I-TASSER results

I-TASSER results for job id Rv0471c

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

Input Sequence in FASTA format

>protein (162 residues)
MPDAGAGSRLRSWAYALRTTNPPADGPTDTVTRWLVVTRAAVLPMTLVSGLVAGLLAIGE
PGLDWRWLVLWWESHAPHIANNLMNDLYDTDVGTDSATYARARYAQHPAATGANRAAYTT
PRRTTSCGSPERALEPTTPRWARAVGRSCWRRSPTGCCAPRC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPDAGAGSRLRSWAYALRTTNPPADGPTDTVTRWLVVTRAAVLPMTLVSGLVAGLLAIGEPGLDWRWLVLWWESHAPHIANNLMNDLYDTDVGTDSATYARARYAQHPAATGANRAAYTTPRRTTSCGSPERALEPTTPRWARAVGRSCWRRSPTGCCAPRC
Prediction	CCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCC
Conf.Score	987767654567777765579988885699999999865577889999999999999757888899999999999999988887887654578888887644446665445876555567754456787544445677577888777776557877777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPDAGAGSRLRSWAYALRTTNPPADGPTDTVTRWLVVTRAAVLPMTLVSGLVAGLLAIGEPGLDWRWLVLWWESHAPHIANNLMNDLYDTDVGTDSATYARARYAQHPAATGANRAAYTTPRRTTSCGSPERALEPTTPRWARAVGRSCWRRSPTGCCAPRC
Prediction	656435454043104203335444543242044103123234132232223200111243341311112202211331122223202323442234751444423422245354433243344345254464325443441042114411443343113568
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCC
MPDAGAGSRLRSWAYALRTTNPPADGPTDTVTRWLVVTRAAVLPMTLVSGLVAGLLAIGEPGLDWRWLVLWWESHAPHIANNLMNDLYDTDVGTDSATYARARYAQHPAATGANRAAYTTPRRTTSCGSPERALEPTTPRWARAVGRSCWRRSPTGCCAPRC

4tq3A1

0.12

0.09

0.74

1.44

wdPPAS

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYD----VDRHDGLNLSMQP-------LVTGEISVREAWLYCIAFLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A1

0.14

0.11

0.77

1.23

wMUSTER

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYDRD--VDRL-HDGLNLSMQPLVTGEISEAWL---YCIAFLALSLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A1

0.12

0.09

0.74

1.79

wPPAS

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYD----VDRLDGLNLSMQP-------LVTGEISVREAWLYCIAFLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A1

0.15

0.11

0.76

1.61

dPPAS2

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYDRD--VDRL-HDGLNLSMQPLVTGE-----ISVREAWLYCIAFLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A1

0.14

0.10

0.75

1.27

PPAS

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYD----VD-RLHDGLNLSMQPLVTGE-----ISVREAWLYCIAFLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A

0.12

0.09

0.74

0.97

wPPAS

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYD----VDRLDGLNLSMQP-------LVTGEISVRECIAFLALSLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4od4A1

0.16

0.10

0.64

0.96

wPPAS

------------------------------------LVR-FSLPFAYVGALLSR------YPFTADAILMAAAVVGLRMAGMAYNNIADL---IDRL--PRTAKRP-------LVVGAVSLREAWALVAAGFASAALLNTYALLLSPLVLAIALT----PRL

4tq3A1

0.13

0.10

0.78

0.97

MUSTER

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYDRD--VDRL-HDGLNLSMQPLVTGEISVREAW-LYCIAFLALSLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4tq3A1

0.13

0.10

0.78

0.80

dPPAS

-------------------------------SKYLRLLRPVAWLCFLLPYAVGFGFGITPNASLQHAVLGLLSFAFWMAFSFTINALYDRD--VDRL-HDGLNLSMQPLVTGEISVREAW-LYCIAFLALSLATAAAINEKFFLAMLGANIIGYVYSAPPRF

4od4A1

0.13

0.09

0.68

0.84

wdPPAS

------------------------------------LVR--EHTIFSLPFAYVGALLSRYPFTLADAILMAAAVVGLRMAGMAYNNIADL---ID-RLNPRTAKRP-------LVVGAVSLREVAAGSAIYFASAALLNTYALLLSPLVLAIALTY---PHA

(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=-1.21

Estimated TM-score = 0.56±0.15

Estimated RMSD = 7.5±4.3Å

Download Model 2

C-score=-2.18

Download Model 3

C-score=-3.03

Download Model 4

C-score=-2.17

Download Model 5

C-score=-1.97

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	4tq3A	0.693	1.58	0.122	0.759
2	2o1oA2	0.640	3.82	0.065	0.889
3	3saeA	0.639	3.65	0.065	0.876
4	4kk2A2	0.637	3.69	0.061	0.858
5	3s9vA2	0.632	3.52	0.053	0.870
6	3llwA	0.631	3.87	0.065	0.920
7	2ewgA2	0.629	3.90	0.079	0.883
8	1fpsA	0.625	3.99	0.046	0.920
9	2f8zF	0.625	3.93	0.059	0.901
10	5aypA	0.623	3.81	0.094	0.895

(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	0.12	5	1ubxA	MG	Rep, Mult	85,86,89
2	0.12	4	4tq4C	DMA	Rep, Mult	39,81,82,85,89,102,156,161
3	0.09	3	4tq4D	MG	Rep, Mult	85,89,95,161
4	0.07	3	1mkdB	MG	Rep, Mult	78,86
5	0.05	2	3qqvA	IPE	Rep, Mult	41,42,45,46,81,103
6	0.02	1	2wsc2	CLA	Rep, Mult	39,147
7	0.02	1	3n5hF	GO0	Rep, Mult	14,17,31,35,40
8	0.02	1	4dz4A	UNK	Rep, Mult	95,112
9	0.02	1	1d4m1	MYR	Rep, Mult	93,95

	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	2ewgA	0.612	3.84	0.047	0.895	2.5.1.10	39
2	0.060	2j1pB	0.599	3.95	0.128	0.901	2.5.1.1,2.5.1.10,2.5.1.29	NA
3	0.060	1wmwA	0.604	3.92	0.104	0.889	2.5.1.-	39
4	0.060	1di1A	0.560	3.76	0.071	0.784	4.2.3.9	NA
5	0.060	2oa6D	0.587	4.16	0.093	0.876	4.2.3.9	NA
6	0.060	2f8zF	0.625	3.93	0.059	0.901	2.5.1.10,2.5.1.1	51,136
7	0.060	1hxgA	0.603	3.85	0.059	0.870	4.2.3.9,4.1.99.7	46
8	0.060	2azkA	0.603	3.89	0.061	0.846	2.5.1.1,2.5.1.29,2.5.1.10	NA
9	0.060	1hm7A	0.542	3.74	0.120	0.765	4.2.3.7,4.6.1.5	NA
10	0.060	5coxA	0.497	4.83	0.040	0.802	1.14.99.1	NA
11	0.060	3b8eC	0.492	4.31	0.079	0.784	3.6.3.9	80
12	0.060	3lmdA	0.610	3.75	0.073	0.858	2.5.1.30	NA
13	0.060	1prhA	0.502	4.93	0.047	0.815	1.14.99.1	NA
14	0.060	2ftzA	0.568	4.00	0.080	0.852	2.5.1.10	NA
15	0.060	3m9uA	0.617	3.99	0.066	0.907	2.5.1.10	76,131,133
16	0.060	2h8oA	0.603	3.94	0.095	0.889	2.5.1.10	NA
17	0.060	2azjA	0.609	3.87	0.075	0.852	2.5.1.1	39
18	0.060	3npkA	0.578	4.12	0.063	0.889	2.5.1.10	NA
19	0.060	1rqiA	0.618	3.35	0.082	0.815	2.5.1.10	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	0.32	0.612	3.84	0.05	0.90	2ewgA	GO:0008299 GO:0016740 GO:0046872
1	0.31	0.602	3.89	0.07	0.86	1n1zA	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046211 GO:0046872 GO:0047926
2	0.28	0.625	3.99	0.05	0.92	1fpsA	GO:0004161 GO:0004337 GO:0005737 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008299 GO:0016126 GO:0016740 GO:0033384 GO:0045337 GO:0046872
3	0.28	0.613	3.94	0.03	0.90	2o1oA	GO:0008299 GO:0016740
4	0.24	0.614	3.76	0.08	0.86	3p5rA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0042617 GO:0046872 GO:0050553
5	0.12	0.604	3.89	0.05	0.88	2ongA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
6	0.09	0.628	3.49	0.05	0.86	3s9vB	GO:0000287 GO:0003824 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046872 GO:0050554 GO:0050559
7	0.09	0.695	1.83	0.13	0.77	4tq4D	GO:0004659 GO:0016020 GO:0016021
8	0.08	0.624	4.11	0.05	0.93	4dxjA	GO:0008299 GO:0016740
9	0.07	0.604	3.92	0.10	0.89	1wmwA	GO:0004311 GO:0008299 GO:0016740 GO:0033386
10	0.07	0.639	3.65	0.07	0.88	3saeA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016829 GO:0046872 GO:0052681
11	0.07	0.594	3.86	0.08	0.83	3rmgA	GO:0008299 GO:0016020 GO:0016021 GO:0016740
12	0.07	0.623	1.40	0.11	0.67	4tq6A	GO:0004659 GO:0016020 GO:0016021
13	0.07	0.599	4.06	0.06	0.91	3ucaA	GO:0004337 GO:0008299 GO:0016740 GO:0045337
14	0.07	0.601	3.76	0.07	0.86	3n0fA	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0034009 GO:0046872
15	0.07	0.599	3.98	0.08	0.87	5c05B	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
16	0.07	0.625	3.91	0.06	0.90	4demF	GO:0004161 GO:0004337 GO:0005654 GO:0005737 GO:0005829 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008299 GO:0016032 GO:0016126 GO:0016740 GO:0033384 GO:0044822 GO:0045337 GO:0046872
17	0.07	0.615	4.03	0.05	0.92	4jzbA	GO:0004161 GO:0004337 GO:0005737 GO:0005783 GO:0005829 GO:0006695 GO:0008299 GO:0016740 GO:0045337 GO:0046872
18	0.07	0.609	3.81	0.06	0.88	5dhiA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0004659	GO:0010333	GO:0000287	GO:0047926
GO-Score	0.56	0.47	0.47	0.31
Biological Processes	GO:0016126	GO:0045338	GO:0008654	GO:0033383	GO:1902653	GO:0042616	GO:0016102	GO:0046211
GO-Score	0.56	0.56	0.56	0.56	0.56	0.47	0.47	0.31
Cellular Component	GO:0009507
GO-Score	0.31

(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.