I-TASSER results

I-TASSER results for job id Rv3517

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

Input Sequence in FASTA format

>protein (279 residues)
MIEPFLGSEAIASGALTRHRLRSAYATIHPDVYVSPGADLTAWSRAQAAWLWSRRRGVIA
GQSAAAMHGAKWVDARQAAELLYDHRRPPAGIHTWSDRVADDEIQPISGMNTTTPARTAL
DLARRYPVGKAVAAIDALARATDLKLADVEMLAERYRGSRGIRNARIALDLVDPGAESPR
ETWLRLLLIRAGFPRPQTQIPVYDEYGQLVAVIDMGWAGIKVGVDYEGDHHRTDRRTFNK
DIKRAEALTELGWTDVRVTVEDTEGGIIWRVSAAWQRRT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MIEPFLGSEAIASGALTRHRLRSAYATIHPDVYVSPGADLTAWSRAQAAWLWSRRRGVIAGQSAAAMHGAKWVDARQAAELLYDHRRPPAGIHTWSDRVADDEIQPISGMNTTTPARTALDLARRYPVGKAVAAIDALARATDLKLADVEMLAERYRGSRGIRNARIALDLVDPGAESPRETWLRLLLIRAGFPRPQTQIPVYDEYGQLVAVIDMGWAGIKVGVDYEGDHHRTDRRTFNKDIKRAEALTELGWTDVRVTVEDTEGGIIWRVSAAWQRRT
Prediction	CCCCEEHHHHHHHCCHHHHHHHCCEEEHCCCEEHCCCCCCCHHHHHHHHHHHHCCCEEEHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCEEEEHCCCCCCCEEEHCCEEHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEEHCCCCCEEEEEEEEHCCEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHHHCHHHHHHHHHHHHHHHC
Conf.Score	987534898998876567887698688669889779999999999999999969985774489999989988889986899779999999789997578888589988888669999999999859888999999999986799999999999985787666899999987656778889999999999989998665589987987567887678668689999869876789999999999999999989989999746556899999999999959
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MIEPFLGSEAIASGALTRHRLRSAYATIHPDVYVSPGADLTAWSRAQAAWLWSRRRGVIAGQSAAAMHGAKWVDARQAAELLYDHRRPPAGIHTWSDRVADDEIQPISGMNTTTPARTALDLARRYPVGKAVAAIDALARATDLKLADVEMLAERYRGSRGIRNARIALDLVDPGAESPRETWLRLLLIRAGFPRPQTQIPVYDEYGQLVAVIDMGWAGIKVGVDYEGDHHRTDRRTFNKDIKRAEALTELGWTDVRVTVEDTEGGIIWRVSAAWQRRT
Prediction	863213222012223021121334012012302024724231110010001003231030130000012031143532010123431322101001122345311414302003002001101221423210000000022342222002202211222222232222232233323422002000001113112321002021443332010000022120001022433244351144034214103614020000015211430042025004628
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCEEHHHHHHHCCHHHHHHHCCEEEHCCCEEHCCCCCCCHHHHHHHHHHHHCCCEEEHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCEEEEHCCCCCCCEEEHCCEEHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEEHCCCCCEEEEEEEEHCCEEEEEEHCCCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEEHHHCHHHHHHHHHHHHHHHC
MIEPFLGSEAIASGALTRHRLRSAYATIHPDVYVSPGADLTAWSRAQAAWLWSRRRGVIAGQSAAAMHGAKWVDARQAAELLYDHRRPPAGIHTWSDRVADDEIQPISGMNTTTPARTALDLARRYPVGKAVAAIDALARATDLKLADVEMLAERYRGSRGIRNARIALDLVDPGAESPRETWLRLLLIRAGFPRPQTQIPVYDEYGQLVAVIDMGWAGIKVGVDYEGDHHRTDRRTFNKDIKRAEALTELGWTDVRVTVEDTEGGIIWRVSAAWQRRT

4oq2A1

0.09

0.04

0.46

1.43

wdPPAS

-------------------------------------------------------------------------------------------------------------------------------------------------------HHHHHEFSKTDYILRALSKISHKRWEHYIINRVVHTLDDPDIEFVCQQCIRKEGHLGKIYLADLLFPQLNLYLEIDE-AHHDSNDARKADAVRRLDVEATGFQEERIPASNIVDEFVRLVKDKKEELE

4oq2A1

0.09

0.04

0.46

1.44

wPPAS

-------------------------------------------------------------------------------------------------------------------------------------------------------HHHHHEFSKTDYILRALSKISHKRWEHYIINRVVHTLDDPDIEFVCQQCIRKEGHLGKIYLADLLFPQLNLYLEIDE-AHHDSNDARKADAVRRLDVEATGFQEERIPASNIVDEFVRLVKDKKEELE

3hrlA

0.18

0.06

0.31

1.26

Env-PPAS

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASEAEAKLWQHLRAGRLNGYKFRRQQPGN-----YIVDFCVT-PKLIVEADGVY----------DHARTVYLNSLGFTVLRFWNHEITNDVLAEILRVLQELE

4parB1

0.14

0.06

0.42

1.09

wdPPAS

---------------------------------------------------------------------------------------------------------------------------------------------------------------ASSDLTDYVIRQLNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKK--IALTDLYFPQLGIHIEVDEGHHFLRISQTESDAMREEDISITGHKIFRVNVFKNIHQQIDKIIEEIKTAK

4parB1

0.14

0.06

0.42

1.13

wPPAS

---------------------------------------------------------------------------------------------------------------------------------------------------------------ASSDLTDYVIRQLNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKK--IALTDLYFPQLGIHIEVDEGHHFLRISQTESDAMREEDISITGHKIFRVNVFKNIHQQIDKIIEEIKTAK

3r3pA

0.14

0.05

0.33

1.03

wPPAS

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTPERRVKEILDEMDIV--FTHHVV--------GWNVAFYLGKKLAIEVNGVYWASKQKNVNKDKRKLSELHSKGYRVLTIEDDELIDKVKQQIQKFWVTHI

3hrlA

0.23

0.07

0.30

1.00

wPPAS

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASEAEAKLWQHLRAGRLNGYK-QQP-----GN--YIVDF--VTPKLIVEADGV----------YDHARTVYLNSLGFTVLRFWNHEITNDVLAEILRVLQELE

4nurA

0.12

0.11

0.96

0.69

MUSTER

EGEAAPDTTNPSLWRQSQLINISGLFEVTDGIYQVRNYDLS-------MTIVEGKDGITIQETAKAALDLKHRPKKPVVAVIYTHSHVYGGV----RGVVDEADVKAGKVKIYAPLGFLEHAVAENVMAGTAMSRRASYMYGNLLPPDAKGQLGATTTSAGTVTLIPPTDIIKETGETHVIDGLTYEFMYAPGSEAPAEMLYYIKEKKALNAAEDSTHTLHNTYSLRGAKIR-DPLAWSKYLNEALKLWGDDVQVMYVWGNKEVREQLSLQRDMYRYIN

4ixjA

0.08

0.06

0.77

0.56

dPPAS

----------------------------------------RNIEKSKAVTCLSNRENIKTQIVIAMAEESSKDKNEVIKEVLENKDGKYFETEPKCKSGGIYSATFDKVYVTCTIEMARDIHQSMKDLIASFAQDPSIIPGASKGNDDFRKYLLDNKYKNGWPTIPDEFKAKYGLSKDTL--YIQPYAYNPTKSDATVVVFANNKTGGNWYTSLVYDYDYKGKNGISVAGRSWDVDTDSVKSVKTEIHSKEGWGPLN----------------------

3r3pA

0.14

0.05

0.34

1.01

wdPPAS

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTPERRVKEILDEMDI-VYFTHHVVEG-------WNVAFYLGKKLAIEVNGVYWASKQKNVNKDKRKLSELHSKGYRVLTIEDDELIDKVKQQIQKFWVTHI

(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=-3.76

Estimated TM-score = 0.31±0.10

Estimated RMSD = 15.3±3.4Å

Download Model 2

C-score=-4.17

Download Model 3

C-score=-3.46

Download Model 4

C-score=-4.56

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	2yheA	0.521	5.67	0.060	0.814
2	2cg2A1	0.516	5.70	0.081	0.817
3	4nurA1	0.515	5.68	0.093	0.814
4	4pdxA	0.494	5.61	0.078	0.778
5	5l43A	0.452	5.61	0.063	0.717
6	2iwhB	0.448	6.14	0.075	0.742
7	1gkuB	0.441	6.04	0.063	0.724
8	1y791	0.435	6.14	0.060	0.724
9	5kf6A	0.432	6.67	0.045	0.792
10	2eidA	0.426	6.21	0.063	0.720

(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	0.14	7	3povA	MG	Rep, Mult	177,214,225,226,227
2	0.06	3	1w1xC	SIA	Rep, Mult	29,31,33,47,48,49,50
3	0.06	3	3odhA	CA	Rep, Mult	199,214
4	0.02	1	1t5bA	FMN	Rep, Mult	144,149
5	0.02	1	2vz3A	CU	Rep, Mult	184,215,226
6	0.02	1	2qt0A	MG	Rep, Mult	182,214
7	0.02	1	4bg1A	16D	Rep, Mult	25,33
8	0.02	1	2b0qA	MG	Rep, Mult	205,214
9	0.02	1	4zfzA	ZN	Rep, Mult	261,264
10	0.02	1	3c61A	AZI	Rep, Mult	245,249
11	0.02	1	1w20A	UUU	Rep, Mult	220,221,222,271
12	0.02	1	3rl3A	MN	Rep, Mult	252,255
13	0.02	1	2r9rB	PGW	Rep, Mult	120,138
14	0.02	1	2o6nA	YB2	Rep, Mult	177,181
15	0.02	1	2ih9B	5AX	Rep, Mult	68,69

	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	2jfdA	0.302	5.99	0.081	0.495	2.3.1.85	NA
2	0.060	2q5lA	0.410	6.47	0.080	0.724	4.1.1.74,4.1.1.43	215
3	0.060	2cmlC	0.414	5.60	0.067	0.663	3.2.1.18	52,195
4	0.060	2pdaA	0.411	5.75	0.070	0.649	1.2.7.1	62,96
5	0.060	1ddzA	0.407	6.18	0.050	0.685	4.2.1.1	NA
6	0.060	3e2tA	0.411	6.14	0.050	0.688	1.14.16.4	NA
7	0.060	2vjyA	0.408	6.03	0.066	0.677	4.1.1.1	NA
8	0.060	1ingA	0.405	5.58	0.050	0.642	3.2.1.18	NA
9	0.060	2vk1A	0.318	6.69	0.057	0.577	4.1.1.1	NA
10	0.060	1mhyB	0.405	6.05	0.055	0.670	1.14.13.25	NA
11	0.060	1b0pA	0.410	5.76	0.070	0.649	1.2.7.1	NA
12	0.060	1j38A	0.402	6.10	0.041	0.685	3.4.15.1	167,182
13	0.060	1phzA	0.423	6.02	0.053	0.695	1.14.16.1	NA
14	0.060	2v3wA	0.408	5.88	0.045	0.645	4.1.1.7	NA
15	0.060	1yniB	0.402	5.90	0.066	0.670	3.5.3.23	190
16	0.060	2eabA	0.412	6.40	0.053	0.713	3.2.1.63	NA
17	0.060	2vz9B	0.352	6.72	0.039	0.642	2.3.1.85	NA
18	0.060	2htrA	0.406	5.68	0.057	0.652	3.2.1.18	50,100
19	0.060	1j36A	0.400	6.04	0.032	0.677	3.4.15.1	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	0.07	0.521	5.67	0.06	0.81	2yheA	GO:0046872 GO:0046983
1	0.07	0.513	5.74	0.08	0.82	5aijA	GO:0016787 GO:0042802 GO:0046872 GO:0046983
2	0.07	0.512	5.61	0.09	0.81	4nurA	GO:0046872 GO:0046983
3	0.07	0.505	5.54	0.07	0.78	4pdxA	GO:0016787 GO:0018741 GO:0030288 GO:0046983
4	0.07	0.411	5.79	0.06	0.66	3lvzB	GO:0046872
5	0.06	0.400	5.41	0.09	0.62	3faiA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
6	0.06	0.388	5.84	0.05	0.63	4awyB	GO:0046872
7	0.06	0.397	5.61	0.05	0.63	3adrA	GO:0008270 GO:0046872
8	0.06	0.358	5.42	0.06	0.55	1m2xA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
9	0.06	0.345	5.29	0.10	0.53	2zwrB	GO:0046872
10	0.06	0.304	6.12	0.03	0.51	3jyhA	GO:0004177 GO:0004185 GO:0005576 GO:0005764 GO:0005794 GO:0005829 GO:0006508 GO:0008233 GO:0008236 GO:0008239 GO:0016023 GO:0016787 GO:0031410 GO:0031982 GO:0043231 GO:0070062
11	0.06	0.351	5.57	0.05	0.56	2m5cA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
12	0.06	0.332	6.37	0.06	0.57	2p4zB	GO:0016787 GO:0046872
13	0.06	0.338	6.59	0.05	0.61	1ikpA	GO:0016740 GO:0016757 GO:0047286
14	0.06	0.323	5.96	0.06	0.53	3zwfA	GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005829 GO:0008033 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
15	0.06	0.297	6.71	0.03	0.54	3eoeD	GO:0000287 GO:0003824 GO:0004743 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955
16	0.06	0.313	6.25	0.04	0.53	4r4xA	GO:0003824 GO:0016715 GO:0055114
17	0.06	0.348	6.05	0.05	0.57	2i7tA	GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
18	0.06	0.259	5.02	0.06	0.38	1ufrA	GO:0003723 GO:0004845 GO:0006351 GO:0006353 GO:0006355 GO:0009116 GO:0016740 GO:0016757

Consensus prediction of GO terms

Molecular Function	GO:0005515	GO:0043169
GO-Score	0.48	0.48
Biological Processes
GO-Score
Cellular Component	GO:0030288
GO-Score	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.