I-TASSER results

I-TASSER results for job id Rv3142c

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

Input Sequence in FASTA format

>protein (142 residues)
MTEQEMTEQWLEGCAVQRIMFRDGLVLNFDDYNELVISVPLQLTLPAIETSPAEVVAIDP
NDPADHERPLFDFAGATCTAFVWYDTGDLHLEFSDGHQIDVHPDDRVTAWELYGKYHGYA
ACLAPGKLRVVRHDVADANGDQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTEQEMTEQWLEGCAVQRIMFRDGLVLNFDDYNELVISVPLQLTLPAIETSPAEVVAIDPNDPADHERPLFDFAGATCTAFVWYDTGDLHLEFSDGHQIDVHPDDRVTAWELYGKYHGYAACLAPGKLRVVRHDVADANGDQ
Prediction	CCCCCHHHHHHCCCCEEEEEHCCEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCEEEHCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEEEEHCCCCEEEHCCCCCCCEEEEEHCCCCEEEHCCCCCEEEEHCCCCCCCCCC
Conf.Score	9887656666548758999988889999779978999976999957878787866885899976899999998586688999969985999987997899689988866888858996799857986899976788655789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTEQEMTEQWLEGCAVQRIMFRDGLVLNFDDYNELVISVPLQLTLPAIETSPAEVVAIDPNDPADHERPLFDFAGATCTAFVWYDTGDLHLEFSDGHQIDVHPDDRVTAWELYGKYHGYAACLAPGKLRVVRHDVADANGDQ
Prediction	7674623432166240330234320203045333010313030333444624444040427535522430251144303404147524020304442303043455242131225441200002414010033415566788
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHCCCCEEEEEHCCEEEEEHCCCCEEEEEEEEEEEHCCCCCCCCCEEEHCCCCCHHHHHHHHHHHCCEEEEEEEHCCCEEEEEHCCCCEEEHCCCCCCCEEEEEHCCCCEEEHCCCCCEEEEHCCCCCCCCCC
MTEQEMTEQWLEGCAVQRIMFRDGLVLNFDDYNELVISVPLQLTLPAIETSPAEVVAIDPNDPADHERPLFDFAGATCTAFVWYDTGDLHLEFSDGHQIDVHPDDRVTAWELYGKYHGYAACLAPGKLRVVRHDVADANGDQ

4ld1A

0.19

0.17

0.87

1.33

dPPAS2

FPNGTRKELSADGQTVKVMFFNGDVKHTMPDQRVIYYYAEAQTTHITYPD--GMEVLQFPN-------------NQTEKHF---PDGRKEITFPDQTVKTLHPDGREETIIQLNPDGSKVIQFNTGQREIHTADYPDSDGRQ

4by2A

0.15

0.13

0.90

1.17

dPPAS2

AAVFKREITNADGS--KDIWYPNGNLKKISDGMNLRMLYFIKETNIREGAETNTWHTSYLDGLEILEFP----NGQTEHRR---KDGTVEIHFPNNSIKIVDPSDTEKLEEWRYADGTHLVQLRNGDKILNLPN-----GQK

4ld1A

0.16

0.15

0.90

0.78

MUSTER

FPNGTRKELSADGQTVKVMFFNGDVKHTMPDQRVIYYYAEAQTTHITYPD--GMEVLQFPNNQTEKHFP-----GRKEIT----PDQTVKTLHPDGREESVLTD---GTIIQLNPDGSKVIQFNTGQREIHTADFPDSDGRQ

4ld1A

0.15

0.13

0.92

0.83

dPPAS

FPNGTRKELSADGQTVKVMFFNGDVKHTMPDQRVIYYYAEAQTTHITYPD--GMEVLQFPNNQTEKHFP----DGRKEITF---PDQTVKTLHPDGREESVLTDGT---IIQLNPDGSKVIQFNTGQREIHTADFKRREYPD

4ld1A

0.17

0.15

0.88

0.83

wdPPAS

FPNGTRKELSADGQTVKVMFFNGDVKHTMPDQRVIYYYQTTHITYPD-----GMEVLQFPNNQTEKHFP-----GRKEIT----PDQTVKTLHPDGREESVLTDGT---IIQLNPDGSKVIQFNTGQREIHTADYPDSDGRQ

4ld1A

0.17

0.15

0.88

0.82

wMUSTER

FPNGTRKELSADGQTVKVMFFNGDVKHTMPDQRVIYYYATTHITYPD-----GMEVLQFPNNQTEKHFP-----GRKEIT----PDQTVKTLHPDGREESVLTD---GTIIQLNPDGSKVIQFNTGQREIHTADYPDSDGRQ

2bvbA

0.20

0.17

0.83

0.73

wPPAS

KTEKATLE---EGQQLTLTFISTKLDVAVGSCHSLVANLDGFLKFQTGSNSAFDVVEVEP-------------AGPAVLTIGLGHKGRLAVVLDLGSAAYVVEDSSSEEVSFQGVG-------SGATLVVTTGESPTAVSA-

3e5dA

0.18

0.12

0.67

1.15

dPPAS2

ATANDLYENKTKG--------FNSYFLSFEDGARLEISRTDVTGKTTGENLGWAHIAISTGTKVDELTEKLRQDGFAIAGEPRTGDGYYESVVLEGNRIEITW---------------------------------------

4csqA

0.19

0.15

0.77

0.76

PPAS

MTTQRYLLDELETADMLEIDGLHAWRFELNE--NLLDQADLAAEADQPFASEDWVLAVE------------SLDGR----------TRREWRFSYNAVMEAEPQADGESWRLTTGEGAQLRCLG---------AVSASGEDE

3n1sA

0.16

0.12

0.77

0.76

Env-PPAS

MAEETIFSKIIRREIPSDIVYQDDLVTAFRDISILIIPN-----------ILIPTVNVSAEH-EQALGRMITVAAKIAEQEGIAEDG-YRLIMNTN------RHGGQEVYHIH------MHLLGGRPLPMLAHK--------

(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=-1.60

Estimated TM-score = 0.52±0.15

Estimated RMSD = 8.1±4.4Å

Download Model 2

C-score=-2.84

Download Model 3

C-score=-4.98

Download Model 4

C-score=-5.00

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	4ld1A	0.846	1.56	0.131	0.915
2	4by2A	0.791	2.46	0.106	0.922
3	2fkjA	0.659	3.82	0.065	0.958
4	4iglA	0.618	3.80	0.050	0.873
5	4dvyP	0.584	3.85	0.059	0.852
6	5dl8B	0.579	3.92	0.069	0.852
7	3uauA	0.579	3.67	0.058	0.796
8	3rfzB	0.571	3.99	0.080	0.824
9	5ixmA	0.565	4.20	0.066	0.831
10	4fspA	0.564	4.04	0.029	0.831

(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	0.09	3	1pumB	GOL	Rep, Mult	70,112,113,114
2	0.06	2	2grxA	FTT	Rep, Mult	15,27,35,37,42
3	0.06	2	1ujwA	UUU	Rep, Mult	91,99,110,112
4	0.03	1	3t5tB	MG	Rep, Mult	100,104
5	0.03	1	1a0tP	CA	Rep, Mult	61,64,81,83,84
6	0.03	1	2bgaA	AZI	Rep, Mult	127,142
7	0.03	1	4bxrB	III	Rep, Mult	38,57,59,60,61,79,81,86,90,100,102,109,111,123,131
8	0.03	1	3ea1A	ZN	Rep, Mult	30,31
9	0.03	1	3v4pA	CA	Rep, Mult	23,28,30,32,33,34
10	0.03	1	1ujwA	UUU	Rep, Mult	10,17,25,26,27,35
11	0.03	1	3thpA	MN	Rep, Mult	102,104,133
12	0.03	1	3ta4E	TO2	Rep, Mult	7,8,11
13	0.03	1	1nh0A	III	Rep, Mult	108,110

	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	1ofdA	0.473	4.96	0.063	0.838	1.4.7.1	NA
2	0.060	1i78A	0.484	3.79	0.039	0.662	3.4.23.49	120
3	0.060	1euuA	0.468	5.18	0.036	0.859	3.2.1.18	95
4	0.060	2g3mF	0.454	5.17	0.070	0.817	3.2.1.20	NA
5	0.060	1ogoX	0.442	5.54	0.015	0.873	3.2.1.11	77,102,114
6	0.060	2zxqA	0.479	4.89	0.066	0.817	3.2.1.97	NA
7	0.060	1ogmX	0.457	5.32	0.066	0.887	3.2.1.11	30
8	0.060	1bheA	0.477	5.21	0.082	0.873	3.2.1.15	85,88
9	0.060	1dboA	0.494	5.48	0.063	0.944	4.2.2.19	47,49
10	0.060	3ffzA	0.459	5.16	0.045	0.859	3.4.24.69	NA
11	0.060	3c5wA	0.406	5.61	0.091	0.838	3.1.3.16	72
12	0.060	1rmgA	0.480	5.33	0.086	0.915	3.2.1.-	NA
13	0.060	1eurA	0.420	5.18	0.054	0.775	3.2.1.18	96,121,124
14	0.060	1eutA	0.469	5.18	0.036	0.859	3.2.1.18	NA
15	0.060	1ia5A	0.467	5.22	0.087	0.866	3.2.1.15	NA
16	0.060	1oacB	0.461	4.71	0.039	0.704	1.4.3.21,1.4.3.6	NA
17	0.060	1hm9B	0.450	5.24	0.114	0.845	2.3.1.157,2.7.7.23	NA
18	0.060	2agsA	0.476	4.90	0.059	0.824	3.2.1.18	55
19	0.060	1ib4A	0.456	5.40	0.038	0.852	3.2.1.15	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	0.24	0.773	2.58	0.11	0.92	4by2B	GO:0000132 GO:0000242 GO:0005813 GO:0005814 GO:0007052 GO:0007099 GO:0007140 GO:0008356 GO:0010457 GO:0034454 GO:0035186 GO:0040011 GO:0042384 GO:0045298 GO:0046785 GO:0051297 GO:0051298 GO:0051299 GO:0055059
1	0.17	0.716	3.36	0.07	0.94	3ckaB	GO:0009279
2	0.15	0.659	3.82	0.07	0.96	2fkjA	GO:0009279 GO:0016020
3	0.07	0.606	4.08	0.08	0.90	1fj1E	GO:0009279 GO:0016020
4	0.07	0.582	4.25	0.07	0.90	2oy5O	GO:0009279 GO:0016020
5	0.07	0.621	3.91	0.06	0.92	2af5A	GO:0009279 GO:0016020
6	0.07	0.618	3.80	0.05	0.87	4iglA	GO:0005737
7	0.07	0.503	4.44	0.06	0.78	3ckfA	GO:0009279
8	0.07	0.425	5.67	0.09	0.85	2y7cB	GO:0003676 GO:0003677 GO:0005829 GO:0006306 GO:0008168 GO:0008170 GO:0009007 GO:0009307 GO:0016740 GO:0032259 GO:0032775
9	0.07	0.393	4.60	0.04	0.68	1k32A	GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0016787
10	0.06	0.356	4.53	0.01	0.58	2e4vB	GO:0001641 GO:0004871 GO:0004930 GO:0005886 GO:0005887 GO:0007165 GO:0007186 GO:0007196 GO:0016020 GO:0016021 GO:0019233 GO:0042734 GO:0050804 GO:0051966 GO:0097449
11	0.06	0.383	3.62	0.07	0.51	4rs6A	GO:0000082 GO:0000166 GO:0000278 GO:0000785 GO:0004672 GO:0004674 GO:0004871 GO:0005524 GO:0005622 GO:0005737 GO:0005813 GO:0005814 GO:0005829 GO:0005856 GO:0006468 GO:0006977 GO:0007052 GO:0007093 GO:0007265 GO:0007613 GO:0010508 GO:0016301 GO:0016310 GO:0016740 GO:0018105 GO:0030425 GO:0032092 GO:0032403 GO:0032436 GO:0032486 GO:0042995 GO:0043008 GO:0043066 GO:0043123 GO:0045732 GO:0046599 GO:0048167 GO:0060291 GO:0060292 GO:0061000
12	0.06	0.380	4.28	0.04	0.62	1p4pA	GO:0009279 GO:0016020
13	0.06	0.344	5.65	0.03	0.69	2ar0A	GO:0003676 GO:0003677 GO:0005829 GO:0006306 GO:0008168 GO:0008170 GO:0009007 GO:0009307 GO:0016740 GO:0032259 GO:0032775
14	0.06	0.317	5.61	0.04	0.63	1ujmA	GO:0003824 GO:0008106 GO:0016491 GO:0050662 GO:0055114
15	0.06	0.339	5.16	0.01	0.63	3zpyA	GO:0016829 GO:0045135
16	0.06	0.299	5.39	0.03	0.56	1k38A	GO:0008658 GO:0008800 GO:0016787 GO:0017001 GO:0046677
17	0.06	0.318	5.50	0.04	0.62	5dqrC	GO:0009507 GO:0009536 GO:0015994 GO:0016491 GO:0033354 GO:0046872 GO:0051536 GO:0055114 GO:0090415
18	0.06	0.338	3.80	0.05	0.48	3mw4A	GO:0005246 GO:0007155 GO:0007268 GO:0007269 GO:0007416 GO:0007612 GO:0016020 GO:0016021 GO:0030534 GO:0035176 GO:0042734 GO:0043234 GO:0046872 GO:0051965 GO:0071625 GO:0090129

Consensus prediction of GO terms

Molecular Function
GO-Score
Biological Processes	GO:0031109	GO:0045448	GO:0051294	GO:0051298	GO:0044782	GO:0051258	GO:0098534	GO:0040001	GO:0098722	GO:0007126	GO:0033301	GO:0010927	GO:0045165	GO:0030031	GO:0072393	GO:0060271	GO:0055057
GO-Score	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48	0.48
Cellular Component	GO:0043234	GO:0005813	GO:0044450	GO:0009279
GO-Score	0.48	0.48	0.48	0.39

(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.