I-TASSER results

I-TASSER results for job id Rv3242c

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

Input Sequence in FASTA format

>protein (213 residues)
MLDLVLPLECGGCGAPATRWCAACAAELSVAAGEPHVVSPRVDPQVPVFALGRYAGVRRQ
AILAMKEHGRRDLVAPLACALIVGVDHLLSWGMLENPLTMVPAPTRRWAARRRGGDPVSR
MARIAGATLGRHHDVTVVPALRMRALARDSVGLGASARERNITGRVLLRGQRPRNEVVLV
DDIITTGATARESVRVLQAAGVRVGAVLAVAAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLDLVLPLECGGCGAPATRWCAACAAELSVAAGEPHVVSPRVDPQVPVFALGRYAGVRRQAILAMKEHGRRDLVAPLACALIVGVDHLLSWGMLENPLTMVPAPTRRWAARRRGGDPVSRMARIAGATLGRHHDVTVVPALRMRALARDSVGLGASARERNITGRVLLRGQRPRNEVVLVDDIITTGATARESVRVLQAAGVRVGAVLAVAAA
Prediction	CCEEHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEHCCCCCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEEEEEHCC
Conf.Score	954557899888998775458788766876678875444688888758999857789999999998669678999999999999999998777788859975889999999878979999999999998997788534357875888675679999999986575445677899589999667667699999999999989959999999879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLDLVLPLECGGCGAPATRWCAACAAELSVAAGEPHVVSPRVDPQVPVFALGRYAGVRRQAILAMKEHGRRDLVAPLACALIVGVDHLLSWGMLENPLTMVPAPTRRWAARRRGGDPVSRMARIAGATLGRHHDVTVVPALRMRALARDSVGLGASARERNITGRVLLRGQRPRNEVVLVDDIITTGATARESVRVLQAAGVRVGAVLAVAAA
Prediction	857253033202143324404652255044334412402642442220000023441013003301442233003000310130043025444344010000021234324434221002003200320444261401400333553551452435202411442333345343210000121331220022004104724053010000026
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEHCCCCCHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHCCCEEEEEEEHCC
MLDLVLPLECGGCGAPATRWCAACAAELSVAAGEPHVVSPRVDPQVPVFALGRYAGVRRQAILAMKEHGRRDLVAPLACALIVGVDHLLSWGMLENPLTMVPAPTRRWAARRRGGDPVSRMARIAGATLGRHHDVTVVPALRMRALARDSVGLGASARERNITGRVLLRGQRPRNEVVLVDDIITTGATARESVRVLQAAGVRVGAVLAVAAA

1vchD

0.20

0.12

0.62

1.20

wPPAS

--------------------------------------------------METYPITVGGVTRHV-R-GDPEFTRAAAEALRPLVP--------KEAEILFTTET-----------SPIPLTHVLAEALGLPYRPYMEDPIIQEVQTTVGEVLWLDRRFAEKL---------LNQRVVLVSDVVASGETMRAMEKMVLRAGGHVVARLAVFRQ

1w30B

0.18

0.11

0.59

1.23

dPPAS2

---------------------------------------------------------------------EGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIP-------TRGVTLANRLAGNITEYSGIHVGHGALDITLYRDPPRPLASTS------------IPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGPRAVQLAVLVDR

1g2qA

0.15

0.10

0.69

1.26

Env-PPAS

------------------------------------------------MPIASYAQELKLALHQYPFPSEFRNPGLFQKLIDAFKLHLEEAFPEVKIDYIVGLES-------RGFL----FGPTLALALGVG------FVPVRKAGKLPGECFKATYEKEYGSDLFEIQKNAAGSNVIIVDDIIATGGSAAAAGELVEQLEANLLEYNFVMEL

1vdmG

0.17

0.10

0.56

1.15

wPPAS

---------------------------------------------------------MDKVY--LTWWQVDRAIFALAEKLREY------------PDVIIGV---------RG---GLIPAVRLSHILGD---IPL-KVIDVKFYKGIDER-GEKPVIT-----IPIHGDLKDKRVVIVDDVSDTGKTLEVVIEEVKKLGAKEIKIACLAMK

1ufrA

0.23

0.13

0.57

1.16

dPPAS2

-------------------------------------------------------------------RFKAELNAPERRALYRIAHEIVEANKGTEGLALVGIH-------TRGIPLAHRIARFIAEFEGKEVP---VGVLDITLPQ---------------VRETRIPFDLTGKAIVLVDDVLYTGRTARAALDALIDLGPRRIYLAVLVDR

1vchD

0.18

0.13

0.70

1.24

Env-PPAS

---------------------------METYPITVGGVTRHVPLIEPLPGRRIP---LVEFL------GDPEFTRAAAEALRPLV--------PKEAEILFTTET-----------SPIPLTHVLAEALGLPYRPYMEDPIIQEVQTLTVGEVLWLDRRFAEK--------LLNQRVVLVSDVVASGETMRAMEKMVLRAGGHVVARLAVFRQ

1w30B

0.16

0.09

0.60

1.09

wPPAS

-----------------------------------------------------------------E--SAANVGRTISRIAHQIIEKTALDDPVGPPRVVL-LGIP-----TRGVTLANRLAGNITEYSGIHVGHGALDITLYRDPPRPLASTS------------IPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGPRAVQLAVLVDR

1vdmG

0.16

0.09

0.56

1.14

dPPAS2

------------------------------------------------------------------------MDKVYWWQVDRAIFALAEKLREYKPDVIIGVA--------RG---GLIPAVRLSHILGDI--PLKVIDVKFYKGIDERGEK--------PVITIPIHGDLKDKRVVIVDDVSDTGKTLEVVIEEVKKLGAKEIKIACLAMK

5eswA

0.16

0.10

0.65

1.18

Env-PPAS

-----------------------------------------------------HHMTIPDKIKAVYEKSTCLYSNEVEAALDRMAIKIHETLQDKN-PVIICVM--------VG---GLVPLGNLLHRLDFPLEV---DYVHATRYRGDLTGGD-------ILWKVRPSSNLAGRTVLVVDDILDGGITLAAIINEIKAMGAAEVYSAVLVDK

1ecgB2

0.19

0.11

0.60

1.04

wPPAS

-----------------SNPC--------------------------------Y-----SFI---VYSARVNMGTKLGEKIAREWED-------LDIDVVIPIP-----------ETSCDIALEIARILGKPYRQG----FVKNRYTPGQQLRRKSVRRKNNRAEF------RDKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLASAAPE

(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=-3.66

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-3.83

Download Model 3

C-score=-4.13

Download Model 4

C-score=-4.47

Download Model 5

C-score=-5.00

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	3dmpA	0.540	3.46	0.148	0.700
2	1jlrA	0.540	3.89	0.125	0.709
3	1qcdA	0.538	4.43	0.106	0.751
4	1vstA	0.529	3.50	0.075	0.685
5	1i5eA	0.525	3.61	0.159	0.671
6	1o5oA	0.524	3.51	0.160	0.676
7	5e38A	0.522	3.61	0.144	0.681
8	2ehjA	0.516	3.55	0.127	0.667
9	1fsgA	0.514	4.00	0.144	0.700
10	1cjbC	0.513	3.58	0.089	0.671

(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	0.21	13	1ao0A	5GP	Rep, Mult	54,115,181,182,183,185,186,187,188,189
2	0.12	7	1dbrA	MG	Rep, Mult	181,182,183
3	0.04	2	1qb7A	MG	Rep, Mult	104,181,189
4	0.03	2	1bd4C	URA	Rep, Mult	101,103,193,194,205,206,207
5	0.03	2	3jueA	ZN	Rep, Mult	10,13,21,24
6	0.03	2	3ozfC	PO4	Rep, Mult	185,186,187,188,189
7	0.03	2	1jlrB	GTP	Rep, Mult	86,89,95,96,97,98,129,133,175

	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	0.066	3dmpD	0.530	3.75	0.161	0.700	2.4.2.9	NA
2	0.060	1dozA	0.506	5.27	0.045	0.812	4.99.1.1	NA
3	0.060	1ct9A	0.496	4.54	0.057	0.723	6.3.5.4	87
4	0.060	1oreA	0.503	4.04	0.112	0.667	2.4.2.7	NA
5	0.060	1fsgA	0.514	4.00	0.144	0.700	2.4.2.8	180,186
6	0.060	1hrkA	0.504	4.94	0.084	0.789	4.99.1.1	192
7	0.060	1o5oD	0.534	3.24	0.167	0.676	2.4.2.9	NA
8	0.060	1pwhA	0.497	4.08	0.082	0.690	4.3.1.17,4.3.1.19	NA
9	0.060	1o5oA	0.524	3.51	0.160	0.676	2.4.2.9	144
10	0.060	3dezA	0.506	3.87	0.109	0.648	2.4.2.10	NA
11	0.060	2c8jA	0.509	5.02	0.046	0.793	4.99.1.1	NA
12	0.060	2e55D	0.509	3.49	0.156	0.662	2.4.2.9	109,118
13	0.060	1g2qA	0.512	3.96	0.123	0.681	2.4.2.7	113
14	0.060	1p5jA	0.456	5.42	0.049	0.751	4.3.1.17	NA
15	0.060	1cjbC	0.513	3.58	0.089	0.671	2.4.2.8	NA
16	0.060	1ve5A	0.487	4.27	0.106	0.700	4.3.1.19	NA
17	0.060	1y7lA	0.486	4.30	0.062	0.690	2.5.1.47	NA
18	0.060	1ve5D	0.488	4.27	0.106	0.700	4.3.1.19	NA
19	0.060	1mzvA	0.542	4.36	0.123	0.751	2.4.2.7	159
20	0.060	1f2dA	0.502	4.85	0.061	0.775	3.5.99.7	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	0.540	3.46	0.15	0.70	3dmpA	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0005525 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0044206
1	0.07	0.540	3.89	0.12	0.71	1jlrA	GO:0000166 GO:0003824 GO:0004845 GO:0005525 GO:0008152 GO:0016740 GO:0016757 GO:0044206
2	0.07	0.516	3.65	0.17	0.67	1v9sB	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0005525 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0044206
3	0.07	0.529	3.91	0.17	0.70	5e38D	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0005886 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
4	0.07	0.516	3.55	0.13	0.67	2ehjA	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016020 GO:0016740 GO:0016757 GO:0042802 GO:0043097 GO:0044206
5	0.07	0.519	3.93	0.11	0.70	3g6wA	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
6	0.07	0.525	3.61	0.16	0.67	1i5eA	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0005525 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0044206
7	0.07	0.524	3.51	0.16	0.68	1o5oA	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
8	0.07	0.511	3.46	0.15	0.66	2e55A	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
9	0.07	0.400	5.37	0.06	0.66	4lygB	GO:0000166 GO:0000287 GO:0002189 GO:0004749 GO:0005524 GO:0005829 GO:0006015 GO:0006144 GO:0006164 GO:0006167 GO:0006221 GO:0007399 GO:0009156 GO:0009165 GO:0016208 GO:0016301 GO:0016310 GO:0016740 GO:0019003 GO:0019693 GO:0030246 GO:0031100 GO:0034418 GO:0042803 GO:0043234 GO:0043531 GO:0044249 GO:0046101 GO:0046872
10	0.07	0.478	4.13	0.15	0.65	4s2uA	GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0005829 GO:0006015 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0042301 GO:0044249 GO:0046872
11	0.07	0.452	4.21	0.14	0.62	3dahC	GO:0000166 GO:0000287 GO:0004749 GO:0005524 GO:0005737 GO:0006015 GO:0009156 GO:0009165 GO:0016301 GO:0016310 GO:0016740 GO:0044249 GO:0046872
12	0.06	0.430	4.11	0.13	0.61	5e38B	GO:0000166 GO:0000287 GO:0003824 GO:0004845 GO:0004849 GO:0005525 GO:0005829 GO:0005886 GO:0006206 GO:0006223 GO:0008152 GO:0008655 GO:0016740 GO:0016757 GO:0043097 GO:0044206
13	0.06	0.481	4.15	0.14	0.65	1l1qA	GO:0009116 GO:0016740 GO:0016757
14	0.06	0.402	4.88	0.07	0.61	2cd9A	GO:0000166 GO:0005534 GO:0005536 GO:0005975 GO:0008270 GO:0016491 GO:0019151 GO:0019595 GO:0033222 GO:0033498 GO:0046872 GO:0047910 GO:0047936 GO:0051262 GO:0055114 GO:0070401 GO:0070403
15	0.06	0.383	5.92	0.06	0.66	1jqnA	GO:0000287 GO:0003824 GO:0005829 GO:0006099 GO:0006107 GO:0008152 GO:0008964 GO:0015977 GO:0016829
16	0.06	0.353	5.75	0.04	0.63	3zdrA	GO:0004022 GO:0006066 GO:0008152 GO:0008774 GO:0015976 GO:0016491 GO:0016620 GO:0046872 GO:0055114
17	0.06	0.279	6.27	0.04	0.51	4htgA	GO:0004418 GO:0006779 GO:0006782 GO:0009507 GO:0009536 GO:0009570 GO:0009941 GO:0015995 GO:0016740 GO:0018160 GO:0033014 GO:0042742 GO:0048046
18	0.06	0.484	3.16	0.12	0.60	2igbB	GO:0003723 GO:0004845 GO:0006351 GO:0006353 GO:0006355 GO:0009116 GO:0016740 GO:0016757

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032550	GO:0032561	GO:0016763	GO:0046872
GO-Score	0.58	0.58	0.58	0.58	0.48
Biological Processes	GO:0010138	GO:0043097	GO:0006222	GO:0043100	GO:0046107
GO-Score	0.58	0.58	0.58	0.48	0.48
Cellular Component	GO:0005829	GO:0005886
GO-Score	0.13	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.