I-TASSER results

I-TASSER results for job id Rv2137c

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

Input Sequence in FASTA format

>protein (137 residues)
MRNMKSTSHESESGKLLSISSCRPREMVLQRYSLGMTVTADRHLADKREEFAVEDISTGI
FASGYGQVGDGRSFSFHIEHRSLVVEIYRPRVAGPVPQAEDVVAMAVRGLVDIDLTDERS
LAAAVRDSVASAAPVSR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRNMKSTSHESESGKLLSISSCRPREMVLQRYSLGMTVTADRHLADKREEFAVEDISTGIFASGYGQVGDGRSFSFHIEHRSLVVEIYRPRVAGPVPQAEDVVAMAVRGLVDIDLTDERSLAAAVRDSVASAAPVSR
Prediction	CCCCCCCCCCCCCCCEEEHCCCCCCHHHHHHHHHCCEEEEEHHHCCCCCCEEEEEEEHCCCCCCCEHCCCCCEEEEEEEEEEEEEEEEHCCCCCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCC
Conf.Score	98655565555578666545688754666655545446543455588887588887654556676557899668999985599999985667899999665678887656665588768999999998776578889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRNMKSTSHESESGKLLSISSCRPREMVLQRYSLGMTVTADRHLADKREEFAVEDISTGIFASGYGQVGDGRSFSFHIEHRSLVVEIYRPRVAGPVPQAEDVVAMAVRGLVDIDLTDERSLAAAVRDSVASAAPVSR
Prediction	75536545454543422304513434110332143231223352376445030431332331222143454440013144430203023341755135664123335341340303444300210341146445368
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCEEEHCCCCCCHHHHHHHHHCCEEEEEHHHCCCCCCEEEEEEEHCCCCCCCEHCCCCCEEEEEEEEEEEEEEEEHCCCCCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCC
MRNMKSTSHESESGKLLSISSCRPREMVLQRYSLGMTVTADRHLADKREEFAVEDISTGIFASGYGQVGDGRSFSFHIEHRSLVVEIYRPRVAGPVPQAEDVVAMAVRGLVDIDLTDERSLAAAVRDSVASAAPVSR

2mqdA

0.23

0.20

0.87

0.69

MUSTER

-GHMKFTDQ--QIGVLAGL-AISP-EWLKQNIAANQLVYGIVKPSDTVPA-GVDDYSY-LVAAD---DQDGTIIFFKAEGQTVIIKYTSQR-NTKL----KAKALTLSQLKK-EFYQTRSQKREVDDYVAGLRTE--

2mj7A

0.08

0.07

0.94

0.62

dPPAS

HHHHSHMQELPDSGALMLVPNRQLTADYFEKTWLSLKVAHQQVLRGEFHPDTLQMAVVNIQTIAMSRAGSRPWKAYLSAQDLFLTELLL--------EPGNSEMQISVKQNEARTETLNSFISVLETVIGTIEEIKS

1h7sA2

0.25

0.20

0.82

0.62

wdPPAS

--SIKEN------GSLIPFVQLPPSDSVCEEYGLSCS-------DALHNLFYISGFISQC-THGVGRSSTDRQFFFINRRPRLVNEVYHYN-RHQYPF---VVLNIS-ECVDINLQEEKLLLAVLKTSLIGFDS---

2mqdA

0.23

0.20

0.85

0.70

wMUSTER

--HMKFTDQQ---GVLAGLAI-SP-EWLKQNIAANQLVYGIVKPSDTVPA-GVDDYSY-LVAAD---DQDGTIIFFKAEGQTVIIKYTSQR-NTKL----KAKALTLSQLKK-EFYQTRSQKREVDDYVAGLRTE--

1h7sA2

0.27

0.22

0.80

0.57

wPPAS

--SIK----EN--GQLIPFVQLPPSDSVCEEYGLSC---SD----ALHNLFYISGFISQC-THGVGRSSTDRQFFFINRRPKVLVEVYH---RHQYP----VVLNIS-ECVDINLQEEKLLLAVLKTSLIGFD--S-

2o6tA

0.13

0.11

0.84

0.70

dPPAS2

--HMATAPRPEQYLHFQPI---STRVTYYAFFDTAVNTYLIERGGLDIQGGLVVSSSCDYFAPVA--FPQGNS------SVQYELALFLE-------GQREACAAGRFVHVFVERRSSRPIPQELRDALAALQSS--

1h7sA2

0.24

0.20

0.85

0.67

PPAS

--SIKEN---KQLQSLIPFVQLPPSDSVCEEYGLSCS-------DALHNLFYISGFISQC-THGVGRSSTDRQFFFINRRPRLVNEVYHNRHQYPF-----VVLNISSECVDINLQEEKLLLAVLKTSLIGFDS---

3fspA2

0.11

0.09

0.89

0.74

Env-PPAS

MKKTAVKQVPDDEGRVLIRK--RDSTGLLALWEFSCETDGADGKEKLEQMVGEQ---YGLQVELTEPIV---SFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVHQRVWREYKEWAS-------

2mj7A

0.10

0.09

0.95

0.67

MUSTER

HHHHSHMQELPDSGALMLVPNRQLTADYFEKTWLSLKVAHQQVL-PWRGEFHPDTLQMALQVVNIQTIAMSRA-----GSRPWKAYLSAQDDTGCL-EPGNSEMQISVKQNEARTETLNSFISVLETVIGTIEEIKS

3m86A

0.17

0.13

0.76

0.59

dPPAS

PHMAIHILTEKEDHATLHISFNDLIKIQLTNPSTGYAWNIE----YPTDTFSLSQDTIKAEPHPSGMVGFPREIQLKPGTTTIKLGYSRPWEKGKEPLRSLTYSVVIR-----------------------------

(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=-3.20

Estimated TM-score = 0.36±0.12

Estimated RMSD = 11.9±4.4Å

Download Model 2

C-score=-4.56

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.52

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	1h7sA	0.565	3.87	0.143	0.839
2	3h4lB	0.524	4.06	0.084	0.803
3	3fahA2	0.514	4.70	0.063	0.883
4	3lnuA	0.509	3.69	0.105	0.730
5	4urlA	0.508	3.53	0.105	0.730
6	1ei1A	0.507	3.65	0.057	0.737
7	4i3hA	0.506	3.76	0.106	0.730
8	1dgjA2	0.504	4.78	0.031	0.883
9	3zkbA	0.504	3.87	0.067	0.737
10	2cg9B	0.503	3.60	0.059	0.715

(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	0.20	10	3hx2A	CA	Rep, Mult	114,117
2	0.06	3	1nhiA	K	Rep, Mult	121,122,123,128
3	0.04	2	5d56B	78M	Rep, Mult	122,125,129
4	0.04	2	3jcuH	CLA	Rep, Mult	124,131
5	0.04	2	2il1A	CA	Rep, Mult	117,118
6	0.02	1	1rfuF	ZN	Rep, Mult	101,103
7	0.02	1	1dxeA	MG	Rep, Mult	79,114
8	0.02	1	1dgjA	FES	Rep, Mult	58,59,60,61,95,96,97,133
9	0.02	1	3fahA	GOL	Rep, Mult	83,84,85,87
10	0.02	1	2iubC	MG	Rep, Mult	54,55
11	0.02	1	3m9iA	3PE	Rep, Mult	132,136

	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	2pgiA	0.482	4.79	0.055	0.825	5.3.1.9	129
2	0.060	2o2dB	0.495	4.86	0.087	0.839	5.3.1.9	NA
3	0.060	3dnyT	0.449	3.99	0.055	0.686	3.6.5.3	NA
4	0.060	2q2eB	0.453	4.53	0.054	0.759	5.99.1.3	NA
5	0.060	1rm6A	0.497	4.61	0.056	0.854	1.3.99.20	NA
6	0.060	2q8nB	0.470	4.92	0.087	0.847	5.3.1.9	NA
7	0.060	2hkjA	0.331	4.59	0.009	0.577	5.99.1.3	NA
8	0.060	3hjbA	0.490	4.72	0.040	0.803	5.3.1.9	NA
9	0.060	1darA	0.454	4.08	0.115	0.679	3.6.5.3	NA
10	0.060	1vz6A	0.486	4.33	0.073	0.796	2.3.1.35	NA
11	0.060	2a2dA	0.467	4.31	0.041	0.745	2.7.1.157,2.7.1.-	NA
12	0.060	2wu8A	0.478	4.85	0.096	0.818	5.3.1.9	NA
13	0.060	1ffuB	0.424	4.82	0.063	0.759	1.2.99.2	NA
14	0.060	1pieA	0.473	4.00	0.034	0.715	2.7.1.6	NA
15	0.060	2rdo7	0.463	3.95	0.104	0.679	3.6.5.3	NA
16	0.060	2v4iH	0.295	4.30	0.091	0.482	2.3.1.35	56,90
17	0.060	3ifsE	0.484	4.78	0.056	0.818	5.3.1.9	NA
18	0.060	1zzgB	0.458	4.70	0.089	0.781	5.3.1.9	129
19	0.060	1efgA	0.455	4.00	0.101	0.701	3.6.5.3	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	0.07	0.577	3.90	0.14	0.85	1h7sA	GO:0003677 GO:0003697 GO:0004518 GO:0004519 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0006281 GO:0006298 GO:0006974 GO:0015630 GO:0016446 GO:0016787 GO:0016887 GO:0030983 GO:0032138 GO:0032300 GO:0032389 GO:0032407 GO:0042493 GO:0090305
1	0.07	0.504	3.89	0.07	0.74	1b63A	GO:0000018 GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006281 GO:0006298 GO:0006974 GO:0016887 GO:0030983 GO:0032300 GO:0042802
2	0.07	0.485	3.57	0.14	0.68	4p7aA	GO:0000289 GO:0000712 GO:0000793 GO:0000794 GO:0000795 GO:0001673 GO:0002204 GO:0003682 GO:0003697 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0005712 GO:0006281 GO:0006298 GO:0006303 GO:0006974 GO:0007049 GO:0007060 GO:0007126 GO:0007129 GO:0007131 GO:0007140 GO:0007283 GO:0008630 GO:0016020 GO:0016321 GO:0016446 GO:0016447 GO:0016887 GO:0030983 GO:0032137 GO:0032389 GO:0032407 GO:0043060 GO:0045132 GO:0045141 GO:0045143 GO:0045190 GO:0045950 GO:0048477 GO:0051257
3	0.07	0.436	5.24	0.10	0.80	1jroB	GO:0016491 GO:0030151 GO:0046872 GO:0055114
4	0.06	0.503	4.65	0.04	0.87	1dgjA	GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
5	0.06	0.424	4.82	0.06	0.76	1ffuB	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
6	0.06	0.404	5.08	0.07	0.72	1jroA	GO:0000166 GO:0003824 GO:0004854 GO:0004855 GO:0009055 GO:0016491 GO:0016614 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
7	0.06	0.404	4.63	0.05	0.66	5g06A	GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0006396 GO:0017091 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0043928 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071035 GO:0071038 GO:0071042 GO:0071051
8	0.06	0.481	4.66	0.05	0.82	4zohA	GO:0016491 GO:0055114
9	0.06	0.391	4.72	0.07	0.66	1t3qB	GO:0016491 GO:0055114
10	0.06	0.480	4.58	0.05	0.82	1n63B	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
11	0.06	0.511	4.64	0.07	0.88	3fahA	GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
12	0.06	0.399	3.56	0.06	0.58	2wp8A	GO:0000176 GO:0000177 GO:0000178 GO:0000467 GO:0003723 GO:0005634 GO:0005730 GO:0005737 GO:0006364 GO:0006396 GO:0017091 GO:0034427 GO:0034473 GO:0034475 GO:0034476 GO:0043928 GO:0070478 GO:0070481 GO:0070651 GO:0071028 GO:0071035 GO:0071038 GO:0071042 GO:0071051
13	0.06	0.424	5.03	0.05	0.77	3hrdB	GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114
14	0.06	0.497	4.61	0.06	0.85	1rm6A	GO:0016491 GO:0018525 GO:0055114
15	0.06	0.432	4.96	0.05	0.77	3zyvB	GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0030151 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114
16	0.06	0.431	4.46	0.00	0.71	3hrdA	GO:0016491 GO:0046872 GO:0050138 GO:0051187 GO:0055114
17	0.06	0.304	4.87	0.05	0.55	4evyA	GO:0008080 GO:0016740 GO:0016746 GO:0046677 GO:0047663
18	0.06	0.331	4.27	0.07	0.53	4zohC	GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003690	GO:0032559	GO:0032550	GO:0035639	GO:0017111
GO-Score	0.37	0.37	0.37	0.37	0.37
Biological Processes	GO:0006281
GO-Score	0.37
Cellular Component	GO:0005654	GO:0032389	GO:0015630	GO:0005737	GO:0005712	GO:0000795	GO:0001673	GO:0016020
GO-Score	0.13	0.13	0.07	0.07	0.07	0.07	0.07	0.07

(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.