I-TASSER results

I-TASSER results for job id Rv2811

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

Input Sequence in FASTA format

>protein (202 residues)
MVTVEADVDQVERRLAAGELSCPSCGGVLAGWGRARSRQLRGPAGPVELCPRRSRCTGCG
VTHVLLPVSALLRRADTAAVIVSALAAKATSRVGFRRIATDVARPAETVRGWLRRFAERV
EAVRSVFTVWLCAVDADPVMPDAGGGGFVDAVVAIGALAAAIGRRFSLPTVSLAETAVAV
SGGRLLAPGWPGEWVQHESTLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVTVEADVDQVERRLAAGELSCPSCGGVLAGWGRARSRQLRGPAGPVELCPRRSRCTGCGVTHVLLPVSALLRRADTAAVIVSALAAKATSRVGFRRIATDVARPAETVRGWLRRFAERVEAVRSVFTVWLCAVDADPVMPDAGGGGFVDAVVAIGALAAAIGRRFSLPTVSLAETAVAVSGGRLLAPGWPGEWVQHESTLP
Prediction	CEEEEHCHHHHHHHHHCCCCCCCCCCCEEHCCCCCEEEEEHCCCCEEEEEEEEEHCCCCCEEEEEHCCEEEEHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCHCCCCCCCCCCCCCCCCC
Conf.Score	9788746666677765588889888866655666455566657875788655565678875788745434433456899999999999866787556677767886889999999999999999999888764378766777788757899999999998887645678888888554445875558888876777777899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVTVEADVDQVERRLAAGELSCPSCGGVLAGWGRARSRQLRGPAGPVELCPRRSRCTGCGVTHVLLPVSALLRRADTAAVIVSALAAKATSRVGFRRIATDVARPAETVRGWLRRFAERVEAVRSVFTVWLCAVDADPVMPDAGGGGFVDAVVAIGALAAAIGRRFSLPTVSLAETAVAVSGGRLLAPGWPGEWVQHESTLP
Prediction	7130525453044304635131330413044223235341534744141434414056032100101210113423214101300233067434343134427345730230032005304302220210013341433144243330220000011033304432424423132000003312000122336135476638
	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

CEEEEHCHHHHHHHHHCCCCCCCCCCCEEHCCCCCEEEEEHCCCCEEEEEEEEEHCCCCCEEEEEHCCEEEEHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCHCCCCCCCCCCCCCCCCC
MVTVEADVDQVERRLAAGELSCPSCGGVLAGWGRARSRQLRGPAGPVELCPRRSRCTGCGVTHVLLPVSALLRRADTAAVIVSALAAKATSRVGFRRIATDVARPAETVRGWLRRFAERVEAVRSVFTVWLCAVDADPVMPDAGGGGFVDAVVAIGALAAAIGRRFSLPTVSLAETAVAVSGGRLLAPGWPGEWVQHESTLP

5cwbA

0.13

0.96

0.78

MUSTER

CEEKARRVAEKVERLKRSGTSEDEIAEEVAREISEVIRTLKESGSSYEVICECVAVAEIVEALKRSGTSEDEIAEIVARVISEVIRTLKESGSSYEVICECVARIVAEIVEALKRSGTSEDEIAEIVARVISEVIRTLKESGSSYEVIKECVQRIVEEIVEALKRSGTSEDEINEIVRRVKSEVERTLKESGS---------

2qwtA

0.14

0.12

0.82

0.57

dPPAS

--PLRADAARNRARVLEVAYDT---------------FAAEGLGVPMDEIARRAGVG---------AGTVYRHFPTKQALVVAVAEDRVRRIVDHARTLLAAEGPGEALFVFMRDMVRSAAADYGLVDALVGYGLDLEVAAPGAEAAFLATLGELLAAAQRAGTRADVDVAVIKALLVSERVVRVIEDGLRV----------

3gn5A

0.10

0.05

0.53

0.69

wdPPAS

------------------HMKCPVCHGEMVS----KDIPYTFRGKTVLKGIHGLYCVHCEESIM----------KEESDAFMAQVKAFRASSLTQKEASEIFGGGVNAFSRYEK-----------------------NAQPHP---STIKLLRVLDKHPELLNER-------------------------------------

5dfzC

0.13

0.12

0.94

0.67

wMUSTER

ELLVHLLETKVRPLVKVRPIALPLDPDVLICDVCPETSKVFKSSLS---LKITFKTTL-NQPYHLMFKV---RQDQLVVQIISLMNELLKNDLKLTPYKILATGPQEGAIEFIPNDLASILSKYHGILGYLKLHYPDENATLGVQGWVLDNFVKSCAGYCVITYILGVGDRHLDNLLV-TPDGHFF--GY-GQDPKPFPP-L

2rekB

0.21

0.16

0.78

0.79

wPPAS

----RADARRNYDRIIEAAAAE------VARHGA---------DASLEI--RR-----AGVGSATL------HRHFRWGLLQAVFQERVAQLCDERSLAAEHP-PATALTRWLTSLAVFGAVTRGAARSLL-------ALDSRCEQLLTEAGADLLARAQEDGTR---DDVTALELLSLANAVSLAAPDAAHHATR-GG-LP

2zb9A2

0.12

0.07

0.57

0.80

dPPAS2

-----------------------------------------------------------------FPDTVRADLLAQLRAFTHVMTRTPGGRI-LTELIGAAQTDADLATAYRQLYSAQRRALAAERLRHARELG--QIRPDVD----VQVLVDQLWGAVYHRLLIPDEPVDDAFVTALVTDG--VCPR-------------

2rekB

0.19

0.16

0.82

0.89

PPAS

----RADARRNYDRIIEAAAAE------VARHGA---------DASLEEIARR-----AGVGSATL------HRHFRWGLLQAVFQERVAQLCDEARSLAAEHPPATALTRWLTSLAVFGAVTRGAARSLLA------ALDSRCEQLLTEAGADLLARAQEDGTRDDVTALELLSLANAVSLAAEHTPDAAHHATRLMGIAP

2jmuA

0.12

0.11

0.94

0.66

Env-PPAS

LIEVERKGPDTEERLQELGATLSELS--LMLSDHWLRQRE-GSGWELKCPGVTGVSGPHNEYVEVTS------EAAIVAQLFELLGSGEQKPAGVAAVLGSLKQEVASFI--TTRSSWKLALSGAHGQEPQLTIDLDSADFGHEKAEVPAALEKIITVSSMLGVPAQEEAPAKLMVYLQRFRQRLLEAASSGEATGDSAS--

5cr4A

0.08

0.94

0.71

MUSTER

TAHGDKDRTFWRNVLWSDETKIELFGHNDHRYVWRKKGEACKPKN--TIPTVKHGGGSIMLWGCFAAGGTGALHKIDGIMDAVQYVDILKQH--LKTSVRKLKLGR----KWVFQHDNDPKHTSKVVAKWLKDNKVKVLEWPSQSPDLNPIENLWAELKKRVRARRPTNLTQLHQLCQEEWAK--IHPNYCGKLVE---GYP

5cwdA

0.14

0.12

0.85

0.54

dPPAS

----TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMPTKEAAR----------------SFCEAAARAAAESNDEEVAKIAAKAC-LEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESNDEEVEKIAKKACKEVAKQAGMPWLE----------

(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=-2.67

Estimated TM-score = 0.41±0.14

Estimated RMSD = 11.5±4.5Å

Download Model 2

C-score=-4.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.10

Download Model 5

C-score=-4.94

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	2rekB	0.628	3.32	0.141	0.807
2	2q24B	0.593	3.48	0.203	0.782
3	2oerB	0.587	3.93	0.131	0.807
4	2gfnB	0.579	4.11	0.120	0.827
5	2o7tA	0.561	4.31	0.090	0.807
6	2nx4A	0.554	4.40	0.075	0.842
7	4ichA	0.547	4.54	0.115	0.817
8	2hkuA	0.545	4.45	0.055	0.807
9	3geuA	0.544	4.33	0.048	0.787
10	3vuqA	0.540	4.33	0.112	0.767

(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	0.20	10	3jueA	ZN	Rep, Mult	22,25,56,59
2	0.06	3	5bq6A	EFB	Rep, Mult	81,84,85,88
3	0.04	2	5ezmA	MPG	Rep, Mult	120,123
4	0.02	1	2uxpA	CLM	Rep, Mult	117,148,152,178,180
5	0.02	1	3btjB	DEQ	Rep, Mult	82,85,127
6	0.02	1	1jt0C	QNA	Rep, Mult	1,71,72,73,74,75,78,79
7	0.02	1	1jt0A	QNA	Rep, Mult	1,71,78,79,82,83
8	0.02	1	4xlrM	NUC	Rep, Mult	82,141,142,143
9	0.02	1	3aqtB	RCO	Rep, Mult	95,109,112,113,116,151,152,155,178
10	0.02	1	3h45O	PO4	Rep, Mult	83,86
11	0.02	1	3ze3A	78M	Rep, Mult	123,130
12	0.02	1	3ehbB	HEA	Rep, Mult	120,148
13	0.02	1	2rek0	III	Rep, Mult	109,163,176,177,179,183,186,187,198,200

	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	2vuaA	0.342	6.08	0.026	0.644	3.4.24.69	71
2	0.060	1i8qA	0.443	5.12	0.071	0.703	4.2.2.1	29
3	0.060	3evhA	0.441	5.33	0.048	0.718	4.2.2.3	NA
4	0.060	2pflA	0.442	4.96	0.044	0.698	2.3.1.54	NA
5	0.060	2ztgA	0.436	5.16	0.076	0.698	6.1.1.7	27,129
6	0.060	2q8gA	0.443	5.33	0.073	0.718	2.7.11.2	121
7	0.060	1s4bP	0.440	4.18	0.067	0.619	3.4.24.15	NA
8	0.060	2v8tA	0.459	4.47	0.046	0.683	1.11.1.6	NA
9	0.060	1fa2A	0.452	5.35	0.046	0.733	3.2.1.2	NA
10	0.060	1tazA	0.441	4.90	0.036	0.668	3.1.4.17	NA
11	0.060	2vr5A	0.473	4.62	0.032	0.698	3.2.1.-	NA
12	0.060	1i1iP	0.458	4.03	0.063	0.629	3.4.24.16	19
13	0.060	2d0tB	0.453	5.24	0.049	0.718	1.13.11.52	NA
14	0.060	3btaA	0.436	4.43	0.052	0.639	3.4.24.69	NA
15	0.060	2e9bA	0.455	4.65	0.032	0.683	3.2.1.41	NA
16	0.060	2pnrB	0.440	5.36	0.040	0.703	2.7.11.2	NA
17	0.060	2fhcA	0.499	4.68	0.064	0.762	3.2.1.41	79
18	0.060	1lj8A	0.451	5.38	0.087	0.767	1.1.1.67	NA
19	0.060	1y8pA	0.456	5.25	0.045	0.713	2.7.11.2	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	0.21	0.537	3.88	0.10	0.72	3vuqC	GO:0003677 GO:0006351 GO:0006355
1	0.09	0.628	3.32	0.14	0.81	2rekB	GO:0003677 GO:0006351 GO:0006355
2	0.09	0.511	5.11	0.05	0.83	3bhqA	GO:0003677 GO:0006351 GO:0006355
3	0.08	0.551	4.59	0.11	0.83	4ichA	GO:0003677 GO:0006351 GO:0006355
4	0.07	0.604	3.53	0.20	0.80	2q24B	GO:0003677 GO:0006351 GO:0006355
5	0.07	0.587	3.93	0.13	0.81	2oerB	GO:0003677 GO:0006351 GO:0006355
6	0.07	0.526	4.72	0.12	0.81	2g7sA	GO:0003677 GO:0006351 GO:0006355
7	0.07	0.539	4.04	0.13	0.76	2qwtA	GO:0003677 GO:0006351 GO:0006355
8	0.07	0.568	4.37	0.10	0.82	2o7tA	GO:0003677 GO:0006351 GO:0006355
9	0.07	0.543	4.53	0.04	0.80	3f0cA	GO:0003677 GO:0006351 GO:0006355
10	0.07	0.531	4.55	0.09	0.80	2qtqA	GO:0003677 GO:0006351 GO:0006355
11	0.07	0.535	4.54	0.10	0.80	4gclB	GO:0003677 GO:0005737 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
12	0.07	0.526	4.50	0.06	0.79	3on4A	GO:0003677 GO:0006351 GO:0006355
13	0.07	0.502	4.86	0.11	0.80	2id3A	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046872
14	0.07	0.504	4.93	0.10	0.81	2g3bA	GO:0003677 GO:0006351 GO:0006355
15	0.07	0.508	4.51	0.09	0.75	4g12A	GO:0003677 GO:0006351 GO:0006355
16	0.07	0.525	4.33	0.12	0.76	2hytA	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.518	4.57	0.08	0.78	4gctC	GO:0000976 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006355 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
18	0.07	0.486	4.99	0.12	0.78	3on2B	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.44
Biological Processes	GO:0006355
GO-Score	0.44
Cellular Component
GO-Score

(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.