I-TASSER results

I-TASSER results for job id Rv3136A

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

Input Sequence in FASTA format

>protein (110 residues)
MGWEFGVLLILIAVLAVFLAPRLIPRGPRGDLASGTLLVTGVSPRPDAGGQQYVTIAGII
TGPTVNEYAVYQRMAVDVDQWPTVGQILPVVYSPKNPDNWTFTPNGPPVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MGWEFGVLLILIAVLAVFLAPRLIPRGPRGDLASGTLLVTGVSPRPDAGGQQYVTIAGIITGPTVNEYAVYQRMAVDVDQWPTVGQILPVVYSPKNPDNWTFTPNGPPVG
Prediction	CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEHCCCCCCCCEEEEEEEEEEHCCCCCCCEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCCEEHCCCCCCCC
Conf.Score	96679999999999999998754678888766656899998568999986589999999978989974688788875788999865666886899998567657899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MGWEFGVLLILIAVLAVFLAPRLIPRGPRGDLASGTLLVTGVSPRPDAGGQQYVTIAGIITGPTVNEYAVYQRMAVDVDQWPTVGQILPVVYSPKNPDNWTFTPNGPPVG
Prediction	64333233333333323122434345445452341302020125437752432020333042473533422331224365124314413031436426405135575588
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEHCCCCCCCCEEEEEEEEEEHCCCCCCCEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCCEEHCCCCCCCC
MGWEFGVLLILIAVLAVFLAPRLIPRGPRGDLASGTLLVTGVSPRPDAGGQQYVTIAGIITGPTVNEYAVYQRMAVDVDQWPTVGQILPVVYSPKNPDNWTFTPNGPPVG

5g25A

0.17

0.13

0.73

1.08

dPPAS2

--------QTVVREMENFMERLRQDPQGIPALCNGALALGG---KQGTCTAIPCNVAGGLACPTAGDVRAFQVVLRVEEK-----RLETVVYRPLE--------------

4bhrA

0.15

0.11

0.72

1.00

dPPAS2

----TAAQAYVRNVATAVEAERDPTTGALPQLP--QACDQFVANPP--ASVTQCNVTANNDGVNFTVTAQLGSVSFDSST----GQFSFQL-------------------

5g2fA

0.21

0.16

0.78

0.83

MUSTER

-ANLAAGQSYVRNVALALEAQRDPSTGALPTHLTDCL--SGFGQRPK------TVTACTITYL--NALDYVIEASLDGA---ALK---KVVYKSSDG---TLTSLP----

4bhrA

0.20

0.15

0.74

0.80

dPPAS

----TAAQAYVRNVATAVEAERDPTTGALPQLP--QACDQFVANPPASVTQCNVTANNDGVNFTVTAQLTYGSVSFDSST----GQFSFQL-------------------

5g25A

0.19

0.14

0.70

0.68

wdPPAS

--------QTVVREMENFMERLRQDPQGIPALCNGALALGG------KQGAIPCNVAGGLACPTAGDVRAFQVVLRVEEK-----RLETVVYRPLE--------------

5g2fA

0.22

0.16

0.75

0.80

wMUSTER

-----ANLAAGQSYVRNVALALEAQRDPSTGALP-TDCLSGFGQRPK------TVTACTITYL--NALDYVIEASLDGA---ALK---KVVYKSSDG---TLT--SLP--

2ee9A

0.32

0.19

0.59

0.67

wPPAS

----------------------------------GSSGSSGVSDKPVRKGE----ITGEVHMPSTATPEIVDTVTV-----PTVGHEMHIKYMPESP--LQFYVNYPNSG

5g2fA

0.17

0.13

0.76

0.91

dPPAS2

-----ANLAAGQSYVRNVALALEAQRDPSTGALPTHLTDSGFGQRPKT-------VTACTITY-LNALDYVIEASLDGA---ALK---KVVYKSSDG---TLTSLP----

4bhrA

0.11

0.08

0.73

0.79

PPAS

----TAAQAYVRNVATAVEAERDPTTGALPQLP--QACDQFVANPP--ASVTQCNVTAN---NDGVNFTVTAQLTYG-----------SVSFDSSTGQSFQL--------

2ciuA

0.11

0.98

0.76

Env-PPAS

DTQLFNRAVSMVEKNKDIRSLLQCDDGITKERLKAYGELITNDKRPDKEGRTHHYMRFHVESKK-KIALVHLEAKESKQNYQPDFINMYVDV-PGEKRYYLIKPKLHPVS

(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=-1.79

Estimated TM-score = 0.50±0.15

Estimated RMSD = 7.9±4.4Å

Download Model 2

C-score=-3.65

Download Model 3

C-score=-4.61

Download Model 4

C-score=-4.00

Download Model 5

C-score=-2.70

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	3kvnX2	0.621	3.46	0.108	0.891
2	1uynX	0.614	3.62	0.076	0.891
3	3ci0K1	0.581	3.76	0.079	0.900
4	3bitA2	0.568	3.66	0.051	0.836
5	2opdA	0.564	3.43	0.085	0.818
6	3aehA	0.562	3.66	0.062	0.855
7	2yijA	0.561	4.01	0.057	0.927
8	3sokA	0.556	3.74	0.060	0.864
9	2oryB	0.554	4.03	0.059	0.918
10	3cb5A	0.548	3.99	0.096	0.891

(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	0.10	5	4f8hB	LMD	Rep, Mult	12,13,16
2	0.06	3	2zc6D	III	Rep, Mult	11,36,37,38,39,41,42,43,44,46
3	0.04	2	3i2bA	MG	Rep, Mult	20,92
4	0.04	2	2h6bA	3C4	Rep, Mult	11,14
5	0.04	2	1uwcA	FER	Rep, Mult	94,99
6	0.02	1	2ogfB	OXG	Rep, Mult	10,13,44
7	0.02	1	1o7lD	CA	Rep, Mult	47,51,53
8	0.02	1	1d7bA	HEM	Rep, Mult	44,47
9	0.02	1	2hrgA	CA	Rep, Mult	34,64
10	0.02	1	1htwA	MG	Rep, Mult	41,47
11	0.02	1	3rbxC	CA	Rep, Mult	77,82
12	0.02	1	1smyF	MG	Rep, Mult	15,90,91
13	0.02	1	3zweA	FUC	Rep, Mult	92,100
14	0.02	1	1vf5C	III	Rep, Mult	19,23
15	0.02	1	1uynX	CXE	Rep, Mult	55,57,59,72,74
16	0.02	1	3zw2B	UUU	Rep, Mult	82,84,92,100

	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	3mr1A	0.494	3.79	0.067	0.773	3.4.11.18	NA
2	0.060	1kp0A	0.503	4.32	0.081	0.846	3.5.3.3	NA
3	0.060	1jawA	0.511	4.12	0.063	0.818	3.4.11.9	NA
4	0.060	2gk9B	0.491	4.01	0.096	0.754	2.7.1.149,2.7.1.68	NA
5	0.060	2oknA	0.499	4.27	0.071	0.836	3.4.13.9	NA
6	0.060	2p3nA	0.512	4.20	0.097	0.864	3.1.3.25	NA
7	0.060	1pv9B	0.497	3.87	0.044	0.782	3.4.13.9	NA
8	0.060	1bo1A	0.503	3.67	0.058	0.746	2.7.1.149	NA
9	0.060	1dt5C	0.503	3.98	0.065	0.809	3.1.1.3	31,71
10	0.060	2dfiA	0.496	4.21	0.063	0.818	3.4.11.18	NA
11	0.060	3b9jJ	0.398	4.58	0.009	0.718	1.17.1.4,1.17.3.2	NA
12	0.060	2q4iC	0.496	3.96	0.061	0.800	5.3.99.6	57
13	0.060	4matA	0.504	3.72	0.079	0.773	3.4.11.18	NA
14	0.060	3hriA	0.499	4.34	0.042	0.864	6.1.1.21	NA
15	0.060	1rp5A	0.506	4.69	0.102	0.927	3.4.-.-	NA
16	0.060	2e1qA	0.392	4.31	0.028	0.673	1.17.3.2,1.17.1.4	NA
17	0.060	1m0wA	0.494	4.25	0.018	0.818	6.3.2.3	NA
18	0.060	1fo4A	0.395	4.39	0.009	0.682	1.17.1.4	NA
19	0.060	2v2fF	0.483	4.58	0.067	0.900	3.4.16.4	16

(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	0.08	0.621	3.46	0.11	0.89	3kvnX	GO:0006629 GO:0008610 GO:0009247 GO:0009279 GO:0016020 GO:0016021 GO:0016298 GO:0016787 GO:0016788 GO:0042710 GO:0044010 GO:0048870 GO:0052689 GO:0071973 GO:0071978
1	0.07	0.614	3.62	0.08	0.89	1uynX	GO:0004252 GO:0006508
2	0.07	0.570	3.38	0.12	0.81	3ci0K	GO:0005886 GO:0006810 GO:0009306 GO:0016020 GO:0016021 GO:0046872
3	0.07	0.458	4.44	0.04	0.80	3q6dA	GO:0006508 GO:0016787 GO:0016805 GO:0046872 GO:0102009
4	0.07	0.471	4.20	0.13	0.79	2zsgA	GO:0004177 GO:0006508 GO:0016787 GO:0046872
5	0.07	0.487	4.04	0.08	0.78	2howA	GO:0016787
6	0.07	0.480	4.40	0.07	0.86	3pgrA	GO:0006810 GO:0006869 GO:0009279 GO:0015483 GO:0015718 GO:0015909 GO:0016020 GO:0016021 GO:0022834 GO:0055085
7	0.07	0.530	3.99	0.06	0.87	5e5bA	GO:0005634 GO:0005654 GO:0005694 GO:0006260 GO:0006281 GO:0006337 GO:0006351 GO:0006355 GO:0006366 GO:0006368 GO:0006974 GO:0032786 GO:0044822 GO:1901796
8	0.07	0.492	4.21	0.06	0.84	4fkcA	GO:0004177 GO:0006508 GO:0016787 GO:0046872
9	0.06	0.415	3.09	0.05	0.58	1tbuB	GO:0005777 GO:0006635 GO:0006637 GO:0016290 GO:0016787 GO:0019395 GO:0047617 GO:0052689
10	0.06	0.408	4.62	0.01	0.76	4kwyA	GO:0019867 GO:0043165
11	0.06	0.498	3.82	0.06	0.78	1pv9A	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
12	0.06	0.400	4.21	0.04	0.70	1a0kA	GO:0003779 GO:0003785 GO:0005618 GO:0005634 GO:0005730 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005886 GO:0005938 GO:0008154 GO:0009506 GO:0009524 GO:0009826 GO:0010229 GO:0015629 GO:0042989 GO:0048046 GO:0048366 GO:0048527
13	0.06	0.386	3.52	0.05	0.59	3i2nA	GO:0006915 GO:0043130
14	0.06	0.480	4.38	0.06	0.88	3cb5A	GO:0000790 GO:0005634 GO:0005694 GO:0006260 GO:0006281 GO:0006334 GO:0006338 GO:0006351 GO:0006355 GO:0006368 GO:0006974 GO:0034724 GO:0035101 GO:0043486 GO:0044732
15	0.06	0.552	4.22	0.01	0.91	3bitA	GO:0000790 GO:0003682 GO:0005634 GO:0005658 GO:0005694 GO:0006260 GO:0006261 GO:0006281 GO:0006334 GO:0006351 GO:0006355 GO:0006368 GO:0006974 GO:0008023 GO:0031298 GO:0031491 GO:0034724 GO:0035101 GO:0042393 GO:0045899 GO:0060261
16	0.06	0.471	4.38	0.04	0.80	3l24B	GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
17	0.06	0.316	4.89	0.05	0.57	3lh4A	GO:0004869 GO:0005576 GO:0010466 GO:0030414 GO:2000117
18	0.06	0.387	4.63	0.05	0.73	3fcxB	GO:0005737 GO:0005788 GO:0016023 GO:0016787 GO:0016788 GO:0018738 GO:0031410 GO:0046294 GO:0047374 GO:0052689 GO:0070062 GO:1901687

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.37
Biological Processes	GO:0019538
GO-Score	0.37
Cellular Component	GO:0016021	GO:0009279	GO:0005886
GO-Score	0.14	0.08	0.07

(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.