I-TASSER results

Input Sequence in FASTA format

>protein (76 residues)
MLAGLRPSIGIVGDALDNALCETTTGPHRTECSHGSPFRSGPIRTLADLEDIASAWVEHT
CHTQQGVRIPGRLQPA

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MLAGLRPSIGIVGDALDNALCETTTGPHRTECSHGSPFRSGPIRTLADLEDIASAWVEHTCHTQQGVRIPGRLQPA
Prediction	CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Conf.Score	9888733568888746668999999998887646877667766788999999998788875664489885678999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MLAGLRPSIGIVGDALDNALCETTTGPHRTECSHGSPFRSGPIRTLADLEDIASAWVEHTCHTQQGVRIPGRLQPA
Prediction	7444144233442423321104313442312103444245542532430330014103322143144335753468
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
MLAGLRPSIGIVGDALDNALCETTTGPHRTECSHGSPFRSGPIRTLADLEDIASAWVEHTCHTQQGVRIPGRLQPA

4tq1B

0.09

0.04

0.42

1.62

dPPAS2

-----------QTAAWRKQIFQQLTERTKRELENFRHYEQAVE---------------------------------

2kegA

0.06

0.03

0.42

1.31

dPPAS2

--------RRSRKNGIGYAIGYAFGAVERAVLGGSRDYNK------------------------------------

2lpeA1

0.12

0.97

MUSTER

MDGGAGAAVSRA-QCGQQKLIDISIGSLRGLRTKCSVSNDLTQQEIRTLEAKLVKYICKQQQSKLS-VTPSDRTAE

4tq1B

0.09

0.04

0.42

0.88

dPPAS

-----------QTAAWRKQIFQQLTERTKRELENFRHYEQAVE---------------------------------

2xnsC

0.10

0.05

0.51

0.89

wdPPAS

----------------D---IEGLVELLNRVQSSGAH-DQRGLLSNEEVFRALRDFDRW-----------------

3jcaA

0.18

0.17

0.96

0.93

wMUSTER

ARWKISHVTGIPYNPQGQAIVERTHQNIKAQL--NKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTA-GPISAD

4a1qA

0.16

0.12

0.76

0.87

wPPAS

VES---KKIAKKKTAFD----EDVYHTLKLVSVYLNR------DMTEIIEEAVVMWLIQNKE-----KLPNELKPK

4xkhE

0.16

0.09

0.57

1.28

dPPAS2

-----------NGLSEDEALQRALELSLAE--AKPQVLSSQEEDDLALAQALSASE--------------------

2kw3C

0.15

0.12

0.79

0.86

PPAS

-GHG-TGSFGDRPA----TLLEQVLNQKRLSLLRS--------PEVVQFLQKQQQLLNQQVLEQRQQQFPGTSM--

2lepA

0.07

0.05

0.78

0.95

Env-PPAS

--------MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSADESQAERVRAELARFLEN-------PADLD--

(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=-2.72

Estimated TM-score = 0.40±0.13

Estimated RMSD = 9.2±4.6Å

Download Model 2

C-score=-3.35

Download Model 3

C-score=-3.32

Download Model 4

C-score=-3.70

Download Model 5

C-score=-3.96

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	4cz8A	0.636	3.00	0.068	0.947
2	4j72A	0.619	3.09	0.053	0.947
3	3lsjA2	0.612	3.10	0.111	0.895
4	5ek8A	0.603	3.28	0.066	0.908
5	4r1zA1	0.592	2.79	0.031	0.816
6	3siaA	0.591	3.64	0.039	0.961
7	3lwjA	0.586	2.77	0.103	0.855
8	2pg6A1	0.584	2.63	0.047	0.803
9	3kkcA	0.582	3.09	0.042	0.895
10	5cjeA	0.581	3.02	0.092	0.855

(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	0.12	5	3r1bC	TB2	Rep, Mult	19,23
2	0.07	3	2wpzB	CL	Rep, Mult	15,18
3	0.05	2	3a50B	VD3	Rep, Mult	16,17,20,58,61,66
4	0.05	2	2uxpB	CLM	Rep, Mult	21,24,50,57
5	0.05	2	2o011	CLA	Rep, Mult	57,58
6	0.05	2	3re7H	CU	Rep, Mult	58,62
7	0.05	2	2uxoB	TAC	Rep, Mult	23,27,57,60
8	0.02	1	4u5tA	3CG	Rep, Mult	22,29
9	0.02	1	2uxiA	G50	Rep, Mult	20,23,73
10	0.02	1	4khyA	CA	Rep, Mult	29,32
11	0.02	1	1xrmA	III	Rep, Mult	43,46

	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	1hbmA	0.537	3.11	0.069	0.803	2.8.4.1	NA
2	0.060	3i3kA	0.507	3.45	0.111	0.842	1.14.13.70	NA
3	0.060	1e6yA	0.547	3.17	0.055	0.816	2.8.4.1	57
4	0.060	1xjtA	0.521	3.09	0.058	0.776	3.2.1.17	32,41
5	0.060	3dwcB	0.523	3.52	0.103	0.842	3.4.17.19	54
6	0.060	3bowB	0.550	3.00	0.000	0.789	3.4.22.53	59
7	0.060	3d3lA	0.551	3.44	0.066	0.882	1.13.11.31	NA
8	0.060	3eifA	0.548	3.61	0.072	0.895	3.4.21.110	NA
9	0.060	2etfB	0.464	3.79	0.055	0.829	3.4.24.69	NA
10	0.060	2uvnA	0.537	3.27	0.067	0.868	1.14.-.-	NA
11	0.060	1lgfA	0.530	3.34	0.081	0.829	1.14.-.-	NA
12	0.060	1kblA	0.525	3.68	0.042	0.895	2.7.9.1	NA
13	0.060	3juvA	0.522	3.38	0.067	0.855	1.14.13.70	NA
14	0.060	1yvgA	0.556	2.86	0.122	0.816	3.4.24.68	NA
15	0.060	1z7hA	0.557	2.81	0.122	0.816	3.4.24.68	NA
16	0.060	1kywC	0.518	4.17	0.069	0.908	2.1.1.68	NA
17	0.060	3g17G	0.533	3.10	0.063	0.776	1.1.1.169	NA
18	0.060	1dmtA	0.546	3.28	0.069	0.829	3.4.24.11	59
19	0.060	1m1tA	0.521	3.57	0.068	0.829	2.3.1.9	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	0.15	0.483	3.73	0.00	0.84	3c6gB	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006766 GO:0008395 GO:0010038 GO:0010164 GO:0010212 GO:0016020 GO:0016491 GO:0016705 GO:0020037 GO:0030343 GO:0031090 GO:0036378 GO:0042359 GO:0043231 GO:0046872 GO:0055114
1	0.08	0.458	3.44	0.05	0.70	3t3zA	GO:0000139 GO:0004497 GO:0005506 GO:0005739 GO:0005783 GO:0005789 GO:0006641 GO:0006805 GO:0008202 GO:0008392 GO:0008395 GO:0010193 GO:0010243 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016709 GO:0016712 GO:0017144 GO:0018885 GO:0018910 GO:0019373 GO:0019825 GO:0019899 GO:0020037 GO:0031090 GO:0031227 GO:0042197 GO:0042493 GO:0043231 GO:0045471 GO:0046483 GO:0046872 GO:0055114
2	0.07	0.497	3.61	0.10	0.89	3lsjA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045922
3	0.07	0.453	3.85	0.08	0.86	1ygeA	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016165 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
4	0.07	0.491	3.72	0.07	0.88	2p0mA	GO:0001503 GO:0002820 GO:0004052 GO:0005506 GO:0005546 GO:0005737 GO:0005811 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006646 GO:0008289 GO:0010811 GO:0016020 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0030282 GO:0030838 GO:0031234 GO:0034976 GO:0035358 GO:0035963 GO:0042060 GO:0043277 GO:0043651 GO:0046872 GO:0050473 GO:0051122 GO:0051213 GO:0055114 GO:0070374 GO:0071277 GO:1901074 GO:2001303
5	0.07	0.470	2.99	0.06	0.70	1z11A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0005881 GO:0008202 GO:0008389 GO:0008392 GO:0008395 GO:0009804 GO:0016020 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019373 GO:0019899 GO:0020037 GO:0031090 GO:0042738 GO:0043231 GO:0046226 GO:0046872 GO:0055114
6	0.07	0.645	2.99	0.07	0.96	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
7	0.07	0.474	3.24	0.03	0.74	2hi4A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006629 GO:0006706 GO:0006725 GO:0006778 GO:0006805 GO:0008202 GO:0009055 GO:0009403 GO:0009404 GO:0009791 GO:0009820 GO:0010033 GO:0010468 GO:0014070 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0018894 GO:0019373 GO:0019825 GO:0019899 GO:0020037 GO:0030324 GO:0031090 GO:0032259 GO:0032355 GO:0032451 GO:0032496 GO:0032787 GO:0034875 GO:0035902 GO:0042493 GO:0042737 GO:0042738 GO:0043231 GO:0045333 GO:0046483 GO:0046872 GO:0050665 GO:0055114 GO:0070330 GO:0070989 GO:0071276 GO:0071615 GO:0097267
8	0.07	0.575	3.13	0.01	0.87	4r21B	GO:0004497 GO:0004508 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0042448 GO:0046872 GO:0055114
9	0.07	0.603	3.28	0.07	0.91	5ek8A	GO:0016702 GO:0046872 GO:0055114
10	0.07	0.446	4.39	0.03	0.86	1no3A	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
11	0.07	0.399	3.64	0.04	0.62	4nreA	GO:0005506 GO:0005509 GO:0005622 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0006629 GO:0006915 GO:0008285 GO:0008289 GO:0010744 GO:0016020 GO:0016165 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0019898 GO:0030336 GO:0030850 GO:0030856 GO:0035360 GO:0036403 GO:0043651 GO:0045618 GO:0045786 GO:0045926 GO:0046872 GO:0050473 GO:0051122 GO:0051213 GO:0055114 GO:0070062 GO:0090197
12	0.07	0.559	3.38	0.07	0.88	3rdeA	GO:0001503 GO:0002820 GO:0004052 GO:0005506 GO:0005546 GO:0005737 GO:0005811 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006646 GO:0008289 GO:0010811 GO:0016020 GO:0016491 GO:0016702 GO:0019369 GO:0019372 GO:0030282 GO:0030838 GO:0031234 GO:0034976 GO:0035358 GO:0035963 GO:0042060 GO:0043277 GO:0043651 GO:0046872 GO:0050473 GO:0051213 GO:0055114 GO:0070374 GO:0071277 GO:1901074 GO:2001303
13	0.07	0.527	3.56	0.05	0.87	4r1zA	GO:0004497 GO:0004508 GO:0005506 GO:0006694 GO:0007548 GO:0016491 GO:0016705 GO:0020037 GO:0042448 GO:0046872 GO:0047006 GO:0047442 GO:0055114 GO:1903449
14	0.07	0.549	3.23	0.04	0.87	3o8yA	GO:0002526 GO:0002540 GO:0004051 GO:0005506 GO:0005615 GO:0005634 GO:0005635 GO:0005641 GO:0005737 GO:0005829 GO:0006691 GO:0006954 GO:0007584 GO:0016020 GO:0016363 GO:0016491 GO:0016702 GO:0019233 GO:0019369 GO:0019370 GO:0019372 GO:0030425 GO:0031965 GO:0042383 GO:0045907 GO:0046872 GO:0051213 GO:0055093 GO:0055114 GO:2001300
15	0.07	0.485	3.84	0.04	0.84	2vn0A	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0006082 GO:0006805 GO:0008392 GO:0008395 GO:0016020 GO:0016491 GO:0016705 GO:0017144 GO:0019373 GO:0019825 GO:0020037 GO:0031090 GO:0034875 GO:0042738 GO:0043231 GO:0046872 GO:0055114 GO:0070330 GO:0070989 GO:0097267
16	0.07	0.394	3.99	0.05	0.68	2iukA	GO:0005737 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0016702 GO:0031408 GO:0046872 GO:0051213 GO:0055114
17	0.07	0.470	3.89	0.04	0.84	3tbgA	GO:0004497 GO:0005506 GO:0005739 GO:0005783 GO:0005789 GO:0006629 GO:0006805 GO:0008144 GO:0008202 GO:0008392 GO:0008395 GO:0009804 GO:0009820 GO:0009822 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016712 GO:0017144 GO:0019369 GO:0019825 GO:0020037 GO:0031090 GO:0033076 GO:0042737 GO:0043231 GO:0046483 GO:0046872 GO:0051100 GO:0055114 GO:0070330 GO:0070989 GO:0090350
18	0.07	0.469	4.17	0.11	0.80	1n6bA	GO:0004497 GO:0005506 GO:0005783 GO:0005789 GO:0016020 GO:0016491 GO:0016705 GO:0020037 GO:0031090 GO:0043231 GO:0046872 GO:0055114 GO:0070330

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0046906	GO:0004497
GO-Score	0.53	0.43	0.43
Biological Processes	GO:0055114
GO-Score	0.32
Cellular Component	GO:0042175	GO:0044432	GO:0044425
GO-Score	0.43	0.43	0.33

(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 Rv2087

[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]