I-TASSER results

I-TASSER results for job id Rv2140c

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

Input Sequence in FASTA format

>protein (176 residues)
MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETR
SFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVG
AAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR
Prediction	CCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEHCCCCCCCEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCEEEEEEEEEHCCCCCCCCCCCCHHHHHHHHHCCEEEEEEEEEEEEHC
Conf.Score	99998875556778766999877789976788885567788898877656767999875699999987999999985999999679988766789888888899868876799998767899999999769999999958888889999999999999866767899999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR
Prediction	86434421441472360403053155644025521444443626423240437612740200000010231344321000000113243440444155455134203203033444324211116553312020101004375171776242630251056212140302030558
	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

CCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEHCCCCCCCEEEEEEEHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCEEEEEEEEEHCCCCCCCCCCCCHHHHHHHHHCCEEEEEEEEEEEEHC
MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

4.31

MUSTER

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

5.66

dPPAS

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

5.83

wdPPAS

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

5.13

wMUSTER

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

6.13

wPPAS

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

10.84

dPPAS2

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

5.21

PPAS

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

4begA

1.00

6.45

Env-PPAS

MTTSPDPYAALPKLPSFSLTSTSITDGQPLATPQVSGIMGAGGADASPQLRWSGFPSETRSFAVTVYDPDAPTLSGFWHWAVANLPANVTELPEGVGDGRELPGGALTLVNDAGMRRYVGAAPPPGHGVHRYYVAVHAVKVEKLDLPEDASPAYLGFNLFQHAIARAVIFGTYEQR

1vi3A

0.47

0.41

0.89

3.69

MUSTER

---------------SLKLISNDLRDGDKLPHRHVFNG-GYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAPDGVLQTRTDFGKTGYDGAAPPKGE-THRYIFTVHALDIERIDVDEGASGA-VGFNVHFHSLASASITAFSE--

1vi3A

0.47

0.41

0.89

4.88

dPPAS

---------------SLKLISNDLRDGDKLPHRHVFNG-GYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAPDGVLQTRTDFGKTGYDGAAPPKGE-THRYIFTVHALDIERIDVDEGASGA-VGFNVHFHSLASASITAFSE--

(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 3 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=2.00

Estimated TM-score = 0.99±0.04

Estimated RMSD = 1.3±1.3Å

Download Model 2

C-score=-3.83

Download Model 3

C-score=-4.01

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	4begA	0.989	0.55	1.000	1.000
2	1fuxA	0.860	1.31	0.463	0.909
3	1vi3A	0.848	1.25	0.462	0.886
4	3n08A	0.758	1.81	0.347	0.835
5	1vw41	0.693	3.10	0.130	0.869
6	2evvB	0.691	2.63	0.262	0.824
7	1wpxB	0.683	3.30	0.219	0.852
8	2gzqA	0.673	3.09	0.187	0.847
9	4v1ab	0.655	3.09	0.146	0.812
10	4ce4b	0.649	3.08	0.140	0.801

(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	0.58	23	2qyqA	PTR	Rep, Mult	68,77,79,121,122,123,130,132
2	0.02	1	1yi9A	CU	Rep, Mult	79,137
3	0.02	1	3t9wA	CU	Rep, Mult	127,130

	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	2jlpD	0.453	4.44	0.095	0.676	1.15.1.1	NA
2	0.060	1r58A	0.439	4.80	0.015	0.710	3.4.11.18	NA
3	0.060	2dewX	0.452	4.24	0.074	0.665	3.5.3.15	165
4	0.060	1to5C	0.444	3.91	0.078	0.619	1.15.1.1	NA
5	0.060	1l9mB	0.448	4.28	0.100	0.682	2.3.2.13	NA
6	0.060	2je8B	0.442	3.71	0.056	0.614	3.2.1.25	174
7	0.060	3eifA	0.471	4.03	0.032	0.699	3.4.21.110	NA
8	0.060	1srdC	0.441	4.15	0.133	0.631	1.15.1.1	NA
9	0.060	2i0eA	0.312	5.49	0.060	0.557	2.7.11.13	NA
10	0.060	2ea4A	0.440	4.87	0.063	0.716	3.4.11.18	NA
11	0.060	2bsyA	0.453	4.36	0.054	0.676	3.6.1.23	56,82,90,91
12	0.060	2uzpB	0.454	3.39	0.072	0.602	2.7.11.13	NA
13	0.060	1a25A	0.452	3.25	0.037	0.597	2.7.11.13	NA
14	0.060	1zvyA	0.457	3.41	0.109	0.619	3.2.1.17	NA
15	0.060	1kv3A	0.456	4.35	0.057	0.693	2.3.2.13	NA
16	0.060	2q3zA	0.446	4.20	0.050	0.659	2.3.2.13	NA
17	0.060	1srdA	0.440	4.02	0.124	0.619	1.15.1.1	166
18	0.060	1wd9A	0.450	4.10	0.079	0.648	3.5.3.15	163
19	0.060	2jcwA	0.446	4.23	0.101	0.642	1.15.1.1	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	0.71	0.989	0.55	1.00	1.00	4begA	GO:0005576 GO:0005886 GO:0042802
1	0.50	0.865	1.31	0.46	0.91	1fuxA	GO:0004857 GO:0030288 GO:0042597 GO:0043086
2	0.27	0.632	3.23	0.17	0.81	1wkoA	GO:0003712 GO:0005634 GO:0005737 GO:0005773 GO:0005886 GO:0006623 GO:0007275 GO:0009744 GO:0009908 GO:0009910 GO:0030154 GO:0031982 GO:0090344 GO:1903506
3	0.24	0.643	3.17	0.24	0.81	1kn3A	GO:0000166 GO:0004867 GO:0005524 GO:0005737 GO:0008289 GO:0010466 GO:0010951 GO:0030414
4	0.21	0.632	3.26	0.16	0.81	3axyA	GO:0005634 GO:0005737 GO:0007275 GO:0008429 GO:0009908 GO:0009909 GO:0010229 GO:0030154 GO:0048510 GO:0048572 GO:0048573 GO:0048575
5	0.20	0.866	1.16	0.46	0.90	1vi3A	GO:0005737
6	0.10	0.664	3.28	0.18	0.85	2r77A	GO:0008429 GO:0016301 GO:0016310 GO:0019887 GO:0045859
7	0.09	0.683	3.30	0.22	0.85	1wpxB	GO:0000328 GO:0000329 GO:0004867 GO:0005543 GO:0005737 GO:0008289 GO:0010466 GO:0010951 GO:0030162 GO:0030414 GO:0046578
8	0.07	0.646	3.08	0.22	0.80	2iqyA	GO:0000165 GO:0000166 GO:0001505 GO:0001933 GO:0002026 GO:0004867 GO:0005102 GO:0005524 GO:0005615 GO:0005737 GO:0005739 GO:0005741 GO:0005791 GO:0005794 GO:0006979 GO:0007286 GO:0007568 GO:0008021 GO:0008289 GO:0009408 GO:0009611 GO:0009636 GO:0009986 GO:0010033 GO:0010243 GO:0010466 GO:0010951 GO:0014070 GO:0014823 GO:0016020 GO:0019900 GO:0019901 GO:0021766 GO:0030414 GO:0042493 GO:0042755 GO:0043005 GO:0043025 GO:0043209 GO:0043409 GO:0043679 GO:0043950 GO:0045177 GO:0045471 GO:0045840 GO:0048240 GO:0051019 GO:0051412 GO:0051591 GO:0051592 GO:0051602 GO:0060409
9	0.07	0.633	3.17	0.17	0.81	1wkpA	GO:0005634 GO:0005737 GO:0007275 GO:0008429 GO:0009908 GO:0009909 GO:0009911 GO:0010119 GO:0030154 GO:0048573
10	0.07	0.624	3.39	0.22	0.81	2l7wA	GO:0000165 GO:0000166 GO:0004867 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0008289 GO:0008429 GO:0010466 GO:0010951 GO:0019899 GO:0019901 GO:0030414 GO:0044822 GO:0070062
11	0.07	0.582	3.77	0.20	0.81	2jyzA
12	0.06	0.408	3.57	0.07	0.55	4f9lA	GO:0002250 GO:0002376 GO:0005886 GO:0016020 GO:0016021 GO:0050663 GO:0050798 GO:0050852 GO:0072643
13	0.06	0.278	5.08	0.02	0.48	5buyE	GO:0005737 GO:0006629 GO:0006633 GO:0009245 GO:0016829 GO:0016836 GO:0019171 GO:0047451
14	0.06	0.267	5.86	0.02	0.53	4gy5A	GO:0000122 GO:0000790 GO:0000791 GO:0000792 GO:0000987 GO:0003677 GO:0003700 GO:0004842 GO:0005634 GO:0005657 GO:0005720 GO:0006281 GO:0006351 GO:0006355 GO:0006974 GO:0007049 GO:0008270 GO:0008283 GO:0008327 GO:0010216 GO:0010390 GO:0016363 GO:0016567 GO:0016568 GO:0016574 GO:0016874 GO:0031493 GO:0032270 GO:0035064 GO:0042393 GO:0042787 GO:0042802 GO:0044729 GO:0045944 GO:0046872 GO:0051865 GO:0061630 GO:0090308 GO:2000373
15	0.06	0.236	5.67	0.05	0.45	2l3rA	GO:0000122 GO:0000790 GO:0000791 GO:0000792 GO:0000987 GO:0003677 GO:0003700 GO:0004842 GO:0005634 GO:0005657 GO:0005720 GO:0006281 GO:0006351 GO:0006355 GO:0006974 GO:0007049 GO:0008270 GO:0008283 GO:0008327 GO:0010216 GO:0010390 GO:0016363 GO:0016567 GO:0016568 GO:0016574 GO:0016874 GO:0031493 GO:0032270 GO:0035064 GO:0042393 GO:0042787 GO:0042802 GO:0044729 GO:0045944 GO:0046872 GO:0051865 GO:0061630 GO:0090308 GO:2000373
16	0.06	0.392	3.71	0.11	0.55	4jkwA	GO:0002250 GO:0002376 GO:0005886 GO:0016020 GO:0016021 GO:0050663 GO:0050798 GO:0050852 GO:0072643
17	0.06	0.218	5.72	0.03	0.39	2nyiA	GO:0008152 GO:0016597
18	0.06	0.691	2.63	0.26	0.82	2evvB

Consensus prediction of GO terms

Molecular Function	GO:0042802	GO:0000989	GO:0032559	GO:0032550	GO:0035639	GO:0004866	GO:0005543
GO-Score	0.71	0.53	0.47	0.47	0.47	0.47	0.42
Biological Processes	GO:0097659	GO:0090342	GO:0006605	GO:0048581	GO:0007034	GO:2001141	GO:2000242	GO:0009909	GO:0034285	GO:0072666	GO:0010466	GO:0052548	GO:0048572	GO:0048506	GO:0010228	GO:0030154
GO-Score	0.53	0.53	0.53	0.53	0.53	0.53	0.53	0.53	0.53	0.53	0.47	0.47	0.42	0.42	0.42	0.42
Cellular Component	GO:0005886	GO:0005576	GO:0044444	GO:0030288	GO:0005634
GO-Score	0.79	0.71	0.53	0.50	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.