I-TASSER results

I-TASSER results for job id Rv2617c

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

Input Sequence in FASTA format

>protein (146 residues)
MSIRPTTSPALADQLKDPAYSAYVLLRTLFTVAPILFGLDKFFNLLTHPQHWNMYLAGWI
NDLVPGTADQCMYLVGAIEIVAGVLVAVAPRIGAWVVAAWLAGIILNLVTGPGFYDIALR
DFGLLVGAIALARLAQGVHSGGIGRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSIRPTTSPALADQLKDPAYSAYVLLRTLFTVAPILFGLDKFFNLLTHPQHWNMYLAGWINDLVPGTADQCMYLVGAIEIVAGVLVAVAPRIGAWVVAAWLAGIILNLVTGPGFYDIALRDFGLLVGAIALARLAQGVHSGGIGRP
Prediction	CCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Conf.Score	98888888567776568656688999999999999976577777764876556677788888567888887789989999999999874567899999999999999997687345667899999999999999987577777899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSIRPTTSPALADQLKDPAYSAYVLLRTLFTVAPILFGLDKFFNLLTHPQHWNMYLAGWINDLVPGTADQCMYLVGAIEIVAGVLVAVAPRIGAWVVAAWLAGIILNLVTGPGFYDIALRDFGLLVGAIALARLAQGVHSGGIGRP
Prediction	75444464543454255403201210233113102301323114101436404410142034114243420020021021201001123343202001311121300313333131001321021111221130153245544558
	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

CCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
MSIRPTTSPALADQLKDPAYSAYVLLRTLFTVAPILFGLDKFFNLLTHPQHWNMYLAGWINDLVPGTADQCMYLVGAIEIVAGVLVAVAPRIGAWVVAAWLAGIILNLVTGPGFYDIALRDFGLLVGAIALARLAQGVHSGGIGRP

3jbrE

0.15

0.12

0.85

0.74

MUSTER

MS------PTEAPKV----RVTLFCILVGIVLAMTAVVSDHWAVLSEFTTQKEYSISAAAISV----FSLGFLIMGTICALMKRDYLLRPASMFYVFAGLCLFVSLEVMRQSSFACACAAFVLLFLGGISLLLFSLPR--------

4clvA

0.13

0.11

0.86

0.58

dPPAS

------------------SRTFRLSVSTLVGALVGVLMAIVGVYVTHSTEEPHTSLHEMLHDAVPLDSNEREILELKEEEFTARRREI--ESRLRAANGKLAESIAKNPQWSPEVEEATREVERAAADLQRATLVHVFEMRAGLKP

4za6A2

0.12

0.10

0.83

0.57

wdPPAS

-----ATERTYRKAMSQSGQGPEYILDVFGRVMRSVESSTELRALTKEPMVFIKLAM--------PGSIESISASITAEILQSQVDALTITLSPQVLGEALVRICDVHLYA----PLL--EIETALDLIALLLVTRNHHH------

5a9q4

0.17

0.16

0.95

0.70

wMUSTER

LIPQPTFTEKVAHEHKEKKYEMDFGIWKGHLDALTADVKEKMYNVLLFVDGW---MVDVREDAKEDHERTHQMVLLRKLCLPMLCFLLHTSTGQYQECLQLADMVSSLYLV--FSKEELRKLLQKLRESSLMLLDQGL--DPLGYE

4k70A3

0.14

0.12

0.81

0.71

wPPAS

QAVHVAAAADLDH-TQVDATGVWEAVQASAS--PLQV-VTAFT-----RRHCDLLERAVLDR-APR--TDAQRAVGCTAVVGGVVHRLLDDYG----LDYVRAYTDVADTL----EPLYGDV---TAALGLKGVEHV-----VRHP

3wdoA2

0.18

0.16

0.94

0.80

dPPAS2

-RESGMVKGSFSKVLAEPIMCLHMLLMSTFVALPGQLAAG-----FPAAEHWKVYLATMLIAFGPRKMKQVFVFCVGLIVVAEIVLWNQTQFWQLVVGVQLFFVAFNLMEAAGYVYSTSQFLGVAIGGSLGGWIDGMFDGQGV---

4za6A2

0.13

0.12

0.88

0.76

PPAS

-----ATERTYRKAMSQSGQGPEYILDVFGRVMRSVESSTELRALTKEPMVFIKLAMM-------PGSIESISASITAEILQSQVDALTITLSPQVLGEALVRICDVHLYA----PLLGREKAEIETALDLIALLLGVTRNHHH--

4b89A1

0.13

0.12

0.87

0.75

Env-PPAS

LKFFAVDEVSCQINQEGAP--KDVVEKVLFVLNNLNNKVDELKKSL-TPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMG------SGLLHQFMVNVTLRQLFVLLSTEQAIDKKHLKNLASWLGCITLALN----------KP

4hzuS

0.13

0.98

0.74

MUSTER

MTKGSLKENTIAAVLIAMTVALSILVVIPIGIVTLCEVGIYTSAILYGRRMLVGGASGFLIDILTGYCLFSLVIHGTQGLVVGWLLPRHHKGIRSMLLPLLVGSLVMVIGYAGLASIFGNVVQVGFGAGVTLSIVGPLTR---LKP

4za6A2

0.13

0.12

0.89

0.58

dPPAS

----ATERTYRKAMSQASGQGPEYILDVFGRVMRSVESSTELRALTKRE------PMVFIKLAMMPGSIESISASITAEILQSQVDALTITLSPQVLGEALVRICDVHLYA----PLLGREKAEIETALDLIALLLGVTRNHHH--

(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=-2.77

Estimated TM-score = 0.40±0.13

Estimated RMSD = 10.9±4.6Å

Download Model 2

C-score=-4.57

Download Model 3

C-score=-4.46

Download Model 4

C-score=-4.75

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	5do7B2	0.669	3.45	0.045	0.918
2	4za6A	0.666	2.86	0.131	0.849
3	1n1zA	0.634	3.73	0.051	0.897
4	3c07A	0.631	3.75	0.101	0.931
5	3f0cA	0.630	2.93	0.092	0.815
6	5c05A	0.630	3.60	0.051	0.897
7	5do7A2	0.623	3.83	0.067	0.918
8	5d1wA	0.621	3.33	0.109	0.863
9	2oerB	0.620	3.19	0.067	0.815
10	3lwjA2	0.618	3.34	0.046	0.843

(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	3b6aA	ZCT	Rep, Mult	3,36,53,54,73,74,106
2	0.06	3	2jstA	HLT	Rep, Mult	100,128
3	0.04	2	2uxiB	G50	Rep, Mult	10,13,14,26,29,33,77,81,84,98,101,105
4	0.04	2	2y30B	SM8	Rep, Mult	48,52,53,57,60,106
5	0.04	2	3s7bA	BU3	Rep, Mult	95,133,137
6	0.04	2	3lsjB	COA	Rep, Mult	29,84,129,132,133
7	0.02	1	2y30A	SM8	Rep, Mult	56,60,99,106,107
8	0.02	1	2uxhA	QUE	Rep, Mult	29,30,47,51,77,81,97,101,105
9	0.02	1	3v5uA	CA	Rep, Mult	109,112,113,114,121
10	0.02	1	2o012	CLA	Rep, Mult	72,76,79
11	0.02	1	2y31A	SMQ	Rep, Mult	36,67,74,77,99,102,106
12	0.02	1	3b6cA	SDN	Rep, Mult	32,36,69,70,73
13	0.02	1	1h55A	O	Rep, Mult	27,30
14	0.02	1	3zt6A	ACX	Rep, Mult	34,38
15	0.02	1	2qx6A	ML1	Rep, Mult	52,113

	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	1inpA	0.504	3.60	0.071	0.733	3.1.3.57	NA
2	0.060	1z45A	0.488	4.67	0.026	0.774	5.1.3.2,5.1.3.3	73
3	0.060	1qmgA	0.482	4.09	0.035	0.740	1.1.1.86	79
4	0.060	1di1A	0.501	4.70	0.075	0.877	4.2.3.9	36
5	0.060	2z1qB	0.488	4.52	0.092	0.808	1.3.99.3	NA
6	0.060	3npkA	0.489	4.41	0.043	0.760	2.5.1.10	26,35,125
7	0.060	1ezfB	0.529	4.49	0.082	0.870	2.5.1.21	26,77,101
8	0.060	1mosA	0.494	4.34	0.060	0.781	2.6.1.16	24
9	0.060	2h8oA	0.505	4.30	0.090	0.781	2.5.1.10	91,122
10	0.060	1hm7A	0.511	4.81	0.095	0.904	4.2.3.7,4.6.1.5	NA
11	0.060	3ckeD	0.503	4.45	0.055	0.822	4.2.3.9	37
12	0.060	1n1zA	0.634	3.73	0.051	0.897	5.5.1.8	122
13	0.060	1yewB	0.523	4.22	0.064	0.808	1.14.13.25	31,35
14	0.060	1gy8C	0.495	4.29	0.053	0.767	5.1.3.2	NA
15	0.060	1dgpA	0.502	4.88	0.075	0.884	4.2.3.9,4.1.99.7	NA
16	0.060	1hxgA	0.592	3.68	0.045	0.856	4.2.3.9,4.1.99.7	21
17	0.060	1bucB	0.487	4.10	0.018	0.760	1.3.99.2	105,111
18	0.060	1rqiA	0.515	4.27	0.068	0.788	2.5.1.10	91
19	0.060	1yrlC	0.482	3.97	0.076	0.740	1.1.1.86	74

(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	0.597	3.25	0.14	0.80	4jl3C	GO:0003677 GO:0006351 GO:0006355
1	0.21	0.546	4.16	0.10	0.84	3c2bA	GO:0003677 GO:0006351 GO:0006355
2	0.18	0.589	3.87	0.06	0.88	5f1jA	GO:0003677 GO:0006351 GO:0006355
3	0.14	0.608	3.18	0.10	0.79	3b6aA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
4	0.13	0.506	4.65	0.08	0.84	3s5rA	GO:0003677 GO:0006351 GO:0006355
5	0.12	0.520	3.96	0.07	0.79	4me9A	GO:0003677 GO:0006351 GO:0006355
6	0.12	0.561	3.30	0.10	0.77	2fq4A	GO:0003677 GO:0006351 GO:0006355
7	0.12	0.561	3.88	0.09	0.82	3vprA	GO:0003677 GO:0006351 GO:0006355 GO:0042802
8	0.12	0.529	3.63	0.06	0.75	3zqfA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
9	0.09	0.666	2.86	0.13	0.85	4za6A	GO:0003677
10	0.08	0.646	3.50	0.04	0.92	5do7D	GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
11	0.08	0.601	3.57	0.03	0.83	3g7rB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
12	0.07	0.650	2.99	0.10	0.84	3f0cA	GO:0003677 GO:0006351 GO:0006355
13	0.07	0.612	3.74	0.10	0.92	5do7A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045177 GO:0045796 GO:0046982 GO:0055085
14	0.07	0.562	3.78	0.09	0.82	3frqA	GO:0003677 GO:0006351 GO:0006355 GO:0016740
15	0.07	0.574	3.41	0.06	0.76	2q24B	GO:0003677 GO:0006351 GO:0006355
16	0.07	0.616	3.42	0.09	0.87	5d1wD	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.543	4.25	0.11	0.83	3jsjA	GO:0003677 GO:0006351 GO:0006355
18	0.07	0.551	3.84	0.10	0.78	2nx4A	GO:0003677 GO:0006351 GO:0006355
19	0.07	0.534	3.85	0.07	0.76	2oi8A	GO:0003677 GO:0006351 GO:0006355
20	0.07	0.513	4.20	0.06	0.79	2o7tA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.61
Biological Processes	GO:0006355
GO-Score	0.61
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.