I-TASSER results

Input Sequence in FASTA format

>protein (82 residues)
MSGMQTQTIERTDADERVDDGTGSDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTR
APKPGSPVCPDCKRIYDTLKKG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MSGMQTQTIERTDADERVDDGTGSDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTRAPKPGSPVCPDCKRIYDTLKKG
Prediction	CCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHCCCEEEHCCEEHCCCCCCCCCCCCCCCHHHHHHHCCCC
Conf.Score	9998875566454555556789999885767773688899887498589856768857889999999998679999986899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MSGMQTQTIERTDADERVDDGTGSDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTRAPKPGSPVCPDCKRIYDTLKKG
Prediction	8656536416455455545757676443211214454124332444302010343121443475622313504512662588
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHCCCEEEHCCEEHCCCCCCCCCCCCCCCHHHHHHHCCCC
MSGMQTQTIERTDADERVDDGTGSDTPKYFHYVKKDKIAESAVMGSHVVALCGEVFPVTRAPKPGSPVCPDCKRIYDTLKKG

2wdn4

0.32

0.11

0.34

1.27

dPPAS2

-------------------------------------------VPARIICGCGNVIE-TYSTKPEVEVCSKC----------

1v87A

0.26

0.20

0.74

1.07

dPPAS2

MEKLAVA----SGYSDMTDSKALGPMTKCSHAFHLLCLLAMYCNGN----------------KDGSLQCPSCKTIY-GEKTG

2k17A

0.22

0.17

0.79

MUSTER

GSHMAMAYVIRDE---------WGNQIWICPGCNKPD------DGSPMIG-CDDWY-IMAAPPEEMQFCPKCANKIKKDKKH

2d8sA

0.15

0.12

0.83

0.88

dPPAS

SGSSGTSITPSSQDICRICHCEGDDESPLIHFVHQACLQQWIKSSDTRCELCKYEFIMETKLSGPSSG--------------

2k17A

0.21

0.16

0.77

0.83

wdPPAS

--GSHMA-------MAYVIRDEWGNQIWICPGCNK--------DGSPMIG-CDDWY-IMAAPPEEMQFCPKCANKIKKDKKH

4tpuA

0.19

0.18

0.94

0.77

wMUSTER

ALYVSDEVIRGEKEVESIPERRPPREKREAIRAEEASRAEMMETMSKPVWRCGYLCAMDEAPG----VCPICKERFERFMH-

2k17A

0.18

0.15

0.79

0.85

wPPAS

----GSH----MAMAYVIRD-EWGNQIWICPGCNKPD------DGSPMIG-CDDWY-IMAAPPEEMQFCPKCANKIKKDKKH

2m6oA

0.29

0.10

0.34

1.01

dPPAS2

---------------------------------------------QAVEYACGHRFEMPFSVEAEIPPCKVC---------G

2k17A

0.22

0.17

0.79

0.94

PPAS

GSHMAMAYVIRDE---------WGNQIWICPGCNKPD------DGSPMIG-CDDWY-IMAAPPEEMQFCPKCANKIKKDKKH

1mulA

0.26

0.23

0.89

0.85

Env-PPAS

M--NKTQLIDVIAEKAELSKT---QAKAALEST-LAAITESLKEGDA-VQLVGGTFKVNRAEAAAVPAFVSGKALKDAVK--

(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=-3.35

Estimated TM-score = 0.34±0.12

Estimated RMSD = 10.9±4.6Å

Download Model 2

C-score=-3.34

Download Model 3

C-score=-3.62

Download Model 4

C-score=-4.30

Download Model 5

C-score=-4.68

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	3r4vA	0.541	3.54	0.078	0.927
2	4ifqA4	0.530	3.36	0.042	0.866
3	4kf8A	0.517	3.31	0.042	0.866
4	4xriA	0.507	3.53	0.029	0.842
5	1faeA	0.505	3.44	0.043	0.842
6	5ijoJ	0.504	3.29	0.029	0.854
7	2x1gF5	0.501	3.50	0.014	0.854
8	2bnxB	0.501	3.85	0.042	0.842
9	1rw9A2	0.501	3.74	0.088	0.817
10	3x17B2	0.500	3.69	0.132	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	0.27	14	2hw7A	ZN	Rep, Mult	52,69,72
2	0.12	6	4u0bK	III	Rep, Mult	76,79
3	0.04	2	3fu0A	22F	Rep, Mult	56,58,62,65,66,70
4	0.02	1	3fueA	11S	Rep, Mult	9,49,51
5	0.02	1	3obvA	SUC	Rep, Mult	38,72,73,76
6	0.02	1	4iqdA	PYR	Rep, Mult	73,74,77

	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	1h6dA	0.485	3.67	0.013	0.842	1.1.99.28	76
2	0.060	1gw6A	0.489	3.47	0.060	0.817	3.3.2.6	NA
3	0.060	2fbnA	0.463	3.59	0.074	0.829	5.2.1.8	22,25,27,48
4	0.060	2ejwA	0.460	3.92	0.059	0.805	1.1.1.3	71
5	0.060	2vn7A	0.495	3.61	0.071	0.854	3.2.1.3	NA
6	0.060	1wmdA	0.370	4.64	0.024	0.756	3.4.21.-	NA
7	0.060	2drsA	0.494	3.72	0.038	0.842	3.2.1.156	29,42,76,79
8	0.060	2o48X	0.473	3.90	0.095	0.866	1.1.1.179,1.3.1.20	NA
9	0.060	2qnoA	0.504	3.56	0.057	0.854	3.2.1.4	NA
10	0.060	3ciaA	0.467	3.74	0.090	0.817	3.4.11.-	NA
11	0.060	1j0mA	0.465	3.78	0.074	0.817	4.2.2.12	NA
12	0.060	3c5wA	0.411	4.35	0.029	0.793	3.1.3.16	47
13	0.060	1gcuA	0.471	4.01	0.101	0.902	1.3.1.24	32
14	0.060	1iwpA	0.472	4.19	0.049	0.915	4.2.1.30	NA
15	0.060	1h7aA	0.460	3.84	0.075	0.805	1.17.4.2	NA
16	0.060	1fp3A	0.464	4.25	0.042	0.854	5.1.3.8	11,43,49
17	0.060	1b41A	0.470	3.73	0.068	0.817	3.1.1.7	NA
18	0.060	1cb7B	0.460	4.26	0.038	0.866	5.4.99.1	NA
19	0.060	2vn4A	0.499	3.38	0.059	0.829	3.2.1.3	54

(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	0.07	0.391	4.30	0.03	0.78	4knhB	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
1	0.07	0.429	4.25	0.05	0.83	4n03A	GO:0006865
2	0.07	0.389	4.45	0.07	0.77	3w3zA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
3	0.07	0.430	3.96	0.03	0.79	4jlqA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
4	0.07	0.483	3.49	0.04	0.84	1ialA	GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0042826 GO:0044822
5	0.07	0.507	3.53	0.03	0.84	4xriA	GO:0005622 GO:0006886 GO:0008536
6	0.07	0.427	4.29	0.09	0.84	5cwuA	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0016020 GO:0031965 GO:0051028
7	0.07	0.469	3.93	0.03	0.84	5hb4B	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
8	0.07	0.456	3.33	0.03	0.71	3w3uA	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
9	0.06	0.435	3.96	0.06	0.84	3nd2A	GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
10	0.06	0.435	4.47	0.05	0.82	1qgkA	GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
11	0.06	0.457	3.76	0.08	0.74	3ltjA
12	0.06	0.407	4.20	0.03	0.82	5ijnD	GO:0000059 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0006406 GO:0006409 GO:0006810 GO:0006913 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0031965 GO:0034399 GO:0044611 GO:0051028 GO:0051292 GO:0075733 GO:1900034
13	0.06	0.437	3.99	0.04	0.80	1qbkB	GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
14	0.06	0.431	3.94	0.03	0.84	2q5dB	GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
15	0.06	0.421	3.98	0.10	0.80	4knhA	GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
16	0.06	0.440	3.78	0.04	0.77	5dlqA	GO:0005049 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0046827
17	0.06	0.457	3.85	0.03	0.85	4kf8B	GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
18	0.06	0.519	3.26	0.04	0.85	4kf8A	GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611

Consensus prediction of GO terms

Molecular Function	GO:0005048	GO:0022892
GO-Score	0.37	0.37
Biological Processes	GO:0006606
GO-Score	0.37
Cellular Component	GO:0043231
GO-Score	0.48

(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.

I-TASSER results for job id Rv2708c

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

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