I-TASSER results

I-TASSER results for job id Rv3655c

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

Input Sequence in FASTA format

>protein (125 residues)
MEAALAIATLVLVLVLCLAGVTAVSMQVRCIDAAREAARLAARGDVRSATDVARSIAPRA
ALVQVHRDGEFVVATVTAHSNLLPTLDIAARAISVAEPGSTAARPPCLPSRWSRCCCASP
VRVHI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEAALAIATLVLVLVLCLAGVTAVSMQVRCIDAAREAARLAARGDVRSATDVARSIAPRAALVQVHRDGEFVVATVTAHSNLLPTLDIAARAISVAEPGSTAARPPCLPSRWSRCCCASPVRVHI
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCEEEEEEHCCEEEEEEEHCCCCCCCEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	86458999999999999999999999999999999999999989988999999998999858999976889999999868888867999999874688878888888865445544568764469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEAALAIATLVLVLVLCLAGVTAVSMQVRCIDAAREAARLAARGDVRSATDVARSIAPRAALVQVHRDGEFVVATVTAHSNLLPTLDIAARAISVAEPGSTAARPPCLPSRWSRCCCASPVRVHI
Prediction	54203022233333223322121022332023103400323144447403520463227514030455343030303153432330303142323443646637645334414311024425346
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCEEEEEEHCCEEEEEEEHCCCCCCCEEEEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MEAALAIATLVLVLVLCLAGVTAVSMQVRCIDAAREAARLAARGDVRSATDVARSIAPRAALVQVHRDGEFVVATVTAHSNLLPTLDIAARAISVAEPGSTAARPPCLPSRWSRCCCASPVRVHI

3h0nA

0.17

0.16

0.96

0.79

MUSTER

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLAIGHQNVRNAHRRNGTRQY---CCQN--RVKA

3sokA

0.11

0.98

0.78

dPPAS

--FTLIELMIVVAIIGILAAFAIPAYNDYIARSQAAEGLTLADGLKVRISDHLESANPASGSLGNDDKGKYALATIDNKDAKTADEKNGCKVVITYGQGTAGEKISKLIVGYKYNEGETDLELKF

3h0nA

0.16

0.15

0.95

0.86

wdPPAS

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLAREAHRCD-DTSRNGTRQY--C-CQN--RVKA

3h0nA

0.17

0.16

0.96

1.00

wMUSTER

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLAIGHQNVRNAHRRNGTRQY--C-CQN--RVKA

3h0nA

0.18

0.17

0.94

0.87

wPPAS

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLAIGHQNVR-NAHRCD-SQY--C-CQN--RVKA

3h0nA

0.16

0.15

0.93

0.99

dPPAS2

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLARE---IGHQN----VRRFGI--CNAHDRVYF

3h0nA

0.18

0.95

0.93

PPAS

GCVIEDLHDLLKDDPASVAQLDHVEGFVELARLLHTAIDALSNGQVATAATALNHLLPATPELAQDPDGTWRLHHHPLDAELVPWTAICAEGLAIGHQNVR-NAHRC---DRSRNCCQN--RVKA

1fifA

0.13

0.12

0.91

0.62

Env-PPAS

AEINTLKSKLELTNKLHAFSMGKKSGK-KFFSKVKALCSELAIPRNAEENKAIQEVAKTSAFLGITTEGQFMYVT---------GGRLTYSNWKKDQPDDWYGHGLGVDNLWNDDSCQRPYTA-V

4ok0A1

0.14

0.13

0.89

0.78

MUSTER

SEQALNHEKLMRAIVKNLADTPMVLKGETALYLGYGLNRFSDCHKKINLLGRVKSAIPNGIDIHIKKDTDRYMVRYATKDNK-EEQTLKLEISY---------RDAPKESEV---NVIEGMRIA-

4fmyA

0.11

0.10

0.97

0.76

dPPAS

AANTKAINILEVRLTTAEGKIVVLRSDVDYLLDEVIDIQAHLVTVDQRLDGVESDV----SDIKSDYVSKTVTESQSLASPLDVKTSYSVDGIQVVGARQTGWTAATGTPLLGSFNANQSYTVGT

(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=-2.21

Estimated TM-score = 0.45±0.15

Estimated RMSD = 9.2±4.6Å

Download Model 2

C-score=-3.32

Download Model 3

C-score=-4.34

Download Model 4

C-score=-4.33

Download Model 5

C-score=-3.84

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	4s2rP2	0.589	4.01	0.071	0.872
2	5jqkA	0.580	3.81	0.025	0.864
3	4b28A	0.579	3.90	0.067	0.888
4	4r60A	0.574	3.60	0.076	0.856
5	1fsaA1	0.568	3.93	0.037	0.864
6	3fmrA	0.568	3.87	0.035	0.848
7	3ctzA	0.567	3.84	0.041	0.848
8	2qvrA1	0.567	3.69	0.062	0.848
9	1yw8A	0.561	3.94	0.018	0.856
10	2bwxA	0.561	3.82	0.057	0.848

(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	0.13	9	2fieA	A74	Rep, Mult	7,8,10,11,12,14,15,16,19,20,23,24,27,108
2	0.10	6	2wbbH	RO3	Rep, Mult	34,37,38,40,49,50,53,54,55,56
3	0.06	4	3erzD	HG	Rep, Mult	41,45,49
4	0.04	3	5e3kB	CO3	Rep, Mult	35,39
5	0.04	3	2i0mA	ZN	Rep, Mult	32,36
6	0.03	2	4khyA	CA	Rep, Mult	39,42
7	0.03	2	1h9mA	MOO	Rep, Mult	76,77,80
8	0.01	1	1qb4A	MN	Rep, Mult	2,32
9	0.01	1	3h0nA	ZN	Rep, Mult	115,116,117
10	0.01	1	1htwA	MG	Rep, Mult	44,45
11	0.01	1	5jreH	ADE	Rep, Mult	34,35,91
12	0.01	1	1nv0A	PO4	Rep, Mult	19,20,22,23,86,87
13	0.01	1	4mhlA	ARF	Rep, Mult	25,29
14	0.01	1	5hzzB	MN	Rep, Mult	29,32

	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	1hxgA	0.550	4.70	0.068	0.904	4.2.3.9,4.1.99.7	9
2	0.060	2j5cB	0.514	4.46	0.034	0.824	4.2.3.-	NA
3	0.060	2iw2A	0.557	3.80	0.025	0.840	3.4.13.9	NA
4	0.060	1pv9B	0.506	3.79	0.063	0.760	3.4.13.9	97
5	0.060	2oknA	0.557	3.80	0.025	0.840	3.4.13.9	NA
6	0.060	1o0xA	0.533	3.77	0.107	0.800	3.4.11.18	NA
7	0.060	1hm7B	0.526	4.22	0.071	0.832	4.2.3.7,4.6.1.5	NA
8	0.060	1n1zA	0.523	4.92	0.033	0.928	5.5.1.8	NA
9	0.060	1qxyA	0.529	3.75	0.078	0.808	3.4.11.18	30,77,125
10	0.060	1fuiA	0.515	4.34	0.062	0.872	5.3.1.25	36,51
11	0.060	3kb9A	0.555	4.79	0.097	0.952	4.2.3.37	NA
12	0.060	2hb6A	0.525	4.70	0.073	0.912	3.4.11.1	NA
13	0.060	2hb6B	0.525	4.70	0.073	0.912	3.4.11.1	34,39
14	0.060	4matA	0.534	3.81	0.065	0.816	3.4.11.18	27
15	0.060	1jawA	0.560	3.82	0.057	0.848	3.4.11.9	NA
16	0.060	2qvrA	0.567	3.69	0.062	0.848	3.1.3.11	NA
17	0.060	1ftaA	0.555	3.93	0.043	0.872	3.1.3.11	NA
18	0.060	3ctzA	0.567	3.84	0.041	0.848	3.4.11.9	NA
19	0.060	2zsgA	0.542	3.64	0.069	0.808	3.4.11.9	97

(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	0.12	0.557	3.80	0.03	0.84	2iw2A	GO:0004177 GO:0004181 GO:0006508 GO:0006520 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0030145 GO:0030574 GO:0046872 GO:0070062 GO:0102009
1	0.08	0.506	3.79	0.06	0.76	1pv9B	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
2	0.07	0.573	3.61	0.08	0.86	4r60B	GO:0016787 GO:0046872
3	0.07	0.589	4.01	0.07	0.87	4s2rP	GO:0004177 GO:0006508 GO:0016787 GO:0046872
4	0.07	0.564	3.80	0.07	0.85	4pv4A	GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
5	0.07	0.567	3.84	0.04	0.85	3ctzA	GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0010815 GO:0016787 GO:0030145 GO:0042803 GO:0046872 GO:0070006 GO:0070062
6	0.07	0.544	3.66	0.03	0.79	4zwuA	GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
7	0.07	0.544	3.66	0.04	0.79	3l24B	GO:0004063 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0009636 GO:0016311 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0047862 GO:0102009
8	0.07	0.549	3.50	0.03	0.80	3rvaA	GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0016795 GO:0016805 GO:0046872 GO:0102009
9	0.07	0.519	3.93	0.08	0.80	1pv9A	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
10	0.07	0.546	3.80	0.07	0.85	4fukA	GO:0004177 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0022626 GO:0046872 GO:0070006 GO:0070084
11	0.07	0.494	3.92	0.07	0.74	4fkcA	GO:0004177 GO:0006508 GO:0016787 GO:0046872
12	0.07	0.538	3.67	0.09	0.80	4egeA	GO:0016787 GO:0046872
13	0.07	0.564	3.73	0.04	0.84	3ig4A	GO:0004177 GO:0006508 GO:0016787 GO:0030145 GO:0046872
14	0.07	0.436	5.02	0.06	0.79	3ct9B	GO:0006508 GO:0006526 GO:0008152 GO:0008237 GO:0008270 GO:0008777 GO:0016787 GO:0043171 GO:0070573
15	0.06	0.553	3.65	0.08	0.82	3q6dA	GO:0006508 GO:0016787 GO:0016805 GO:0046872 GO:0102009
16	0.06	0.320	4.75	0.03	0.58	4m05B	GO:0016491 GO:0046872 GO:0050587 GO:0055114
17	0.06	0.544	3.61	0.06	0.81	2howA	GO:0016787
18	0.06	0.562	3.80	0.06	0.85	2bh3A	GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008235 GO:0008237 GO:0016787 GO:0030145 GO:0042802 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0008238	GO:0046914
GO-Score	0.46	0.36
Biological Processes	GO:0019538
GO-Score	0.59
Cellular Component	GO:0070062	GO:0005737
GO-Score	0.12	0.08

(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.