I-TASSER results

I-TASSER results for job id Rv2240c

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

Input Sequence in FASTA format

>protein (196 residues)
MLIGWRAVPRRHGGELPRRGALALGCIALLLMGIVGCTTVTDGTAMPDTNVAPAYRSSVS
ASVSASAATSSIRESQRQQSLTTKAIRTSCDALAATSKDAIDKVNAYVAAFNQGRNTGPT
EGPAIDALNNSASTVSGSLSAALSAQLGDALNAYVDAARAVANAIGAHASTAEFNRRVDR
LNDTKTKALTMCVAAF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLIGWRAVPRRHGGELPRRGALALGCIALLLMGIVGCTTVTDGTAMPDTNVAPAYRSSVSASVSASAATSSIRESQRQQSLTTKAIRTSCDALAATSKDAIDKVNAYVAAFNQGRNTGPTEGPAIDALNNSASTVSGSLSAALSAQLGDALNAYVDAARAVANAIGAHASTAEFNRRVDRLNDTKTKALTMCVAAF
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	9876566776566776558999999999999999755655588888887674456777888899998888899999999999999999999998765778899999999975898875556689999999999988764667897899999999999999999986589877767888998899999999987659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLIGWRAVPRRHGGELPRRGALALGCIALLLMGIVGCTTVTDGTAMPDTNVAPAYRSSVSASVSASAATSSIRESQRQQSLTTKAIRTSCDALAATSKDAIDKVNAYVAAFNQGRNTGPTEGPAIDALNNSASTVSGSLSAALSAQLGDALNAYVDAARAVANAIGAHASTAEFNRRVDRLNDTKTKALTMCVAAF
Prediction	6333233024534442221102000111120000010133362634255741442344244434434444444445444424452144304423433442043024103122546735544431252045325414542456136604530440153044004214652435403523542454353026205667
	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

CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
MLIGWRAVPRRHGGELPRRGALALGCIALLLMGIVGCTTVTDGTAMPDTNVAPAYRSSVSASVSASAATSSIRESQRQQSLTTKAIRTSCDALAATSKDAIDKVNAYVAAFNQGRNTGPTEGPAIDALNNSASTVSGSLSAALSAQLGDALNAYVDAARAVANAIGAHASTAEFNRRVDRLNDTKTKALTMCVAAF

4ke2A

0.17

0.99

1.02

MUSTER

MNID--AARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAA

4ke2A

0.17

0.16

0.94

1.10

dPPAS2

------------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAA

4ke2A

0.15

0.14

0.95

1.13

PPAS

----------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAA

5cwnA

0.11

0.98

0.90

MUSTER

SLERAREASERGDEEEFRKAAEKALELAKRLVEQAK----KEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLAKKQGDEEVYEKARETAREVKEELKRVREEKGGWL

4ke2A

0.17

0.16

0.94

0.78

dPPAS

------------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAA

2oerB

0.12

0.11

0.90

0.61

wdPPAS

--------------SSELVASILEAAVQVLA----RFTARVAERAGVSIGSLYQYKAAILFRLQSDEWRRTTRLLGEILEDPLERLRRLVLAFVRSECEEAAIRVALSDAAPLYRDADEAREVKAEGARVFQAFLREALPEVAEAERSLAGDLLTTTLGAVGKQFSQPRSEAEIERYAEALADLCAYLAALGER--

4ke2A

0.18

0.17

0.97

0.88

wMUSTER

IDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALEKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP------

2dg8B

0.10

0.08

0.84

0.73

wPPAS

--------PQ-------RRERILAATLDLIAEEIARVSRRIAQRAGVPLGSMTYHIEQLLREAFGRFTDHIVAVFDEHLGARDEAREAVADLVHELSEDSQRDLVLTQELYTLA----ARQPAYRELTHEWMRRSRVHLEKHFDPGTARQLDALIEGLTLHRALAREPHGRALTLEAIARITTT------------

5cwnA

0.11

0.10

0.96

0.79

dPPAS2

LERAREASERGDEEEFRKAAEKALELAKRLVEQAKK-----EGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLAKKQGD---EEVYEKARETAREVKEELKRVREEKG

5cwbA

0.12

0.98

0.87

PPAS

--DECEEKARRVAEKVERLKRSGTSEDEIAEEVAREISEVISGSSYEVICECVARIVAEIVEALKRSGTSEDEIAEIVARVISEVIRTLKESGSSYEVICECVARIVAEIVEALKRSGTSEDEIAEIVARVISEVIRTLKESGSSYEVIKECVQRIVEEIVEALKRSGTSEDEINEIVRRVKSEVERTLKESGS--

(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=-1.08

Estimated TM-score = 0.58±0.14

Estimated RMSD = 7.6±4.3Å

Download Model 2

C-score=-3.35

Download Model 3

C-score=-3.89

Download Model 4

C-score=-4.33

Download Model 5

C-score=-4.40

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	5cwnA	0.920	1.36	0.104	0.980
2	5cwmA	0.815	2.44	0.074	0.969
3	5dlqB	0.715	3.22	0.073	0.929
4	2x1gF	0.691	3.55	0.039	0.918
5	3s4wA	0.688	3.03	0.051	0.878
6	2r17C	0.664	2.99	0.060	0.837
7	2x19B2	0.661	3.69	0.056	0.888
8	3icqT2	0.659	3.46	0.046	0.857
9	4c0oA	0.655	3.29	0.095	0.847
10	4u1dC	0.650	3.26	0.063	0.837

(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	0.05	3	2ie7A	CA	Rep, Mult	43,44
2	0.03	2	5jreH	ADE	Rep, Mult	133,134,180
3	0.03	2	5lj3S	NUC	Rep, Mult	31,33,34,51,54,102,103,106,107,153
4	0.03	2	3c9iB	XE	Rep, Mult	139,143
5	0.03	2	3ebbB	III	Rep, Mult	94,97,98,101,130,134
6	0.03	2	4ryoA	MPG	Rep, Mult	104,120,127
7	0.03	2	4tnwE	POV	Rep, Mult	159,163,174,175,178
8	0.02	1	3wguB	CLR	Rep, Mult	190,193
9	0.02	1	3qdnA	CA	Rep, Mult	146,149
10	0.02	1	1upkA	III	Rep, Mult	103,106,107,111,156,157,160,161,164
11	0.02	1	3u24A	ZN	Rep, Mult	173,176
12	0.02	1	3rkoL	LFA	Rep, Mult	148,151,152,181
13	0.02	1	1kktA	MAN	Rep, Mult	125,174
14	0.02	1	1cnoA	HEC	Rep, Mult	55,73
15	0.02	1	4u5oA	3D5	Rep, Mult	56,60,106,107,110,154,157,161
16	0.02	1	1qgk1	III	Rep, Mult	167,172,173,176,177,180,183,184,185,188,192,195,196
17	0.02	1	3obvA	SUC	Rep, Mult	148,151,174,175,178
18	0.02	1	1f59B	III	Rep, Mult	99,103,106,107,157,161
19	0.02	1	1o6pA	III	Rep, Mult	130,175,179
20	0.02	1	3obvC	SUC	Rep, Mult	95,127,128,131

	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	3dsxA	0.498	4.27	0.058	0.719	2.5.1.60	103
2	0.060	2vn7A	0.503	5.21	0.049	0.827	3.2.1.3	103
3	0.060	2pfdB	0.544	4.48	0.088	0.791	2.1.2.5,4.3.1.4	96
4	0.060	2d0tB	0.512	4.03	0.068	0.725	1.13.11.52	NA
5	0.060	1hn0A	0.532	4.92	0.051	0.847	4.2.2.20	NA
6	0.060	1z1wA	0.510	3.80	0.038	0.689	3.4.11.-	NA
7	0.060	1gaiA	0.512	5.27	0.056	0.847	3.2.1.3	173
8	0.060	3ismC	0.527	3.44	0.076	0.694	3.6.1.3	104,136,139
9	0.060	1ojnA	0.535	4.81	0.036	0.832	4.2.2.1	NA
10	0.060	1cb8A	0.541	4.03	0.043	0.750	4.2.2.5	107
11	0.060	1f1sA	0.569	4.65	0.082	0.867	4.2.2.1	NA
12	0.060	1hcuB	0.518	4.66	0.049	0.775	3.2.1.113	102
13	0.060	2ri9B	0.515	4.64	0.070	0.781	3.2.1.113	NA
14	0.060	3c5wA	0.589	3.56	0.096	0.786	3.1.3.16	91
15	0.060	1dl2A	0.526	4.76	0.018	0.796	3.2.1.113	56,102
16	0.060	1ayxA	0.525	5.42	0.067	0.878	3.2.1.3	NA
17	0.060	1dceA	0.542	3.16	0.069	0.699	2.5.1.60	NA
18	0.060	1r76A	0.529	4.81	0.073	0.827	4.2.2.2	NA
19	0.060	1fo2A	0.504	5.12	0.062	0.821	3.2.1.113	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	0.12	0.619	3.21	0.06	0.80	4uvkA	GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
1	0.08	0.658	3.02	0.09	0.84	4ol0B	GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
2	0.08	0.630	4.13	0.07	0.90	3zkvA	GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
3	0.07	0.691	3.55	0.04	0.92	2x1gF	GO:0005737 GO:0006606 GO:0006886 GO:0007270 GO:0008139 GO:0008536 GO:0008565 GO:0031965 GO:0042331 GO:0050804
4	0.07	0.639	4.02	0.05	0.89	2xwuB	GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
5	0.07	0.627	3.78	0.06	0.86	4c0qA	GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
6	0.07	0.661	3.03	0.10	0.84	4c0qB	GO:0004872 GO:0005634 GO:0005737 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0035048 GO:0042802 GO:0043231
7	0.07	0.644	3.80	0.07	0.90	3wyfC	GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
8	0.07	0.626	4.06	0.07	0.90	3zjyE	GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
9	0.07	0.644	3.90	0.07	0.90	5difC	GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
10	0.07	0.468	5.06	0.06	0.74	3renA	GO:0003824 GO:0004553 GO:0005975 GO:0016020 GO:0016021 GO:0016787
11	0.07	0.469	4.82	0.07	0.74	2y4uA	GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
12	0.07	0.444	5.48	0.05	0.72	3l0oA	GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0006351 GO:0006353 GO:0006355 GO:0008186 GO:0016787
13	0.06	0.367	4.96	0.03	0.58	5bmwB	GO:0003824 GO:0004807 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853 GO:0042802
14	0.06	0.371	5.86	0.03	0.66	2gieA	GO:0003677 GO:0004518 GO:0004519 GO:0009036 GO:0009307 GO:0016787 GO:0090305
15	0.06	0.381	4.32	0.07	0.56	1x87A	GO:0005737 GO:0006547 GO:0006548 GO:0016153 GO:0016829 GO:0019556 GO:0019557
16	0.06	0.389	4.07	0.10	0.54	1n0rA
17	0.06	0.361	5.43	0.06	0.61	2cuzA	GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039
18	0.06	0.343	5.16	0.04	0.55	4p7kA	GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0005048	GO:0022892	GO:0017016
GO-Score	0.54	0.54	0.41
Biological Processes	GO:1902593	GO:0017038	GO:0044744
GO-Score	0.41	0.41	0.41
Cellular Component	GO:0005635	GO:0031090
GO-Score	0.54	0.54

(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.