I-TASSER results

I-TASSER results for job id Rv2474c

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

Input Sequence in FASTA format

>protein (217 residues)
MVERGLWLPDPAHRADLATFVDHALRLDDAAVIRIRARSTGLLSAWVATGFDVLASRVVA
GKVRPDDLSVAARSLAHGLATTDASGYVDPGYSMDSAWRGGLPPESGFTYLDDVPARVML
DLAHRGARLAKEHGSSAGPPVSLLDQEVIQVSSADVVVGLPMRCVFALTAMGFLPQSAET
ISADELIRVRISPAWLRLDARFGSVYRHRGHAALVLR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVERGLWLPDPAHRADLATFVDHALRLDDAAVIRIRARSTGLLSAWVATGFDVLASRVVAGKVRPDDLSVAARSLAHGLATTDASGYVDPGYSMDSAWRGGLPPESGFTYLDDVPARVMLDLAHRGARLAKEHGSSAGPPVSLLDQEVIQVSSADVVVGLPMRCVFALTAMGFLPQSAETISADELIRVRISPAWLRLDARFGSVYRHRGHAALVLR
Prediction	CCCCEEEHCCHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCCEEEEEHCCCCCEEEEEEEHCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEEEHCCEEHCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEEEHCCCEEEEHCCCCEEEEHCCCCCCCCC
Conf.Score	9987589789567778999999999859875799999689589999868985899999876677897788788999999866788877899888988888899999868858778999999999999999975888888656646679999949966655489999999978888998888888658999769889997699779997688887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MVERGLWLPDPAHRADLATFVDHALRLDDAAVIRIRARSTGLLSAWVATGFDVLASRVVAGKVRPDDLSVAARSLAHGLATTDASGYVDPGYSMDSAWRGGLPPESGFTYLDDVPARVMLDLAHRGARLAKEHGSSAGPPVSLLDQEVIQVSSADVVVGLPMRCVFALTAMGFLPQSAETISADELIRVRISPAWLRLDARFGSVYRHRGHAALVLR
Prediction	7654304033654253012003203413750102022334310000022411000001130435433010304401420464556442424443435031312255214424614162034016402621573546543232314332030337744140101001002110002444553557331302333300101032000012364413427
	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

CCCCEEEHCCHHHHHHHHHHHHHHHHCCCCCEEEEEEHCCCEEEEEHCCCCCEEEEEEEHCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCEEEEEEHCCEEHCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEEEHCCCEEEEHCCCCEEEEHCCCCCCCCC
MVERGLWLPDPAHRADLATFVDHALRLDDAAVIRIRARSTGLLSAWVATGFDVLASRVVAGKVRPDDLSVAARSLAHGLATTDASGYVDPGYSMDSAWRGGLPPESGFTYLDDVPARVMLDLAHRGARLAKEHGSSAGPPVSLLDQEVIQVSSADVVVGLPMRCVFALTAMGFLPQSAETISADELIRVRISPAWLRLDARFGSVYRHRGHAALVLR

2fr0A1

0.15

0.10

0.68

1.29

dPPAS2

LDGTWLVAKYAGTADETSTAAREALE----------SAGARVRELVVDARCG-------------------RDELAERLRSVGEVAGVLSLLAVDEA--------------EPEEAPLALASLADTLSLVQAMVSAELGCP------LWTVTESAVATFERVRNAAHGALWGVVPAGSVGGAGEDQLALRADGVYGR--------------------

1u0kA

0.14

0.13

0.91

1.07

dPPAS2

TLEEELPFAG-HPLLGAAALLHHLRGGDNEQHWTLHLASKSVALRSVRAGSGFYAEDQGRAEFGATPDAGTCRWFAEAFSLSANDLSGHPPRVVSTGLP---------YLLLPVTAEALGRARQDLQEALDKLGAAFVYLLDVDGREGRTWDNLGLVEDVAGPVAAYLVEYGLAARGEPFLERPSRLDVQVATD--------GSVRVG-GHVQLLAR

3el6A

0.19

0.18

0.95

0.66

MUSTER

VPGHRLSTDEQPWLAEGSVLVDLALA-EDVGLPVLEEL--VLQRPLVLAGAGALLRMSVGAPDESGRRTIDVHAAEDVADLADAQGTLAQGVAAGPRDTEQWPPEDA-VRIP--LDDHYDGLAEQGYEYGPSFQALRAAWRK--DSVYAEVSIAADEEGYPVLLDAVAQTLSLGALGEKHASGATSVRVVATPAALRVTDPAGHLVATVDS--LVVR

2fr0A1

0.12

0.10

0.80

0.73

dPPAS

LDGTWLVAKYAGTADETSTAAREALESAGARVRELVVDARCAERLRSVGEVAGVLSLLAVDEAEPEEAPLALASLADTLSLVQAMVSAELGCPLWTVTESAVATGPF-ERVRNAAHGALWGVGRVIALENPAVWG-----------GLVDVPAGS-----VAELARHLAAV------VSGGAGEDQLALRADGVYGR--------------------

2fr0A1

0.12

0.09

0.75

0.68

wdPPAS

LDGTWLVAKYAGTADETSTAAREALE-SAGARVRELVVDARLAERLRSVG-GVLSLLAVDEAEPEEASLADTLSLVQAMVSAELGCPL---------WESAVATGPF-ERVRNAAHGALWGVGRVIALENPAVWG-----------GLVDVPAGS-----VAELARHLAAV-------SGGAGEDQLALRADGVYGR--------------------

1u0kA

0.14

0.13

0.93

0.67

wMUSTER

TLEEELPFAG-HPLLGAAALLHHLRGGDNEQHWTLHLASKSVALRSVRAGSGFYAEDQGRAEFGATPDAGTCRWFAEAFSLSANDLSGHPPRVVSTGLP--------YLLLP-VTAEALGRA-NDLQEALDKLGAAFVYLLDVDGREGRTWDNLGLVEDVATGSAAGPVAA-YLVEYGL-AARGEPFVLHQLERDVQVATD-GSVRVG-GHVQLLAR

2fr0A1

0.18

0.13

0.73

0.69

wPPAS

LDGTWLVAKYAGTADETSTAAREALE-SAGARVRELVVDARLAERLRSVG-GVLSLLAVDEAEPEEAPLADTLSLVQAMVSAELGCPL---------WESAVATGPF----ERVRNAAHGALWGVGRVIALEN-----PAV-LVD------------AGSVAELARHLAAV--VSGGAG----EDQLALRADGVYGR--------------------

3tt2A

0.12

0.11

0.91

1.03

dPPAS2

LPDRIARAPVPADAPAIARLIAACQEADLGQEAVLVVAPDGYADVLNRRYVQLSVYGYVHPRFRGG----LGTWLVQWGEEWIQDRHLAPAEAQVTV-----------QHYIRASSTSALRLEQHGYRPVRDILDQPPPAPEWPEGITARTFVPGLD----ERATYEAVEEAFPPSTFERWLSTQSERKDPELWLLAVETDSGTCLGQETAGKGWIG

2fr0A1

0.13

0.10

0.76

0.77

PPAS

LDGTWLVAKYAGTADETSTAAREALESAGARVRELVVDARCAERLRSVGEVAVLSLLAVDEAEPEEAPLADTLSLVQAMVSAELGCPL---------WESAVATGPF----ERVRNAAHGALWGVGRVIALEN--------PAVWGGLVDVPAGS-----VAELARHLAAV-------SGGAGEDQLALRADGVYGR--------------------

3eyxA

0.09

0.08

0.88

0.75

Env-PPAS

---------NQDILAANAKWASQMNNIQPTLTLFIGCSDSRYNENCLGVLPEVFTWKNVANICHSEDLTL-KATLEFAIICLKVNKVIICGHTDCGGIKTCLNQREALPKVNCSHLYKYLDDIDTMYHEESQNLIHLKTQREKSHYLS--------HCNV-KRQFNRIIENPTVQ---TAVQNGE-LQVYGL--LYNVED--GLLQTVSTYTKVTPK

(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=-2.04

Estimated TM-score = 0.47±0.15

Estimated RMSD = 10.1±4.6Å

Download Model 2

C-score=-4.42

Download Model 3

C-score=-4.40

Download Model 4

C-score=-4.89

Download Model 5

C-score=-3.52

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	2et6A	0.633	3.99	0.087	0.889
2	3qp9A	0.626	3.27	0.166	0.793
3	1wvgA	0.623	4.33	0.064	0.889
4	2fr0A1	0.622	3.08	0.130	0.779
5	4lisA	0.620	4.08	0.037	0.843
6	4pvcA	0.617	4.18	0.080	0.853
7	2c29F	0.614	4.11	0.085	0.857
8	4qtzA	0.613	4.15	0.090	0.853
9	1kewA	0.613	4.26	0.063	0.862
10	1t2aA	0.612	3.96	0.086	0.839

(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	7	4xymC	COA	Rep, Mult	8,9,16,17,36,37,38,56,57,58,75,97,98,150,189,190
2	0.07	4	3bxxA	QUE	Rep, Mult	98,100,115,116
3	0.03	2	3dayA	UNX	Rep, Mult	20,160,163
4	0.03	2	2xquB	CVM	Rep, Mult	123,127
5	0.03	2	1xcbA	NAD	Rep, Mult	16,17,20,152
6	0.03	2	4rlfA	3SK	Rep, Mult	16,17,96,97,151,152,153,160,163,164
7	0.03	2	1yb1A	AE2	Rep, Mult	77,129,132
8	0.02	1	1cpoA	UUU	Rep, Mult	167,169
9	0.02	1	5d51S	KR	Rep, Mult	5,7,20,31,168
10	0.02	1	2o01I	CLA	Rep, Mult	171,173
11	0.02	1	1z450	III	Rep, Mult	65,66,70,73,77,114,120,124,125,128,129
12	0.02	1	2f2hA	XTG	Rep, Mult	144,145
13	0.02	1	2wse1	CLA	Rep, Mult	172,173,198
14	0.02	1	2islB	OXY	Rep, Mult	107,160
15	0.02	1	2dysG	DMU	Rep, Mult	98,100

	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	1he4A	0.553	3.67	0.068	0.733	1.3.1.24,1.5.1.30	174
2	0.066	3e9nG	0.512	4.10	0.089	0.710	1.1.1.36	167
3	0.066	3e9nA	0.511	4.12	0.096	0.710	1.1.1.36	NA
4	0.060	3dwfB	0.591	4.11	0.078	0.825	1.1.1.146	NA
5	0.060	3ch6B	0.594	4.05	0.089	0.825	1.1.1.146	NA
6	0.060	1y5mA	0.592	4.05	0.063	0.825	1.1.1.146	NA
7	0.060	2et6A	0.633	3.99	0.087	0.889	1.1.1.-	NA
8	0.060	3enkA	0.610	4.31	0.073	0.871	5.1.3.2	NA
9	0.060	1keuA	0.613	4.24	0.058	0.857	4.2.1.46	NA
10	0.060	1y1pA	0.618	4.31	0.083	0.871	1.1.1.2	NA
11	0.060	1z45A	0.607	4.37	0.046	0.871	5.1.3.2,5.1.3.3	NA
12	0.060	1udpB	0.599	4.41	0.052	0.862	5.1.3.2	NA
13	0.060	2c20A	0.604	4.33	0.058	0.866	5.1.3.2	NA
14	0.060	1sb8A	0.603	4.20	0.079	0.857	5.1.3.7	NA
15	0.060	1rpnC	0.594	4.12	0.096	0.843	4.2.1.47	NA
16	0.060	1a4uA	0.594	4.01	0.060	0.816	1.1.1.1	114
17	0.060	2hunA	0.611	4.27	0.042	0.862	4.2.1.46	NA
18	0.060	1kerB	0.604	4.24	0.042	0.853	4.2.1.46	NA
19	0.060	1i3kA	0.601	4.45	0.084	0.866	5.1.3.2	NA
20	0.060	1bxkB	0.610	4.30	0.058	0.862	4.2.1.46	NA
21	0.060	2p5uA	0.599	3.98	0.093	0.830	5.1.3.2	NA
22	0.060	3m2pA	0.603	4.43	0.063	0.862	5.1.3.7	166

(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	0.08	0.633	3.99	0.09	0.89	2et6A	GO:0003824 GO:0005777 GO:0006629 GO:0006631 GO:0006635 GO:0008152 GO:0016491 GO:0016616 GO:0016829 GO:0016853 GO:0055114
1	0.07	0.602	4.07	0.07	0.84	3u9lA	GO:0004316 GO:0016491 GO:0055114 GO:0102132
2	0.07	0.576	4.08	0.10	0.80	4bmvC	GO:0000166
3	0.07	0.598	4.18	0.10	0.84	4kzpC	GO:0004316 GO:0016491 GO:0055114 GO:0102132
4	0.07	0.594	4.01	0.06	0.82	1a4uA	GO:0004022 GO:0006066 GO:0008152 GO:0016491 GO:0042802 GO:0055114
5	0.07	0.599	3.89	0.12	0.82	2gdzA	GO:0003824 GO:0004957 GO:0005654 GO:0005737 GO:0005829 GO:0006629 GO:0006631 GO:0006693 GO:0007179 GO:0007565 GO:0007567 GO:0016323 GO:0016404 GO:0016491 GO:0019372 GO:0030728 GO:0042803 GO:0045786 GO:0051287 GO:0055114 GO:0070062 GO:0070403 GO:0070493 GO:0097070 GO:2001300
6	0.07	0.578	3.84	0.10	0.78	3lqfA	GO:0000166
7	0.07	0.565	4.10	0.10	0.80	3gvcB	GO:0016491 GO:0055114
8	0.07	0.559	4.00	0.10	0.77	4jigA	GO:0016491 GO:0055114
9	0.07	0.570	4.01	0.10	0.78	2jahC	GO:0000166
10	0.07	0.574	4.17	0.11	0.81	4trrB	GO:0003858 GO:0016491 GO:0055114
11	0.07	0.583	3.88	0.06	0.80	1bdbA	GO:0016491 GO:0016628 GO:0018509 GO:0019439 GO:0055114
12	0.07	0.570	4.02	0.07	0.79	3rd5A
13	0.07	0.579	3.85	0.11	0.79	2b4qA	GO:0004316 GO:0016491 GO:0055114 GO:0102132
14	0.07	0.570	4.05	0.08	0.79	3uf0A	GO:0000166 GO:0008678 GO:0016491 GO:0055114
15	0.07	0.570	4.00	0.11	0.79	4yqzA	GO:0016491 GO:0055114
16	0.07	0.577	3.94	0.10	0.80	3ak4A	GO:0000166 GO:0016491 GO:0055114
17	0.07	0.573	3.99	0.10	0.79	2d1yC	GO:0000166 GO:0016491 GO:0055114
18	0.07	0.565	4.12	0.08	0.79	2bfpD	GO:0004799 GO:0006729 GO:0016491 GO:0019889 GO:0031427 GO:0032259 GO:0034599 GO:0047040 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003824
GO-Score	0.35
Biological Processes	GO:0044710
GO-Score	0.50
Cellular Component	GO:0005777
GO-Score	0.08

(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.