I-TASSER results

I-TASSER results for job id Rv3705c

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

Input Sequence in FASTA format

>protein (214 residues)
MRIAAAVVSIGLAVIAGFAVPVADAHPSEPGVVSYAVLGKGSVGNIVGAPMGWEAVFTRP
FQAFWVELPACNNWVDIGLPEVYDDPDLASFNGATTQTSATDQTHLVKQAVGVFASNDAA
DRAFHRVVDRTVGCSGQTTAIHLDDGTTQVWSFAGGPSTGTDEAWTKQEAGTDRRCFVQT
RLRENVLLQAKVCQSGNAGPAVNVLAGAMQNTLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRIAAAVVSIGLAVIAGFAVPVADAHPSEPGVVSYAVLGKGSVGNIVGAPMGWEAVFTRPFQAFWVELPACNNWVDIGLPEVYDDPDLASFNGATTQTSATDQTHLVKQAVGVFASNDAADRAFHRVVDRTVGCSGQTTAIHLDDGTTQVWSFAGGPSTGTDEAWTKQEAGTDRRCFVQTRLRENVLLQAKVCQSGNAGPAVNVLAGAMQNTLG
Prediction	CCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHCCCCEEHCCCCCCCCCCCCCCHHHHHHHHHCHHHHCCCCCCEEEEEEEEHCCCCCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCEEEEEEEEEHCCCCEEEEEEEHCCCCCCEEEEEEHCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHCC
Conf.Score	9854677765445677888899899999977757577999999998798766764567888888899977766665544554578884578889986799998758999999988999999999999999986698789997799976689997555689879999987799874446555434488999985699987899999999997569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRIAAAVVSIGLAVIAGFAVPVADAHPSEPGVVSYAVLGKGSVGNIVGAPMGWEAVFTRPFQAFWVELPACNNWVDIGLPEVYDDPDLASFNGATTQTSATDQTHLVKQAVGVFASNDAADRAFHRVVDRTVGCSGQTTAIHLDDGTTQVWSFAGGPSTGTDEAWTKQEAGTDRRCFVQTRLRENVLLQAKVCQSGNAGPAVNVLAGAMQNTLG
Prediction	7402000000011213344344463533527505513043730351143424444434443444424342032124223541164531211222224347844411010000001347304510440164047144442424357454440414434446531313345447322022113232100000200243464500430152057468
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHCCCCEEHCCCCCCCCCCCCCCHHHHHHHHHCHHHHCCCCCCEEEEEEEEHCCCCCCCEEEEEEEEEHCCHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCEEEEEEEEEHCCCCEEEEEEEHCCCCCCEEEEEEHCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHCC
MRIAAAVVSIGLAVIAGFAVPVADAHPSEPGVVSYAVLGKGSVGNIVGAPMGWEAVFTRPFQAFWVELPACNNWVDIGLPEVYDDPDLASFNGATTQTSATDQTHLVKQAVGVFASNDAADRAFHRVVDRTVGCSGQTTAIHLDDGTTQVWSFAGGPSTGTDEAWTKQEAGTDRRCFVQTRLRENVLLQAKVCQSGNAGPAVNVLAGAMQNTLG

4esqA

0.20

0.18

0.89

2.62

MUSTER

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSMQPGKPITSMDSSPVVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVTN-KAKTYRWTFADVKGSPPTITVIDTQEGEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.18

0.16

0.89

3.57

dPPAS

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSSMQPGKTSMDSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVTN-KAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.18

0.16

0.89

5.51

wdPPAS

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSSMQPGKTSMDSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVT-NKAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.20

0.17

0.88

3.33

wMUSTER

------------------------HQPVAEERLSALLLNSSEVNAVMGSSMQPGKPITSMDSSPVVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVT-NKAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.18

0.16

0.89

5.77

wPPAS

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSSMQPGKTSMDSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVT-NKAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.18

0.16

0.89

9.59

dPPAS2

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSSMQPGKTSMDSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVTN-KAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.19

0.17

0.89

4.44

PPAS

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSMQPGKPITSMSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVT-NKAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4esqA

0.19

0.17

0.89

4.76

Env-PPAS

-----------------------GHQPVAEERLSALLLNSSEVNAVMGSSMQPGKPITSMSSPVTVSLPDCQGALYTSQDPVYAGTGYTAINGLISSEPGDNYEHWVNQAVVAFPTADKARAFVQTSADKWKNCAGKTVTVT-NKAKTYRWTFADVKGSPPTITVIDTQGAEGWECQRAMSVANNVVVDVNACGYQITNQAGQIAAKIVDKVNK

4tmdA

0.08

0.07

0.83

0.74

MUSTER

--------------------AYPDADIAKVAQLKSSFGPEFKVSEVAPTGIDPKLLSPQKLPEVKFEPADCAKFAEGQQ---FPPGLQGNMAATAAE--GEGNRFIVMAVETSEPVP---------LSDPGDECK--RVKFLGTGARGQVDVVESPQIDDAGTHRIIQTMRTGELYNYVASFDNYMVIVTANPLVLPDKRARELLSAAVAAVRA

4nx9A

0.09

0.97

0.69

dPPAS

QQSTNILQRRDLSLQSANGSNSDSERTALNGEVKQLQKELDRISNTTGSFGVASFQVGSAANEESAESLNGTYFKADGGGAVTAATASGTVDIAIDITGGS------AVNVKVDKGNETAEQAAAKIAAAVNDANVGIGAFTDGAQISYVSKASADGTTSAVSGVAITDTGSTGAGTAAGTTTFTEANDTVAKIDISTAKGAQSAVLVIDEAIK

(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=-0.03

Estimated TM-score = 0.71±0.12

Estimated RMSD = 5.5±3.5Å

Download Model 2

C-score=-0.16

Download Model 3

C-score=-2.64

Download Model 4

C-score=-1.29

Download Model 5

C-score=-2.44

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	4esqA	0.860	1.09	0.189	0.888
2	4tmdA	0.571	3.67	0.063	0.748
3	2lnjA	0.503	3.96	0.026	0.668
4	4rthA	0.482	3.52	0.050	0.617
5	4r1dB	0.479	4.10	0.054	0.640
6	1v2bB	0.467	3.58	0.074	0.598
7	2xb3A	0.466	4.23	0.077	0.654
8	3wiqA1	0.466	4.49	0.043	0.635
9	4ol4A	0.463	3.81	0.059	0.608
10	3hlzB	0.460	3.53	0.111	0.584

(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	1h3uB	NAG	Rep, Mult	91,113,186
2	0.06	3	2ckjA	FES	Rep, Mult	117,119,121,183,184,185
3	0.06	3	3jadA	SY9	Rep, Mult	96,107,109,179,181,188
4	0.06	3	1py2B	ZN	Rep, Mult	125,129
5	0.04	2	3eubS	FES	Rep, Mult	132,133,134,136,153
6	0.02	1	2zyqB	TAR	Rep, Mult	30,31
7	0.02	1	3uufA	MAN	Rep, Mult	101,102
8	0.02	1	1t5bA	FMN	Rep, Mult	38,43
9	0.02	1	2bq8X	ZN	Rep, Mult	81,85
10	0.02	1	4flfA	XXH	Rep, Mult	116,118
11	0.02	1	4zr2A	RET	Rep, Mult	71,180,189
12	0.02	1	4xniA	78M	Rep, Mult	120,127
13	0.02	1	3kdnA	CAP	Rep, Mult	151,211
14	0.02	1	1mpxA	CA	Rep, Mult	81,84,87,92
15	0.02	1	2ckjC	FES	Rep, Mult	43,47,49,97

	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	1t3qB	0.423	5.15	0.032	0.678	1.3.99.17	NA
2	0.060	1nyqB	0.403	5.32	0.050	0.664	6.1.1.3	NA
3	0.060	1n63B	0.431	5.08	0.053	0.682	1.2.99.2	NA
4	0.060	2c6fA	0.406	5.75	0.087	0.696	3.4.15.1	NA
5	0.060	2vsmA	0.352	5.82	0.066	0.608	3.2.1.18	NA
6	0.060	1f1sA	0.357	5.82	0.060	0.622	4.2.2.1	183
7	0.060	2cqsA	0.437	4.76	0.041	0.626	2.4.1.20	NA
8	0.060	2e1qA	0.415	5.85	0.056	0.729	1.17.3.2,1.17.1.4	NA
9	0.060	2wafA	0.446	4.38	0.046	0.617	3.4.-.-	NA
10	0.060	2ow6A	0.419	5.48	0.070	0.687	3.2.1.114	121
11	0.060	3b9jI	0.242	5.07	0.063	0.383	1.17.1.4,1.17.3.2	207
12	0.060	2e0wB	0.419	5.58	0.054	0.724	2.3.2.2	180
13	0.060	1z11A	0.303	6.08	0.055	0.551	1.14.14.1	176
14	0.060	2z8kC	0.349	5.29	0.055	0.570	2.3.2.2	78,123,124,133
15	0.060	3b9jJ	0.330	6.08	0.070	0.589	1.17.1.4,1.17.3.2	55
16	0.060	1i8qA	0.404	5.03	0.043	0.617	4.2.2.1	111
17	0.060	2ckjA	0.428	5.38	0.038	0.692	1.17.1.4,1.17.3.2	NA
18	0.060	1ffuB	0.430	5.10	0.032	0.682	1.2.99.2	NA
19	0.060	3fwmA	0.443	4.89	0.053	0.659	2.4.1.129,	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	0.41	0.860	1.09	0.19	0.89	4esqA	GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005618 GO:0005886 GO:0005887 GO:0006468 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0043085 GO:0043086 GO:0043388 GO:0045893 GO:0045926 GO:0046777 GO:0046890 GO:0052572
1	0.07	0.482	3.52	0.05	0.62	4rthA	GO:0005509 GO:0009523 GO:0009654 GO:0015979 GO:0019898
2	0.07	0.466	4.23	0.08	0.65	2xb3A	GO:0005509 GO:0009523 GO:0009654 GO:0015979 GO:0019898 GO:0046872
3	0.07	0.503	3.96	0.03	0.67	2lnjA	GO:0005509 GO:0009523 GO:0009654 GO:0015979 GO:0019898
4	0.07	0.464	3.49	0.07	0.59	2vu4A	GO:0005509 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009579 GO:0009654 GO:0015979 GO:0016020 GO:0019898
5	0.07	0.467	3.58	0.07	0.60	1v2bB	GO:0005509 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009579 GO:0009654 GO:0015979 GO:0016020 GO:0019898
6	0.07	0.462	4.05	0.05	0.64	4rtiA	GO:0005509 GO:0009507 GO:0009523 GO:0009535 GO:0009536 GO:0009579 GO:0009654 GO:0015979 GO:0016020 GO:0019898
7	0.06	0.303	6.29	0.05	0.57	4n0qB	GO:0006810 GO:0006865
8	0.06	0.319	6.09	0.05	0.57	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
9	0.06	0.281	6.09	0.05	0.50	2yntA	GO:0046872
10	0.06	0.310	5.71	0.07	0.52	4pz2B	GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
11	0.06	0.319	6.09	0.02	0.57	2i7xA	GO:0003723 GO:0005634 GO:0005847 GO:0005849 GO:0006378 GO:0006379 GO:0006397 GO:0098789
12	0.06	0.332	5.34	0.04	0.55	3h3eA	GO:0016787 GO:0046872
13	0.06	0.346	5.27	0.07	0.58	4qi7A	GO:0004553 GO:0005576 GO:0005975 GO:0016491 GO:0016614 GO:0030248 GO:0047735 GO:0050660 GO:0055114
14	0.06	0.301	6.23	0.06	0.56	1onkA	GO:0006952 GO:0016787 GO:0017148 GO:0030246 GO:0030598
15	0.06	0.370	6.07	0.05	0.69	5c97A	GO:0000209 GO:0002480 GO:0004177 GO:0005576 GO:0005622 GO:0005765 GO:0005829 GO:0005886 GO:0005887 GO:0006508 GO:0007165 GO:0007267 GO:0007565 GO:0008217 GO:0008233 GO:0008237 GO:0008270 GO:0016020 GO:0016021 GO:0016787 GO:0030163 GO:0030659 GO:0031905 GO:0042277 GO:0043171 GO:0046872 GO:0048471 GO:0060395 GO:0061024 GO:0070006
16	0.06	0.302	5.51	0.07	0.51	4uttA	GO:0003824 GO:0005975 GO:0006051 GO:0008152 GO:0016853 GO:0016857 GO:0019262 GO:0047465
17	0.06	0.269	6.37	0.05	0.52	3pmqA	GO:0009055 GO:0046872
18	0.06	0.331	5.94	0.08	0.59	3g5sA	GO:0005737 GO:0008033 GO:0008168 GO:0016491 GO:0016740 GO:0030698 GO:0032259 GO:0047151 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0005524	GO:0004674
GO-Score	0.47	0.41	0.41
Biological Processes	GO:0043086	GO:0045926	GO:0043085	GO:0045893	GO:0043388	GO:0046890	GO:0052572	GO:0046777
GO-Score	0.41	0.41	0.41	0.41	0.41	0.41	0.41	0.41
Cellular Component	GO:0009521	GO:0042651	GO:1990204	GO:0005887	GO:0005618
GO-Score	0.47	0.47	0.47	0.41	0.41

(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.