I-TASSER results

I-TASSER results for job id Rv1773c

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

Input Sequence in FASTA format

>protein (248 residues)
MPPTEGKSTTNRDEGIQVLRRAVAALDEIAAEPGHLRLVDLCERLGLAKSTTRRLLVGLV
EVGLVSVDSHGRFALGERLLGFGSVTGAHIAAAFRPTVERVARATDGETVDLSVLRGQRM
WFVDQIESSYRLRAVSAVGLRFPLNGTANGKAALAALDDADAEAALCRLDPMVAEGLRRE
IVEIRRTGIAFDRNEHTPGISAAAIARRALGDNVIAISVPAPTARFLEKEQRIIAALRAA
ADSPDWTR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MPPTEGKSTTNRDEGIQVLRRAVAALDEIAAEPGHLRLVDLCERLGLAKSTTRRLLVGLVEVGLVSVDSHGRFALGERLLGFGSVTGAHIAAAFRPTVERVARATDGETVDLSVLRGQRMWFVDQIESSYRLRAVSAVGLRFPLNGTANGKAALAALDDADAEAALCRLDPMVAEGLRREIVEIRRTGIAFDRNEHTPGISAAAIARRALGDNVIAISVPAPTARFLEKEQRIIAALRAAADSPDWTR
Prediction	CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEHCCCCCEEHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCCEEEEEEEHCCCCCEEEHCCCCCEHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEEHCCCCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCC
Conf.Score	99888888888898864999999999999859998789999999999989999999999999998986999677638999999986697999999999999999679679999986998999998578985688757885666656689999986899999999987579999999999999999989767667677885799855589998799999877566689689999999999999986579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MPPTEGKSTTNRDEGIQVLRRAVAALDEIAAEPGHLRLVDLCERLGLAKSTTRRLLVGLVEVGLVSVDSHGRFALGERLLGFGSVTGAHIAAAFRPTVERVARATDGETVDLSVLRGQRMWFVDQIESSYRLRAVSAVGLRFPLNGTANGKAALAALDDADAEAALCRLDPMVAEGLRREIVEIRRTGIAFDRNEHTPGISAAAIARRALGDNVIAISVPAPTARFLEKEQRIIAALRAAADSPDWTR
Prediction	74568676677785303002100200200275644020120053271432102000103353310233774331001100000222544024102210440174044100000024542000002040633020313133201010103200000113472045105723242163036204501743102233031300000000133743000000000113204652550152035006315658
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEHCCCCCEEHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCCEEEEEEEHCCCCCEEEHCCCCCEHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCEEHCCCCCCCCEEEEEEHCCCCCEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCC
MPPTEGKSTTNRDEGIQVLRRAVAALDEIAAEPGHLRLVDLCERLGLAKSTTRRLLVGLVEVGLVSVDSHGRFALGERLLGFGSVTGAHIAAAFRPTVERVARATDGETVDLSVLRGQRMWFVDQIESSYRLRAVSAVGLRFPLNGTANGKAALAALDDADAEAALCRLDPMVAEGLRREIVEIRRTGIAFDRNEHTPGISAAAIARRALGDNVIAISVPAPTARFLEKEQRIIAALRAAADSPDWTR

1mkmB

0.25

0.24

0.94

3.52

MUSTER

--------------HMNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLFNIRDIAHDHLVDIMKRT-GETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKINTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHGYPVAGVSISGVARKFTEKIEEYSDVLKEKAEEISR-K

1mkmB

0.25

0.24

0.94

6.76

dPPAS

--------------HMNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLFNIRDIAHDHLVDIMKRT-GETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKINTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFHNGYPVAGVSISGVARKFTEKIEEYSDVLKEKAEEISRKL

1mkmB

0.25

0.24

0.94

6.26

wdPPAS

--------------HMNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFV-FNIRDIAHDHLVDIMKRT-GETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKINTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDNGYPVAGVSISGVARKFTEKIEEYSDVLKEKAEEISRKL

1mkmB

0.26

0.24

0.93

4.25

wMUSTER

---------------MNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLFNIRDIAHDHLVDIMKRT-GETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKINTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHGYPVAGVSISGVARKFTEKIEEYSDVLKEKAEEISR-K

5tjjA

0.26

0.25

0.95

4.55

wPPAS

------------DYQVPSVALAARVLKLLSRHKRQSTLTEIAERLGVNKTTCLRVLRTLEREDFVSYDPQRRYSLGPYLIPLGARAANDVYAHALAELHQVAAHT-GTAVLVKRLRDDRVIYIGSAEPPDGVRIAVSVGQQFPVYGAAFGRCFLAYDDESTWRRVLRENSITDEEEYVRLLQEVREKGYAVSHGELWPGISAVAVPVFNQNKVDLVLSCLTTSVIQGEDVERAVKALKESAAKVSAWQ

1mkmB

0.25

0.24

0.94

6.80

dPPAS2

--------------HMNTLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYGSFVLFNIRDIAHDHLVDIMKRT-GETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKINTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFHNGYPVAGVSISGVARKFTEKIEEYSDVLKEKAEEISRKL

5tjjA

0.26

0.25

0.94

4.04

PPAS

------------DYQVPSVALAARVLKLLSRHKRQSTLTEIAERLGVNKTTCLRVLRTLEREDFVSYDPQRRYSLGPYLIPLGARAANDVYAHALAELHQVAAHT-GTAVLVKRLRDDRVIYIGSAEPPDGVRIAVSVGQQFPVYGAAFGRCFLAYDDESTWRRVLRENSITDEEEYVRLLQEVREKGYAVSHGELWPGISAVAVPV-QQNKVDLVLSCLTTSVIQGEDVERAVKALKESAAKVSAWQ

5tjjA

0.26

0.25

0.95

5.83

Env-PPAS

------------DYQVPSVALAARVLKLLSRHKRQSTLTEIAERLGVNKTTCLRVLRTLEREDFVSYDPQRRYSLGPYLIPLGARAANDVYAHALAELHQVAAHT-GTAVLVKRLRDDRVIYIGSAEPPDGVRIAVSVGQQFPVYGAAFGRCFLAYDDESTWRRVLRENSITDEEEYVRLLQEVREKGYAVSHGELWPGISAVAVPVFQQNKVDLVLSCLTTSVIQGEDVERAVKALKESAAKVSAWQ

2xrnA

0.29

0.27

0.92

3.47

MUSTER

----------------QVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEEL-DESVSLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALTSNTLG-RKALVKQLSEVRQSGVASDLDEHIDGVSSFATLLDTY-LGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAR

2o0yC

0.25

0.98

6.54

dPPAS

--TDSAEKPAVADAGVRSVTRVIDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATCARSVLTSRA-DGSYSLGPELRWVRLAGRTWAPPEEVVDIRQLSADT-GETVNLYIRQGLSRVVVAQCESTATVRSVIPLGVPYPLWAGAAGKILLLAAPELIDDVAADPHGPEFADQLREKVEDGRERGYQLVHGERELGSSGLSFPLVSHGTVVAALTLGGPTGRFTDRTPHYIECTRAAAEEISAIG

(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=0.87

Estimated TM-score = 0.83±0.08

Estimated RMSD = 4.0±2.7Å

Download Model 2

C-score=-1.43

Download Model 3

C-score=-2.00

Download Model 4

C-score=-2.16

Download Model 5

C-score=-1.73

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	1mkmB	0.917	1.04	0.249	0.940
2	2o0yC	0.759	3.52	0.234	0.948
3	1tf1A	0.604	2.10	0.212	0.657
4	1ysqA	0.602	1.76	0.236	0.649
5	2ia2A	0.594	1.67	0.177	0.633
6	3r4kA2	0.590	1.80	0.268	0.633
7	2xrnA	0.590	2.46	0.200	0.653
8	5hpfA	0.590	1.85	0.176	0.641
9	2o9aA	0.589	2.19	0.226	0.653
10	2g7uA	0.587	1.85	0.154	0.637

(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	0.74	21	2o9aD	PYR	Rep, Mult	142,147,148,149,192,200,202,218,220
2	0.02	1	2o9a0	III	Rep, Mult	131,136,196,199,200,221,222,224
3	0.02	1	2ia20	III	Rep, Mult	16,18,19,20,22,23,26,27,29,34,54,58,59,61,62,64,75,76,77,78,79,80,141

	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	2v2fF	0.442	4.41	0.056	0.617	3.4.16.4	207
2	0.060	1rp5A	0.471	5.24	0.097	0.718	3.4.-.-	NA
3	0.060	3eqvA	0.477	5.11	0.061	0.718	3.4.16.4	NA
4	0.060	2q8nB	0.407	6.05	0.059	0.706	5.3.1.9	NA
5	0.060	3hz6A	0.414	6.42	0.082	0.746	2.7.1.17	139,148,219
6	0.060	1sj2A	0.343	5.97	0.036	0.593	1.11.1.6,1.11.1.7	21
7	0.060	1pn0C	0.405	6.02	0.063	0.690	1.14.13.7	NA
8	0.060	3flcX	0.410	6.51	0.064	0.758	2.7.1.30	NA
9	0.060	1a3wA	0.430	5.19	0.040	0.673	2.7.1.40	NA
10	0.060	3hztA	0.274	6.30	0.042	0.484	2.7.11.17	147
11	0.060	2d4wA	0.422	6.09	0.056	0.754	2.7.1.30	4
12	0.060	2o9bA	0.424	3.73	0.066	0.532	2.7.13.3	153
13	0.060	1y9mA	0.436	5.71	0.033	0.714	3.2.1.80	224
14	0.060	1zaoA	0.444	5.37	0.078	0.698	2.7.11.1	NA
15	0.060	2zmfB	0.402	3.26	0.056	0.484	3.1.4.17	112,153,241
16	0.060	3fwlA	0.444	5.54	0.085	0.718	2.4.1.129	NA
17	0.060	1y4wA	0.432	5.79	0.056	0.714	3.2.1.80	43
18	0.060	2agsA	0.437	6.07	0.080	0.738	3.2.1.18	162
19	0.060	2zf5Y	0.417	6.32	0.060	0.754	2.7.1.30	187,191,203

(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	0.49	0.917	1.04	0.25	0.94	1mkmB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
1	0.35	0.769	3.51	0.23	0.96	2o0yC	GO:0003677 GO:0006351 GO:0006355
2	0.28	0.596	2.05	0.30	0.65	3bjnA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
3	0.27	0.604	2.10	0.21	0.66	1tf1A	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0006974 GO:0042802 GO:0045892
4	0.26	0.581	2.01	0.14	0.64	3mq0B	GO:0003677 GO:0006351 GO:0006355
5	0.24	0.596	1.95	0.19	0.65	3r4kA	GO:0003677 GO:0006351 GO:0006355
6	0.23	0.590	2.46	0.20	0.65	2xrnB	GO:0003677 GO:0006351 GO:0006355
7	0.23	0.602	1.76	0.24	0.65	1ysqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
8	0.22	0.578	1.54	0.26	0.61	1yspA	GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
9	0.21	0.604	1.75	0.23	0.65	2o99C	GO:0003677 GO:0003700 GO:0005829 GO:0006097 GO:0006351 GO:0006355 GO:0045892
10	0.19	0.583	2.17	0.20	0.65	3obfA	GO:0003677 GO:0006351 GO:0006355
11	0.18	0.604	1.72	0.17	0.65	2ia2A	GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
12	0.14	0.565	2.51	0.15	0.64	3d3oA	GO:0003677 GO:0006351 GO:0006355
13	0.07	0.597	1.88	0.15	0.65	2g7uA	GO:0003677 GO:0006351 GO:0006355 GO:0045893 GO:0046278
14	0.06	0.324	6.40	0.06	0.58	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
15	0.06	0.287	5.47	0.08	0.46	3k2zB	GO:0003677 GO:0004252 GO:0006260 GO:0006281 GO:0006351 GO:0006355 GO:0006508 GO:0006974 GO:0009432 GO:0016787 GO:0045892
16	0.06	0.290	5.67	0.05	0.48	1ig0B	GO:0000166 GO:0004788 GO:0005524 GO:0009229 GO:0016301 GO:0016310 GO:0016740 GO:0030975
17	0.06	0.316	6.31	0.06	0.57	4ylfB	GO:0004355 GO:0005737 GO:0016491 GO:0051536 GO:0055114
18	0.06	0.276	3.38	0.07	0.33	2fxaB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0030435 GO:0045892

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0003700	GO:0005515
GO-Score	0.87	0.73	0.54
Biological Processes	GO:0045892	GO:0033554
GO-Score	0.73	0.54
Cellular Component	GO:0044444
GO-Score	0.54

(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.