I-TASSER results

I-TASSER results for job id Rv3054c

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

Input Sequence in FASTA format

>protein (184 residues)
MSDTKSDIKILALVGSLRAASFNRQIAELAAKVAPDGVTVTMFEGLGDLPFYNEDIDTAT
EVPAPVSALREAASDAHAALVVTPEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGG
SMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPFQTLGKSVADDAGLAANVRDAVGNLA
AEVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSDTKSDIKILALVGSLRAASFNRQIAELAAKVAPDGVTVTMFEGLGDLPFYNEDIDTATEVPAPVSALREAASDAHAALVVTPEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGGSMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPFQTLGKSVADDAGLAANVRDAVGNLAAEVG
Prediction	CCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEEHCCCCCHCHHHHHHHHHHHHHHCCHCCCCCEEEHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
Conf.Score	9989998589999878999885699999999985789969999588889998998888889999999999999989968999679999988899999998756789854489869999868986556899999999999879855787567653555456788875789999999999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSDTKSDIKILALVGSLRAASFNRQIAELAAKVAPDGVTVTMFEGLGDLPFYNEDIDTATEVPAPVSALREAASDAHAALVVTPEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGGSMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPFQTLGKSVADDAGLAANVRDAVGNLAAEVG
Prediction	8664554010000002026412043004101620576040300143460111143256576326304401620460411000000323323212100001023436552044110000002213301320141024104406042153131323243247531547612640351055027418
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEEHCCCCCHCHHHHHHHHHHHHHHCCHCCCCCEEEHCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
MSDTKSDIKILALVGSLRAASFNRQIAELAAKVAPDGVTVTMFEGLGDLPFYNEDIDTATEVPAPVSALREAASDAHAALVVTPEYNGSIPAVIKNAIDWLSRPFGDGALKDKPLAVIGGSMGRYGGVWAHDETRKSFSIAGTRVVDAIKLSVPFQTLGKSVADDAGLAANVRDAVGNLAAEVG

3svlA

0.31

0.29

0.96

2.97

MUSTER

------KLQVVTLLGSLRKGSFNGMVARTLPKIAPASMEVNALPSIADIPLYDADVQQEEGFPATVEALAEQIRQADGVVIVTPEYNYSVPGGLKNAIDWLSR-LPDQPLAGKPVLIQTSSMGVIGGARCQYHLRQILVFLDAMVMNKPEFMGGVIQNKTGEVIDQGTLDHLTGQLTAFGEFIQ

3svlA

0.31

0.29

0.96

3.97

dPPAS

------KLQVVTLLGSLRKGSFNGMVARTLPKIAPASMEVNALPSIADIPLYDADVQQEEGFPATVEALAEQIRQADGVVIVTPEYNYSVPGGLKNAIDWLSR-LPDQPLAGKPVLIQTSSMGVIGGARCQYHLRQILVFLDAMVMNKPEFMGGVIQNKTGEVIDQGTLDHLTGQLTAFGEFIQ

1x77A

0.31

0.29

0.93

4.02

wdPPAS

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISNAFDAQGRLLDDKARELIQQQLQALQL---

3svlA

0.31

0.29

0.95

3.40

wMUSTER

L-------QVVTLLGSLRKGSFNGMVARTLPKIAPASMEVNALPSIADIPLYDADVQQEEGFPATVEALAEQIRQADGVVIVTPEYNYSVPGGLKNAIDWLSRL-PDQPLAGKPVLIQTSSMGVIGGARCQYHLRQILVFLDAMVMNKPEFMGGVIQ-QTGEVIDQGTLDHLTGQLTAFGEFIQ

1x77A

0.31

0.29

0.93

4.23

wPPAS

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISNAFDAQGRLLDDKARELIQQQLQALQL---

1x77A

0.31

0.29

0.93

6.65

dPPAS2

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISSAQNAQGRLLDDKARELIQQQLQALQL---

1x77A

0.31

0.29

0.93

3.76

PPAS

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISSAQNAQGRLLDDKARELIQQQLQALQL---

1x77A

0.31

0.29

0.93

4.26

Env-PPAS

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISSAQNAQGRLLDDKARELIQQQLQALQL---

1x77A

0.31

0.29

0.92

2.91

MUSTER

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISSAQ-AQGRLLDDKARELIQQQLQALQL---

1x77A

0.31

0.29

0.93

3.94

dPPAS

-------IKVLGISGSLRSGSYNSAALQEAIGLVPPGMSIELAD-ISGIPLYNEDVY-ALGFPPAVERFREQIRAADALLFATPEYNYSMAGVLKNAIDWASRP-PEQPFSGKPAAILGASAGRFGTARAQYHLRQTLVFLDVHPLNKPEVMISNAFDAQGRLLDDKARELIQQQLQALQL---

(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 1 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=1.19

Estimated TM-score = 0.88±0.07

Estimated RMSD = 2.9±2.1Å

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	3svlA	0.940	0.82	0.305	0.962
2	3s2yA	0.936	0.88	0.339	0.962
3	1x77A	0.892	1.08	0.304	0.929
4	2fzvB	0.864	2.12	0.230	0.967
5	2q62D	0.851	2.14	0.243	0.962
6	3u7rA	0.814	2.13	0.325	0.918
7	3fvwB	0.812	2.24	0.287	0.929
8	3gfrD	0.807	1.84	0.215	0.886
9	4ptyC	0.777	2.38	0.138	0.908
10	4c76A	0.776	2.44	0.160	0.918

(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	0.69	44	4c0xA	FMN	Rep, Mult	16,18,21,22,23,84,85,86,87,88,120,121,122,123
2	0.37	24	1x77A	FMN	Rep, Mult	52,54,99,102,103,140
3	0.02	3	3o73A	O73	Rep, Mult	87,122,123,156,157
4	0.02	3	2vzfA	PO4	Rep, Mult	16,18,21,22,23,84,155
5	0.01	1	1t0iA	FMN	Rep, Mult	59,99
6	0.01	1	3o2nB	MZX	Rep, Mult	88,93,133
7	0.01	1	3svlB	CA	Rep, Mult	17,18
8	0.01	1	3svlA	CA	Rep, Mult	53,55
9	0.01	1	1t0iA	CA	Rep, Mult	132,136

	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	0.353	1t0iA	0.760	2.77	0.217	0.902	1.5.1.29	46,86,95,99,132
2	0.164	1s2gB	0.563	4.20	0.096	0.783	2.4.2.6	74,76,113
3	0.135	1cb7A	0.524	3.45	0.124	0.701	5.4.99.1	76,80,119
4	0.099	1y80A	0.513	3.28	0.129	0.674	2.1.1.13	NA
5	0.067	1b1cA	0.592	3.94	0.135	0.815	1.6.2.4	16
6	0.067	1m2oB	0.557	3.51	0.107	0.750	3.6.5.-	131
7	0.067	1s2dB	0.564	4.21	0.096	0.783	2.4.2.6	NA
8	0.066	1f8xA	0.539	3.64	0.109	0.707	2.4.2.6	NA
9	0.066	1bdjA	0.487	3.75	0.120	0.674	2.7.13.3	141
10	0.066	3lwzA	0.505	3.55	0.126	0.690	4.2.1.10	139
11	0.066	1h0rA	0.498	3.60	0.119	0.685	4.2.1.10	NA
12	0.066	2r25B	0.481	3.67	0.072	0.668	2.7.13.3	NA
13	0.066	1d0iH	0.521	4.14	0.154	0.739	4.2.1.10	NA
14	0.060	1e0sA	0.585	3.64	0.075	0.788	3.6.1.47	NA
15	0.060	1qr2A	0.732	3.14	0.172	0.918	1.10.99.2,1.6.99.2	119
16	0.060	1ycfA	0.666	2.68	0.178	0.799	1.7.99.7	NA
17	0.060	2qx9B	0.729	3.19	0.172	0.918	1.10.99.2	50,89,95
18	0.060	1eloA	0.591	3.31	0.075	0.777	3.6.5.3	NA
19	0.060	1ob2A	0.635	3.46	0.128	0.837	3.6.1.48	NA
20	0.060	1h65A	0.602	4.32	0.073	0.880	3.6.5.-	NA
21	0.060	1de0A	0.614	3.43	0.086	0.821	1.18.6.1	NA
22	0.060	1darA	0.587	3.46	0.069	0.783	3.6.5.3	NA
23	0.060	1fuiA	0.593	3.76	0.145	0.821	5.3.1.25	28
24	0.060	2z9dB	0.716	3.12	0.166	0.902	1.7.1.6	96,99
25	0.060	1d4aA	0.736	3.12	0.144	0.918	1.6.5.2	NA
26	0.060	1etuA	0.626	3.55	0.116	0.842	3.6.5.3	NA
27	0.060	2ohhA	0.673	2.54	0.179	0.793	1.-.-.-	NA
28	0.060	1gy8C	0.583	4.12	0.064	0.826	5.1.3.2	NA
29	0.060	2rg1B	0.690	2.59	0.175	0.815	1.6.5.2	NA
30	0.060	1tllA	0.602	3.52	0.112	0.799	1.14.13.39	NA
31	0.060	1ja1A	0.587	3.99	0.128	0.815	1.6.2.4	NA
32	0.060	3fjoA	0.585	4.02	0.140	0.804	1.6.2.4	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	0.58	0.934	0.90	0.33	0.96	4h6pA	GO:0000166 GO:0016491 GO:0055114
1	0.54	0.939	0.82	0.30	0.96	3svlB	GO:0003955 GO:0005829 GO:0006805 GO:0010181 GO:0016491 GO:0055114
2	0.53	0.895	1.03	0.30	0.93	1rttA	GO:0000166 GO:0010181 GO:0016491 GO:0042802 GO:0042803 GO:0052873 GO:0055114
3	0.46	0.846	2.10	0.31	0.95	3u7rA	GO:0016491 GO:0055114
4	0.41	0.817	2.24	0.28	0.93	3fvwB	GO:0016491 GO:0055114
5	0.40	0.851	2.14	0.24	0.96	2q62D	GO:0000166 GO:0010038 GO:0010181 GO:0016491 GO:0051289 GO:0052873 GO:0055114
6	0.39	0.864	2.12	0.23	0.97	2fzvB	GO:0000166 GO:0010181 GO:0016491 GO:0050446 GO:0051289 GO:0052873 GO:0055114
7	0.38	0.807	1.84	0.21	0.89	3gfrD	GO:0016491 GO:0042802 GO:0055114
8	0.37	0.754	2.47	0.17	0.90	4ltdA	GO:0000166 GO:0008752 GO:0016491 GO:0046306 GO:0055114
9	0.35	0.760	2.77	0.22	0.90	1t0iA	GO:0003955 GO:0005634 GO:0005737 GO:0005829 GO:0006915 GO:0008134 GO:0016491 GO:0034599 GO:0042994 GO:0052873 GO:0052874 GO:0055114
10	0.34	0.778	2.40	0.14	0.91	4ptyD	GO:0006974 GO:0008752 GO:0009970 GO:0016491 GO:0046306 GO:0051289 GO:0052873 GO:0055114
11	0.33	0.767	2.61	0.17	0.91	3k1yA	GO:0016491 GO:0055114
12	0.33	0.779	2.45	0.16	0.92	4c76A	GO:0016491 GO:0052873 GO:0055114
13	0.30	0.723	3.08	0.22	0.90	3r6wA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
14	0.30	0.727	3.02	0.18	0.90	1t5bA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
15	0.30	0.726	2.94	0.18	0.90	4eseA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
16	0.29	0.730	3.14	0.17	0.92	1tikA	GO:0005829 GO:0006979 GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016655 GO:0016661 GO:0050446 GO:0055114
17	0.27	0.735	3.31	0.16	0.94	4fglD	GO:0005654 GO:0005737 GO:0007613 GO:0008753 GO:0009055 GO:0016491 GO:0046872 GO:0055114 GO:0070062
18	0.25	0.690	3.00	0.16	0.87	3p0rA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
19	0.23	0.715	3.19	0.16	0.92	3u7iB	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
20	0.23	0.696	3.13	0.17	0.89	3w78A	GO:0000166 GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
21	0.22	0.690	3.25	0.15	0.88	4c0wA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
22	0.22	0.725	2.44	0.14	0.84	2zkiA	GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0055114
23	0.22	0.691	3.14	0.14	0.88	2hpvA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
24	0.19	0.585	3.65	0.18	0.79	1bvyF	GO:0003824 GO:0003958 GO:0004497 GO:0005506 GO:0005737 GO:0008152 GO:0010181 GO:0016491 GO:0016705 GO:0016712 GO:0020037 GO:0042802 GO:0046872 GO:0055114 GO:0070330

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0003955	GO:0042803	GO:0052873
GO-Score	0.79	0.54	0.53	0.53
Biological Processes	GO:0055114	GO:0006805
GO-Score	0.97	0.54
Cellular Component	GO:0005829
GO-Score	0.54

(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.