I-TASSER results

I-TASSER results for job id Rv3098c

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

Input Sequence in FASTA format

>protein (150 residues)
MASLRIAEVDPVDRSPNHHASGSVETSSSRSRSASVRACLIHTSRSSSCSARRMTSLLRS
PLRIAALMICSSFSVGRKPMVAVMSTTIADVAQSYSNCSTHSGTPTPAFAASFLLDAINA
PRVIAGRFASESVRFPAAAPHGSVPSRLPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MASLRIAEVDPVDRSPNHHASGSVETSSSRSRSASVRACLIHTSRSSSCSARRMTSLLRSPLRIAALMICSSFSVGRKPMVAVMSTTIADVAQSYSNCSTHSGTPTPAFAASFLLDAINAPRVIAGRFASESVRFPAAAPHGSVPSRLPV
Prediction	CCCEEEEHCCCCCCCCCCCCCCCEHCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEHCCCCCEHCCCCCCCCCCCCCCCC
Conf.Score	985445555777889887777765545665544456555544477766557889999886889999998754556888645654557788888765666678999856799999998657634544446665445667888888888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MASLRIAEVDPVDRSPNHHASGSVETSSSRSRSASVRACLIHTSRSSSCSARRMTSLLRSPLRIAALMICSSFSVGRKPMVAVMSTTIADVAQSYSNCSTHSGTPTPAFAASFLLDAINAPRVIAGRFASESVRFPAAAPHGSVPSRLPV
Prediction	745142452443554454434242544554544240300102144544142430241143303000011033243444211111333034115425414446434332201321141141332012403464151323144452465358
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCEEEEHCCCCCCCCCCCCCCCEHCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEHCCCCCEHCCCCCCCCCCCCCCCC
MASLRIAEVDPVDRSPNHHASGSVETSSSRSRSASVRACLIHTSRSSSCSARRMTSLLRSPLRIAALMICSSFSVGRKPMVAVMSTTIADVAQSYSNCSTHSGTPTPAFAASFLLDAINAPRVIAGRFASESVRFPAAAPHGSVPSRLPV

5kodA2

0.14

0.13

0.92

0.53

MUSTER

VLSIDTDEVE-VKNAVTHLVPFDASLSTSSIPGHYVLFWELCLDGNTPIPPSVFEDCCLAVEESFNTVYRQGVSDKSPLEIKIVEPTFDKLMDYAISLGASINQYTPRCVFAPIIELLNS-RVVDSYFSP-------KCPK--VPGH-KQ

4y7sA

0.13

0.09

0.72

0.55

dPPAS

---------NPYTIYPPVPKTASINGFADRIYDKCAQECVKQSTSSTPCPYWDTGCLCVIPNFTGAVGNCVASKCRGADVTNFRKLAVGACAAAGVWDPYWIIPASVSSALDAAATA---------------------------------

1scuA2

0.18

0.15

0.79

0.50

wdPPAS

PGECKIGIQ-----PGHIHKPGKVG----------------IVSRSGTLTYEAVKQTTDYGFGQSTCV-----GIGGDPIP---GSNFIDILEMFEK-QTEAGGSAEEEAAAYIKEHVTKP-YIAGVTAPKGKRMGAGAIIAGGKGTADE

5b00A2

0.30

0.26

0.85

0.57

wMUSTER

----R-AVTDILEQDAVHLCGGQIRT--KRSRATNLREWRAHASTYGSTFLGRYGALAAAC-ADSVREFAEAFA---------MTITMADDLTDYDRNGERDGNRTGAVAGQDVVDLLEE---LRGR-ALAAVAAPPGAP-GLVPVRLPR

1scuA2

0.24

0.18

0.74

0.48

wPPAS

ITECKIG-------QPGHHKPGKVG----------------IVSRSGTLTYEAVKQTTDYGF--------STCGIGGDPIP---GSNFIDILEMFEK-QTEAGS---EEAAAYIKEHVTKP-YIAGVTAPKGKRMGAGAIIGTVLADIGE

1scuA2

0.19

0.15

0.75

0.51

dPPAS2

QPG-------------HIHKPGKVG----------------IVSRSGTLTYEAVKQTTDYGFGQSTCV-----GIGGDPIP---GSNFIDILEMFEKDQTEAGGSAEEEAAAYIKEHVTKPGYIAGVTAPKGKRMGAGAIIGGKGTAVKT

1scuA2

0.23

0.17

0.76

0.59

PPAS

PGECKIG-------QPGHHKPGKVG----------------IVSRSGTLTYEAVKQTTDYGF--------STCGIGGDPIP---GSNFIDILEMFEK-QTEAGGSAEEEAAAYIKEHVTKP-YIAGVTAPKGKRMGAGAIIGGKGTAVKT

3wc4A3

0.18

0.13

0.72

0.62

Env-PPAS

------------------------WPNVSCSLSLYFNIDLIRDKCSKDAKNATLDFLL-SKLRVEDV---PQDMLDVGEKETLFSRTLNSLGVVLPQAKA-------VVVNFF--AELD-PPLFVKYMRS---KLQYVVPLPCPQLLLP-

2lp4A1

0.12

0.11

0.91

0.53

MUSTER

M-SMDISDF--FDEADELLAQHLLDLVPESPDAEQLNAIFRASIKGGAGTFTILQETTHLMENLLDEARRGEMQLNTD-IINLFLETKDIMQEQLDAY--KNSEEPDAASFEYICNALRQ---LALEAKGET---PSAVTRLSVVAK-PQ

2k3pA

0.17

0.15

0.90

0.53

dPPAS

RIAPVTGGTAGISVGVPGYLRTPSSTILAPSNAQTTLAPVLSSSGLSSASASARVSSLAQSLASALS------TSRGTLSLSTFLNLLSSISSEIRASTSLDGT---QATVEVLLEALAALLQVINGAQITDVNV------SSVPSVNAA

(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=-4.07

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.4±3.7Å

Download Model 2

C-score=-4.93

Download Model 3

C-score=-4.98

Download Model 4

C-score=-4.99

Download Model 5

C-score=-4.69

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	5kodA	0.567	4.09	0.067	0.833
2	4ewvA	0.537	4.18	0.106	0.807
3	4eplA2	0.512	3.67	0.079	0.733
4	4b2gA	0.510	4.08	0.066	0.747
5	1p4rA	0.496	4.47	0.076	0.833
6	3owaA	0.480	4.77	0.068	0.813
7	1z5hA	0.478	4.78	0.114	0.813
8	3ucqA	0.475	4.45	0.076	0.773
9	2npaA	0.474	4.26	0.050	0.727
10	3czkA	0.474	4.50	0.099	0.767

(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	0.06	3	4lk3E	POP	Rep, Mult	53,147
2	0.06	3	5k4lA	III	Rep, Mult	56,59,60
3	0.04	2	2i7hB	FMN	Rep, Mult	16,17,18,89
4	0.04	2	4r8hA	SP1	Rep, Mult	92,93,96
5	0.04	2	3wu2h	CLA	Rep, Mult	54,58
6	0.04	2	1i94C	WO2	Rep, Mult	51,53
7	0.02	1	1p4rB	354	Rep, Mult	5,67,70
8	0.02	1	1cc1L	SF4	Rep, Mult	37,141
9	0.02	1	1jdtB	MTA	Rep, Mult	18,37
10	0.02	1	1k7lC	III	Rep, Mult	10,26,33,104
11	0.02	1	1k7lC	III	Rep, Mult	90,116,117,118,120
12	0.02	1	1thzA	326	Rep, Mult	55,127,133
13	0.02	1	3cf2B	ADP	Rep, Mult	78,147
14	0.02	1	4fmaE	MG	Rep, Mult	26,28
15	0.02	1	2ohjE	FMN	Rep, Mult	19,141
16	0.02	1	2axtM	UNK	Rep, Mult	118,123,146
17	0.02	1	2ypaA	NUC	Rep, Mult	59,60,63

	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	2wuzA	0.457	4.59	0.050	0.753	1.14.13.70	21,49
2	0.060	2w0aA	0.336	5.25	0.028	0.613	1.14.13.70	NA
3	0.060	2wz1A	0.447	5.04	0.081	0.807	4.6.1.2	NA
4	0.060	3bxvA	0.453	5.14	0.052	0.833	1.13.11.55	24
5	0.060	1fx2A	0.437	4.83	0.080	0.747	4.6.1.1	NA
6	0.060	3ciaA	0.440	5.07	0.071	0.780	3.4.11.-	NA
7	0.060	1af2A	0.439	4.65	0.096	0.753	3.5.4.5	NA
8	0.060	1s46A	0.454	4.53	0.092	0.747	2.4.1.4	113
9	0.060	2c6fA	0.443	5.11	0.038	0.787	3.4.15.1	25
10	0.060	1g5aA	0.451	4.56	0.102	0.747	2.4.1.4	NA
11	0.060	1u3rA	0.324	4.63	0.029	0.540	2.3.1.48	NA
12	0.060	1r7aA	0.438	4.87	0.065	0.747	2.4.1.7	NA
13	0.060	2ve3A	0.466	4.63	0.067	0.760	1.14.-.-	NA
14	0.060	3dbmA	0.362	5.41	0.042	0.680	4.2.1.92	NA
15	0.060	1cjkB	0.467	4.94	0.073	0.807	4.6.1.1	NA
16	0.060	3ig5A	0.457	4.68	0.062	0.767	6.3.2.2	NA
17	0.060	2vxoB	0.438	4.72	0.064	0.733	6.3.5.2	NA
18	0.060	3hvlB	0.455	4.43	0.048	0.727	2.3.1.48	54,135
19	0.060	1cttA	0.440	4.63	0.096	0.753	3.5.4.5	37

(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	0.533	4.17	0.08	0.80	4ewvB	GO:0006952 GO:0009626 GO:0010112 GO:0016874 GO:0034052 GO:0044419
1	0.07	0.534	4.34	0.07	0.81	4epmA	GO:0006952 GO:0009626 GO:0010112 GO:0016874 GO:0034052 GO:0044419
2	0.07	0.510	4.17	0.06	0.77	4eplA	GO:0002376 GO:0005737 GO:0006952 GO:0009611 GO:0009694 GO:0009864 GO:0010046 GO:0010224 GO:0016874 GO:0019899 GO:0045087 GO:0071365 GO:0080123 GO:2000030
3	0.06	0.350	5.50	0.05	0.67	4avnA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0030246 GO:0030247 GO:0046872
4	0.06	0.344	5.26	0.07	0.63	4zemA	GO:0003743 GO:0006413 GO:0044237
5	0.06	0.368	5.39	0.02	0.68	1a0cA	GO:0000287 GO:0005737 GO:0005975 GO:0006098 GO:0009045 GO:0016853 GO:0042732 GO:0046872
6	0.06	0.418	5.00	0.04	0.73	3r31A	GO:0008152 GO:0008802 GO:0016491 GO:0016620 GO:0019285 GO:0046872 GO:0055114
7	0.06	0.359	5.23	0.04	0.66	5dxfB	GO:0003824 GO:0004805 GO:0005992 GO:0009267 GO:0009405 GO:0016311 GO:0030447 GO:0034599 GO:0034605 GO:0036170 GO:0060257 GO:0071470
8	0.06	0.330	5.35	0.10	0.59	5dboB	GO:0003743 GO:0006413 GO:0044237
9	0.06	0.324	5.24	0.03	0.55	2yv5A	GO:0000166 GO:0003924 GO:0005525 GO:0016787 GO:0046872
10	0.06	0.288	5.42	0.06	0.54	2g7sA	GO:0003677 GO:0006351 GO:0006355
11	0.06	0.361	5.67	0.03	0.72	4nguA	GO:0006810 GO:0030288
12	0.06	0.312	3.81	0.10	0.45	3lxjA	GO:0000166 GO:0003682 GO:0005524 GO:0005634 GO:0016887 GO:0031936 GO:0045944 GO:0070577
13	0.06	0.322	5.13	0.04	0.58	1pbuA	GO:0003746 GO:0004364 GO:0005634 GO:0005737 GO:0005783 GO:0005829 GO:0005913 GO:0006412 GO:0006414 GO:0006749 GO:0009615 GO:0016020 GO:0070062 GO:0098609 GO:0098641
14	0.06	0.346	4.54	0.07	0.54	1tq6A	GO:0000166 GO:0002376 GO:0003924 GO:0005525 GO:0005634 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0010506 GO:0016020 GO:0016787 GO:0019003 GO:0019221 GO:0020005 GO:0031965 GO:0032580 GO:0035458 GO:0042802 GO:0042832 GO:0045087 GO:0050829
15	0.06	0.285	3.87	0.06	0.44	1y3jA	GO:0000166 GO:0001568 GO:0001701 GO:0001974 GO:0002082 GO:0004008 GO:0005375 GO:0005507 GO:0005524 GO:0005737 GO:0005770 GO:0005783 GO:0005794 GO:0005802 GO:0005829 GO:0005886 GO:0005887 GO:0006568 GO:0006584 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0007005 GO:0007595 GO:0007626 GO:0010041 GO:0010043 GO:0010273 GO:0015677 GO:0015679 GO:0016020 GO:0016021 GO:0016323 GO:0016532 GO:0016787 GO:0018205 GO:0019430 GO:0019829 GO:0021702 GO:0021860 GO:0021954 GO:0030001 GO:0030140 GO:0030141 GO:0030198 GO:0030199 GO:0031069 GO:0031526 GO:0032767 GO:0034220 GO:0042093 GO:0042414 GO:0042415 GO:0042417 GO:0042428 GO:0043005 GO:0043025 GO:0043085 GO:0043086 GO:0043473 GO:0043588 GO:0046688 GO:0046872 GO:0048251 GO:0048286 GO:0048471 GO:0048812 GO:0051216 GO:0051353 GO:0051542 GO:0060003
16	0.06	0.319	5.64	0.06	0.61	3mxtA	GO:0000166 GO:0004592 GO:0005524 GO:0005737 GO:0015940 GO:0016874
17	0.06	0.269	4.88	0.09	0.45	2rgnB	GO:0005085 GO:0005089 GO:0005737 GO:0005829 GO:0005886 GO:0016020 GO:0030016 GO:0030017 GO:0035023 GO:0043547
18	0.06	0.364	5.10	0.03	0.63	1bqgA	GO:0000287 GO:0003824 GO:0008152 GO:0008872 GO:0016829 GO:0019394 GO:0042838 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0019899	GO:0080123	GO:0003743	GO:0046872	GO:0030247	GO:0004553
GO-Score	0.07	0.07	0.06	0.06	0.06	0.06
Biological Processes	GO:0006950
GO-Score	0.37
Cellular Component	GO:0005737
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.