GO:0016072	GO:0090501	GO:0002252	GO:2000112	GO:0048874
GO-Score	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36
Cellular Component
GO-Score

(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.