I-TASSER results

I-TASSER results for job id Rv0308

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

Input Sequence in FASTA format

>protein (238 residues)
MTRPQALLAVSLAFVATAVYAVMWVGHSQDWGWLHSFDWSLLNAAHDIGIKNPAWVRFWD
GVSLILGPVVLRPLGLLAAMVALAKRKIRIALLLLACLPLNAIMTIAAKSVAHRPRPATA
LVSAHSTSFPSGHALEATASVLALLTVLLPMLHSRFTRHIAITVGALCVLTVGVARVALN
VHHPTDVVAGWALGYLYFLVCLCVFRPPSIFGAQRASHALSPPVEVSRQPEPEVDTAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTRPQALLAVSLAFVATAVYAVMWVGHSQDWGWLHSFDWSLLNAAHDIGIKNPAWVRFWDGVSLILGPVVLRPLGLLAAMVALAKRKIRIALLLLACLPLNAIMTIAAKSVAHRPRPATALVSAHSTSFPSGHALEATASVLALLTVLLPMLHSRFTRHIAITVGALCVLTVGVARVALNVHHPTDVVAGWALGYLYFLVCLCVFRPPSIFGAQRASHALSPPVEVSRQPEPEVDTAR
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9987578999999999999999999998755678999999999999975778589999999999879679999999999999986976899999999999999999999998589999865678888888979999999999999999997565578999999999999999999998776785899999999999999999999867776655566777888777888888888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MTRPQALLAVSLAFVATAVYAVMWVGHSQDWGWLHSFDWSLLNAAHDIGIKNPAWVRFWDGVSLILGPVVLRPLGLLAAMVALAKRKIRIALLLLACLPLNAIMTIAAKSVAHRPRPATALVSAHSTSFPSGHALEATASVLALLTVLLPMLHSRFTRHIAITVGALCVLTVGVARVALNVHHPTDVVAGWALGYLYFLVCLCVFRPPSIFGAQRASHALSPPVEVSRQPEPEVDTAR
Prediction	8644422001112233233323211022343420230032003001312241220031022103333333222122221211023433210000021233123211003303402103321243432011011000013332312210233244422221112212320330031101031333031301321032213201201232442454445644545464555465655468
	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                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
MTRPQALLAVSLAFVATAVYAVMWVGHSQDWGWLHSFDWSLLNAAHDIGIKNPAWVRFWDGVSLILGPVVLRPLGLLAAMVALAKRKIRIALLLLACLPLNAIMTIAAKSVAHRPRPATALVSAHSTSFPSGHALEATASVLALLTVLLPMLHSRFTRHIAITVGALCVLTVGVARVALNVHHPTDVVAGWALGYLYFLVCLCVFRPPSIFGAQRASHALSPPVEVSRQPEPEVDTAR

4px7A

0.20

0.17

0.85

1.38

MUSTER

-GRSIARRTAVGAALLLVPVAVWISGWRWQ--------------------PGSWLLKAAFWVTETVTQPVITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWVQEPRPRSHWQKETGFAFPSGHTFAASWALLAVGLLWPR-------RRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRI------CGPLTPPEENREIAQREQESLEHH

4px7A

0.15

0.13

0.85

1.20

dPPAS

-----GRSIARRTAVGAALLLVPVAVWISGW----------------RWQPGSWLLKAAFWVTETVTQPWGVITHLILFGWFLWCLRFVLFAILAAAILVGQGVKSWIKDKVQEPRPFVHWQKETGFAFPSGHTFAASWALLAVGLLWPRRR-------TLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTPPEENREIAQREQESLEHH------

4px7A

0.14

0.12

0.85

2.66

wdPPAS

----------GRSIARRTAVGAALLLV------------PVAVWISGWRQPGSWLLKAAFWVTETVTPWGVITHLILFGWFLWCLRFFVLFAILAAAILVGQGVKSWIKDKVQEPRPFSHWQKETGFAFPSGHTFAASWALLAVGLLWPR-------RRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTPPEENREIAQREQESLEHH------

4px7A

0.16

0.14

0.85

1.92

wMUSTER

-----GRSIARRTAVGAALLLVPVAVWISGW----------------RWQPGSWLLKAAFWVTETVTQPGVITHLILFGWFLWCLRFFVLFAILAAAILVGQGVKSWIKDKVQEPRPRSHWQKETGFAFPSGHTFAASWALLAVGLL----WPR---RRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRI---CGPLTPPEENREIAQREQESLEHH---

4px7A

0.14

0.12

0.84

3.64

wPPAS

----------GRSIARRTAVGAALLLV------------PVAVWISGWRQPGSWLLKAAFWVTETVTPWGVITHLILFGWFLWCLRFFVLFAILAAAILVGQGVKSWIKDKVQEPRPFSHWQKETGFAFPSGHTFAASWALLAVGLLWPR-------RRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRI-------CGPLTPPEENREIAQREQESLEH

4px7A

0.16

0.13

0.85

2.96

dPPAS2

-----GRSIARRTAVGAALLLVPVAVWISGW----------------RWQPGSWLLKAAFWVTETVTPWGVITHLILFGWFLWCLRFFVLFAILAAAILVGQGVKSWIKDKVQEPRPFVHWQKETGFAFPSGHTFAASWALLAVGLLWPRRR-------TLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTPPEENREIAQREQESLEHH------

4px7A

0.17

0.15

0.84

2.30

PPAS

-GRSIARRTAVGAALLLVPVAVWISG---------------------RWQPGSWLLKAAFWVTETVTPWGVITHLILFGWFLWCLRFFVLFAILAAAILVGQGVKSWIKDKVQEPRPFSHWQKETGFAFPSGHTFAASWALLAVGLLWPR-------RRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRI-------CGPLTPPEENREIAQREQESLEH

2akcB

0.16

0.14

0.85

2.25

Env-PPAS

HSPEESVNSQFYLPPPPG-----------NDDPAFRYDKEAYFKGYAI--KGSPRWKQAAEDADISVENIARIFSPVVGAKISPKDTETWNMLQNLLKVGGYYATASAKKYYMRTRPFVLFNHSKDGSYPSGHTAYSTLLALVLSQAR----------PERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLS------------

2akcB

0.18

0.15

0.84

1.31

MUSTER

MQ-SPEESVNSQFYLP------------GNDDPAFRYDKEAYFKGYAI--KGSPRWKQAAEDADISVENIARIFSPVVGAKISPKDTPETWNMLQNLLKVGGYYTASAKKYYMRTRPHSTCRPRKDGSYPSGHTAYSTLLALVLSQAR----------PERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLS------------

2akcB

0.16

0.14

0.87

1.10

dPPAS

-------MQPFHSPEESVNSQFYLPPPPGNDDPAFRYDKEAYFKGYAI--KGSPRWKQAAEDADISVENIARIFSPVVGAKISPKDTETWNMLQNLLKVGGYYATASAKKYYMRTRPFVLFNHSTDGSYPSGHTAYSTLLALVLSQAR----------PERAQELARRGWEFGQSRVICGAHWQSDVDAGRYVGAVEFARLQTIPAFQKSLAKVREELNDKNNLLS------------

(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=-0.47

Estimated TM-score = 0.65±0.13

Estimated RMSD = 6.7±4.0Å

Download Model 2

C-score=-1.69

Download Model 3

C-score=-2.96

Download Model 4

C-score=-1.30

Download Model 5

C-score=-4.53

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	4px7A	0.646	3.24	0.148	0.798
2	5aa6A	0.640	4.17	0.132	0.866
3	1qi9A	0.640	3.67	0.123	0.824
4	1qhbA	0.625	4.04	0.127	0.836
5	5lpcA	0.625	4.25	0.121	0.849
6	4citA	0.614	4.19	0.083	0.819
7	1iduA	0.604	4.30	0.143	0.811
8	3w35A	0.579	4.08	0.116	0.794
9	2akcB	0.578	4.31	0.160	0.798
10	1eoiA	0.566	4.39	0.144	0.802

(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	0.30	17	1vneA	VO4	Rep, Mult	109,116,131,132,133,176,182
2	0.04	2	4g86A	BNT	Rep, Mult	116,184,185
3	0.04	2	3feqA	ZN	Rep, Mult	109,133,159
4	0.02	1	2pivA	T3	Rep, Mult	65,66,78,161,165,166,169,172
5	0.02	1	2h2pA	SEK	Rep, Mult	112,118
6	0.02	1	2yloA	YLO	Rep, Mult	96,97,101,194,197,198,201,202
7	0.02	1	3j47V	III	Rep, Mult	170,174,177
8	0.02	1	4citA	VO4	Rep, Mult	116,124,176,182
9	0.02	1	2npjA	IMD	Rep, Mult	105,108,109,190

	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	0.169	2ipbA	0.574	4.35	0.161	0.781	3.1.3.2	133,138,166,177
2	0.134	2a96B	0.576	4.34	0.166	0.781	3.1.3.2	133,176,182,186
3	0.129	1d2tA	0.578	4.62	0.157	0.815	3.1.3.2	133,176,182,186
4	0.060	1syyA	0.427	5.13	0.067	0.643	1.17.4.1	NA
5	0.060	2ouyA	0.413	5.16	0.031	0.634	3.1.4.17	72
6	0.060	3hf1B	0.426	5.07	0.056	0.647	1.17.4.1	NA
7	0.060	1h0nA	0.427	4.69	0.038	0.622	1.17.4.1	NA
8	0.060	1smsA	0.432	4.89	0.064	0.647	1.17.4.1	NA
9	0.060	1vncA	0.605	4.31	0.152	0.811	1.11.1.10	NA
10	0.060	3bjcA	0.401	4.89	0.067	0.601	3.1.4.35	147
11	0.060	2p0mB	0.401	6.03	0.058	0.672	1.13.11.33	106
12	0.060	2p0mA	0.410	5.63	0.067	0.676	1.13.11.33	NA
13	0.060	3b8cA	0.425	4.41	0.040	0.584	3.6.3.6	NA
14	0.060	3ecnB	0.393	4.97	0.036	0.597	3.1.4.17	167
15	0.060	1w07B	0.438	5.63	0.078	0.727	1.3.3.6	NA
16	0.060	2qymA	0.400	4.72	0.046	0.584	3.1.4.17	NA
17	0.060	1biqB	0.415	4.87	0.029	0.622	1.17.4.1	NA
18	0.060	1n1hA	0.423	5.58	0.049	0.702	2.7.7.48	171
19	0.060	2vuxB	0.401	4.45	0.052	0.567	1.17.4.1	NA
20	0.060	1qi9B	0.644	3.94	0.110	0.849	1.11.1.10	109,133,183

(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	0.07	0.604	4.30	0.14	0.81	1iduA	GO:0004601 GO:0005576 GO:0016491 GO:0016691 GO:0046872 GO:0055114 GO:0098869
1	0.06	0.610	4.18	0.09	0.82	4uszA	GO:0004601 GO:0016491 GO:0055114 GO:0098869
2	0.06	0.583	3.98	0.12	0.79	3w36B	GO:0004601 GO:0055114 GO:0098869
3	0.06	0.625	4.05	0.12	0.84	1up8A	GO:0004601 GO:0016491 GO:0046872 GO:0055114 GO:0098869
4	0.06	0.327	6.76	0.05	0.61	1r8gB	GO:0000166 GO:0004357 GO:0005524 GO:0016874 GO:0016879 GO:0042398
5	0.06	0.344	5.82	0.01	0.57	3pgxA	GO:0016491 GO:0055114
6	0.06	0.311	5.85	0.06	0.52	5evlA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
7	0.06	0.305	5.99	0.05	0.53	3wecA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
8	0.06	0.271	5.87	0.03	0.45	4v7fr	GO:0000463 GO:0000465 GO:0002181 GO:0003723 GO:0003735 GO:0005634 GO:0005730 GO:0019843 GO:0022625 GO:0030687 GO:0042254 GO:0042273
9	0.06	0.321	5.93	0.05	0.55	4djaA	GO:0000166 GO:0000719 GO:0003677 GO:0003914 GO:0006281 GO:0006974 GO:0016829 GO:0018298 GO:0046872 GO:0051536 GO:0051539 GO:0071949
10	0.06	0.294	5.64	0.06	0.48	3btnA	GO:0003824 GO:0005634 GO:0005737 GO:0006595 GO:0006596 GO:0033387 GO:0042177 GO:0042978 GO:0043085 GO:1902269
11	0.06	0.640	3.67	0.12	0.82	1qi9A	GO:0004601 GO:0016491 GO:0046872 GO:0055114 GO:0098869
12	0.06	0.246	3.92	0.01	0.33	3iu6A	GO:0000228 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006338 GO:0006351 GO:0006355 GO:0007067 GO:0008285 GO:0016568 GO:0090544
13	0.06	0.253	5.42	0.04	0.41	3im8A	GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
14	0.06	0.275	4.90	0.03	0.40	3s6gA	GO:0000166 GO:0003991 GO:0004042 GO:0005524 GO:0005737 GO:0006526 GO:0008652 GO:0016301 GO:0016310 GO:0016740 GO:0016746
15	0.06	0.273	5.16	0.04	0.45	1z41A	GO:0003824 GO:0003959 GO:0005622 GO:0009636 GO:0010181 GO:0016491 GO:0018548 GO:0050661 GO:0052690 GO:0055114
16	0.06	0.259	6.50	0.02	0.47	2bgwA	GO:0003677 GO:0004518 GO:0004519 GO:0006259 GO:0006281 GO:0046872 GO:0090305
17	0.06	0.246	6.00	0.02	0.42	3ba1A	GO:0000166 GO:0008152 GO:0016491 GO:0016616 GO:0047995 GO:0051287 GO:0055114
18	0.06	0.261	6.11	0.03	0.44	4lygB	GO:0000166 GO:0000287 GO:0002189 GO:0004749 GO:0005524 GO:0005829 GO:0006015 GO:0006144 GO:0006164 GO:0006167 GO:0006221 GO:0007399 GO:0009156 GO:0009165 GO:0016208 GO:0016301 GO:0016310 GO:0016740 GO:0019003 GO:0019693 GO:0030246 GO:0031100 GO:0034418 GO:0042803 GO:0043234 GO:0043531 GO:0044249 GO:0046101 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0016684	GO:0016209
GO-Score	0.47	0.47
Biological Processes	GO:0044710	GO:1990748
GO-Score	0.47	0.47
Cellular Component	GO:0005576
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.