I-TASSER results

I-TASSER results for job id Rv2676c

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

Input Sequence in FASTA format

>protein (231 residues)
MARLDYDALNATLRYLMFSVFSVSPGALGDQRDAIIDDASTFFKQQEERGVVVRGLYDVA
GLRADADFMVWTHAERVEALQATYADFRRTTTLGRACTPVWSGVGLHRPAEFNKSHIPAF
LAGEEPGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYE
WILAFEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRVPVEQLVHSLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MARLDYDALNATLRYLMFSVFSVSPGALGDQRDAIIDDASTFFKQQEERGVVVRGLYDVAGLRADADFMVWTHAERVEALQATYADFRRTTTLGRACTPVWSGVGLHRPAEFNKSHIPAFLAGEEPGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYEWILAFEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRVPVEQLVHSLP
Prediction	CCCCCHHHCCCCEEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEHCCCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEHCCCCCCCCCHHHCCCCCCCEEEEEHCCCCHHHHCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHCCHHHHHHHCC
Conf.Score	998885656554568889998756766655699999999999999998698799999975566665699997489999999999999997888756565446788886467888888566579888777999966668567579999999999999999976998346776544578875688876599999999999999888888764457868998789999998789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MARLDYDALNATLRYLMFSVFSVSPGALGDQRDAIIDDASTFFKQQEERGVVVRGLYDVAGLRADADFMVWTHAERVEALQATYADFRRTTTLGRACTPVWSGVGLHRPAEFNKSHIPAFLAGEEPGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYEWILAFEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRVPVEQLVHSLP
Prediction	765372761454221000001112471365515402630350055147563102010202023000000001215306403501540340240042032110000123336145633463246462340000000333350241347304510550253047254032210001000130000001063054025004503445034303630100004324154027428
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHCCCCEEEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEHCCCCCCEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEHCCCCCCCCCHHHCCCCCCCEEEEEHCCCCHHHHCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEHCCCCCCEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEHCCHHHHHHHCC
MARLDYDALNATLRYLMFSVFSVSPGALGDQRDAIIDDASTFFKQQEERGVVVRGLYDVAGLRADADFMVWTHAERVEALQATYADFRRTTTLGRACTPVWSGVGLHRPAEFNKSHIPAFLAGEEPGAYICVYPFVRSYEWYLLPDEERRRMLAEHGMAARGYKDVRANTVPAFALGDYEWILAFEAPELDRIVDLMRELRATDARRHTRAETPFFTGPRVPVEQLVHSLP

5a12A

0.23

0.98

3.21

MUSTER

MADR-AKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNASDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGPTVLGTIQSADVLVKTLS

5a12A

0.23

0.98

6.16

dPPAS

MADR-AKLLTTPGVFGNFSTYKVRADLPAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYISKDKSPDLNSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHRWGNPTVLGTIQSADVLVKTLS

5a12A

0.24

0.98

6.21

wdPPAS

MADR-AKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNAGDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHRWGNPTVLGTIQSADVLVKTLS

5a12A

0.23

0.98

3.80

wMUSTER

ADR--AKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNASDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGPTVLGTIQSADVLVKTLS

5a12A

0.24

0.98

5.52

wPPAS

MAD-RAKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNAGDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHRWGNPTVLGTIQSADVLVKTLS

5a12A

0.24

0.98

8.66

dPPAS2

MADR-AKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNAGDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHRWGNPTVLGTIQSADVLVKTLS

5a12A

0.24

0.98

4.59

PPAS

MAD-RAKLLTTPGVFGNFSTYKVRADYMAAERKAAAAEAQMVIDKHK--DKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRAT-KLGMYSDVTENLVGITKALNYSKDKSPDLNAGDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHRWGNPTVLGTIQSADVLVKTLS

3nn1A

0.24

0.98

6.31

Env-PPAS

-ADR-EKLLTESGVYGTFATFQMDHDWWGESRVISVAEVKGLVEQWS--GKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTR-LGRHLTSGGLLHGVSKKPTYVAGFPESMKTESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRGHPTLLGTMSPLDEILEKFA

3nn1A

0.24

0.98

3.17

MUSTER

-ADR-EKLLTESGVYGTFATFQMDHDWWGESRVISVAEVKGLVEQWS--GKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTR-LGRHLTSGGLLHGVSKKPTYVAGFPESMKTESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRGHPTLLGTMSPLDEILEKFA

3nn1A

0.24

0.23

0.98

6.12

dPPAS

--ADREKLLTESGVYGTFATFQMDHDWWGESRVISVAEVKGLVEQWS--GKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTR-LGRHLTSGGLLHGVSKKPTYVAGFPESMKTESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRGHPTLLGTMSPLDEILEKFA

(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 1 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=1.65

Estimated TM-score = 0.95±0.05

Estimated RMSD = 2.4±1.8Å

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	5a12A	0.950	1.15	0.229	0.983
2	3nn1A	0.934	1.33	0.252	0.978
3	2vxhB	0.902	1.21	0.217	0.939
4	4wwsA	0.805	2.48	0.218	0.909
5	1vdhA	0.799	2.64	0.190	0.909
6	1t0tV	0.796	2.37	0.216	0.896
7	4grcA	0.796	3.20	0.112	0.961
8	4gt2B	0.792	3.31	0.129	0.965
9	4gs1A	0.791	3.33	0.142	0.970
10	5jxuA	0.789	3.36	0.098	0.965

(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	0.71	52	5a12A	HEM	Rep, Mult	110,111,112,113,133,135,137,141,153,156,157,160,168,170,181,183,185,196,197,200
2	0.03	2	3q08A	CA	Rep, Mult	63,216
3	0.02	2	2vxhB	CO3	Rep, Mult	10,11,107,108
4	0.01	1	2dyo1	III	Rep, Mult	145,149,151,152,153,155,156,159,160,161,162,163,191,192

	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	0.414	3nn1A	0.934	1.33	0.252	0.978	1.13.11.49	176,178
2	0.060	3i4zA	0.429	5.44	0.052	0.693	2.5.1.34	58,106
3	0.060	1peuA	0.428	5.73	0.049	0.719	1.17.4.1	78
4	0.060	1e6yA	0.442	5.13	0.037	0.680	2.8.4.1	199
5	0.060	1f1hA	0.419	5.52	0.089	0.667	6.3.1.2	NA
6	0.060	1i19A	0.442	5.62	0.072	0.753	1.1.3.6	NA
7	0.060	2vvmA	0.422	5.53	0.048	0.688	1.4.3.4	NA
8	0.060	1t7nA	0.429	5.79	0.034	0.723	2.3.1.7	NA
9	0.060	3b9jJ	0.298	5.77	0.051	0.502	1.17.1.4,1.17.3.2	NA
10	0.060	1reoA	0.418	5.31	0.028	0.671	1.4.3.2	NA
11	0.060	1hbmA	0.443	5.26	0.032	0.697	2.8.4.1	NA
12	0.060	1e6vA	0.448	5.15	0.042	0.701	2.8.4.1	NA
13	0.060	2yr4A	0.454	5.51	0.060	0.732	1.13.12.9	104
14	0.060	2z5xA	0.428	5.68	0.027	0.710	1.4.3.4	NA
15	0.060	1jrpB	0.428	5.67	0.069	0.723	1.17.1.4	NA
16	0.060	1jroB	0.432	5.65	0.050	0.736	1.1.1.204	212
17	0.060	3d2jA	0.468	4.93	0.037	0.723	1.21.3.3	182
18	0.060	2lgsA	0.405	5.11	0.098	0.623	6.3.1.2	83,103,107,136
19	0.060	1f8rA	0.425	5.47	0.048	0.684	1.4.3.2	NA
20	0.060	1n63B	0.425	5.67	0.045	0.732	1.2.99.2	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	0.42	0.941	1.28	0.21	0.98	3q08A	GO:0016491 GO:0042597 GO:0046872 GO:0050587 GO:0055114
1	0.34	0.796	2.37	0.22	0.90	1t0tV	GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
2	0.33	0.805	2.48	0.22	0.91	4wwsA	GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
3	0.31	0.934	1.50	0.25	0.99	4m05B	GO:0016491 GO:0046872 GO:0050587 GO:0055114
4	0.31	0.799	2.64	0.19	0.91	1vdhA	GO:0004601 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
5	0.19	0.597	2.13	0.16	0.66	3qpiA	GO:0046872
6	0.06	0.357	4.71	0.07	0.51	3et6A	GO:0000166 GO:0004016 GO:0004383 GO:0005886 GO:0006182 GO:0007165 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556
7	0.06	0.350	5.85	0.09	0.61	2o5rA	GO:0000049 GO:0000166 GO:0003723 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039
8	0.06	0.268	6.29	0.03	0.49	5ibqA	GO:0046872
9	0.06	0.333	6.12	0.04	0.59	3ebgA	GO:0004177 GO:0005737 GO:0005829 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
10	0.06	0.322	5.65	0.05	0.53	2okkA	GO:0000139 GO:0003824 GO:0004351 GO:0005737 GO:0005794 GO:0005829 GO:0005886 GO:0006540 GO:0007268 GO:0007269 GO:0016020 GO:0016023 GO:0016595 GO:0016829 GO:0016831 GO:0019752 GO:0030054 GO:0030170 GO:0030424 GO:0030672 GO:0031225 GO:0031410 GO:0042136 GO:0042493 GO:0042734 GO:0045202 GO:0046982 GO:0048471 GO:0060077 GO:0061202
11	0.06	0.294	5.75	0.02	0.48	5c9eA	GO:0009405 GO:0019867 GO:0046903
12	0.06	0.310	5.57	0.03	0.52	3k31A	GO:0000166 GO:0004318 GO:0006633 GO:0016491 GO:0055114
13	0.06	0.241	5.86	0.04	0.42	2bovA	GO:0000166 GO:0000910 GO:0001843 GO:0003924 GO:0005525 GO:0005886 GO:0005925 GO:0006887 GO:0006935 GO:0007049 GO:0007165 GO:0007264 GO:0007265 GO:0009986 GO:0016020 GO:0016032 GO:0017022 GO:0017157 GO:0019003 GO:0030139 GO:0030496 GO:0030659 GO:0031532 GO:0031625 GO:0031755 GO:0032154 GO:0043209 GO:0051117 GO:0051301 GO:0051491 GO:0051665 GO:0061024 GO:0070062
14	0.06	0.224	5.53	0.04	0.36	2lroA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245
15	0.06	0.233	5.92	0.06	0.41	3neyA	GO:0004385 GO:0005622 GO:0005887 GO:0007165 GO:0016020 GO:0030863 GO:0032420 GO:0042995 GO:0046037 GO:0046710 GO:0090022
16	0.06	0.245	5.58	0.03	0.41	4drrA	GO:0016032 GO:0019012 GO:0019028 GO:0019058 GO:0019062 GO:0039624 GO:0039665 GO:0044165 GO:0044168 GO:0046718
17	0.06	0.223	5.38	0.03	0.37	1to0D	GO:0005737 GO:0006364 GO:0008168 GO:0016740 GO:0031167 GO:0032259 GO:0070038
18	0.06	0.238	4.33	0.02	0.34	3d6rB	GO:0003723 GO:0016032 GO:0030430 GO:0030683 GO:0039502 GO:0039503 GO:0039524 GO:0039540 GO:0039580 GO:0039657 GO:0042025

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0020037	GO:0004601	GO:0050587
GO-Score	0.88	0.70	0.70	0.60
Biological Processes	GO:0055114	GO:0098869
GO-Score	0.88	0.70
Cellular Component	GO:0042597
GO-Score	0.42

(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.