I-TASSER results

I-TASSER results for job id Rv1571

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

Input Sequence in FASTA format

>protein (169 residues)
MVHSIELVFDSDTEAAIRRIWAGLAAAGIPSQAPASRPHVSLAVAERIAPEVDEPLGAVA
RRLPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLCGPHLAPAPMANSLPGQW
TAHVTLARRVGGHQLGRALRIAGRPSRIDGRFAGLRRWDGNTRAEYLLG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVHSIELVFDSDTEAAIRRIWAGLAAAGIPSQAPASRPHVSLAVAERIAPEVDEPLGAVARRLPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLCGPHLAPAPMANSLPGQWTAHVTLARRVGGHQLGRALRIAGRPSRIDGRFAGLRRWDGNTRAEYLLG
Prediction	CCEEEEEHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEHCCCCEEEEHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEEEEEEHCCCCEEEHCC
Conf.Score	9868999779999999999999999989976678899958999757778799999999986798799996789858998599985789999999999999999986687776678888767588876589988999999998467786589999999857887788779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MVHSIELVFDSDTEAAIRRIWAGLAAAGIPSQAPASRPHVSLAVAERIAPEVDEPLGAVARRLPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLCGPHLAPAPMANSLPGQWTAHVTLARRVGGHQLGRALRIAGRPSRIDGRFAGLRRWDGNTRAEYLLG
Prediction	4310000202761153036105403736043346643000000005403640451055147524040304010303554200001233374035104301510473354633631424301000100341467412400410462551703020003124744443338
	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

CCEEEEEHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEHCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEHCCCCEEEEHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEEEEEEHCCCCEEEHCC
MVHSIELVFDSDTEAAIRRIWAGLAAAGIPSQAPASRPHVSLAVAERIAPEVDEPLGAVARRLPLDCVIGAPVLFGRANVVFTRLVVPTSELLALHAEVHRLCGPHLAPAPMANSLPGQWTAHVTLARRVGGHQLGRALRIAGRPSRIDGRFAGLRRWDGNTRAEYLLG

2fyhA

0.14

0.96

1.93

MUSTER

MRAFIAIDVSESVRDALVRAQDYIGSKEAKIFVERENFHITLKFLGEITEEIKKILEKIAKKYKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGRVKDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTIYETLA

2d4gA

0.15

0.14

0.92

2.14

dPPAS

-KYGIVLFPSKKLQDLANSYRKRYD-----PSYSLIPPHLTLRASFECADQLVSHLRNIAKESHPLVLKTKYSSFAPVNNVIYIKAEPTEELKTLNEKLYTGVLA--------GEQEYNFVPHVTVGQNLSDDEHSDVLGQLKQEVSHEEIVDRFHLLYQLENETFLLG

2fyhA

0.14

0.96

3.01

wdPPAS

MRAFIAIDVSESVRDALVRAQDYIGSKEAKKFVERENFHITLKFLGEITEEQAEEIKKILEKKKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGR-KDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTARFELS

2fyhA

0.14

0.96

2.43

wMUSTER

-RAFIAIDVSESVRDALVRAQDYIGSKEAKKFVERENFHITLKFLGEITEEIKKILEKIAKKYKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGRVKDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTARFELS

2fyhA

0.14

0.96

3.20

wPPAS

MRAFIAIDVSESVRDALVRAQDYIGSKEAKKFVERENFHITLKFLGEITEEQAEEIKKILEKKKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGRVKDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTARFELS

2fyhA

0.13

0.96

6.71

dPPAS2

MRAFIAIDVSESVRDALVRAQDYIGSKEAKKFVERENFHITLKFLGEITEEQAEEIKKILEKKKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGRVKDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTIYETLA

2d4gA

0.16

0.15

0.91

2.53

PPAS

-KYGIVLFPSKKLQDLANSYRKRYDP-----SYSLIPPHLTLRASFECADQLVSHLRNIAKESPLVLK-TKYSSFAPVNNVIYIKAEPTEELKTLNEKLYTGVLA--------GEQEYNFVPHVTVGQNLSDDEHSDVLGQLKQEVSHEEIVDRFHLLYQLENETFLLG

4qakA

0.14

0.13

0.92

2.96

Env-PPAS

QRLFFAIDLPAEIREQIIHWRATHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIGFTLTLDDAGQWLR-SRVVWLGRQPPRGLIQLANLRSQAARSGCF--------QSPFHPHITLLRDAS-----EAVTIPPPGFNWSYAVTEFTLYASSFAKRWALT

1iuhA

0.15

0.14

0.96

1.90

MUSTER

MRLFYAVFLPEEVRAALVEAQTKVRPFRGWKPVPPHQLHLTLLFLGERPPDYLALGHRLARLEPFRARLRGTGYFPGTPRVWFAKA-EAEGFLRLAEGLRAGVEELLGEEAVRIPGWDKFKPHITLARRKAPAP-----RVPPVLFGLEWPVEGFALVRSELKVYTVLE

2fyhA

0.13

0.96

2.04

dPPAS

MRAFIAIDVSESVRDALVRAQDYIGSKEAKKFVERENFHITLKFLGEITEEQAEEIKKILEKKKHEVNVRGIGVFPNPNRVIWAGVENDEIIKKIAKEIDDELAKLGFKKEGN------FVAHITLGRVKDKLGLAMKLKELANEDFGSFIVEAIELKKSTLTIYETLA

(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=0.50

Estimated TM-score = 0.78±0.10

Estimated RMSD = 4.0±2.7Å

Download Model 2

C-score=-1.60

Download Model 3

C-score=-3.58

Download Model 4

C-score=-5.00

Download Model 5

C-score=-1.04

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	2fyhA	0.817	2.28	0.135	0.965
2	1iuhA	0.808	2.19	0.157	0.941
3	2vflA	0.789	2.64	0.098	0.965
4	2d4gA	0.755	2.50	0.161	0.917
5	4h7wA	0.743	3.00	0.110	0.953
6	4qakA	0.734	2.78	0.109	0.917
7	1jh7A	0.733	2.75	0.153	0.917
8	2fsqA	0.713	2.84	0.125	0.899
9	4z5vA	0.670	2.74	0.120	0.834
10	5af2A	0.625	2.77	0.136	0.781

(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	0.25	7	4qakB	2AM	Rep, Mult	4,39,41,44,123,125,128
2	0.12	4	2vfkA	AMP	Rep, Mult	41,75,121,123,125
3	0.06	2	2vfkA	AMP	Rep, Mult	41,75,118,119,121,123,125
4	0.06	2	1jh7A	UVC	Rep, Mult	18,34,37,38
5	0.03	1	1fsiA	SO4	Rep, Mult	71,73,74,139
6	0.03	1	2ehzA	MCT	Rep, Mult	72,84,85,86

	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	3e2dA	0.416	5.24	0.036	0.722	3.1.3.1	137
2	0.060	2veoB	0.399	5.00	0.079	0.669	3.1.1.3	95
3	0.060	1zefA	0.404	4.95	0.036	0.675	3.1.3.1	106
4	0.060	1cjxA	0.425	5.09	0.055	0.751	1.13.11.27	NA
5	0.060	1fftA	0.410	5.19	0.030	0.698	1.10.3.-	NA
6	0.060	1eilA	0.442	4.93	0.081	0.746	1.13.11.39	NA
7	0.060	2wk5A	0.405	5.20	0.079	0.710	2.4.2.4	NA
8	0.060	1wojA	0.565	4.00	0.090	0.805	3.1.4.37	39,123,125
9	0.060	1azyA	0.405	5.38	0.040	0.722	2.4.2.4	NA
10	0.060	3iayA	0.400	3.72	0.043	0.556	2.7.7.7	NA
11	0.060	2pflA	0.393	4.94	0.066	0.657	2.3.1.54	NA
12	0.060	1sqiA	0.432	5.35	0.065	0.775	1.13.11.27	NA
13	0.060	1jh7A	0.733	2.75	0.153	0.917	3.1.4.-	39,123
14	0.060	1q16A	0.385	5.63	0.036	0.716	1.7.99.4	NA
15	0.060	3bq1A	0.402	4.70	0.043	0.645	2.7.7.7	NA
16	0.060	1iyxA	0.391	4.77	0.073	0.627	4.2.1.11	NA
17	0.060	2ivfA	0.411	5.41	0.049	0.722	1.17.99.2	NA
18	0.060	1t47A	0.431	4.92	0.087	0.757	1.13.11.27	82,129
19	0.060	1zedA	0.403	4.97	0.036	0.675	3.1.3.1	137

(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	0.29	0.817	2.28	0.14	0.96	2fyhA	GO:0004113 GO:0008081 GO:0008664 GO:0016787
1	0.27	0.790	2.63	0.10	0.96	3j4qA	GO:0005634 GO:0005737 GO:0005829 GO:0005886 GO:0008022 GO:0008104 GO:0010738 GO:0016020 GO:0016208 GO:0016324 GO:0016529 GO:0019904 GO:0030315 GO:0032947 GO:0034237 GO:0043234 GO:0051018 GO:0070382
2	0.21	0.625	2.77	0.14	0.78	5af2A	GO:0000166 GO:0003723 GO:0003824 GO:0004482 GO:0004484 GO:0005525 GO:0006370 GO:0006397 GO:0008152 GO:0008168 GO:0016032 GO:0016740 GO:0016779 GO:0019012 GO:0019013 GO:0032259 GO:0036265
3	0.18	0.808	2.19	0.16	0.94	1iuhA	GO:0004113 GO:0008081 GO:0008664 GO:0016787
4	0.17	0.686	2.69	0.13	0.85	4z5vA	GO:0030430
5	0.17	0.767	2.47	0.19	0.92	2d4gA	GO:0016787 GO:0016788
6	0.15	0.749	2.77	0.11	0.93	4qakB	GO:0004113 GO:0008081 GO:0008664 GO:0016787
7	0.13	0.743	3.00	0.11	0.95	4h7wA	GO:0000175 GO:0004518 GO:0005634 GO:0006397 GO:0008380 GO:0016787 GO:0034477 GO:0045171 GO:0090305 GO:0090503
8	0.12	0.733	2.75	0.15	0.92	1jh7A	GO:0004112 GO:0005737 GO:0006388 GO:0016787
9	0.11	0.713	2.84	0.12	0.90	2fsqA
10	0.07	0.624	2.85	0.14	0.78	4rptA	GO:0000166 GO:0003723 GO:0004482 GO:0004484 GO:0005525 GO:0006370 GO:0006397 GO:0008168 GO:0016032 GO:0016740 GO:0016779 GO:0019012 GO:0019013 GO:0032259 GO:0036265
11	0.06	0.350	5.55	0.04	0.63	4iv9A	GO:0004497 GO:0009851 GO:0016491 GO:0050361 GO:0055114
12	0.06	0.311	5.96	0.04	0.61	1zm5A	GO:0046872
13	0.06	0.309	5.58	0.07	0.57	3hjnA	GO:0000166 GO:0004798 GO:0005524 GO:0005737 GO:0006227 GO:0006233 GO:0006235 GO:0009041 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046939
14	0.06	0.263	6.39	0.07	0.57	1texD	GO:0016740
15	0.06	0.332	4.67	0.05	0.54	2f7lA	GO:0000287 GO:0005975 GO:0008966 GO:0016853 GO:0016868 GO:0046872 GO:0071704
16	0.06	0.354	5.57	0.06	0.63	3ln6A	GO:0000166 GO:0000287 GO:0003824 GO:0004357 GO:0004363 GO:0005524 GO:0006750 GO:0008152 GO:0016874 GO:0030145 GO:0046872
17	0.06	0.236	6.19	0.09	0.49	2gbzA	GO:0000175 GO:0003676 GO:0004518 GO:0004527 GO:0005737 GO:0016787 GO:0016788 GO:0016896 GO:0090305 GO:0090503
18	0.06	0.303	6.00	0.05	0.59	4dwjB	GO:0000166 GO:0004798 GO:0005524 GO:0006233 GO:0006235 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0046939

Consensus prediction of GO terms

Molecular Function	GO:0005198	GO:0032550	GO:0005515	GO:0032559	GO:0004113	GO:0008664	GO:0008192	GO:0008174	GO:0003676	GO:0035639	GO:0032561	GO:0008170
GO-Score	0.55	0.55	0.55	0.55	0.42	0.42	0.41	0.41	0.41	0.41	0.41	0.41
Biological Processes	GO:0033036	GO:1902531	GO:0010737	GO:0009452	GO:0001510	GO:0006397	GO:0044764	GO:0044403
GO-Score	0.55	0.55	0.55	0.41	0.41	0.41	0.41	0.41
Cellular Component	GO:0005783	GO:0016528	GO:0042383	GO:0030133	GO:0098590	GO:0045177	GO:0032991	GO:0099503	GO:0019028	GO:0033646
GO-Score	0.55	0.55	0.55	0.55	0.55	0.55	0.55	0.55	0.41	0.34

(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.