I-TASSER results

I-TASSER results for job id Rv1312

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

Input Sequence in FASTA format

>protein (147 residues)
MSAPMIGMVVLVVVLGLAVLALSYRLWKLRQGGTAGIMRDIPAVGGHGWRHGVIRYRGGE
AAFYRLSSLRLWPDRRLSRRGVEIISRRAPRGDEFDIMTDEIVVVELCDSTQDRRVGYEI
ALDRGALTAFLSWLESRPSPRARRRSM

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSAPMIGMVVLVVVLGLAVLALSYRLWKLRQGGTAGIMRDIPAVGGHGWRHGVIRYRGGEAAFYRLSSLRLWPDRRLSRRGVEIISRRAPRGDEFDIMTDEIVVVELCDSTQDRRVGYEIALDRGALTAFLSWLESRPSPRARRRSM
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEHCCCCCCCCEEEEEEEEHCCEEEEEEEEHCCCCCCEEEHCCCEEEEEHCCCCCHHHHHCCCCEEEEEEEHCCCCCCCEEEEEHCCCHHHHHHHHHHHCCCCCCCCCCC
Conf.Score	987589999999999999999999999984687589999858999998577999996998999998875678867998575799876689985676468988999999689888766999968756788999998689877777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSAPMIGMVVLVVVLGLAVLALSYRLWKLRQGGTAGIMRDIPAVGGHGWRHGVIRYRGGEAAFYRLSSLRLWPDRRLSRRGVEIISRRAPRGDEFDIMTDEIVVVELCDSTQDRRVGYEIALDRGALTAFLSWLESRPSPRARRRSM
Prediction	652221121212122222123223223334340120001324467642022010213553042120212333242304144040254152565334214632200202354764523010003462230020011233573555478
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEHCCCCCCCCEEEEEEEEHCCEEEEEEEEHCCCCCCEEEHCCCEEEEEHCCCCCHHHHHCCCCEEEEEEEHCCCCCCCEEEEEHCCCHHHHHHHHHHHCCCCCCCCCCC
MSAPMIGMVVLVVVLGLAVLALSYRLWKLRQGGTAGIMRDIPAVGGHGWRHGVIRYRGGEAAFYRLSSLRLWPDRRLSRRGVEIISRRAPRGDEFDIMTDEIVVVELCDSTQDRRVGYEIALDRGALTAFLSWLESRPSPRARRRSM

2metA

0.15

0.03

0.22

1.33

dPPAS2

LEIIILEGTAVIAMFFWLLLVIILRTVKRANGG------------------------------------------------------------------------------------------------------------------

2mv6A

0.21

0.05

0.22

1.25

dPPAS2

ILTLSLILVVILVLLTVLALLSHRRALKQKIWP------------------------------------------------------------------------------------------------------------------

4ipuA

0.13

0.12

0.88

0.79

MUSTER

ID-PFTERNELQSAAEELNALQYARSEAVSQRR-AISIQAL---KDKDWGKGLSIGVLGSIA--RKHDGFRAATLTAKEKSAVEHLTFTANG--TLVPPTERTFAICQNGKTDG--GRVLSISQAGR------IQLEPSSKAPQSCY

5bw0B

0.16

0.10

0.61

0.90

dPPAS

-------NASRLEDKTLAMWIADNRLNELQ---------LEQTPPSSGRNQGELEFAGRRWEWRTQVDSTAEQDM----RRVIVWVAAKPLGRGSIEERAAARLVGFLG--------------------------------------

1btnA

0.12

0.07

0.61

0.84

wdPPAS

---------------------------------MEGFLNRKHEASSRSWHNVYCVINNQEMGFYK--GIPYHSEVPVSLKEAICEVALDYKKKK---------VFKLRLSDGN-----EYLFQAKDDEEMNTWIQA--------SA-

4ipuA

0.15

0.13

0.86

0.88

wMUSTER

ID-PFTERNELQSAAEELNALQYARSEAVSQRR-AISIQAL---KDKDWGKGLSIGVLGSIA--RKHDGFRAATLTAK-SAVEHLTFT-ANG--TLVPPTERTFAICQNGKTDG--GRVLSISQ---AG----IQLEPSSKAPQSCY

3a8pA1

0.20

0.14

0.69

0.87

wPPAS

------------VVR-----WLFFKPLVTLQKE-----RKLELVARRKWKQYWVTLKGCTLLFYE----KSAPRCALFAEDSIVQSVPEHPKKE---------VFCLSNSC---GDVYLFQ---TSQTDLENWVTA--FAKKHGK--

3j2wE

0.15

0.03

0.18

1.22

dPPAS2

ITGGVGLIVAVAALILIVVLCVSFSRH------------------------------------------------------------------------------------------------------------------------

2lcgA

0.10

0.09

0.91

0.80

PPAS

MNITV---TVAAPVGKVWRAYTTPEDIKQ-SDDWHTTAATVDLREGGAFSSRMEAKDGSMGFDFAGTYTKVVENIEYAFGDRTAKVEFLEAPQ------GVTVRVSFVAETEYPVEQQQQGW-QAILNNFKRHVESHLEHHHHHH--

4xydB

0.12

0.11

0.88

0.89

Env-PPAS

MANIFYGGSLFFILIFVGLSVHSHRYIVTTST--------DAATLTAEVEHGKHLWEIHGVNCHSIEGAYFAPELG------NVMTRWGVEDDPDAAFEALKGWMDAMPTGIEGRRQMNFGLNDEEYRALSDFLLWTPPNDAG----

(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=-2.98

Estimated TM-score = 0.38±0.13

Estimated RMSD = 11.5±4.5Å

Download Model 2

C-score=-4.09

Download Model 3

C-score=-4.29

Download Model 4

C-score=-4.25

Download Model 5

C-score=-4.58

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	4ipuA	0.628	3.66	0.105	0.898
2	2knqA	0.576	3.73	0.074	0.830
3	2qv8A	0.516	3.88	0.060	0.769
4	4gdgA	0.510	3.96	0.055	0.748
5	3kvnX2	0.508	4.28	0.066	0.782
6	5djfA	0.506	3.92	0.132	0.762
7	2bjiA	0.500	3.80	0.093	0.735
8	5ce6A	0.500	4.26	0.017	0.762
9	2qvrA	0.498	4.33	0.111	0.789
10	1ka1A	0.497	4.03	0.061	0.748

(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	0.11	6	4gx0B	GLC	Rep, Mult	25,35
2	0.08	4	3prqX	CLA	Rep, Mult	15,22
3	0.06	3	4fvkA	ZN	Rep, Mult	133,135
4	0.06	3	2w4yC	AMP	Rep, Mult	41,56,65
5	0.04	2	3hykB	A3P	Rep, Mult	79,88
6	0.02	1	1izlB	CLA	Rep, Mult	11,139
7	0.02	1	3t7dB	MG	Rep, Mult	88,91
8	0.02	1	2rh1A	CLR	Rep, Mult	26,131
9	0.02	1	1vdfB	CL	Rep, Mult	22,25
10	0.02	1	5d5aA	CLR	Rep, Mult	26,131,136
11	0.02	1	3mgnD	DPR	Rep, Mult	27,31
12	0.02	1	3hxtA	MG	Rep, Mult	77,79
13	0.02	1	1eyiA	PO4	Rep, Mult	6,7,10,11,72,73

	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	1lbzA	0.482	4.47	0.051	0.762	3.1.3.25	95
2	0.060	1lbvA	0.487	4.21	0.073	0.748	3.1.3.25,	NA
3	0.060	1imaA	0.489	3.88	0.075	0.721	3.1.3.25	96
4	0.060	2qvrA	0.498	4.33	0.111	0.789	3.1.3.11	134
5	0.060	4matA	0.480	4.79	0.054	0.803	3.4.11.18	NA
6	0.060	3fxxA	0.471	4.90	0.066	0.762	2.7.10.1	NA
7	0.060	2qflA	0.494	3.99	0.075	0.721	3.1.3.25	NA
8	0.060	3kulB	0.449	4.73	0.086	0.708	2.7.10.1	NA
9	0.060	1awbA	0.490	3.84	0.085	0.721	3.1.3.25	NA
10	0.060	1yvjA	0.462	4.60	0.059	0.735	2.7.10.2	NA
11	0.060	2q74A	0.494	4.13	0.100	0.748	3.1.3.25	40
12	0.060	1yrlA	0.478	3.93	0.043	0.660	1.1.1.86	NA
13	0.060	1spiA	0.480	4.04	0.054	0.735	3.1.3.11	NA
14	0.060	3d1rA	0.485	4.10	0.124	0.735	3.1.3.11	NA
15	0.060	1bk4A	0.494	4.16	0.061	0.769	3.1.3.11	NA
16	0.060	2r2pA	0.453	4.77	0.050	0.721	2.7.10.1	NA
17	0.060	1jpaA	0.447	4.53	0.072	0.687	2.7.10.1	121,124
18	0.060	3dlaD	0.472	4.77	0.063	0.809	6.3.5.1	NA
19	0.060	1mqbB	0.461	4.67	0.053	0.721	2.7.10.1,2.7.1.112	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	0.08	0.634	3.64	0.10	0.90	4ipuA	GO:0008565 GO:0015627 GO:0015628 GO:0016020 GO:0016021 GO:0043107 GO:0043683
1	0.07	0.576	3.73	0.07	0.83	2knqA	GO:0006810 GO:0008565 GO:0015031 GO:0015627 GO:0015628
2	0.07	0.521	3.93	0.07	0.78	4dq9A	GO:0006810 GO:0008565 GO:0009306 GO:0015031 GO:0015627 GO:0015628
3	0.07	0.507	3.96	0.06	0.75	4hxvA	GO:0000103 GO:0000166 GO:0000287 GO:0005737 GO:0008441 GO:0009086 GO:0016311 GO:0046854 GO:0046872
4	0.07	0.494	4.13	0.10	0.75	2q74A	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0007165 GO:0008934 GO:0016787 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
5	0.07	0.498	4.65	0.08	0.81	2wefA	GO:0000287 GO:0004441 GO:0005737 GO:0005829 GO:0006139 GO:0007399 GO:0008441 GO:0016311 GO:0016787 GO:0046854 GO:0046872 GO:0050427 GO:0070062
6	0.07	0.497	3.59	0.08	0.70	2pcrB	GO:0000287 GO:0005737 GO:0005975 GO:0006020 GO:0006094 GO:0007165 GO:0008934 GO:0016787 GO:0042132 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
7	0.07	0.480	3.92	0.06	0.71	2p3nA	GO:0000287 GO:0005737 GO:0005975 GO:0006020 GO:0006094 GO:0007165 GO:0008934 GO:0016787 GO:0042132 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834
8	0.07	0.506	3.83	0.08	0.73	3b8bA	GO:0000103 GO:0000287 GO:0005737 GO:0008441 GO:0016020 GO:0016311 GO:0046854
9	0.07	0.487	4.71	0.05	0.80	4qxdB	GO:0000287 GO:0005737 GO:0016311 GO:0016791 GO:0046854 GO:0046872
10	0.07	0.506	3.81	0.08	0.73	4as4A	GO:0000287 GO:0005737 GO:0005829 GO:0006020 GO:0006021 GO:0006661 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0030145 GO:0031403 GO:0042802 GO:0042803 GO:0043647 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834 GO:0070062
11	0.07	0.498	3.69	0.10	0.71	5eq9B	GO:0004401 GO:0016311 GO:0046854
12	0.07	0.500	3.80	0.09	0.73	2bjiA	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0006661 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0030145 GO:0031403 GO:0042802 GO:0042803 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834 GO:0070062
13	0.07	0.494	3.99	0.07	0.72	2qflA	GO:0000287 GO:0005737 GO:0005829 GO:0006020 GO:0007165 GO:0008934 GO:0016787 GO:0031403 GO:0046854 GO:0046855 GO:0046872 GO:0047954 GO:0052832 GO:0052833 GO:0052834
14	0.07	0.493	3.95	0.12	0.72	3t0jA	GO:0046854
15	0.07	0.505	3.76	0.09	0.73	4as5A	GO:0000287 GO:0005737 GO:0006020 GO:0006021 GO:0006661 GO:0006796 GO:0007165 GO:0008934 GO:0016787 GO:0030145 GO:0031403 GO:0042802 GO:0042803 GO:0046854 GO:0046855 GO:0046872 GO:0052832 GO:0052833 GO:0052834 GO:0070062
16	0.07	0.498	4.12	0.06	0.76	1k9yA	GO:0000103 GO:0000287 GO:0005634 GO:0005737 GO:0006790 GO:0008441 GO:0009086 GO:0016311 GO:0016787 GO:0042538 GO:0046854 GO:0046872
17	0.07	0.493	3.89	0.11	0.72	3lv0A	GO:0008934 GO:0046854 GO:0046855
18	0.07	0.487	4.21	0.07	0.75	1lbvA	GO:0005975 GO:0006094 GO:0008934 GO:0016311 GO:0016787 GO:0042132 GO:0046854 GO:0046872 GO:0052832 GO:0052833 GO:0052834

Consensus prediction of GO terms

Molecular Function	GO:0022892
GO-Score	0.40
Biological Processes	GO:0009306	GO:0098776
GO-Score	0.40	0.40
Cellular Component	GO:0043234	GO:0044464
GO-Score	0.40	0.33

(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.