I-TASSER results

I-TASSER results for job id Rv2599

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

Input Sequence in FASTA format

>protein (143 residues)
MSRNRLFLVAGSLAVAAAVSLISGITLLNRDVGSYIASHYRQESRDVNGTRYLCTGSPKQ
VATTLVKYQTPAARASHTDTEYLRYRNNIVTVGPDGTYPCIIRVENLSAGYNHGAYVFLG
PGFTPGSPSGGSGGSPGGPGGSK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRNRLFLVAGSLAVAAAVSLISGITLLNRDVGSYIASHYRQESRDVNGTRYLCTGSPKQVATTLVKYQTPAARASHTDTEYLRYRNNIVTVGPDGTYPCIIRVENLSAGYNHGAYVFLGPGFTPGSPSGGSGGSPGGPGGSK
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCEEEEHCCCHHHHHHHHHHHCCHHHHCCCCCCEEEEHCCEEEEEHCCCCCCEEEEEEHCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98746688999999999999999997589997788877643356677866999599989999999985796775568997788868958999768999859999867888767757887788889998888888889998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRNRLFLVAGSLAVAAAVSLISGITLLNRDVGSYIASHYRQESRDVNGTRYLCTGSPKQVATTLVKYQTPAARASHTDTEYLRYRNNIVTVGPDGTYPCIIRVENLSAGYNHGAYVFLGPGFTPGSPSGGSGGSPGGPGGSK
Prediction	75442111001111211111101101233641352025305544574424313176415500540375442544466653311214520000114464413030342453243111011131133333444646456355768
	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

CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCEEEEHCCCHHHHHHHHHHHCCHHHHCCCCCCEEEEHCCEEEEEHCCCCCCEEEEEEHCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCC
MSRNRLFLVAGSLAVAAAVSLISGITLLNRDVGSYIASHYRQESRDVNGTRYLCTGSPKQVATTLVKYQTPAARASHTDTEYLRYRNNIVTVGPDGTYPCIIRVENLSAGYNHGAYVFLGPGFTPGSPSGGSGGSPGGPGGSK

2hi2A

0.10

0.95

0.71

MUSTER

----TLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGSAVTEYYLNHGKWPENNTS-AGVASSPTDIKGKYVKEVEVKNGVVTATMLSSGGKKLSLWARREN--GSVKWFCGQPVTRTDDDTVADAKDGKPSTCR

3wprA

0.12

0.11

0.97

0.60

dPPAS

IEEILSKIYHIENEIARIKKLIKAVGNQVVTTQTTLVNSLGGNAKNVAQGNQTNVGDALTALDNAINTAATTSKSTVSNG-----QNIVVSKSKNADGSDNYEVSTAKDLTVDGDTVLNNAGITIGNNANTGLTISGGPSVTL

2e76D

0.16

0.13

0.83

0.67

wdPPAS

MG-RRQFMNLLAFGTVTGVALGALYP-----LVKYFIP----PSGGAVTTAKDKLGNNVKVSKFLESHNAGDRVLVQGLK-----GDPTYIVVESKEAIRDYGINAV----TH-----LGVPWNAAENHGSQYDETGGPAPLS

4ixjA1

0.19

0.16

0.85

0.77

wMUSTER

MARDIHQSMKDLIASFA-PSIIPGASKGNDDFRKYLLDNKY-------------KNGWPTIPDEFKAKYG----LSKDTLYIQPY-DATVVVFANNKTGYTSLVYDYDEGYKKNGISVAGRSWDVDTDSVKSHSKEGGPLN--

4qanA2

0.15

0.13

0.85

0.72

wPPAS

ISTPQRAVEQFIYAIEKGLTRALAFATTESSYAKELKTLYG---GTEDARLY---GKSEEQLNKLRGKLNP---------EYV-YLDKVIPIETEENTET---VKQYAGLYSYNGKNYL--GYTLCRQEDGWQQSLSAPSSGE

2qqpF

0.18

0.08

0.47

0.88

dPPAS2

-------FAGTVSALASIGLGLLGKSSATPSVIKGIAQQAVGAVQANPGILEGAVKAIGSVGARLVGSIK--ARRA-------------------------------------------------------------------

3wprA

0.15

0.99

0.77

PPAS

IEEILSKIYHIENEIARIKKLIKAVGNQVVTTQTTLVNSLGGNAKVNADGTITGPGNQTNVGDALTALDNAINTAATTSKSTVSNGQNIVVSK-NADGSDNYEVSTAKDLTVDGDTVLNNAGITIGNNAVVLNNTSGGPAGNK

4edgA1

0.11

0.10

0.85

0.72

Env-PPAS

SNADDLQMIEMHELIQEFYYYALTKTVEGEQALTYLQERFTDALIKERGIGFAPDSS-HFCHDFLQKKGYDIELAYEAG--LLSRNEENFSYYDRFRNRIMFPLKN-----AQGRIVGYS-------------GRTYTGQEPK

4n0nA3

0.16

0.15

0.90

0.69

MUSTER

--------VNKALKNAAASEYVEG--PPGSGKTFHLVKDVLAV--VGSATLVVPTASMLDCINKLKQAADPYVVPKYTVLDFPR-GNITVRLPQVGTSEGETFVDEVAYFSTQGRVKGYG-DLNQLGCVGPASVPRNLSLEPL

2n11A

0.05

0.03

0.52

0.59

dPPAS

---QQQAVLEQERRDRELALRIAQSEAELISDEAQADLALRRSLDSYPVSKNDGTRPKMTPEQMAKEMSEFLSRGPA------------------------------------------------------------------

(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=-4.04

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-4.50

Download Model 3

C-score=-4.60

Download Model 4

C-score=-4.84

Download Model 5

C-score=-4.88

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	2zf5O	0.479	5.21	0.059	0.909
2	1ka1A	0.478	4.80	0.028	0.818
3	4e1jA	0.478	5.06	0.053	0.860
4	1i5pA	0.477	4.61	0.075	0.811
5	2dpnA	0.477	5.33	0.059	0.916
6	3ctzA2	0.476	4.78	0.051	0.797
7	5iwkA2	0.476	4.54	0.043	0.776
8	1yiqA1	0.474	4.92	0.030	0.846
9	2im9A	0.473	5.01	0.063	0.839
10	1cvuA2	0.473	4.87	0.071	0.804

(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	0.06	3	1xvhA	ZN	Rep, Mult	39,43
2	0.06	3	1lqoB	PO4	Rep, Mult	111,113
3	0.06	3	3h3oX	EDO	Rep, Mult	81,92,93,94
4	0.04	2	4evpA	URE	Rep, Mult	5,87,89
5	0.04	2	1mfuA	GLC	Rep, Mult	31,35,48
6	0.04	2	3f8fB	DM1	Rep, Mult	9,111
7	0.04	2	3ctzA	MN	Rep, Mult	77,80,82,93
8	0.04	2	3kqzL	CO3	Rep, Mult	12,31,32,33,34,92
9	0.02	1	5hk7D	VVA	Rep, Mult	11,33,40,43
10	0.02	1	4il6R	HEM	Rep, Mult	18,22
11	0.02	1	2hf8A	ZN	Rep, Mult	54,100
12	0.02	1	3h3oO	PO4	Rep, Mult	103,105,116,137
13	0.02	1	1a34A	U	Rep, Mult	55,56
14	0.02	1	1glfX	PO4	Rep, Mult	105,114,116
15	0.02	1	1swiC	BNZ	Rep, Mult	6,10
16	0.02	1	3kziX	CLA	Rep, Mult	8,11

	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	3ij3A	0.448	4.78	0.060	0.797	3.4.11.1	31
2	0.060	2vdcA	0.458	4.13	0.038	0.720	1.4.1.13	NA
3	0.060	2e8iA	0.447	4.76	0.060	0.769	3.5.1.46	63,73,103
4	0.060	1ftaA	0.419	5.03	0.056	0.748	3.1.3.11	NA
5	0.060	1kv9A	0.470	4.88	0.035	0.832	1.1.99.-	NA
6	0.060	1ofdA	0.456	4.14	0.066	0.720	1.4.7.1	NA
7	0.060	2aeyA	0.444	5.17	0.098	0.811	3.2.1.80	55
8	0.060	1st8A	0.444	5.17	0.098	0.818	3.2.1.80	81
9	0.060	2j0wA	0.444	5.14	0.034	0.804	2.7.2.4	NA
10	0.060	1b0pA	0.449	4.77	0.071	0.769	1.2.7.1	NA
11	0.060	3flcX	0.454	5.51	0.028	0.923	2.7.1.30	NA
12	0.060	2gmjA	0.404	5.67	0.065	0.797	1.5.5.1	NA
13	0.060	1yiqA	0.446	5.12	0.043	0.839	1.1.99.-	NA
14	0.060	2vdcF	0.458	4.13	0.038	0.720	1.4.1.13	NA
15	0.060	1ci8A	0.446	5.11	0.069	0.811	3.1.1.1	117
16	0.060	3g5sA	0.454	5.14	0.087	0.832	2.1.1.74	NA
17	0.060	1y9mA	0.463	5.14	0.066	0.839	3.2.1.80	80
18	0.060	3ezwG	0.461	5.38	0.058	0.916	2.7.1.30	NA
19	0.060	1pj6A	0.447	4.89	0.049	0.811	1.5.3.10	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	0.20	0.455	5.36	0.07	0.85	3h3nO	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
1	0.07	0.324	5.44	0.03	0.62	3ifrA	GO:0004856 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
2	0.07	0.448	5.51	0.06	0.85	4e1jD	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
3	0.07	0.462	5.34	0.05	0.90	1bu6Y	GO:0000166 GO:0003824 GO:0004370 GO:0005524 GO:0005829 GO:0005975 GO:0006071 GO:0006072 GO:0006974 GO:0008152 GO:0008270 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563 GO:0046872
4	0.06	0.479	5.21	0.06	0.91	2zf5O	GO:0000166 GO:0004370 GO:0005524 GO:0005737 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
5	0.06	0.424	5.79	0.04	0.90	3wxiA	GO:0000166 GO:0004370 GO:0005975 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773
6	0.06	0.477	5.33	0.06	0.92	2dpnA	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
7	0.06	0.425	5.81	0.02	0.88	2d4wA
8	0.06	0.428	5.59	0.04	0.88	2w41B	GO:0000166 GO:0004370 GO:0005524 GO:0005739 GO:0005975 GO:0006071 GO:0006072 GO:0006641 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046167
9	0.06	0.359	5.36	0.02	0.67	2itmA	GO:0000166 GO:0004856 GO:0005524 GO:0005737 GO:0005975 GO:0005997 GO:0005998 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0042732 GO:0042843 GO:0046835
10	0.06	0.429	5.52	0.07	0.87	3i8bA	GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046872
11	0.06	0.392	5.23	0.04	0.73	3g25A	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
12	0.06	0.401	5.55	0.04	0.82	3l0qB	GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773
13	0.06	0.395	5.67	0.04	0.78	3kzbA	GO:0000166 GO:0004856 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
14	0.06	0.319	5.22	0.05	0.59	5huxA	GO:0005975 GO:0016301 GO:0016310 GO:0016773
15	0.06	0.391	5.61	0.06	0.76	4c23A	GO:0005975 GO:0008737 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
16	0.06	0.345	4.48	0.05	0.58	4hf7A	GO:0016787
17	0.06	0.358	5.12	0.01	0.67	1ak2A	GO:0000166 GO:0004017 GO:0005524 GO:0005739 GO:0005743 GO:0005758 GO:0006139 GO:0006172 GO:0016301 GO:0016310 GO:0016740 GO:0016776 GO:0019205 GO:0036126 GO:0046033 GO:0046034 GO:0046939 GO:0070062 GO:0097226
18	0.06	0.306	5.68	0.07	0.62	3am8A	GO:0000139 GO:0001916 GO:0002250 GO:0002376 GO:0002474 GO:0002476 GO:0002479 GO:0002480 GO:0002715 GO:0002717 GO:0005102 GO:0005886 GO:0006955 GO:0009986 GO:0012507 GO:0016020 GO:0016021 GO:0019731 GO:0019882 GO:0030670 GO:0030881 GO:0031901 GO:0032398 GO:0032736 GO:0032753 GO:0032759 GO:0032760 GO:0036037 GO:0042270 GO:0042288 GO:0042605 GO:0042612 GO:0045087 GO:0046703 GO:0050776 GO:0050830 GO:0051024 GO:0060333 GO:0060337 GO:0070062 GO:0071556 GO:2000566

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0004370
GO-Score	0.35	0.35
Biological Processes	GO:0016310	GO:0019563	GO:0006072
GO-Score	0.39	0.35	0.35
Cellular Component	GO:0005829
GO-Score	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.