I-TASSER results

I-TASSER results for job id Rv3072c

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

Input Sequence in FASTA format

>protein (174 residues)
MACVRRSCDVTGTARAGIGAGADPAVVDAVAVAADDCGFATLWVGEHVVMVDRPASRYPY
SRDGVIAVPAQADWLDPMIALSFAAAASSRVDVATGVLLLPEHNPVIVAKEAASLDRLSG
RRLTLGVASDGPRRSSTRSECHSSGAQSAPPNTSLQCAHYGATTSHRSTATVGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MACVRRSCDVTGTARAGIGAGADPAVVDAVAVAADDCGFATLWVGEHVVMVDRPASRYPYSRDGVIAVPAQADWLDPMIALSFAAAASSRVDVATGVLLLPEHNPVIVAKEAASLDRLSGRRLTLGVASDGPRRSSTRSECHSSGAQSAPPNTSLQCAHYGATTSHRSTATVGS
Prediction	CCCCCCCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEHCEHCCCCCCHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEEEHCCC
Conf.Score	998877766455665788889999999999999999899889976666667777778888888888788888877899999999998884897554554777889999999998898769959998758998756658985776555789999999998589865889997689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MACVRRSCDVTGTARAGIGAGADPAVVDAVAVAADDCGFATLWVGEHVVMVDRPASRYPYSRDGVIAVPAQADWLDPMIALSFAAAASSRVDVATGVLLLPEHNPVIVAKEAASLDRLSGRRLTLGVASDGPRRSSTRSECHSSGAQSAPPNTSLQCAHYGATTSHRSTATVGS
Prediction	454463413231033031332331520240042026130200001101122444444334444443434543412101100020033243020100001034330030032002013015110100001124434224341552344264024104311564424240423448
	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

CCCCCCCCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEHCEHCCCCCCHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEEEHCCC
MACVRRSCDVTGTARAGIGAGADPAVVDAVAVAADDCGFATLWVGEHVVMVDRPASRYPYSRDGVIAVPAQADWLDPMIALSFAAAASSRVDVATGVLLLPEHNPVIVAKEAASLDRLSGRRLTLGVASDGPRRSSTRSECHSSGAQSAPPNTSLQCAHYGATTSHRSTATVGS

2b81C

0.20

0.18

0.91

1.95

MUSTER

YNRFAKDQLTLGVHIPNYQFHAPTEKQVELVQKAEQYGFTGVWLRDVLLQDPDFGDPAT--------------GQIYDIYLTYLASKTEKIAFGTSATVLSLRHPLRVAKEIATLDQLFPERI-LGVSSGDRRADFLGVSHETRGEKFREAFAYLEEILYKNFPSIQSTLGEVH

1f07A1

0.19

0.15

0.80

3.68

dPPAS

--------MKFGIEFVP---NEPIEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVK

1f07A1

0.19

0.15

0.80

4.59

wdPPAS

--------MKFGIEFV---PNEPIEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVK

2b81C

0.20

0.18

0.91

2.60

wMUSTER

YNRFAKDQLTLGVHIPNYQFHAPTEKQVELVQKAEQYGFTGVWLRDVLLQDPDFGDPAT--------------GQIYDIYLTYLASKTEKIAFGTSATVLSLRHPLRVAKEIATLDQLFPERI-LGVSSGDRRADFLGVSHETRGEKFREAFAYLEEILYKNFPSIQSTLGEVH

1f07A1

0.19

0.15

0.80

4.68

wPPAS

--------MKFGIEFVPNEP---IEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMKAV

1f07A1

0.19

0.15

0.80

7.92

dPPAS2

--------MKFGIEFVP---NEPIEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMKAV

1f07A1

0.19

0.15

0.80

3.79

PPAS

--------MKFGIEFVPNEP---IEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMKAV

1f07A1

0.19

0.15

0.80

4.31

Env-PPAS

--------MKFGIEFV---PNEPIEKIVKLVKLAEDVGFEYAWITDHYN------------------------NKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMKAV

1f07A1

0.19

0.16

0.80

1.88

MUSTER

MKF--------GIE---FVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNK------------------------NVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKTFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMKAV

1z69A1

0.18

0.14

0.80

3.54

dPPAS

--------MKFGIEFVP---SDPALKIAYYAKLSEQQGFDHVWITDHYNNR------------------------DVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKTFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFA

(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=-0.45

Estimated TM-score = 0.66±0.13

Estimated RMSD = 6.0±3.7Å

Download Model 2

C-score=-0.98

Download Model 3

C-score=-0.81

Download Model 4

C-score=-0.39

Download Model 5

C-score=-3.12

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	2b81C	0.749	2.35	0.212	0.874
2	5dqpA	0.737	2.59	0.105	0.874
3	3sdoA	0.734	2.82	0.201	0.885
4	3b9nB	0.727	2.86	0.135	0.885
5	1yw1A	0.722	2.91	0.123	0.879
6	1rhcA	0.719	2.67	0.153	0.862
7	3raoA2	0.717	2.95	0.211	0.862
8	2wgkA	0.714	2.40	0.163	0.839
9	2i7gB	0.709	2.52	0.152	0.833
10	1z69A	0.709	1.92	0.174	0.793

(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	0.12	5	3kgfB	PO4	Rep, Mult	45,46,97,128
2	0.10	5	3s47A	MG	Rep, Mult	14,43,97,126
3	0.09	4	1z69A	F42	Rep, Mult	45,46,47,96,97,129,130,131,141,143,144,145,146
4	0.08	4	1bsl0	III	Rep, Mult	49,50,51,76,79,80,82,83,85,86,87,102,103,104,107,110,111,114,115,117,118
5	0.03	1	1ezwA	MG	Rep, Mult	85,88,89
6	0.02	1	2vpnB	MG	Rep, Mult	116,119
7	0.02	1	4ytrC	TGK	Rep, Mult	35,38,41
8	0.02	1	3b4yA	FLC	Rep, Mult	51,131
9	0.02	1	1cs1D	DHD	Rep, Mult	109,110
10	0.02	1	1djnA	SF4	Rep, Mult	100,104,147,148,149,152,154,170
11	0.02	1	1yw1A	GLC	Rep, Mult	15,45,46,47,58,132

	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	1qhoA	0.580	4.30	0.055	0.862	3.2.1.133	NA
2	0.060	3i4eA	0.581	3.65	0.054	0.759	4.1.3.1	NA
3	0.060	1cygA	0.583	4.21	0.070	0.851	2.4.1.19	NA
4	0.060	2pbgA	0.579	4.34	0.054	0.874	3.2.1.85	NA
5	0.060	9cgtA	0.583	3.87	0.065	0.828	2.4.1.19	82,84
6	0.060	1k87A	0.581	3.33	0.054	0.776	1.5.99.8	94,145,152
7	0.060	2cerA	0.566	4.17	0.036	0.839	3.2.1.23	NA
8	0.060	1g0cA	0.582	3.37	0.080	0.793	3.2.1.4	NA
9	0.060	1djnA	0.584	3.81	0.057	0.822	1.5.8.2,1.5.99.7	47
10	0.060	1tiwA	0.536	4.15	0.074	0.770	1.5.1.12,1.5.99.8	56
11	0.060	3c8nA	0.691	2.95	0.156	0.845	1.-.-.-	NA
12	0.060	1d7fA	0.577	4.29	0.071	0.845	2.4.1.19	NA
13	0.060	2q3rA	0.587	3.78	0.082	0.833	1.3.1.42	108
14	0.060	1np2A	0.568	4.30	0.055	0.851	3.2.1.21	NA
15	0.060	2tmdA	0.585	3.80	0.057	0.822	1.5.8.2	17,95,123
16	0.060	1a47A	0.575	4.31	0.064	0.856	2.4.1.19	NA
17	0.060	1cdgA	0.559	4.45	0.064	0.851	2.4.1.19	46
18	0.060	1dquA	0.576	3.49	0.035	0.747	4.1.3.1	NA
19	0.060	1f8iA	0.576	3.67	0.088	0.753	4.1.3.1	103

(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	0.729	2.90	0.21	0.87	3raoB	GO:0016705 GO:0055114
1	0.27	0.702	2.49	0.18	0.83	1lucA	GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
2	0.25	0.720	2.51	0.15	0.84	2i7gB	GO:0004497 GO:0016705 GO:0055114
3	0.25	0.768	2.37	0.21	0.90	2b81C	GO:0004497 GO:0005886 GO:0016491 GO:0016705 GO:0055114
4	0.15	0.734	2.82	0.20	0.89	3sdoA	GO:0004497 GO:0016491 GO:0016705 GO:0055114
5	0.14	0.737	2.79	0.14	0.89	1yw1A	GO:0004497 GO:0016491 GO:0016705 GO:0055114
6	0.13	0.735	2.79	0.21	0.89	3sdoB	GO:0004497 GO:0016491 GO:0016705 GO:0055114
7	0.12	0.727	2.86	0.14	0.89	3b9nB	GO:0000166 GO:0004497 GO:0016705 GO:0055114
8	0.12	0.737	2.59	0.10	0.87	5dqpA	GO:0004497 GO:0016705 GO:0055114
9	0.12	0.696	2.43	0.18	0.81	1nqkA	GO:0004497 GO:0008726 GO:0009408 GO:0016491 GO:0016705 GO:0042802 GO:0046306 GO:0055114
10	0.11	0.719	2.67	0.15	0.86	1rhcA	GO:0016705 GO:0055114
11	0.10	0.701	1.74	0.18	0.77	1f07A	GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
12	0.10	0.709	1.92	0.17	0.79	1z69A	GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
13	0.10	0.702	2.18	0.18	0.81	1ezwA	GO:0005737 GO:0006730 GO:0015948 GO:0016491 GO:0016705 GO:0018537 GO:0019386 GO:0055114
14	0.10	0.692	2.67	0.18	0.83	3fgcD	GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
15	0.10	0.675	2.83	0.20	0.81	4us5C	GO:0004497 GO:0016705 GO:0055114
16	0.09	0.701	2.50	0.18	0.83	3fgcA	GO:0004497 GO:0008218 GO:0016491 GO:0016705 GO:0047646 GO:0055114
17	0.07	0.576	3.49	0.04	0.75	1dquA	GO:0003824 GO:0004451 GO:0005777 GO:0005782 GO:0006097 GO:0006099 GO:0008152 GO:0009062 GO:0009514 GO:0015976 GO:0016829 GO:0019752 GO:0045733 GO:0046421 GO:0046872 GO:0046912
18	0.07	0.714	2.90	0.15	0.87	3c8nA	GO:0004497 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0016491 GO:0016614 GO:0016705 GO:0045454 GO:0052749 GO:0055114 GO:0070967
19	0.07	0.480	4.03	0.04	0.69	2yswA	GO:0003824 GO:0003855 GO:0008652 GO:0009073 GO:0009423 GO:0016829

Consensus prediction of GO terms

Molecular Function	GO:0016712
GO-Score	0.54
Biological Processes	GO:0055114	GO:0044237
GO-Score	0.75	0.45
Cellular Component	GO:0071944	GO:0016020
GO-Score	0.49	0.37

(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.