I-TASSER results

I-TASSER results for job id Rv0992c

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

Input Sequence in FASTA format

>protein (197 residues)
MAMASKSALRDQLLAARRRVADDVRAAEARMLRGHLERMVTSDSTVCAYVPVGGEPGSIE
MLDVLLRRAGRVLLPVARTAGGDLPLPLRWGEYRAGGLARARWGLLEPPEPWLPEAALAQ
ASLVLVPALAVDRQGVRLGRGRGFYDRSLRCRDPHARLVAVVRTVELVDVLPSEPHDVPM
THALTPERGLIALPCGE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAMASKSALRDQLLAARRRVADDVRAAEARMLRGHLERMVTSDSTVCAYVPVGGEPGSIEMLDVLLRRAGRVLLPVARTAGGDLPLPLRWGEYRAGGLARARWGLLEPPEPWLPEAALAQASLVLVPALAVDRQGVRLGRGRGFYDRSLRCRDPHARLVAVVRTVELVDVLPSEPHDVPMTHALTPERGLIALPCGE
Prediction	CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCEEHCCCCCEHCCCCCHHHHHHHHCCCCCCEEEEEHCEEHCCCCCCCCCCCCCCEEEHCCCEEEHCCCCC
Conf.Score	98899999999999999959999999999999999999999799899997699999999999999998998999998679986678887775787667778889989998877777765676999766488589986578987567888876899858999854466588999988776788997897799868999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MAMASKSALRDQLLAARRRVADDVRAAEARMLRGHLERMVTSDSTVCAYVPVGGEPGSIEMLDVLLRRAGRVLLPVARTAGGDLPLPLRWGEYRAGGLARARWGLLEPPEPWLPEAALAQASLVLVPALAVDRQGVRLGRGRGFYDRSLRCRDPHARLVAVVRTVELVDVLPSEPHDVPMTHALTPERGLIALPCGE
Prediction	75464255115412521671466214520441053025004603000000116412203400430174504000000246655141313034245741463324020145742553424301000000011044120002132201310541475020000012212156134451623011000354001305548
	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

CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCHHHHHHHHHHHCCEEEEEEEHCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCEEHCCCCCEHCCCCCHHHHHHHHCCCCCCEEEEEHCEEHCCCCCCCCCCCCCCEEEHCCCEEEHCCCCC
MAMASKSALRDQLLAARRRVADDVRAAEARMLRGHLERMVTSDSTVCAYVPVGGEPGSIEMLDVLLRRAGRVLLPVARTAGGDLPLPLRWGEYRAGGLARARWGLLEPPEPWLPEAALAQASLVLVPALAVDRQGVRLGRGRGFYDRSLRCRDPHARLVAVVRTVELVDVLPSEPHDVPMTHALTPERGLIALPCGE

2jcbA

0.18

0.17

0.95

3.57

MUSTER

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQIS---NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

7.04

dPPAS

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETR---TMSFRQISNFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYK--GKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

6.13

wdPPAS

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQI----NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

4.48

wMUSTER

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEW-KTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQIS---NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.94

5.33

wPPAS

V-REEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQI----NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

10.10

dPPAS2

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQIS---NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYK--GKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

4.63

PPAS

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQIS---NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

2jcbA

0.18

0.17

0.95

4.30

Env-PPAS

HVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQIS---NFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHY--KGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN----

3hy6A

0.20

0.19

0.94

3.43

MUSTER

MASSAKRSLRGELKQRLRAMSAEERLRQSRVLSQKVIAHSEYQKRISIFLSMQDEIETEEIIKDIFQRGKICFIPRYRFQSNHMDMVRIESPEEISLLPKTSWNIPQPGEGDVRELSTGGLDLIFMPGLGFDKHGNRLGRGKGYYDAYLKRCLVKPYTLALAFKEQICLQVPVNENDMKVDEVLYE-----------

1ydmB

0.22

0.20

0.90

6.84

dPPAS

-------QLRKKTLEALSALSNEDILQKTERYKYLFSPEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKQFRTYQ----TDDQLETVYAGLLEPVIKT-KEVNPSQIDLI-VPGVCFDVNGFRVGFGGGYYDRYLSEYE--GKTVSLLLECQLFAHVPRLPHDIPVHKLITEDRIISCF----

(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 3 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=1.58

Estimated TM-score = 0.94±0.06

Estimated RMSD = 2.3±1.7Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=1.58

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	2jcbA	0.935	0.76	0.181	0.954
2	3hy6A	0.873	1.70	0.204	0.944
3	1souA	0.831	2.11	0.234	0.934
4	1ydmB	0.812	2.30	0.220	0.898
5	1wkcA	0.757	1.93	0.329	0.833
6	1sbqA	0.736	1.97	0.194	0.812
7	2a0uA	0.643	4.05	0.098	0.853
8	2yvkA	0.636	4.02	0.071	0.843
9	1t9kC	0.630	4.16	0.082	0.843
10	5b04G	0.625	4.50	0.072	0.858

(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	0.60	22	1u3fA	ADP	Rep, Mult	6,10,138,139,140,141,142,143,146,147,150,176,177
2	0.21	10	1u3fA	MG	Rep, Mult	6,137,146,177
3	0.17	9	1u3gA	THF	Rep, Mult	49,50,52,55,75,77,127,137,140,142,144,145
4	0.04	3	3hxtA	MG	Rep, Mult	25,52,53,55
5	0.03	3	3hy6A	MG	Rep, Mult	85,86,116,117,118,148,151
6	0.03	2	3hxtA	MG	Rep, Mult	20,25,163
7	0.02	2	3hy6A	MG	Rep, Mult	98,99,100
8	0.02	2	3hy3A	MG	Rep, Mult	78,79,80
9	0.01	1	3hy6A	MG	Rep, Mult	185,186
10	0.01	1	3hy6A	MG	Rep, Mult	90,94,114
11	0.01	1	3hy6A	MG	Rep, Mult	41,43,122
12	0.01	1	3hy6A	MG	Rep, Mult	136,173,177,179
13	0.01	1	3hy3A	MG	Rep, Mult	79,101,102
14	0.01	1	3hxtA	MG	Rep, Mult	168,169
15	0.01	1	3hxtA	MG	Rep, Mult	83,84,151

	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	0.328	1u3fA	0.745	1.86	0.194	0.812	6.3.3.2	75,127,146,178
2	0.159	2jcbA	0.935	0.76	0.181	0.954	6.3.3.2	137
3	0.159	1souA	0.831	2.11	0.234	0.934	6.3.3.2	137
4	0.157	3hy6A	0.873	1.70	0.204	0.944	6.3.3.2	137
5	0.128	1sbqA	0.736	1.97	0.194	0.812	6.3.3.2	137
6	0.067	3cdkB	0.588	3.51	0.112	0.756	2.8.3.5	143
7	0.060	1o98A	0.513	4.58	0.068	0.766	5.4.2.1	NA
8	0.060	1hwxA	0.547	4.45	0.090	0.827	1.4.1.3	NA
9	0.060	1gtmA	0.538	4.48	0.067	0.817	1.4.1.3	NA
10	0.060	1hrdA	0.541	4.51	0.053	0.812	1.4.1.2	18,29
11	0.060	1uj6A	0.558	3.64	0.126	0.721	5.3.1.6	75,78,141
12	0.060	3i5tA	0.508	4.22	0.042	0.701	2.6.1.-	NA
13	0.060	3etdA	0.547	4.39	0.090	0.822	1.4.1.3	NA
14	0.060	2pjmD	0.553	3.61	0.106	0.711	5.3.1.6	54
15	0.060	2bmaA	0.551	4.62	0.094	0.843	1.4.1.4	NA
16	0.060	2nrcB	0.597	3.86	0.073	0.797	2.8.3.5	NA
17	0.060	1t9kD	0.629	4.08	0.082	0.838	5.3.1.23	78,128,148,178
18	0.060	1uwkA	0.515	4.49	0.028	0.756	4.2.1.49	53
19	0.060	1v9lA	0.517	4.89	0.078	0.822	1.4.1.2	NA
20	0.060	1b3bE	0.527	4.61	0.074	0.807	1.4.1.3	17
21	0.060	2ifyA	0.453	4.93	0.078	0.731	5.4.2.1	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	0.58	0.873	1.70	0.20	0.94	3hy6A	GO:0000166 GO:0005524 GO:0005542 GO:0005737 GO:0005759 GO:0005829 GO:0006536 GO:0009396 GO:0015942 GO:0016874 GO:0030272 GO:0035999 GO:0046653 GO:0046655 GO:0046657 GO:0046872
1	0.55	0.762	1.99	0.33	0.84	1wkcA	GO:0000166 GO:0005524 GO:0016874 GO:0030272 GO:0046872
2	0.53	0.935	0.76	0.18	0.95	2jcbA	GO:0000166 GO:0005524 GO:0016874 GO:0030272 GO:0046872
3	0.49	0.736	1.97	0.19	0.81	1sbqA	GO:0000166 GO:0005524 GO:0005737 GO:0016874 GO:0030272 GO:0046872
4	0.48	0.831	2.11	0.23	0.93	1souA	GO:0000166 GO:0005524 GO:0009396 GO:0030272 GO:0035999 GO:0046872
5	0.43	0.827	2.28	0.22	0.91	1ydmB	GO:0000166 GO:0005524 GO:0009396 GO:0030272 GO:0035999
6	0.17	0.578	3.53	0.07	0.74	3rrlB	GO:0008152 GO:0008260 GO:0008410 GO:0016740
7	0.06	0.368	6.15	0.05	0.70	4gq0A	GO:0001523 GO:0001758 GO:0004033 GO:0005576 GO:0005764 GO:0005829 GO:0006081 GO:0007586 GO:0008202 GO:0016488 GO:0016491 GO:0044597 GO:0044598 GO:0045550 GO:0047718 GO:0055114 GO:0070062
8	0.06	0.369	5.85	0.05	0.67	1c9wA	GO:0004032 GO:0005737 GO:0016491 GO:0055114
9	0.06	0.357	5.46	0.04	0.63	4r7pA	GO:0003983 GO:0005536 GO:0005634 GO:0005737 GO:0005829 GO:0005978 GO:0006011 GO:0006065 GO:0008152 GO:0016740 GO:0016779 GO:0019255 GO:0032557 GO:0042802 GO:0046872 GO:0070062 GO:0070569
10	0.06	0.292	5.25	0.07	0.49	4nhzH	GO:0016740
11	0.06	0.367	5.38	0.08	0.61	2jfgA	GO:0000166 GO:0005524 GO:0005737 GO:0007049 GO:0008360 GO:0008764 GO:0009058 GO:0009252 GO:0016874 GO:0042802 GO:0051301 GO:0071555
12	0.06	0.411	4.23	0.06	0.57	1g2iA	GO:0005737 GO:0006508 GO:0008233 GO:0016787 GO:0016798
13	0.06	0.305	5.90	0.04	0.56	2nraC	GO:0003887 GO:0005727 GO:0006260 GO:0006270 GO:0071897
14	0.06	0.301	5.72	0.07	0.53	2rhsC	GO:0000049 GO:0000166 GO:0000287 GO:0004812 GO:0004826 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006432 GO:0016874 GO:0043039 GO:0046872
15	0.06	0.244	4.59	0.09	0.37	1ng6A	GO:0016884
16	0.06	0.211	4.53	0.06	0.32	1m4mA	GO:0000086 GO:0000226 GO:0000228 GO:0000775 GO:0000776 GO:0000777 GO:0000910 GO:0004842 GO:0004869 GO:0005634 GO:0005694 GO:0005737 GO:0005814 GO:0005819 GO:0005829 GO:0005856 GO:0005874 GO:0005876 GO:0005881 GO:0006351 GO:0006355 GO:0006468 GO:0006915 GO:0007049 GO:0007059 GO:0007067 GO:0007346 GO:0008017 GO:0008270 GO:0008536 GO:0009966 GO:0010466 GO:0015631 GO:0016567 GO:0019899 GO:0030414 GO:0030496 GO:0031021 GO:0031503 GO:0031536 GO:0031577 GO:0032133 GO:0042802 GO:0042803 GO:0043027 GO:0043066 GO:0043154 GO:0043524 GO:0045892 GO:0045931 GO:0046872 GO:0046982 GO:0048037 GO:0051087 GO:0051301 GO:0051303 GO:0061178 GO:0061469 GO:0090307 GO:1990001
17	0.06	0.239	5.08	0.08	0.38	2yziB

Consensus prediction of GO terms

Molecular Function	GO:0030272	GO:0046872	GO:0005524	GO:0005542
GO-Score	0.98	0.98	0.98	0.58
Biological Processes	GO:0009396	GO:0035999	GO:0046657	GO:0015942	GO:0006536
GO-Score	0.78	0.78	0.58	0.58	0.58
Cellular Component	GO:0005759	GO:0005829
GO-Score	0.58	0.58

(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.