I-TASSER results

I-TASSER results for job id Rv0047c

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

Input Sequence in FASTA format

>protein (180 residues)
MLELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAG
TPVRRARRVYQLTDKGRRRFGELVADTGPHNYTDDGFGVHLAFFNRTPAEARMRILEGRR
RQVEERREGLREAVARASSSFDRYTRQLHQLGLESSEREVKWLNELIAAERAAPNPAEQT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAGTPVRRARRVYQLTDKGRRRFGELVADTGPHNYTDDGFGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARASSSFDRYTRQLHQLGLESSEREVKWLNELIAAERAAPNPAEQT
Prediction	CHHHHHHHHHHHCCCCHHHHHHHHHHHHCCEEHCCCCHHHHHHHHHHHHCCEEEEEEHCCCCCCCCCEEEEHCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	777999999985999999999999999898676898668999999999899789999668899988658987888999999999878888877778999999976599999999999999999999999999999756789999999999999999999999999999999866666789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAGTPVRRARRVYQLTDKGRRRFGELVADTGPHNYTDDGFGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARASSSFDRYTRQLHQLGLESSEREVKWLNELIAAERAAPNPAEQT
Prediction	524100410045473325402520373154215044211240353037532043433556687445121040175126204511652474734433000001103414473025105511640462154046325635752440231014201321421151055016305746556878
	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

CHHHHHHHHHHHCCCCHHHHHHHHHHHHCCEEHCCCCHHHHHHHHHHHHCCEEEEEEHCCCCCCCCCEEEEHCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MLELAILGLLIESPMHGYELRKRLTGLLGAFRAFSYGSLYPALRRMQADGLIAENAAPAGTPVRRARRVYQLTDKGRRRFGELVADTGPHNYTDDGFGVHLAFFNRTPAEARMRILEGRRRQVEERREGLREAVARASSSFDRYTRQLHQLGLESSEREVKWLNELIAAERAAPNPAEQT

3l9fA

0.23

0.21

0.93

2.88

MUSTER

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.22

0.21

0.93

3.61

dPPAS

QGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.23

0.21

0.93

5.20

wdPPAS

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.22

0.21

0.93

3.48

wMUSTER

QGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.23

0.21

0.93

4.71

wPPAS

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.23

0.21

0.93

9.61

dPPAS2

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.23

0.21

0.93

3.67

PPAS

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

3l9fA

0.23

0.21

0.93

4.61

Env-PPAS

MGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQD--GRPNKNIYAITESGKKELASYLQSDVNDEIFKSDFLMRLFFGNSLNDDDLEQLIREEIERKEEKIKRLSENLEIWKGELTPTQEITIKYGLAQYKSTKKVLEEELAK-----------

1yg2A

0.23

0.21

0.91

2.53

MUSTER

SLPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCV-----------LEVYSITQAGRSALGEWFDQPTAHPTVRDEFSAKLMACSVQSAEPYRLQLAELVEESRKLVAHYQEIEAAYYANPARLERLTLRRNLLVRQAWIQWADEVLAELNAMA------

1yg2A

0.23

0.21

0.91

3.15

dPPAS

SLPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCV-----------LEVYSITQAGRSALGEWFDQPTAHPTVRDEFSAKLMACSVQSAEPYRLQLAELVEESRKLVAHYQEIEAAYYANPARLERLTLRRNLLVRQAWIQWADEVLAELNAMA------

(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=1.00

Estimated TM-score = 0.85±0.08

Estimated RMSD = 3.2±2.2Å

Download Model 2

C-score=-1.05

Download Model 3

C-score=0.50

Download Model 4

C-score=-4.77

Download Model 5

C-score=-2.03

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	3l9fA	0.911	0.69	0.222	0.928
2	1yg2A	0.657	3.40	0.241	0.894
3	2rkhA	0.632	3.06	0.151	0.811
4	1p0yB	0.533	4.56	0.053	0.778
5	1st6A	0.524	4.58	0.058	0.783
6	4ev6A	0.522	4.09	0.057	0.711
7	4ui9I	0.516	4.46	0.074	0.744
8	4egwA	0.506	4.04	0.079	0.683
9	2xu0A	0.506	4.91	0.057	0.811
10	3rkgA	0.504	4.58	0.061	0.728

(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	0.04	2	2h23A	M3L	Rep, Mult	6,7,8,11,12,13,52,70
2	0.04	2	2cbjA	OAN	Rep, Mult	4,5,83
3	0.04	2	3bvdA	XE	Rep, Mult	113,116,166,167
4	0.04	2	1nf4C	FEC	Rep, Mult	120,127,128,131,135,150,157,158,161
5	0.04	2	3b6aD	ZCT	Rep, Mult	153,154
6	0.04	2	3f8fA	DM1	Rep, Mult	4,80,83,84,87
7	0.02	1	5dnmG	RAX	Rep, Mult	125,128
8	0.02	1	5da5E	GOA	Rep, Mult	122,126,156
9	0.02	1	3q8mA	NUC	Rep, Mult	40,119
10	0.02	1	3f38A	2MY	Rep, Mult	35,36,77
11	0.02	1	2bkoA	CA	Rep, Mult	124,157,161
12	0.02	1	4brbB	78N	Rep, Mult	102,109,112
13	0.02	1	3rf3A	III	Rep, Mult	6,17,21
14	0.02	1	3hd7F	GGG	Rep, Mult	158,161
15	0.02	1	2rb1X	261	Rep, Mult	67,70
16	0.02	1	2idkB	C2F	Rep, Mult	38,40
17	0.02	1	3u24A	IMD	Rep, Mult	45,48,49
18	0.02	1	5l8gT	CA	Rep, Mult	130,152,156
19	0.02	1	2cbjB	OAN	Rep, Mult	24,25,34
20	0.02	1	4mteA	NUC	Rep, Mult	18,40,54,70

	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	1bg7A	0.324	2.44	0.013	0.372	1.16.3.1	124
2	0.060	1g8mA	0.444	3.57	0.079	0.600	3.5.4.10,2.1.2.3	NA
3	0.060	1xzpA	0.437	4.39	0.106	0.600	3.6.5.-	69
4	0.060	1z0hB	0.264	5.73	0.041	0.483	3.4.24.69	19
5	0.060	1yqwR	0.443	5.08	0.043	0.739	1.12.2.1	117
6	0.060	2wyhA	0.435	4.81	0.035	0.644	3.2.1.24	NA
7	0.060	2htnG	0.447	3.48	0.165	0.567	1.16.3.1	32
8	0.060	1syyA	0.449	5.11	0.044	0.744	1.17.4.1	NA
9	0.060	2rccA	0.433	5.12	0.030	0.728	1.17.4.1	NA
10	0.060	1xjjA	0.435	4.94	0.032	0.706	1.17.4.1	26
11	0.060	2d0tB	0.453	4.30	0.050	0.633	1.13.11.52	NA
12	0.060	2frvD	0.454	4.96	0.049	0.744	1.12.2.1	6,8
13	0.060	1mhyD	0.442	5.35	0.029	0.761	1.14.13.25	NA
14	0.060	1p4rA	0.439	3.64	0.086	0.600	2.1.2.3,3.5.4.10	NA
15	0.060	3gehA	0.437	3.64	0.034	0.578	3.6.-.-	NA
16	0.060	1mfrW	0.429	4.16	0.054	0.594	1.16.3.1	83
17	0.060	2bq1I	0.439	5.10	0.063	0.733	1.17.4.1	NA
18	0.060	2j62A	0.500	4.02	0.042	0.689	3.2.1.52	39
19	0.060	3ee4A	0.480	3.72	0.082	0.628	1.17.4.1	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	0.19	0.632	3.06	0.15	0.81	2rkhA
1	0.11	0.408	3.45	0.17	0.50	3bpxA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.07	0.532	4.46	0.05	0.77	1ozvB	GO:0008168 GO:0009507 GO:0009536 GO:0016740 GO:0030785 GO:0032259
3	0.07	0.455	4.77	0.12	0.75	3qxyA	GO:0005634 GO:0005737 GO:0008168 GO:0016279 GO:0016740 GO:0018026 GO:0019827 GO:0032088 GO:0032259 GO:0034968 GO:0048863 GO:0050727 GO:0051059
4	0.07	0.482	4.85	0.08	0.81	3smtA	GO:0000790 GO:0001102 GO:0003713 GO:0005634 GO:0005654 GO:0006351 GO:0006355 GO:0008168 GO:0010452 GO:0016568 GO:0016740 GO:0018022 GO:0018023 GO:0018024 GO:0018026 GO:0018027 GO:0032259 GO:0042800 GO:0045893 GO:0045944 GO:0046975 GO:0051149 GO:0051568
5	0.06	0.379	2.76	0.15	0.44	4a5nB	GO:0003677 GO:0006351 GO:0006355
6	0.06	0.367	5.87	0.03	0.68	1p5jA	GO:0003941 GO:0004794 GO:0005737 GO:0005739 GO:0006094 GO:0006520 GO:0006565 GO:0016829 GO:0030170 GO:0042803 GO:0042866
7	0.06	0.291	5.68	0.03	0.55	2brrY
8	0.06	0.307	5.20	0.08	0.52	2zwrB	GO:0046872
9	0.06	0.304	2.90	0.16	0.38	2gmgA
10	0.06	0.313	5.23	0.08	0.53	1fj1B
11	0.06	0.268	6.59	0.04	0.56	1dbaH	GO:0001788 GO:0001798 GO:0001812 GO:0002455 GO:0003823 GO:0005576 GO:0005615 GO:0006910 GO:0006911 GO:0006958 GO:0009897 GO:0016064 GO:0019731 GO:0042571 GO:0042742 GO:0050766 GO:0050778
12	0.06	0.272	5.90	0.06	0.50	3k60A	GO:0005524 GO:0006457 GO:0006950 GO:0006986 GO:0009408 GO:0016887 GO:0051082
13	0.06	0.304	5.52	0.05	0.54	3ojdB
14	0.06	0.366	5.11	0.05	0.63	3ka7A	GO:0000166 GO:0016491 GO:0055114
15	0.06	0.264	5.83	0.05	0.48	2jkiB	GO:0000166 GO:0005524 GO:0006457 GO:0006950 GO:0051082
16	0.06	0.265	5.74	0.01	0.48	3bzwA
17	0.06	0.214	4.98	0.04	0.36	1cl7H
18	0.06	0.222	4.82	0.06	0.34	4v6wAR	GO:0000028 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0022627 GO:0030529

Consensus prediction of GO terms

Molecular Function	GO:0016741
GO-Score	0.37
Biological Processes	GO:1903506	GO:2000112	GO:0010468	GO:0006351
GO-Score	0.34	0.34	0.34	0.34
Cellular Component	GO:0009507	GO:0000790	GO:0005654
GO-Score	0.07	0.07	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.