I-TASSER results

I-TASSER results for job id Rv1271c

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

Input Sequence in FASTA format

>protein (113 residues)
MLSPLSPRIIAAFTTAVGAAAIGLAVATAGTAGANTKDEAFIAQMESIGVTFSSPQVATQ
QAQLVCKKLASGETGTEIAEEVLSQTNLTTKQAAYFVVDATKAYCPQYASQLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MLSPLSPRIIAAFTTAVGAAAIGLAVATAGTAGANTKDEAFIAQMESIGVTFSSPQVATQQAQLVCKKLASGETGTEIAEEVLSQTNLTTKQAAYFVVDATKAYCPQYASQLT
Prediction	CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHCCCC
Conf.Score	99987658899999999999998754678999999767999999998699999999999999999999985999999999999878999999999999999995958755689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MLSPLSPRIIAAFTTAVGAAAIGLAVATAGTAGANTKDEAFIAQMESIGVTFSSPQVATQQAQLVCKKLASGETGTEIAEEVLSQTNLTTKQAAYFVVDATKAYCPQYASQLT
Prediction	74433343333222211001011122333342424643430142057460426337201420330053057454244004203754714462023002201430135336738
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCHHHHCCCC
MLSPLSPRIIAAFTTAVGAAAIGLAVATAGTAGANTKDEAFIAQMESIGVTFSSPQVATQQAQLVCKKLASGETGTEIAEEVLSQTNLTTKQAAYFVVDATKAYCPQYASQLT

5cwpA1

0.11

0.95

0.81

MUSTER

MSSDEEEARELIERAKEAAERAQEAAERTGDPRVRELARELKRLAQEAAEEVPSSSDVNEALKLIVEAIEA---AVRALEAAERTGD-VRELARELVRLAVEAAEEVQRNP--

5l1aA

0.06

0.05

0.91

0.69

dPPAS

MPSYNNARLLEKRLQNCDTQLNQFFNLSIKFLQQLNQIKYFYNSAFNKTENEDDGLEVVEEYENFISLVSQVINADKAFETIKDTTESRQADVIIANFFKVCE----------

3quqA2

0.19

0.11

0.55

0.71

wdPPAS

--------------------------------SMPYHSEAWHQVMKTHGLDL-SREEAYMH----------GRTGASTINIVFQRKEATQEEIESIYHEKSILF-P-------

4hh0A

0.08

0.96

0.65

wMUSTER

LVADNTNIFSFDRIAAVRRFLSDVCAARTLAPDTPVEADTFALYALTE--AQAGRSGRAKAVARLSDLLSTDPLLTEVEELLRAHAPT-AADFARLFEACAERL-TRALARIS

2m7aA

0.23

0.13

0.57

0.76

wPPAS

----------------------------------EDQEQWAMQTLMGSGV--------LA-----CR-LDSGSSAYKLGTYLYQKDN-TLTEARDAIKDAYESYCPQCSKYID

1y04A

0.21

0.06

0.29

1.00

dPPAS2

MNAPARAAAKTAADALAAAKKTAADAAAAAAAA--------------------------------------------------------------------------------

2mqaA

0.18

0.17

0.92

0.84

PPAS

MISSTTSTDQAVSVATSVAQNVGNQLGLDANAMNS-LLGAVSGYVSTLGNAISDSAYANAISSAIGNVLANSGSISE------STASSAASSAASSVTTTLTSYGPAVFYA--

2kzzA3

0.20

0.17

0.84

0.80

Env-PPAS

---QIELRIMAHLSR---DKGLLTAF-------AEGKDIHRATAAEVFGLPLETTSEQRRSAKAINFGLIYGMS----AFGLARQLNIPRKEAQKYMDLYFERY-PGVLEYME

2mqaA

0.08

0.96

0.79

MUSTER

-GNAFAQSLSSNLLSSGDFVQMISSTTSTDQA-VSVATSVAQNVGNQLGLDANAMNSLLGAVSGYVSTLGNAISSSAIGNVLANSGSISASSAASSVTTTLTSYGPAVFYA--

5hiuA3

0.05

0.04

0.88

0.68

dPPAS

IAGFYYEMFPLLTLWLNQAYRAARDARKLALARPASPEDKNLSQLFAL------VKDVIKFNFKFATDDVIAGLIDMLLKICMLTSVEDDLRACIHVIESLVTFG--------

(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=-3.79

Estimated TM-score = 0.30±0.10

Estimated RMSD = 12.9±4.2Å

Download Model 2

C-score=-3.81

Download Model 3

C-score=-3.73

Download Model 4

C-score=-3.69

Download Model 5

C-score=-4.11

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	5l1aA	0.668	2.74	0.040	0.885
2	4q9vA	0.622	3.54	0.045	0.947
3	4k80A	0.609	3.04	0.058	0.885
4	3kv0A	0.601	3.13	0.049	0.867
5	3f4mA	0.595	3.46	0.049	0.894
6	1dvkB	0.589	3.49	0.039	0.876
7	2yruA	0.589	3.24	0.095	0.850
8	1puoB	0.562	3.66	0.084	0.841
9	4zhjA	0.560	4.05	0.057	0.911
10	4c2mA	0.560	4.08	0.028	0.929

(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	0.08	4	4i7nA	1DJ	Rep, Mult	14,17,42,45,58,65,66,69,95
2	0.06	3	1zyrN	STD	Rep, Mult	34,37,38,42
3	0.04	2	2onk2	III	Rep, Mult	64,66,67,68,69,70,71,72,73,74,75,77,80,84,85
4	0.04	2	2p9i3	III	Rep, Mult	92,94,95,97,99,100,102,104
5	0.04	2	4zzcA	XE	Rep, Mult	58,59,62
6	0.02	1	2ie7A	N2O	Rep, Mult	36,41,86,94
7	0.02	1	5l1aA	I3C	Rep, Mult	41,45,57,58,61,87
8	0.02	1	3fk7A	4DM	Rep, Mult	100,104
9	0.02	1	2rjrB	295	Rep, Mult	104,107
10	0.02	1	3serA	CA	Rep, Mult	46,49
11	0.02	1	1sizA	3CO	Rep, Mult	105,110
12	0.02	1	3glnA	XE	Rep, Mult	41,42,61
13	0.02	1	4hlqA	BEF	Rep, Mult	20,63
14	0.02	1	4plrA	CA	Rep, Mult	71,72
15	0.02	1	3eerA	ZN	Rep, Mult	66,105,106
16	0.02	1	3kj1A	ZN	Rep, Mult	63,104
17	0.02	1	4ecgA	CA	Rep, Mult	54,60

	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	2fonB	0.491	4.23	0.072	0.788	1.3.3.6	NA
2	0.060	2pauB	0.484	4.21	0.076	0.814	3.1.3.5	27,99,103
3	0.060	3dc6C	0.487	4.30	0.031	0.805	1.15.1.1	43
4	0.060	3bjcA	0.478	4.36	0.071	0.796	3.1.4.35	85,91
5	0.060	2qykB	0.481	4.22	0.045	0.796	3.1.4.17	NA
6	0.060	3iydD	0.549	4.04	0.029	0.903	2.7.7.6	NA
7	0.060	3djlA	0.487	3.33	0.048	0.699	1.3.99.-	NA
8	0.060	1mc0A	0.434	5.02	0.031	0.841	3.1.4.17	NA
9	0.060	2qymA	0.479	4.37	0.054	0.796	3.1.4.17	99
10	0.060	1ezfB	0.505	3.65	0.056	0.743	2.5.1.21	NA
11	0.060	3mdsA	0.486	4.48	0.040	0.858	1.15.1.1	NA
12	0.060	1gp6A	0.490	3.89	0.087	0.743	1.14.11.19	NA
13	0.060	2pffB	0.516	4.03	0.091	0.779	2.3.1.86	NA
14	0.060	1ma1A	0.486	4.46	0.030	0.858	1.15.1.1	44
15	0.060	1x0xA	0.485	4.58	0.082	0.850	1.1.1.8	NA
16	0.060	3eqlD	0.536	4.26	0.074	0.929	2.7.7.6	NA
17	0.060	2r8qA	0.496	4.17	0.054	0.779	3.1.4.17	NA
18	0.060	1zxiA	0.451	4.35	0.088	0.752	1.2.99.2	NA
19	0.060	2ohyB	0.489	4.78	0.035	0.858	5.4.3.6	41

(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	0.15	0.589	3.24	0.10	0.85	2yruA	GO:0003677 GO:0003712 GO:0003713 GO:0005634 GO:0005654 GO:0005667 GO:0005737 GO:0005831 GO:0005886 GO:0006351 GO:0006355 GO:0006357 GO:0006915 GO:0008283 GO:0010861 GO:0015630 GO:0030154 GO:0030374 GO:0030529 GO:0031252 GO:0042981 GO:0045171 GO:0045944 GO:2000273
1	0.07	0.609	3.04	0.06	0.89	4k80A	GO:0005543 GO:0005548 GO:0005634 GO:0005640 GO:0005730 GO:0005737 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0006687 GO:0006810 GO:0006869 GO:0008289 GO:0010008 GO:0016020 GO:0046836 GO:0051861 GO:1902387 GO:1902388 GO:1902389
2	0.07	0.381	3.16	0.01	0.50	4ntiA	GO:0005737 GO:0006810 GO:0006869 GO:0008219 GO:0008289 GO:0009751 GO:0009816 GO:0010175 GO:0015695 GO:0015791 GO:0017089 GO:0046836 GO:0051861 GO:0072488
3	0.07	0.559	4.00	0.06	0.89	4kbrB	GO:0005543 GO:0005548 GO:0005634 GO:0005640 GO:0005730 GO:0005737 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0006810 GO:0006869 GO:0008289 GO:0010008 GO:0016020 GO:0017089 GO:0046836 GO:0051861 GO:1902387 GO:1902388 GO:1902389
4	0.07	0.601	3.13	0.05	0.87	3kv0A	GO:0005737 GO:0017089 GO:0046836 GO:0051861
5	0.07	0.443	3.68	0.07	0.63	2i3fA
6	0.07	0.612	3.85	0.04	0.96	4q9vB	GO:0005737 GO:0005886 GO:0006810 GO:0006869 GO:0008526 GO:0015914 GO:0016020 GO:0019216 GO:0035091 GO:0043552 GO:0048017 GO:0051897 GO:0070374
7	0.07	0.564	3.48	0.10	0.89	4gxgA	GO:0005737 GO:0005829 GO:0006687 GO:0006810 GO:0006869 GO:0008289 GO:0016020 GO:0017089 GO:0046836 GO:0051861 GO:0070062
8	0.07	0.595	3.46	0.05	0.89	3f4mA	GO:0002376 GO:0005737 GO:0045087 GO:0050728 GO:0050868
9	0.07	0.562	3.66	0.08	0.84	1puoB	GO:0005496 GO:0005576 GO:0005615
10	0.07	0.552	4.10	0.06	0.89	4zhjB	GO:0009058 GO:0015995 GO:0016851
11	0.07	0.589	3.49	0.04	0.88	1dvkB	GO:0000350 GO:0000386 GO:0000398 GO:0005634 GO:0005681 GO:0005682 GO:0006397 GO:0008380 GO:0046540 GO:0071021 GO:0071048
12	0.07	0.551	3.29	0.11	0.83	2mgxA	GO:0003713 GO:0005634 GO:0005654 GO:0005737 GO:0005886 GO:0006351 GO:0006355 GO:0006915 GO:0008283 GO:0015630 GO:0016922 GO:0030154 GO:0030374 GO:0030529 GO:0042981 GO:0045171 GO:1903506 GO:2000273
13	0.07	0.518	4.01	0.12	0.89	2ejnA	GO:0005496 GO:0005576 GO:0005615
14	0.07	0.463	4.33	0.02	0.81	1cvrA	GO:0004197 GO:0004198 GO:0005509 GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0009405 GO:0016787
15	0.07	0.497	3.48	0.06	0.75	3acwA	GO:0009058 GO:0016117 GO:0016740 GO:0016765
16	0.06	0.560	4.05	0.06	0.91	4zhjA	GO:0009058 GO:0015995 GO:0016851
17	0.06	0.359	4.42	0.02	0.62	1byeA	GO:0004364 GO:0016740
18	0.06	0.367	4.98	0.05	0.68	2vs4A	GO:0005794 GO:0005975 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0016758 GO:0031985 GO:0032580 GO:0033580 GO:0046872 GO:0047276

Consensus prediction of GO terms

Molecular Function	GO:0097367	GO:0008289	GO:1901505	GO:0005319
GO-Score	0.49	0.49	0.37	0.37
Biological Processes	GO:0006869	GO:1901264
GO-Score	0.49	0.49
Cellular Component	GO:0071944	GO:0043231	GO:0016020	GO:0005737
GO-Score	0.52	0.52	0.39	0.35

(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.