I-TASSER results

I-TASSER results for job id Rv2680

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

Input Sequence in FASTA format

>protein (210 residues)
MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYAL
GAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLL
PEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLG
AHVQAFCDVLEHAAGLPPAGVTDLGSRSRA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAHVQAFCDVLEHAAGLPPAGVTDLGSRSRA
Prediction	CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCHCCCCCEEEEEEEEHCCCCCCCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Conf.Score	998888866666788888889999999999999969999976999768998788646888888668887877777877775579999789998888985899999967878677569887567789999999875997546776799999755588889998657999998589998589999999999999969999985458888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAHVQAFCDVLEHAAGLPPAGVTDLGSRSRA
Prediction	546545546545555565475325403400420471432460414614224310120100102034665544446654201000000001625661613000000021413562361210140002002410464715243131101213143223144566414000000001536402400400030023104132530251364668
	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

CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEHCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCEEEEEEEHCCCCHHHCCCCCCHHHHHHHHHHHHHHHCCCHCCCCCEEEEEEEEHCCCCCCCCCCEEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAHVQAFCDVLEHAAGLPPAGVTDLGSRSRA

4ae7A

0.13

0.10

0.81

0.60

MUSTER

-----------LKDYALPNASWCSDMLSLYQEFLEKT-SGWIKLSFKSNRDHIR--------GLKLPDCRIFCIQVEGQG-FEYVIFFQPTQK-------KSVCLFQ--PGSYLEGPPAHGGSLAAMMDETFSKT---FLAGEGLFTLSLNIRF--KNLIPVDSLVVMDVEVD-EDQKLYMSCIAHSRVYAKSSGV----FLQLQLEEES

5gaoE

0.14

0.98

0.89

dPPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-----AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAARAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

2lakA

0.16

0.11

0.67

0.69

wdPPAS

MEKAMPESFV---------AAPPAAVFALMTD-----------------PEKIL-MGTEAEVEPEPGGLYLVNVTGARFARGSFREVVPVH---------RLAY--------------------FGW------DGSEVVPPGSSLVEIDLIEQ-------GGGTLLRLTHSGLPSAEQCAGHEEGWAHYLGRLTEVDPGPDPFYGRRLEH

3ttsA2

0.18

0.15

0.85

0.65

wMUSTER

YDWENRWALELSSG-PSIALNYVNEVHKYYDALYKQ----NIQTDMISVEEDLSKYKVVIVMYMVKPGFAERVER---AQGGTFVTTVNENDLGGYPGELR-IWAEEIDLLPGLRQDWLRGSYSCGILCDVIHAETAEYGAYKG-TPVLTRNKFGN-----------GQSYYVASSPD-ADFLQGLIANLCEEQGVKPL----LN-----

5e9aA2

0.19

0.15

0.78

0.57

wPPAS

FD-------DDAMGPRNAGLHYENTVADHYRALWAQ----GIAVDVINADCDLQGYDLVIA---------MLYMVREGVG-GRFVATVNETDLNGFPGPLR-IWAEEIDLTDEQNALGLSGPYRASQLCEVIHLEGAAYGDYAG-NPAVTVNLYG-----------KGQAYYVASRND-QQFHADFFTALAKEMKLPRA-----------

3ct8A

0.11

0.03

0.31

0.99

dPPAS2

VQTEDRFQTPTFHRKRTGLNASREKVDELTQKLKER------------------------GDPILYEDRHPFAGGPNHYANRIKVEIVAP------------------------------------------------------------------------------------------------------------------------

4lmhA2

0.11

0.10

0.87

0.61

PPAS

-SSTDCMACHNATKPYGGTGSAAKRHGDVMKAYNDSLGY-KAKFSNI----GIKNNALTFDVQILDNKDQPIGKE----------FISDPSA---YTKSSIYFSW--IDKDYPAYTA---GSRYSDRGFALSNSKVSTYNEATKTFTIDSTNSNLKLPADLTGMNVELYAGVGYGVEDVVA-TPCSTDTRYAYIQDQPTDTNSAAEKR--

2pp0A1

0.12

0.09

0.72

0.74

Env-PPAS

-SANSDAVTYAKAANTRTAAETGDRIEW-------------VKLSL---------AFLPLATPVSDAKVLTGRQKPLTEVAIIIAEIRSRDGFEGVRAGGQGIYAHAKEIADNLGEDPNDIDKIYTKLLWAGASVG-----RSGMAVQAISP-------------IDI-ALW-----DMKAKRAEQARRWTQLTGKRP------------

4yt2A1

0.12

0.10

0.90

0.60

MUSTER

YGAGNQNLYINKLNLPEKFGGEP-PYGGSRMAIEFAEAGHDVVLAE-PNKNIMSD---DLWKKVEDAGVKVVSDDVEAAKHGEIHVLFTPFG----KATFRIAKTIIEHVPENCNTCTVSPVVLYYSLEPILRT---KRKDV--GISSMHP---AAVPGTPQHGHYVIGGKTTDGKELAEEQIKKAVELAKSAGKVPADVSSVVAD----

4n7rC

0.08

0.07

0.84

0.83

dPPAS

------------------STHKPFPAEVSRSIMELSSV---GTLSTLTHDGW--PLGVGVRFAVDKDGTPVLCLNRSVSPDKRSALHVQLEQCGLRTPQCTIQGSIGRPGD----------DTVLKRLSATWREKFGEEVKEDSLYVVAVDRVLQMEDFMEDGIWVAKNASPDPLRDIAEDIVNQINANNMEDIFRFCNVYVDLDFVVSE

(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=-2.55

Estimated TM-score = 0.42±0.14

Estimated RMSD = 11.3±4.5Å

Download Model 2

C-score=-3.07

Download Model 3

C-score=-3.62

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	5e9aA2	0.669	3.47	0.144	0.862
2	4oifA	0.669	3.53	0.110	0.862
3	3ttsA	0.666	3.47	0.120	0.857
4	4uniA	0.656	3.55	0.126	0.857
5	4uzsA	0.656	3.52	0.105	0.862
6	1kwgA	0.643	3.42	0.098	0.819
7	4e5vA	0.592	3.72	0.084	0.795
8	1t0bG	0.591	4.10	0.062	0.833
9	4jqsA	0.575	4.22	0.068	0.829
10	2gk3E	0.569	4.06	0.068	0.800

(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	0.10	5	4eptA	0QW	Rep, Mult	83,84,85,150,169,171,186
2	0.04	2	1i7qB	GLU	Rep, Mult	73,87,101,102,103,170,171,172,173
3	0.04	2	3mflA	DHY	Rep, Mult	55,56,169
4	0.02	1	3e25A	MG	Rep, Mult	89,91
5	0.02	1	1ox4B	POP	Rep, Mult	61,62,87,88,105
6	0.02	1	3bz1A	PHO	Rep, Mult	186,190,194
7	0.02	1	1w5dA	CA	Rep, Mult	91,94,172
8	0.02	1	2zuvA	NO3	Rep, Mult	48,59,60,84,85
9	0.02	1	4b4yA	OXY	Rep, Mult	182,186
10	0.02	1	1bpyA	MG	Rep, Mult	109,111
11	0.02	1	2b0qA	MG	Rep, Mult	89,111
12	0.02	1	2fkaA	CXS	Rep, Mult	35,180,184
13	0.02	1	1gpmA	AMP	Rep, Mult	85,86,87,171,173,183
14	0.02	1	3q9cA	NA	Rep, Mult	119,143,147
15	0.02	1	1gfmA	C8E	Rep, Mult	154,168
16	0.02	1	2bo6B	MN	Rep, Mult	111,117
17	0.02	1	3mflB	DHY	Rep, Mult	55,56
18	0.02	1	2wl3A	CA	Rep, Mult	90,130
19	0.02	1	3bz1H	CLA	Rep, Mult	186,189

	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	0.066	2ywdA	0.537	3.80	0.123	0.724	2.6.-.-	NA
2	0.066	2ywjA	0.521	4.02	0.058	0.724	2.6.-.-	NA
3	0.066	1kxjA	0.564	3.94	0.037	0.771	2.4.2.-	129
4	0.066	1i7qB	0.529	3.98	0.135	0.729	4.1.3.27	NA
5	0.066	1qdlB	0.529	4.12	0.025	0.738	4.1.3.27	NA
6	0.060	3d54D	0.543	3.98	0.081	0.752	6.3.5.3	NA
7	0.060	1i7sB	0.528	4.07	0.076	0.743	4.1.3.27	NA
8	0.060	1vcnA	0.533	4.46	0.066	0.786	6.3.4.2	NA
9	0.060	2d7jA	0.541	3.95	0.044	0.743	6.3.5.2	NA
10	0.060	2ad5B	0.547	4.80	0.074	0.829	6.3.4.2	21
11	0.060	2issD	0.529	3.95	0.098	0.724	2.6.-.-	30,63,179
12	0.060	2ghrA	0.565	4.08	0.043	0.781	2.3.1.46	NA
13	0.060	2abwB	0.547	4.25	0.101	0.781	2.6.-.-	NA
14	0.060	1kwgA	0.643	3.42	0.098	0.819	3.2.1.23	NA
15	0.060	1vcoA	0.533	4.67	0.054	0.809	6.3.4.2	124
16	0.060	1xfkA	0.485	5.23	0.113	0.781	3.5.3.8	70
17	0.060	1r9gA	0.542	4.21	0.098	0.762	2.6.-.-	NA
18	0.060	1gpmA	0.523	4.21	0.071	0.752	6.3.5.2	NA
19	0.060	1i1qB	0.511	4.14	0.078	0.724	4.1.3.27	NA
20	0.060	2h2wA	0.562	4.05	0.073	0.786	2.3.1.46	NA
21	0.060	1ka9H	0.540	3.81	0.091	0.729	2.4.2.-	NA
22	0.060	1ox4B	0.539	3.91	0.058	0.738	4.1.3.-	NA
23	0.060	1s1mB	0.546	4.90	0.070	0.848	6.3.4.2	NA
24	0.060	2a9vD	0.546	4.15	0.030	0.767	6.3.5.2	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	0.10	0.656	3.52	0.10	0.86	4uzsA	GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798
1	0.09	0.668	3.62	0.12	0.87	5dfaA	GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0046872
2	0.09	0.643	3.42	0.10	0.82	1kwgA	GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798 GO:0046872
3	0.08	0.656	3.55	0.13	0.86	4uniA	GO:0004565 GO:0005975 GO:0006012 GO:0008152 GO:0009341 GO:0016787 GO:0016798
4	0.07	0.521	4.02	0.06	0.72	2ywjA	GO:0004359 GO:0005829 GO:0006541 GO:0006543 GO:0008614 GO:0016787 GO:0016829 GO:0036381 GO:0042819 GO:0042823 GO:1903600
5	0.07	0.455	4.51	0.07	0.69	4n0qB	GO:0006810 GO:0006865
6	0.07	0.434	4.80	0.06	0.65	2f02A	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019512 GO:2001059
7	0.07	0.451	4.57	0.07	0.69	3i45A	GO:0006865
8	0.06	0.415	5.13	0.05	0.66	1be0A	GO:0003824 GO:0009636 GO:0016787 GO:0018786 GO:0019260
9	0.06	0.424	4.21	0.07	0.61	3oi9A
10	0.06	0.358	5.99	0.05	0.65	1rh9A	GO:0004553 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0016985 GO:0046355
11	0.06	0.397	5.65	0.03	0.69	5c70A	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
12	0.06	0.378	4.94	0.04	0.58	1g0cA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
13	0.06	0.358	5.89	0.06	0.65	4d1iG	GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0009341 GO:0016787 GO:0016798
14	0.06	0.386	5.80	0.06	0.68	4jkkA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
15	0.06	0.352	5.59	0.05	0.60	2h00A	GO:0005634 GO:0008168 GO:0016740 GO:0032259 GO:0044822 GO:0052907 GO:0070475
16	0.06	0.354	5.69	0.08	0.61	5a6aB	GO:0004553 GO:0005975 GO:0016787
17	0.06	0.372	5.40	0.09	0.62	2osxA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0047876
18	0.06	0.362	5.79	0.05	0.63	3rdkB	GO:0000272 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0008152 GO:0016052 GO:0016787 GO:0016798 GO:0030246 GO:0031176 GO:0045493
19	0.06	0.369	5.90	0.02	0.66	1b90A	GO:0000272 GO:0005975 GO:0005976 GO:0008152 GO:0016161 GO:0016787 GO:0016798 GO:0046872 GO:2001070

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0004565
GO-Score	0.35	0.31
Biological Processes	GO:0006012
GO-Score	0.31
Cellular Component	GO:0009341
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.