I-TASSER results

I-TASSER results for job id Rv2804c

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

Input Sequence in FASTA format

>protein (209 residues)
MHDHQVLAARHAHQGPHVLQQRPGFVAEAPRPKATPVDLLGRARQPRAGQHLPRRRAAHP
RGGHHRIQNLAVAPPHHRRQQQRGHSRRSIGSTSPSDDSASYSQRPRDVADPPVEASTLE
GQEAVVTVELGGAVVDGVDDQGAGAVVPGTGHGSDEGIEEKIATETGALLLPVERQASED
EHWDRVGSGWPRPGRDGTRIRSMLPMASA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MHDHQVLAARHAHQGPHVLQQRPGFVAEAPRPKATPVDLLGRARQPRAGQHLPRRRAAHPRGGHHRIQNLAVAPPHHRRQQQRGHSRRSIGSTSPSDDSASYSQRPRDVADPPVEASTLEGQEAVVTVELGGAVVDGVDDQGAGAVVPGTGHGSDEGIEEKIATETGALLLPVERQASEDEHWDRVGSGWPRPGRDGTRIRSMLPMASA
Prediction	CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCEEHCCCCCCCCCEEHCCCCCCCCCCHHHHHHHCCCCEEEHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHCCCCCC
Conf.Score	98656766665467874444688755578888888645445557876666777555678888754333445689864566765555566678898888776567887778888765545676578999867756556667788666568788876545666654467566544445554556655567788888887545553456679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MHDHQVLAARHAHQGPHVLQQRPGFVAEAPRPKATPVDLLGRARQPRAGQHLPRRRAAHPRGGHHRIQNLAVAPPHHRRQQQRGHSRRSIGSTSPSDDSASYSQRPRDVADPPVEASTLEGQEAVVTVELGGAVVDGVDDQGAGAVVPGTGHGSDEGIEEKIATETGALLLPVERQASEDEHWDRVGSGWPRPGRDGTRIRSMLPMASA
Prediction	74624112133245234204633412361443532324113314535335413544444454233304411223443445664445444235443565445245434533635253541644411010413211141145631203021324244641554123522100021445256563154226313433451440342144368
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCEEHCCCCCCCCCEEHCCCCCCCCCCHHHHHHHCCCCEEEHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHCCCCCC
MHDHQVLAARHAHQGPHVLQQRPGFVAEAPRPKATPVDLLGRARQPRAGQHLPRRRAAHPRGGHHRIQNLAVAPPHHRRQQQRGHSRRSIGSTSPSDDSASYSQRPRDVADPPVEASTLEGQEAVVTVELGGAVVDGVDDQGAGAVVPGTGHGSDEGIEEKIATETGALLLPVERQASEDEHWDRVGSGWPRPGRDGTRIRSMLPMASA

3gv2A

0.18

0.17

0.94

0.83

MUSTER

VQNLQ---GQMVHQSPRTLNAWVKVVEEAFSPEVIPMSALSEGATPQDLNTMLNTVGGHQAAMQETINEEAAEHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWII----LG---LNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLR--AEQASQEVKNAATETLLVQNANPDKTILKALGPGATL

1mv3A

0.16

0.14

0.89

0.70

dPPAS

------------DGSPAATPEIRVNHEPEPAGGATPGATLPKSSQLRKGPPVPPPPKHTPSKEVKQEQILSLFEDTFVPEISVTTPSQPAEASEVAGGTQPAAGAQEPGETAASEAASSSLPAVV--VETFPATVNGTVEGGSG---AGRLDLPPGFMFKVQAQKAGDVVLVIPFQN-----PEEQDEGWLMGVKESDWNQHKKLEKCR

3s27A2

0.18

0.15

0.83

0.53

wdPPAS

YTEEKR---TKFHSEIEELLYSDVENKEH-KDKKKPILFTARL-DRVKNSGLVE-TRLRELGGDRRKDNEEKAEKKYDLIEEYKLNGQ-ISSQDRVRNGELYRY--KGA--PALEATVVEG--PTFATCKGG-PAEIIVHGKSGFHIDP---YHGDQAADTLAD--------FTKCKEDPSHWDEISKG----GLQ--RIEEKY-----

3gv2A

0.18

0.17

0.93

0.73

wMUSTER

VQNLQ---GQMVHQSPRTLNAWVKVVEEAFSPEVIPMSALSEGATPQDLNTMLNTVGGHQAAMQETINEEAAE-PVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWII----LG---LNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTL---AEQASQEVKNAATETLLVQNANPDKTILKALGPGATL

2gekA1

0.30

0.20

0.68

0.53

wPPAS

--D----VASFA---D--APLLDGYPREGRT-----V-LLGRYDEPRKGMALPKLVARFPDGR---------GDEDELREQAGDLAGH-LGQVDDATKASAMRS-----ADPHLESVLVEG--AVVASDLDAVLADGD----AGRLVPV---DDADGMAAALIG----IL-------EDDQLRAGYVA-----ASE--RVR--------

2xkxA2

0.20

0.13

0.64

0.55

dPPAS2

-----------------------------------------------------------PDITTSYSQHLDNEISH----------SSYLGTDYPTAMTPTSPRRYSPVAKDLLGEEDIPREPRRIVIHLGFNIVGGEDGEGISFILAGSGEGVDRNASHEQAAIAGQVTIIAQYKPEEYS---RFEAHDLREQLMNSSLGS--GTAS-

3s27A2

0.18

0.15

0.84

0.61

PPAS

YTEEKR---TKFHSEIEELLYSDVENKEHLCKDKKKPILTARLD-RVKNSGLVE-TRLRELGGDRRKDNEEKAEKKYDLIEEYKLNGQ-ISSQDRVRNGELYRY--KGA--PALEATVVEG--PTFATCKGG-PAEIIVHGKSGFHID-PYHG--DQAADTLA---DFF----TKCKEDPSHWDEISKG----GLQ--RIEEKY-----

3c4qA2

0.25

0.20

0.82

0.61

Env-PPAS

GNDRATERSRRELGIP---LHTKAFVGRQPF-KG--PQVLIKA--------VAALFDRDP-DRNLR---VIICPTYRHMAEELGVEKRIRDPRPPSELVAVYRA--ADIV---AVPSFNESFEAVIAARVGGAVAEGE----TGLLVDG---HSPHAWADALAT-----LLDETRIRMGEDAVEHARTSWAATAA---QLSSLYNDAIA

1kanA

0.14

1.00

0.69

MUSTER

MNGPIIMTREERMKIVHEIKERIGVYGSLGRQTDGPSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQKFHDAICALIVEELFEYAGKNIRVQGPTTFLPSTVQVAMAGLHHRICYTTSASVLTAVKQSDLPSGYDHLCSGLSDSEKLLESLENFWNGIQE

3gv2A

0.16

0.15

0.93

0.68

dPPAS

QMVHQAISPRTLNAWVKVVEEKAFSPEVIPSEGATPQDLLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAP------GQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILG-------LNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLR--AEQASQEVKNAATETLLVQNANPDKTILKALGPGATL

(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=-3.25

Estimated TM-score = 0.35±0.12

Estimated RMSD = 13.1±4.1Å

Download Model 2

C-score=-3.09

Download Model 3

C-score=-4.52

Download Model 4

C-score=-4.13

Download Model 5

C-score=-5.00

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	4qlbA	0.640	3.83	0.064	0.880
2	3nazA3	0.628	3.95	0.049	0.871
3	1ygpA	0.625	4.29	0.058	0.904
4	2aw3A	0.622	4.15	0.075	0.890
5	2c4mC	0.619	4.25	0.090	0.890
6	2amvA	0.619	4.36	0.037	0.899
7	4bqeA	0.618	4.31	0.053	0.895
8	4l22A	0.616	4.34	0.053	0.899
9	4rbnA	0.613	4.40	0.111	0.890
10	3s27A	0.611	4.44	0.084	0.895

(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	0.13	8	3fs4A	OXY	Rep, Mult	2,6
2	0.06	4	1xoiB	288	Rep, Mult	7,11,107,108
3	0.05	3	2d2mB	HEM	Rep, Mult	10,14
4	0.03	2	1xp3A	ZN	Rep, Mult	152,180,182
5	0.03	2	1l5qA	CFF	Rep, Mult	19,22,24,25
6	0.03	2	1ao0A	MG	Rep, Mult	99,139,140
7	0.02	1	2atiA	IHU	Rep, Mult	36,37,38,40,41
8	0.02	1	3nb0C	G6P	Rep, Mult	4,5,7,8,11
9	0.02	1	2iegB	FRY	Rep, Mult	7,11,121
10	0.02	1	2eb1C	MG	Rep, Mult	180,184
11	0.02	1	3cemA	AVD	Rep, Mult	17,18,19,26
12	0.02	1	2phdA	FE	Rep, Mult	76,77,152
13	0.02	1	4awyB	ZN	Rep, Mult	3,4,152
14	0.02	1	3db1D	PO4	Rep, Mult	10,11,22
15	0.02	1	3v2dF	MG	Rep, Mult	42,43
16	0.02	1	2xgfA	FE2	Rep, Mult	76,77

	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	3i39X	0.493	4.70	0.071	0.756	1.2.99.2	109
2	0.060	7mdhB	0.481	4.72	0.074	0.727	1.1.1.82	NA
3	0.060	1iphA	0.504	4.54	0.119	0.751	1.11.1.6	NA
4	0.060	1sy7B	0.515	4.72	0.072	0.780	1.11.1.6	NA
5	0.060	3cf4A	0.495	4.77	0.043	0.761	1.2.99.2	NA
6	0.060	2c4mC	0.619	4.25	0.090	0.890	2.4.1.1	NA
7	0.060	2qllA	0.620	4.20	0.043	0.885	2.4.1.1	NA
8	0.060	1rzuB	0.594	4.24	0.104	0.861	2.4.1.21	NA
9	0.060	3d5tC	0.476	5.11	0.047	0.770	1.1.1.37	22
10	0.060	1y8zA	0.533	4.37	0.095	0.789	2.4.1.26	4
11	0.060	2azdB	0.621	4.24	0.086	0.890	2.4.1.1	22,121
12	0.060	1ldnA	0.474	5.12	0.053	0.770	1.1.1.27	22
13	0.060	1f0kB	0.516	4.66	0.103	0.785	2.4.1.227	7
14	0.060	1civA	0.498	5.06	0.039	0.804	1.1.1.82	NA
15	0.060	1b8pA	0.476	5.15	0.041	0.775	1.1.1.37	22
16	0.060	1gz5A	0.544	4.59	0.071	0.823	2.4.1.15	187
17	0.060	2gejA	0.550	4.28	0.145	0.794	2.4.1.57	98
18	0.060	1o6cB	0.525	4.00	0.049	0.746	5.1.3.14	NA
19	0.060	3dzcA	0.565	4.04	0.103	0.799	5.1.3.14	3

(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	0.625	4.29	0.06	0.90	1ygpA	GO:0004645 GO:0005737 GO:0005975 GO:0005977 GO:0005980 GO:0008184 GO:0016740 GO:0016757 GO:0030170
1	0.07	0.594	3.93	0.10	0.82	2bisA	GO:0004373
2	0.07	0.595	4.02	0.10	0.83	4zj8A	GO:0004373 GO:0004871 GO:0004930 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007218 GO:0007268 GO:0007631 GO:0008188 GO:0016020 GO:0016021 GO:0016499 GO:0017046 GO:0032870 GO:0042277 GO:0045187 GO:0051480 GO:1901652
3	0.07	0.592	4.03	0.11	0.83	4s0vA	GO:0004373 GO:0004871 GO:0004930 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007200 GO:0007218 GO:0007268 GO:0007631 GO:0008188 GO:0010840 GO:0016020 GO:0016021 GO:0016499 GO:0017046 GO:0022410 GO:0032870 GO:0042277 GO:0045187 GO:0051480 GO:1901652
4	0.07	0.597	4.07	0.10	0.84	2iv7A	GO:0008919 GO:0009103 GO:0009244 GO:0016740 GO:0016757
5	0.06	0.411	5.43	0.05	0.68	3wczA	GO:0006629 GO:0008202 GO:0016491 GO:0055114
6	0.06	0.629	3.91	0.06	0.87	3nazC	GO:0003824 GO:0004373 GO:0005737 GO:0005978 GO:0008152 GO:0016740 GO:0016757
7	0.06	0.640	3.80	0.06	0.88	3nb0C	GO:0003824 GO:0004373 GO:0005737 GO:0005978 GO:0008152 GO:0016740 GO:0016757
8	0.06	0.620	4.21	0.04	0.89	1fa9A	GO:0000166 GO:0002060 GO:0003824 GO:0004645 GO:0005524 GO:0005536 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0005977 GO:0005980 GO:0006015 GO:0008144 GO:0008152 GO:0008184 GO:0016208 GO:0016740 GO:0016757 GO:0019842 GO:0030170 GO:0030246 GO:0032052 GO:0042593 GO:0042803 GO:0070062 GO:0070266
9	0.06	0.616	4.34	0.05	0.90	4l22A	GO:0004645 GO:0005975 GO:0008184 GO:0016740 GO:0016757 GO:0030170
10	0.06	0.620	4.28	0.06	0.89	4bqfB	GO:0003824 GO:0004645 GO:0005737 GO:0005829 GO:0005975 GO:0005980 GO:0008152 GO:0008184 GO:0009414 GO:0009507 GO:0016740 GO:0016757 GO:0030170 GO:0046686
11	0.06	0.619	4.25	0.09	0.89	2c4mC	GO:0004645 GO:0005975 GO:0008184 GO:0016740 GO:0016757 GO:0030170
12	0.06	0.637	3.85	0.07	0.88	4qlbD	GO:0004373 GO:0005978 GO:0016740 GO:0016757
13	0.06	0.624	4.20	0.04	0.89	1e1yA	GO:0000166 GO:0003824 GO:0004645 GO:0005975 GO:0005977 GO:0008152 GO:0008184 GO:0016740 GO:0016757 GO:0030170
14	0.06	0.346	4.93	0.05	0.54	3douA	GO:0001510 GO:0005737 GO:0006364 GO:0008168 GO:0008650 GO:0016740 GO:0031167 GO:0032259
15	0.06	0.597	4.21	0.08	0.85	2r60A	GO:0005985 GO:0016157
16	0.06	0.288	6.20	0.04	0.55	3a7aA	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0006464 GO:0009249 GO:0016874 GO:0016979 GO:0018055
17	0.06	0.331	5.68	0.04	0.59	4amtA	GO:0001822 GO:0001823 GO:0002003 GO:0002016 GO:0002018 GO:0004175 GO:0004190 GO:0005102 GO:0005159 GO:0005576 GO:0005615 GO:0005622 GO:0005737 GO:0005764 GO:0005886 GO:0006508 GO:0008217 GO:0008233 GO:0008584 GO:0009755 GO:0010033 GO:0016020 GO:0016787 GO:0030163 GO:0032496 GO:0035690 GO:0035902 GO:0042493 GO:0042756 GO:0043408 GO:0048469 GO:0050435 GO:0051591 GO:0070305
18	0.06	0.316	5.36	0.05	0.53	3ec1A	GO:0005525

Consensus prediction of GO terms

Molecular Function	GO:0035251
GO-Score	0.37
Biological Processes	GO:0051480	GO:1901652	GO:0032870	GO:0045187	GO:0007268	GO:0007218	GO:0007631	GO:0005980	GO:0010840	GO:0009244	GO:0007200
GO-Score	0.13	0.13	0.13	0.13	0.13	0.13	0.13	0.07	0.07	0.07	0.07
Cellular Component	GO:0005887	GO:0005737
GO-Score	0.13	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.