I-TASSER results

I-TASSER results for job id Rv2570

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

Input Sequence in FASTA format

>protein (129 residues)
MATWDDVARIVGGLPLTAEQAPHDWRVGRKLLAWERPLRKSDREALTRAGSEPPSGDIVG
VRVSDEGVKFALIADEPGVYFTTPHFDGYPAVLVRLAEIEVRDLEELITEAWLMQAPKQL
VQAFLANSG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MATWDDVARIVGGLPLTAEQAPHDWRVGRKLLAWERPLRKSDREALTRAGSEPPSGDIVGVRVSDEGVKFALIADEPGVYFTTPHFDGYPAVLVRLAEIEVRDLEELITEAWLMQAPKQLVQAFLANSG
Prediction	CCCHHHHHHHHHHCCCCEHCCCCCCEHCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHCC
Conf.Score	988999999999899967858887556566888875676655554444456788886899995999999999975998766788778987699984779999999999999998697999999997569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MATWDDVARIVGGLPLTAEQAPHDWRVGRKLLAWERPLRKSDREALTRAGSEPPSGDIVGVRVSDEGVKFALIADEPGVYFTTPHFDGYPAVLVRLAEIEVRDLEELITEAWLMQAPKQLVQAFLANSG
Prediction	754263024003402414457445141343010123243444443334345445433000020446722431365646312313334422001010550437303400451023302440064136768
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHCCCCEHCCCCCCEHCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHCC
MATWDDVARIVGGLPLTAEQAPHDWRVGRKLLAWERPLRKSDREALTRAGSEPPSGDIVGVRVSDEGVKFALIADEPGVYFTTPHFDGYPAVLVRLAEIEVRDLEELITEAWLMQAPKQLVQAFLANSG

2fkiA

0.14

0.12

0.84

1.95

MUSTER

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDGLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.12

0.10

0.84

1.92

dPPAS

-MTISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK-----------------EVENRPAVSLKTSPELAELLRQQHSDVRPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.14

0.12

0.84

3.32

wdPPAS

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.13

0.11

0.84

2.38

wMUSTER

--TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDGLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.14

0.12

0.84

3.28

wPPAS

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.15

0.12

0.84

5.51

dPPAS2

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSDV-RPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.14

0.12

0.84

2.44

PPAS

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVK---------------EVENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2fkiA

0.13

0.11

0.84

2.61

Env-PPAS

M-TISELLQYCMAKPGAEQSVHNDIKVEDVLFAMVKEV---------------ENRPAVSLKT-SPELAELLRQQHSD-VRPSRHLNKAHWSTVYLDSLPDSQIYYLVDASYQQAVPEEKRKLLVQL--

2kfpA

0.14

0.12

0.88

1.52

MUSTER

M-NRQQFIDYAQKKYDTKPDHPWEFRHNDKWYALLM---DIPAEKIGINGD--KRVDVIDLKV-QPELVGSLRKKPG--IYPAYHMNKEHWITVLLNPLGAKEIHSLIEDSFQLTRLEH------HHHH

2kfpA

0.09

0.08

0.90

1.30

dPPAS

-MNRQQFIDYAQKKYDTKPDHPWEKFPDYAVF-----RHSDNDKWYAKIGINGDKRVDVIDLKVQPELVGSLRKKPG--IYPAYHMNKEHWITVLLNGLGAKEIHSLIEDSFQLTRLEHHHHHH-----

(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=0.00

Estimated TM-score = 0.71±0.11

Estimated RMSD = 4.4±2.9Å

Download Model 2

C-score=-2.29

Download Model 3

C-score=-1.86

Download Model 4

C-score=-3.25

Download Model 5

C-score=-3.07

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	2fkiA	0.732	1.85	0.110	0.845
2	2kfpA	0.675	2.62	0.105	0.853
3	2zxlA	0.575	3.41	0.062	0.814
4	3tfhA	0.551	4.03	0.070	0.868
5	2g18G	0.534	3.79	0.063	0.791
6	3ttsA	0.532	3.73	0.076	0.798
7	3i8uX	0.532	3.79	0.036	0.791
8	1vrqC	0.528	3.90	0.075	0.806
9	1kwgA2	0.527	4.19	0.050	0.830
10	2kl4A	0.527	3.11	0.108	0.721

(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	0.05	2	2zxlB	NA	Rep, Mult	12,13,14,15,17
2	0.04	2	4ujht	OHX	Rep, Mult	114,116,117
3	0.04	2	5apwB	CA	Rep, Mult	103,106
4	0.04	2	4bs1A	ADP	Rep, Mult	6,101,102,105
5	0.04	2	3ihiB	SO4	Rep, Mult	72,95
6	0.04	2	3rphA	AMP	Rep, Mult	89,90,101
7	0.04	2	1v98A	MG	Rep, Mult	13,14,105
8	0.04	2	4n0gA	MG	Rep, Mult	100,103
9	0.04	2	1qiyL	IPH	Rep, Mult	108,111
10	0.02	1	3dc7B	MG	Rep, Mult	64,65
11	0.02	1	3f0lA	BLA	Rep, Mult	19,25,27,32,33,34,36,58,59,61,82,84,93
12	0.02	1	3lw52	CLA	Rep, Mult	7,11
13	0.02	1	4rkuL	CLA	Rep, Mult	104,108
14	0.02	1	1c8fA	CA	Rep, Mult	85,87

	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	2ewnA	0.501	4.48	0.090	0.845	6.3.4.15	NA
2	0.060	1v5vA	0.518	4.21	0.047	0.861	2.1.2.10	NA
3	0.060	1ox4B	0.472	4.31	0.041	0.744	4.1.3.-	NA
4	0.060	2g18G	0.534	3.79	0.063	0.791	1.3.7.5	NA
5	0.060	1bibA	0.481	4.45	0.103	0.806	6.3.4.15	30
6	0.060	1skaA	0.480	4.73	0.060	0.822	3.1.3.8	62
7	0.060	1tllA	0.490	4.17	0.041	0.760	1.14.13.39	NA
8	0.060	2veoB	0.469	4.85	0.057	0.806	3.1.1.3	13
9	0.060	2ghrA	0.479	4.29	0.072	0.752	2.3.1.46	NA
10	0.060	1qwoA	0.473	4.72	0.068	0.822	3.1.3.8	NA
11	0.060	1yx2B	0.523	4.08	0.040	0.845	2.1.2.10	16,57
12	0.060	1l9xB	0.486	4.49	0.063	0.791	3.4.19.9	NA
13	0.060	1gpmA	0.525	4.38	0.075	0.861	6.3.5.2	NA
14	0.060	1i7sB	0.481	4.21	0.053	0.767	4.1.3.27	37
15	0.060	2vxoB	0.506	4.34	0.059	0.830	6.3.5.2	NA
16	0.060	1vloA	0.495	4.16	0.057	0.798	2.1.2.10	83,111
17	0.060	3hr4A	0.475	4.71	0.070	0.791	1.14.13.39	NA
18	0.060	2hb6A	0.476	4.77	0.097	0.861	3.4.11.1	NA
19	0.060	2hb6B	0.479	4.93	0.113	0.868	3.4.11.1	24,26,106

(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	0.25	0.732	1.85	0.11	0.84	2fkiA
1	0.09	0.675	2.62	0.10	0.85	2kfpA
2	0.07	0.575	3.41	0.06	0.81	2zxlA	GO:0005737 GO:0005739 GO:0005829 GO:0009507 GO:0009535 GO:0009536 GO:0009570 GO:0009579 GO:0009814 GO:0009941 GO:0010363 GO:0015996 GO:0016020 GO:0016491 GO:0043067 GO:0051743 GO:0055114
3	0.07	0.506	4.61	0.05	0.86	4pabB	GO:0005542 GO:0005739 GO:0006579 GO:0016491 GO:0019695 GO:0035999 GO:0042426 GO:0047865 GO:0050660 GO:0055114
4	0.07	0.532	3.78	0.04	0.79	2d1eA	GO:0010024 GO:0016491 GO:0016636 GO:0050620 GO:0050897 GO:0055114
5	0.07	0.551	4.03	0.07	0.87	3tfhA	GO:0008168 GO:0016740 GO:0032259
6	0.07	0.339	4.09	0.04	0.54	1wsrA	GO:0004047 GO:0005739 GO:0005759 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259 GO:0046487
7	0.07	0.520	3.72	0.10	0.79	2x9oA	GO:0010024 GO:0016491 GO:0016636 GO:0050617 GO:0050897 GO:0055114
8	0.07	0.529	4.02	0.05	0.85	1yx2B	GO:0004047 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259
9	0.07	0.525	4.01	0.04	0.84	1vloA	GO:0004047 GO:0005829 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259
10	0.07	0.534	3.78	0.06	0.79	2g18D	GO:0010024 GO:0016491 GO:0016636 GO:0050620 GO:0050897 GO:0055114
11	0.07	0.535	4.05	0.04	0.85	1wooA	GO:0004047 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259
12	0.07	0.506	3.65	0.06	0.77	2vgrC	GO:0010024 GO:0016491 GO:0016636 GO:0050897 GO:0055114
13	0.07	0.518	4.21	0.05	0.86	1v5vA	GO:0004047 GO:0006546 GO:0008483 GO:0016740 GO:0019464 GO:0032259
14	0.06	0.406	5.41	0.05	0.79	3e74B	GO:0000256 GO:0004038 GO:0005737 GO:0006144 GO:0008270 GO:0009442 GO:0016787 GO:0016810 GO:0046872 GO:0050897
15	0.06	0.393	3.75	0.04	0.61	4cdoA	GO:0000245 GO:0000375 GO:0000380 GO:0000398 GO:0003677 GO:0003713 GO:0005634 GO:0005654 GO:0005681 GO:0005682 GO:0005737 GO:0005813 GO:0006351 GO:0006355 GO:0006397 GO:0007049 GO:0007067 GO:0008022 GO:0008380 GO:0010494 GO:0016607 GO:0031175 GO:0043021 GO:0043484 GO:0046540 GO:0048814 GO:0051301 GO:0060271 GO:0071598 GO:0072372 GO:0097546
16	0.06	0.437	5.17	0.06	0.79	3ad7A	GO:0000166 GO:0008115 GO:0016491 GO:0046653 GO:0055114
17	0.06	0.519	4.44	0.09	0.87	1pj6A	GO:0000166 GO:0016491 GO:0047866 GO:0055114
18	0.06	0.361	5.01	0.05	0.69	4gfrA	GO:0015197 GO:0015833 GO:0030288 GO:0042626 GO:0043190 GO:0046872 GO:0055085

Consensus prediction of GO terms

Molecular Function	GO:0050660	GO:0047865	GO:0050897	GO:0005542	GO:0050620	GO:0051743
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0044710
GO-Score	0.37
Cellular Component	GO:0005739	GO:0009941	GO:0009570	GO:0009535	GO:0005829
GO-Score	0.13	0.07	0.07	0.07	0.07

(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.