I-TASSER results

I-TASSER results for job id Rv0464c

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

Input Sequence in FASTA format

>protein (190 residues)
MTGQNGQVARISPGKFRQLGPVNWLVAKLAARAVGAPQMHLFTTLGYRQYLFWTFAIYTG
RLLHGRLPGVDTELVILRVAHLRSCEYELQHHRRMARRRGLDANTQATIFAWPDVPDGDG
PRKVLSARQQALLQATDELIKDRTITAGTWERLATHLDPRLLIEFCLLATQYDAIAATIT
ALAIPPDNPQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTGQNGQVARISPGKFRQLGPVNWLVAKLAARAVGAPQMHLFTTLGYRQYLFWTFAIYTGRLLHGRLPGVDTELVILRVAHLRSCEYELQHHRRMARRRGLDANTQATIFAWPDVPDGDGPRKVLSARQQALLQATDELIKDRTITAGTWERLATHLDPRLLIEFCLLATQYDAIAATITALAIPPDNPQ
Prediction	CCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	9998899888889997779989999999999867888888999998699999999999999998999998999999999999899556899999999989999999998777677777766556999999999999999985999999999999968989999999999999999999999899999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTGQNGQVARISPGKFRQLGPVNWLVAKLAARAVGAPQMHLFTTLGYRQYLFWTFAIYTGRLLHGRLPGVDTELVILRVAHLRSCEYELQHHRRMARRRGLDANTQATIFAWPDVPDGDGPRKVLSARQQALLQATDELIKDRTITAGTWERLATHLDPRLLIEFCLLATQYDAIAATITALAIPPDNPQ
Prediction	8667645222043252751541243034126644724312002001202500410231231036260454121000000011140310000004204626245621430452442444444442034103001300330166470446004303720456200000000031122022121270437658
	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

CCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MTGQNGQVARISPGKFRQLGPVNWLVAKLAARAVGAPQMHLFTTLGYRQYLFWTFAIYTGRLLHGRLPGVDTELVILRVAHLRSCEYELQHHRRMARRRGLDANTQATIFAWPDVPDGDGPRKVLSARQQALLQATDELIKDRTITAGTWERLATHLDPRLLIEFCLLATQYDAIAATITALAIPPDNPQ

3lvyA

0.11

0.10

0.91

2.36

MUSTER

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPIDD--------DPKLDTLAKFTIAVINTGRVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEQ

3lvyA

0.10

0.09

0.91

2.35

dPPAS

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTKGVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEL

3lvyA

0.10

0.09

0.91

3.59

wdPPAS

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTKGVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEL

3lvyA

0.10

0.09

0.91

3.07

wMUSTER

---------KFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTGRVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEQ

3lvyA

0.10

0.09

0.91

4.17

wPPAS

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTGRVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEQ

3lvyA

0.10

0.09

0.91

6.17

dPPAS2

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTKGVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEL

3lvyA

0.10

0.09

0.91

3.29

PPAS

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTGRVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEL

3lvyA

0.10

0.09

0.91

5.22

Env-PPAS

--------SKFTIHTIETAPERVKETLRTVKKDNGGYIPNLIGLLANAPTALETYRTVGEINRRNSLTPTEREVVQITAAVTNGCAFCVAGHTAFSIKQIQAPDLLEALRNATPID--------DDPKLDTLAKFTIAVINTGRVGDEAFADFLEVYTPENALDVVLGVSLASLCNYANNA-DTPINPEL

2prrK

0.14

0.13

0.94

2.21

MUSTER

--RPAHPISRYPVPELAALPDDIRQRILEVQDKAGF-VPNVFLTLAHRPDEFRAFFAYHDALKDGGLT-KGEREIVVATSAANQCLYCVVAHGAILRIYEKKPLVADQVAVNYLKADIP--------PRQRALDFALKVCKASHVNEADFEALREHFTDEDAWDIAAITAFFGLSNRANTIGRPNDEFFL

2prrK

0.14

0.13

0.95

2.14

dPPAS

--RPAHPISRYPVPELAALPDDIRQRILEVQDKAGF-VPNVFLTLAHRPDEFRAFFAYHDALLKDGGLTKGEREIVVATSAANQCLYCVVAHGAILRIYEKKPLVADQVAVNY-------LKADIPPRQRALDFALKVCKASHEVNEADFEALREHFTDEDAWDIAAITAFFGLSNRANTIGRPNDEFFL

(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=0.90

Estimated TM-score = 0.84±0.08

Estimated RMSD = 3.4±2.4Å

Download Model 2

C-score=-4.15

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

Download Model 5

C-score=-0.70

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	3lvyA	0.876	1.04	0.092	0.910
2	2prrK	0.820	1.96	0.159	0.926
3	2oyoA	0.801	2.16	0.200	0.921
4	2pfxA	0.764	2.27	0.178	0.884
5	3c1lB	0.763	2.43	0.176	0.895
6	2gmyA	0.680	1.96	0.146	0.758
7	5dj4A	0.665	2.48	0.173	0.784
8	2q0tA	0.662	3.11	0.083	0.816
9	2o4dA	0.641	2.10	0.188	0.726
10	1lw1A	0.598	2.61	0.128	0.716

(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	0.08	4	4rkuJ	CLA	Rep, Mult	165,168
2	0.06	3	1e6yA	F43	Rep, Mult	78,79,80,130,133,169
3	0.06	3	2x6pB	ZN	Rep, Mult	88,92
4	0.04	2	5sv1F	III	Rep, Mult	165,168,175
5	0.04	2	1xmeC	HAS	Rep, Mult	163,167
6	0.04	2	4xk8l	CLA	Rep, Mult	153,161,165
7	0.02	1	3jz0A	APC	Rep, Mult	83,88
8	0.02	1	1n4pI	III	Rep, Mult	87,88
9	0.02	1	5d8nB	MG	Rep, Mult	179,181
10	0.02	1	3k30A	SF4	Rep, Mult	132,135,136,166,167,168
11	0.02	1	1xk0A	NO	Rep, Mult	96,100
12	0.02	1	2fug4	SF4	Rep, Mult	10,92
13	0.02	1	1fbmD	RTL	Rep, Mult	62,67
14	0.02	1	3e6sE	FE	Rep, Mult	73,77
15	0.02	1	2nr9A	PA6	Rep, Mult	175,179

	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	2db3A	0.453	5.59	0.074	0.800	3.6.4.13	78
2	0.060	2tmdA	0.474	5.34	0.056	0.800	1.5.8.2	135,157
3	0.060	1gufA	0.457	5.53	0.036	0.789	1.3.1.38,1.3.1.10	NA
4	0.060	1q50A	0.451	5.36	0.019	0.779	5.3.1.9	NA
5	0.060	1ps9A	0.467	5.11	0.089	0.763	1.3.1.34	NA
6	0.060	2dfvA	0.466	5.03	0.082	0.753	1.1.1.103	NA
7	0.060	2dphA	0.453	5.46	0.049	0.768	1.2.99.4	NA
8	0.060	1pl6A	0.460	4.84	0.070	0.732	1.1.1.14	NA
9	0.060	3gfbA	0.474	4.96	0.081	0.763	1.1.1.103	NA
10	0.060	1zsyA	0.455	5.34	0.069	0.774	1.3.1.38	87
11	0.060	2w00B	0.454	5.40	0.056	0.789	3.1.21.3	134
12	0.060	1lw1A	0.598	2.61	0.128	0.716	1.11.1.15	140
13	0.060	2fhbA	0.468	5.53	0.071	0.795	3.2.1.41	NA
14	0.060	1moqA	0.450	5.44	0.044	0.779	2.6.1.16	132
15	0.060	1mosA	0.455	5.28	0.037	0.774	2.6.1.16	NA
16	0.060	1e6yE	0.453	5.94	0.073	0.853	2.8.4.1	50
17	0.060	1gu7A	0.455	5.60	0.042	0.800	1.3.1.38,1.3.1.10	87
18	0.060	1pl7A	0.457	4.94	0.064	0.737	1.1.1.14	182
19	0.060	1l8aA	0.467	5.40	0.040	0.800	1.2.4.1	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	0.39	0.810	2.16	0.20	0.93	2oyoA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
1	0.38	0.840	1.95	0.16	0.95	2prrD	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
2	0.35	0.812	2.24	0.17	0.94	2pfxA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
3	0.33	0.790	2.41	0.17	0.93	3c1lB	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
4	0.32	0.659	2.10	0.18	0.74	2ijcI	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
5	0.31	0.883	1.19	0.09	0.92	3lvyA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
6	0.17	0.680	1.96	0.15	0.76	2gmyA	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
7	0.08	0.661	2.46	0.17	0.78	5cufC	GO:0001932 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0006635 GO:0006914 GO:0007005 GO:0009749 GO:0016239 GO:0016684 GO:0030308 GO:0030330 GO:0031588 GO:0031932 GO:0032042 GO:0032542 GO:0032868 GO:0034599 GO:0036091 GO:0042593 GO:0043491 GO:0046323 GO:0061700 GO:0070328 GO:0070728 GO:0071230 GO:0071233 GO:0072593 GO:0090526 GO:0098869 GO:1900182 GO:1901031 GO:1902010 GO:1904262 GO:1990316 GO:2000479
8	0.07	0.598	2.61	0.13	0.72	1lw1A	GO:0004601 GO:0005829 GO:0005886 GO:0006979 GO:0008785 GO:0015036 GO:0016209 GO:0016491 GO:0032843 GO:0045454 GO:0051920 GO:0055114 GO:0098869
9	0.07	0.503	3.25	0.15	0.63	2ouwB	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
10	0.06	0.355	2.74	0.10	0.42	3beyD	GO:0051920 GO:0055114 GO:0098869
11	0.06	0.435	5.69	0.08	0.76	3acsA	GO:0003824 GO:0005975 GO:0030246
12	0.06	0.297	6.19	0.05	0.58	3n2zB	GO:0002155 GO:0002353 GO:0003085 GO:0004180 GO:0004185 GO:0005764 GO:0005886 GO:0006508 GO:0007597 GO:0008233 GO:0008236 GO:0008239 GO:0016787 GO:0042593 GO:0043535 GO:0045178 GO:0060055 GO:0070062 GO:0097009 GO:2000377
13	0.06	0.271	4.85	0.07	0.41	3hyfA	GO:0000287 GO:0003676 GO:0003964 GO:0004518 GO:0004519 GO:0004523 GO:0005737 GO:0006278 GO:0006401 GO:0016740 GO:0016779 GO:0016787 GO:0042802 GO:0043137 GO:0046872 GO:0090305 GO:0090502
14	0.06	0.249	6.28	0.03	0.49	3wo4C	GO:0004872 GO:0005886 GO:0006954 GO:0006955 GO:0007165 GO:0007166 GO:0016020 GO:0016021 GO:0070301 GO:0071345
15	0.06	0.221	5.02	0.04	0.35	3epuA	GO:0005737 GO:0050708
16	0.06	0.229	5.63	0.04	0.41	3f2zA
17	0.06	0.134	2.57	0.10	0.16	2mulA	GO:0000209 GO:0003677 GO:0004842 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006281 GO:0006284 GO:0006513 GO:0006974 GO:0016020 GO:0016567 GO:0016574 GO:0016874 GO:0030154 GO:0042787 GO:0044822 GO:0070062 GO:1903955
18	0.06	0.270	5.08	0.04	0.43	1zvoC	GO:0003823 GO:0004252 GO:0005576 GO:0005886 GO:0006508 GO:0006898 GO:0006910 GO:0006911 GO:0006955 GO:0006956 GO:0006958 GO:0009897 GO:0016020 GO:0016021 GO:0034987 GO:0038095 GO:0038096 GO:0042571 GO:0042742 GO:0045087 GO:0050776 GO:0050853 GO:0050871 GO:0070062 GO:0072562
19	0.06	0.210	3.97	0.01	0.29	4ds2A

Consensus prediction of GO terms

Molecular Function	GO:0004601	GO:0051920
GO-Score	0.89	0.89
Biological Processes	GO:0055114	GO:0098869
GO-Score	0.89	0.89
Cellular Component
GO-Score

(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.