I-TASSER results

I-TASSER results for job id Rv3807c

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

Input Sequence in FASTA format

>protein (165 residues)
MVAVQSALVDRPGMLATARGLSHFGEHCIGWLILALLGAIALPRRRREWLVAGAGAFVAH
AIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAAALLMGRATGLPLPVVLV
PPMALSRILLGVHYPSDVAVGVALGATVGAIVDSVGGGRQRARKR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVAVQSALVDRPGMLATARGLSHFGEHCIGWLILALLGAIALPRRRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAAALLMGRATGLPLPVVLVPPMALSRILLGVHYPSDVAVGVALGATVGAIVDSVGGGRQRARKR
Prediction	CCHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	954546787786789999999997795899999999999985555899999999999999999999998658899988755665479999999979999999999999999999999999999999998666785889999999999999999999999876559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVAVQSALVDRPGMLATARGLSHFGEHCIGWLILALLGAIALPRRRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAAALLMGRATGLPLPVVLVPPMALSRILLGVHYPSDVAVGVALGATVGAIVDSVGGGRQRARKR
Prediction	541111232322312330330033343312333333322112343322011012023313131303230441221334303130433542320011011022113333333333212220331031113232333331311332033213301311432454578
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MVAVQSALVDRPGMLATARGLSHFGEHCIGWLILALLGAIALPRRRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAAALLMGRATGLPLPVVLVPPMALSRILLGVHYPSDVAVGVALGATVGAIVDSVGGGRQRARKR

1eoiA

0.17

1.00

1.55

MUSTER

AMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTKNGSYPSGHTSIGWATALVLAEPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHPAFQQQLQKAKA

1eoiA

0.17

1.00

1.60

dPPAS

AMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKPALHKLLTNMIEDAGDLATRSAKDHYMRIRPSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKA

1eoiA

0.16

1.00

3.26

wdPPAS

AMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHPAFQQQLQKAKA

1eoiA

0.16

1.00

2.13

wMUSTER

AMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKPALHKLLTNMIEDAGDLATRSAKDHYMRIRPSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHPAFQQQLQKAKA

4px7A

0.20

0.99

3.44

wPPAS

AVWISGRWQPGSWLLKAAFWVTETVTQPITHLILFGWFLWCLRFAFVLFAILAAAILVGQGVKSWIKDKVQEPRPFVIWLEKTHHPVTGFAFPSGHTFAASWALLAVGLRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTP

4px7A

0.20

0.99

5.12

dPPAS2

VWISGWRWQPGSWLLKAAFWVTETVTQVITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWVQEPRPFVIWLEKTHHPVTGFAFPSGHTFAASWALLAVGLRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTP

4px7A

0.20

0.99

2.20

PPAS

VWISGWRWQPGSWLLKAAFWVTETVTQPITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWVQEPRPFVIWLEKTHHPVTGFAFPSGHTFAASWALLAVGLRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTP

1eoiA

0.16

1.00

2.54

Env-PPAS

AMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHPAFQQQLQKAKA

4px7A

0.21

0.99

1.52

MUSTER

LLLVPVAVWISSWLLKAAFWVTETVTQPITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWVQEPRPFVIWLEKTWQKETGFAFPSGHTFAASWALLAVGLRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTP

4px7A

0.20

0.99

1.57

dPPAS

VWISGWRWQPGSWLLKAAFWVTETVTQVITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWVQEPRPFVIWLEKTHHPVTGFAFPSGHTFAASWALLAVGLRTLTIAILLVWATGVGSRLLLG-HWPRDLVVATLISWALVAVATWLAQRICGPLTP

(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=0.62

Estimated TM-score = 0.80±0.09

Estimated RMSD = 3.7±2.5Å

Download Model 2

C-score=-1.16

Download Model 3

C-score=-2.51

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.04

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	1eoiA	0.930	1.44	0.164	1.000
2	2akcB	0.909	1.67	0.164	1.000
3	3w35A	0.748	2.79	0.143	0.915
4	1qhbA	0.746	2.99	0.180	0.933
5	1qi9A	0.744	3.06	0.206	0.933
6	5lpcA	0.741	3.03	0.149	0.927
7	4citA	0.738	3.13	0.153	0.927
8	5aa6A	0.727	3.17	0.162	0.933
9	1iduA2	0.709	2.82	0.227	0.861
10	4px7A	0.604	4.47	0.174	0.921

(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	0.63	16	1eoiA	MOO	Rep, Mult	67,74,86,94,95,96,127,133
2	0.03	1	2ipb0	III	Rep, Mult	1,105,109,113,114,117,118,120,121,143,146,149,150,151,153,154

	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	0.424	2a96B	0.911	1.65	0.164	1.000	3.1.3.2	127,133,137
2	0.098	1d2tA	0.893	1.76	0.166	0.988	3.1.3.2	96,127,133,137
3	0.097	1iduA	0.521	3.85	0.068	0.751	1.11.1.10	67,96
4	0.060	1didA	0.465	4.22	0.055	0.697	5.3.1.5	NA
5	0.060	2ipbA	0.898	1.76	0.164	1.000	3.1.3.2	96,101,146
6	0.060	3b8cB	0.512	4.67	0.047	0.818	3.6.3.6	97,128
7	0.060	3d3lA	0.472	4.61	0.071	0.733	1.13.11.31	NA
8	0.060	1eulA	0.505	4.70	0.073	0.806	3.6.3.8	NA
9	0.060	1wmwA	0.487	4.17	0.061	0.721	2.5.1.-	NA
10	0.060	1jk0A	0.471	4.97	0.029	0.800	1.17.4.1	NA
11	0.060	2iukB	0.493	4.47	0.042	0.758	1.13.11.12	102
12	0.060	1no3A	0.489	4.57	0.056	0.758	1.13.11.12	NA
13	0.060	1up8A	0.743	3.01	0.169	0.927	1.11.1.18	67,96,133
14	0.060	1tazA	0.470	4.52	0.064	0.727	3.1.4.17	NA
15	0.060	3iw0A	0.467	4.32	0.057	0.697	1.14.-.-	NA
16	0.060	1u3rA	0.508	4.11	0.085	0.782	2.3.1.48	106
17	0.060	3ixzA	0.546	4.57	0.044	0.824	3.6.3.10	NA
18	0.060	2p0mB	0.476	4.50	0.105	0.746	1.13.11.33	62
19	0.060	2iukA	0.492	4.48	0.048	0.764	1.13.11.12	NA
20	0.060	3hvlB	0.563	3.98	0.072	0.836	2.3.1.48	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	0.50	0.911	1.65	0.16	1.00	2a96B	GO:0003993 GO:0016311 GO:0016787 GO:0030288
1	0.46	0.893	1.76	0.17	0.99	1d2tA	GO:0003993 GO:0016311 GO:0016787 GO:0030288
2	0.28	0.739	3.12	0.15	0.93	4uszA	GO:0004601 GO:0016491 GO:0055114 GO:0098869
3	0.21	0.521	3.85	0.07	0.75	1iduA	GO:0004601 GO:0005576 GO:0016491 GO:0016691 GO:0046872 GO:0055114 GO:0098869
4	0.13	0.754	2.93	0.14	0.93	3w36B	GO:0004601 GO:0055114 GO:0098869
5	0.12	0.743	3.01	0.17	0.93	1up8A	GO:0004601 GO:0016491 GO:0046872 GO:0055114 GO:0098869
6	0.07	0.461	4.36	0.06	0.69	3wecA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0020037 GO:0046872 GO:0055114
7	0.06	0.357	4.68	0.07	0.56	1z41A	GO:0003824 GO:0003959 GO:0005622 GO:0009636 GO:0010181 GO:0016491 GO:0018548 GO:0050661 GO:0052690 GO:0055114
8	0.06	0.362	5.19	0.09	0.63	4f32B	GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
9	0.06	0.373	4.30	0.04	0.58	3btnA	GO:0003824 GO:0005634 GO:0005737 GO:0006595 GO:0006596 GO:0033387 GO:0042177 GO:0042978 GO:0043085 GO:1902269
10	0.06	0.346	5.81	0.04	0.64	1r8gB	GO:0000166 GO:0004357 GO:0005524 GO:0016874 GO:0016879 GO:0042398
11	0.06	0.317	5.19	0.05	0.53	4i2yA	GO:0000086 GO:0000922 GO:0001975 GO:0002027 GO:0005246 GO:0005509 GO:0005513 GO:0005634 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005876 GO:0005886 GO:0006091 GO:0007190 GO:0008076 GO:0008179 GO:0008218 GO:0010880 GO:0018298 GO:0019722 GO:0019901 GO:0019904 GO:0021762 GO:0030017 GO:0030234 GO:0030235 GO:0030426 GO:0030801 GO:0031432 GO:0031800 GO:0031982 GO:0031996 GO:0031997 GO:0032465 GO:0032516 GO:0034704 GO:0035307 GO:0043005 GO:0043274 GO:0043388 GO:0043548 GO:0044325 GO:0046872 GO:0047485 GO:0048306 GO:0050998 GO:0051000 GO:0051343 GO:0051412 GO:0051592 GO:0055117 GO:0060314 GO:0060316 GO:0070062 GO:0072542 GO:1901339 GO:1901841
12	0.06	0.380	4.94	0.06	0.63	3im8A	GO:0003824 GO:0004314 GO:0008152 GO:0016740 GO:0016746
13	0.06	0.324	5.47	0.07	0.56	3v8hA	GO:0004799 GO:0005737 GO:0006231 GO:0006235 GO:0008168 GO:0009165 GO:0016740 GO:0032259
14	0.06	0.332	4.31	0.06	0.50	1xw8A	GO:0003824 GO:0005975
15	0.06	0.311	5.16	0.05	0.50	3glbD	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0019439
16	0.06	0.328	4.73	0.01	0.50	3waqA	GO:0004871 GO:0007165 GO:0016020 GO:0016021 GO:0046872
17	0.06	0.340	5.25	0.04	0.58	5evlA	GO:0008800 GO:0016787 GO:0017001 GO:0030288 GO:0046677
18	0.06	0.299	5.38	0.05	0.52	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

Consensus prediction of GO terms

Molecular Function	GO:0003993	GO:0004601	GO:0043169
GO-Score	0.73	0.51	0.42
Biological Processes	GO:0016311	GO:0098869	GO:0055114
GO-Score	0.73	0.51	0.51
Cellular Component	GO:0030288
GO-Score	0.73

(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.