I-TASSER results

I-TASSER results for job id Rv0504c

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

Input Sequence in FASTA format

>protein (166 residues)
MTVPEEAQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPL
TFLAIAGRRVQLEIFTKFNIPINIARVFHRDQKFRFHRPILANDKLYFDTYLDSVIESHG
TVLAEIRSEVTDAEGKPVVTSVVTMLGEAAHHEADADATVAAIASI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTVPEEAQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQLEIFTKFNIPINIARVFHRDQKFRFHRPILANDKLYFDTYLDSVIESHGTVLAEIRSEVTDAEGKPVVTSVVTMLGEAAHHEADADATVAAIASI
Prediction	CCCHHHHHHHCCEEHCCCCEEEHCHHHHHHHHHHHCCCCCCHCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEHCCEEEEEHCCCCCCEEEEEEEEEEEEEEHCCCEEEEEEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
Conf.Score	9866999987796877985588779999999999889998558999999859999889868999999877666555655677877567676799995788999899999999999985996599999999959998899999999998688888877776666789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTVPEEAQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQLEIFTKFNIPINIARVFHRDQKFRFHRPILANDKLYFDTYLDSVIESHGTVLAEIRSEVTDAEGKPVVTSVVTMLGEAAHHEADADATVAAIASI
Prediction	7543641461045415354414044630341041141420022136105625266222121000000233334214323332333211313141403210304130304030430364662200203030314643200103010001145654544443562657
	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

CCCHHHHHHHCCEEHCCCCEEEHCHHHHHHHHHHHCCCCCCHCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEHCCEEEEEHCCCCCCEEEEEEEEEEEEEEHCCCEEEEEEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCCCCCCCCCC
MTVPEEAQTLIGKHYRAPDHFLVGREKIREFAVAVKDDHPTHYSEPDAAAAGYPALVAPLTFLAIAGRRVQLEIFTKFNIPINIARVFHRDQKFRFHRPILANDKLYFDTYLDSVIESHGTVLAEIRSEVTDAEGKPVVTSVVTMLGEAAHHEADADATVAAIASI

4rljA

0.44

0.38

0.87

3.33

MUSTER

LS-----ADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

4.54

dPPAS

-----LSADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

5.00

wdPPAS

LS-----ADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.86

4.53

wMUSTER

------LADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

5.19

wPPAS

LS-----ADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

6.93

dPPAS2

-----LSADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

4.80

PPAS

LS-----ADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rljA

0.44

0.38

0.87

4.15

Env-PPAS

LS-----ADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRA-----------------

4rv2A

0.39

0.32

0.81

2.93

MUSTER

---------IVGMHYRYPDFYEVGREKIREHALAIKNDETYFYDEDAAAELGHDALPAPLTFICIFGYQAQSAFFDHADIGVREAKIVQVDQELKFFKPIKAGDRLYCDVYVHAVRRAD---IIVTKNIITNDAGEIVQEAYTTLAG-------------------

4rv2A

0.39

0.32

0.81

4.01

dPPAS

---------IVGMHYRYPDFYEVGREKIREHALAIKNDETYFYDEDAAAELGHDALPAPLTFICIFGYQAQSAFFDHADIGVREAKIVQVDQELKFFKPIKAGDRLYCDVYVHAVRR---ADIIVTKNIITNDAGEIVQEAYTTLAG-------------------

(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=1.44

Estimated TM-score = 0.91±0.06

Estimated RMSD = 2.2±1.7Å

Download Model 2

C-score=-4.01

Download Model 3

C-score=-4.18

Download Model 4

C-score=-4.14

Download Model 5

C-score=-4.78

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	4v12A1	0.884	1.85	0.321	0.970
2	4rljA	0.850	0.71	0.438	0.868
3	4rv2A	0.795	0.73	0.393	0.813
4	1s9cG	0.731	2.52	0.144	0.855
5	2c2iA	0.728	2.23	0.206	0.849
6	1q6wC	0.721	2.61	0.168	0.861
7	2uvcG	0.711	2.83	0.154	0.837
8	3hmjG	0.710	2.79	0.154	0.837
9	4w78A	0.709	3.02	0.151	0.892
10	3kh8A	0.703	2.73	0.130	0.849

(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	0.21	13	1wlvC	COA	Rep, Mult	42,58,96,97,98,99,136
2	0.12	9	2glpA	BDE	Rep, Mult	48,57,98,99
3	0.07	5	3kvzB	ENV	Rep, Mult	33,57,59,60,61,96,99
4	0.03	2	4rltA	FSE	Rep, Mult	63,64,67,68,71,89,92,94,128,143,145
5	0.03	2	2b3m0	III	Rep, Mult	17,21,25,26,27,30,31,33,34,35,36,37,38,39,43,47,61,62,64,65,66,68,69,72,73,83,89,90,91,92,93,94,95,96
6	0.01	1	2cyeD	COA	Rep, Mult	89,90,91,116,117,118,123
7	0.01	1	3zvwC	MG	Rep, Mult	137,138
8	0.01	1	3bwxA	CA	Rep, Mult	99,102
9	0.01	1	2q78G	MLC	Rep, Mult	95,97,137
10	0.01	1	2glmA	SCB	Rep, Mult	43,44,45,57,99
11	0.01	1	2q78D	MLC	Rep, Mult	67,89,90,122,123
12	0.01	1	2xemB	SSV	Rep, Mult	71,72,74,87,110,112,126

	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	0.277	1s9cG	0.731	2.52	0.144	0.855	4.2.1.107	37,42
2	0.142	1lo8A	0.590	2.26	0.098	0.675	3.1.2.23	96,127
3	0.096	2v1oE	0.523	2.69	0.080	0.632	3.1.2.2	74,96
4	0.067	1u1zB	0.561	2.89	0.185	0.693	4.2.1.-	NA
5	0.067	1tbuB	0.469	2.30	0.102	0.542	3.1.2.2	72,140
6	0.067	1z6bA	0.551	2.66	0.168	0.669	4.2.1.-	73
7	0.067	2hx5A	0.552	2.41	0.129	0.645	3.1.2.-	NA
8	0.066	1y7uA	0.542	2.65	0.097	0.669	3.1.2.20	141,143
9	0.066	2qq2C	0.556	2.87	0.116	0.693	3.1.2.2	NA
10	0.066	1mkaA	0.543	3.46	0.101	0.723	4.2.1.60	42,57
11	0.060	1pn4C	0.581	2.25	0.121	0.681	4.2.1.-	37
12	0.060	2vz9B	0.461	4.20	0.069	0.705	2.3.1.85	108
13	0.060	3khpA	0.701	3.17	0.167	0.868	1.-.-.-	37,42
14	0.060	2ortA	0.428	5.05	0.049	0.729	1.14.13.39	NA
15	0.060	1nosA	0.432	5.05	0.042	0.729	1.14.13.39	NA
16	0.060	3b7kC	0.538	3.23	0.066	0.681	3.1.2.1	94,96
17	0.060	2ownB	0.582	3.17	0.071	0.705	3.1.2.14	NA
18	0.060	2vz8B	0.461	4.23	0.069	0.699	2.3.1.85	NA
19	0.060	1iq6B	0.662	2.46	0.152	0.789	4.2.1.17	37,42
20	0.060	2vkzG	0.710	2.79	0.154	0.837	2.3.1.38,3.1.2.14	NA
21	0.060	3d6xB	0.529	2.71	0.078	0.645	4.2.1.-	71
22	0.060	3ebfA	0.449	5.33	0.076	0.789	1.14.13.39	61
23	0.060	2uutA	0.441	4.67	0.048	0.711	3.6.1.15	NA
24	0.060	2cf2C	0.547	3.48	0.094	0.735	2.3.1.85	57
25	0.060	2gllA	0.551	2.90	0.089	0.693	4.2.1.-	73
26	0.060	3e65B	0.449	5.27	0.076	0.783	1.14.13.39	NA
27	0.060	3ir3A	0.586	2.85	0.114	0.723	4.2.1.-	NA
28	0.060	2c2iA	0.728	2.23	0.206	0.849	4.2.1.17	37,42
29	0.060	2vz8A	0.477	3.27	0.093	0.608	2.3.1.85	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	0.47	0.864	1.61	0.41	0.90	4rltA	GO:0005886 GO:0019171 GO:0040007
1	0.28	0.721	2.61	0.17	0.86	1q6wC
2	0.25	0.639	2.92	0.12	0.75	4oobA	GO:0004312 GO:0005835 GO:0005886 GO:0006631 GO:0006633 GO:0018812 GO:0019171 GO:0055114
3	0.25	0.692	2.52	0.16	0.83	3exzB
4	0.24	0.682	2.87	0.16	0.83	5cpgA	GO:0004312 GO:0005835 GO:0006633 GO:0016829 GO:0055114
5	0.24	0.679	2.48	0.16	0.82	4ffuI	GO:0016491 GO:0055114
6	0.20	0.662	2.46	0.15	0.79	1iq6B	GO:0004312 GO:0005835 GO:0006629 GO:0006631 GO:0006633 GO:0016829 GO:0055114
7	0.17	0.586	2.85	0.11	0.72	3ir3A	GO:0005730 GO:0005737 GO:0005739 GO:0006629 GO:0006631 GO:0016829
8	0.16	0.654	2.07	0.17	0.75	3k67A	GO:0004312 GO:0005835 GO:0006633 GO:0055114
9	0.13	0.731	2.52	0.14	0.86	1s9cG	GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
10	0.11	0.703	2.73	0.13	0.85	3kh8A
11	0.10	0.701	3.17	0.17	0.87	3khpA
12	0.09	0.660	2.87	0.10	0.80	1pn4D	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
13	0.08	0.655	2.44	0.14	0.76	1s9cD	GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
14	0.07	0.654	2.47	0.15	0.76	3omlA	GO:0003824 GO:0004300 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0033540 GO:0042803 GO:0055114 GO:0080023
15	0.07	0.584	2.76	0.13	0.72	3khpC
16	0.07	0.581	2.25	0.12	0.68	1pn4C	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
17	0.06	0.323	5.44	0.03	0.60	3kveA	GO:0001716 GO:0005576 GO:0006915 GO:0016491 GO:0019835 GO:0042742 GO:0044179 GO:0046872 GO:0055114
18	0.06	0.238	5.43	0.06	0.45	3nvoA	GO:0005385 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006829 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085 GO:0071577 GO:0098655
19	0.06	0.267	6.45	0.01	0.58	1reoA	GO:0001716 GO:0005576 GO:0006915 GO:0016491 GO:0019835 GO:0042742 GO:0044179 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0019171	GO:0004312
GO-Score	0.60	0.43
Biological Processes	GO:0040007	GO:0055114	GO:0006633
GO-Score	0.47	0.43	0.43
Cellular Component	GO:0005886	GO:0005835
GO-Score	0.60	0.43

(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.