I-TASSER results

I-TASSER results for job id Rv0556

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

Input Sequence in FASTA format

>protein (171 residues)
MISPKPLLHILIHGLSDELPDTRGRIVLRWLRIAVLIVTGLVTLQSVLLVAGAWRNDIAI
QRNMGVAQAEVLSAGPRRSTIEFVTPDRITYRPQLGVLYPSELSTGMRIYVEYNKRDPNL
VRVQHRNAGLAIIPAGSIAVVAWLIAAAALVVLAVLDKRLERRENSASATG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MISPKPLLHILIHGLSDELPDTRGRIVLRWLRIAVLIVTGLVTLQSVLLVAGAWRNDIAIQRNMGVAQAEVLSAGPRRSTIEFVTPDRITYRPQLGVLYPSELSTGMRIYVEYNKRDPNLVRVQHRNAGLAIIPAGSIAVVAWLIAAAALVVLAVLDKRLERRENSASATG
Prediction	CCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCEEEEEEEHCCCCCEEEEEHCCCCCEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEHCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	998656666543688888887757889999999999999999999999999987656888767767899999846885799998599858857987667888999889999984889974556898588876467899999999999999999999888887556666689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MISPKPLLHILIHGLSDELPDTRGRIVLRWLRIAVLIVTGLVTLQSVLLVAGAWRNDIAIQRNMGVAQAEVLSAGPRRSTIEFVTPDRITYRPQLGVLYPSELSTGMRIYVEYNKRDPNLVRVQHRNAGLAIIPAGSIAVVAWLIAAAALVVLAVLDKRLERRENSASATG
Prediction	754344313001314576347344420232033000100021132121002001321440464423030303423443020303277344231730001034145434030304463152030443703012123321210122333331210131243254457546558
	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

CCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCEEEEEEEHCCCCCEEEEEHCCCCCEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCEEHCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MISPKPLLHILIHGLSDELPDTRGRIVLRWLRIAVLIVTGLVTLQSVLLVAGAWRNDIAIQRNMGVAQAEVLSAGPRRSTIEFVTPDRITYRPQLGVLYPSELSTGMRIYVEYNKRDPNLVRVQHRNAGLAIIPAGSIAVVAWLIAAAALVVLAVLDKRLERRENSASATG

5cwjA

0.13

0.12

0.91

0.76

MUSTER

EEEQERIRRILKEARKSGTEESLRQAIEDVAQLAKKSSEVLEEAIRVILRIAKESGSEEALRQAIRAVAEIAKEAQDSEVLEEAIRVILRIAKESGSE--EALRQAIRAVAEIAKEAQD--------PRVLEEAIRVIRQIAEESGSEEARRQAERAEEEIRRRAQ-----

2xqhA2

0.15

0.11

0.70

0.66

dPPAS

------------GGLSDGTRNSDAATVGQLNRKVGGVYDDVKARITVESEKQKKYTDQKTSEVNEKVEAR---------TTVGVDSDGK------------------------------LTRAEGATKTIAVNDGLVALSGRTDRIDYAVGAIDGRVTRNTQSIEKNSKAI

4chvA1

0.23

0.15

0.65

0.64

wdPPAS

---------------------TFFPVLGRVLANEARNLIGVTTLFGVVLFAVALA-AYVIERD---------------------IQPEKFGS------IPQAMTTG------YGDTIPQ---FAGR--VLAGAVMMSGIGIFGLWAGILATGFYQEVRRGDFVRNWQLVAA

4btgA1

0.20

0.18

0.86

0.65

wMUSTER

NIDPVMYARLFFQYAQAGGALSVDELVNQFTEYHQSTAC-EIWRKLTAYITGAIKAD-AVGKVPPTAILELRTLAPSEHEL-FITTDFVCHSP-LGFILPSDLR---RMLTALSSVDSKMLQATFKAKG-ALAP----ALISQHLANAA-------TTAFERSRGN-----

2m47A

0.14

0.12

0.82

0.60

wPPAS

MPKINQVYALV-ITRTGESPVCEKCWW----------------DEDEGPVVGAFTGRNVTPERTWETRSEVIVAEPNR-CFGWSVTDGNVK-------YPLE--EGTVLTESWEFTPKGQRFFHDK---FGDKSIEEIEKRRLAAITGIPETLVAIQRILEVELEHHHHHH

2hynA

0.17

0.05

0.30

1.08

dPPAS2

MEKVQYLTRSAIRRASTIEMPQQARQKLQNLFINFCLILICLLLICIIVMLL-----------------------------------------------------------------------------------------------------------------------

4cgxA

0.13

0.11

0.88

0.69

PPAS

-----------------DRPDHIDSRVWELSETQEDWITQVHGHVRRVVECWKYTICCLISNHTGAPQYDVF-KWQDRSTIEWICSKKKVQYPERDT--PDLYERAVAYKVLLVSDLSDHSPTSGIYHDLAF-ESCALVLRGSQLQDIKGFLCRALEWVVSNNLTQEVVET

2gwgA2

0.09

0.08

0.84

0.65

Env-PPAS

LNADTTAFQCVAGDLFKDFPELK----------FVIPHGGVPYHWGRFRGLAQEKKPLLEDHVLNFDTC-VYHQPGIDLLNTVIPVDNVLF----ASEIGAVRG----IDPRTGFYYDDTKRYIE---ASTILTPEEKQQIYEGNARRVYPRLDAALKAKGKLEH------

5cwdA

0.10

0.95

0.71

MUSTER

RSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAARAAA--------SNDEEVAKIAAKACLEVAKQAGMPTK-EAARSFCEAAKRAAKESNDEEVEKIAKKACKEVAKQAGMPW

4cgxA

0.12

0.11

0.89

0.66

dPPAS

-----------------DRPDHIDSRVWELSETQEDWITQVHGHVRRVVECWKYTICCLISNHTGAPQYDVF-KWQDRSTIEWICSKKKVQYPERDTPDLYDNERAVAYKVLLVSDLSDHSPTSGIYHDLAFNESCALVLRGSQLQDIKGFLCRALEWVVSNNLTQEVVET

(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=-4.59

Estimated TM-score = 0.24±0.07

Estimated RMSD = 16.2±3.1Å

Download Model 2

C-score=-4.79

Download Model 3

C-score=-4.38

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	3aqpA	0.492	4.74	0.073	0.789
2	4mt1A	0.490	4.89	0.093	0.795
3	3k07A	0.485	4.96	0.082	0.807
4	7r1rA	0.482	4.71	0.054	0.795
5	3cf4A	0.480	4.80	0.043	0.807
6	4u3eA	0.477	5.12	0.071	0.825
7	3wajA1	0.476	5.43	0.136	0.830
8	1un8A1	0.475	4.99	0.053	0.784
9	1vb3A	0.473	5.07	0.057	0.801
10	3rceA	0.472	5.43	0.050	0.813

(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	0.11	6	4a25A	MN	Rep, Mult	157,161
2	0.07	4	6r1rA	III	Rep, Mult	60,61,62,64,65,67,87,88
3	0.04	2	3cevA	ARG	Rep, Mult	32,46,50,72
4	0.04	2	3g6wA	POP	Rep, Mult	113,115
5	0.04	2	1y66B	DIO	Rep, Mult	56,59,60
6	0.02	1	4o6mB	MPG	Rep, Mult	149,150
7	0.02	1	4rwdB	OLA	Rep, Mult	52,56,150
8	0.02	1	3wmnF	BCL	Rep, Mult	141,145
9	0.02	1	3r1rC	III	Rep, Mult	133,136,137,145
10	0.02	1	3f1f1	MG	Rep, Mult	96,97
11	0.02	1	3t2hE	TMO	Rep, Mult	60,99
12	0.02	1	2ou3B	I3A	Rep, Mult	99,113
13	0.02	1	1e6aA	MN	Rep, Mult	112,122
14	0.02	1	1ugiC	IMD	Rep, Mult	73,98
15	0.02	1	3se1A	MG	Rep, Mult	154,157
16	0.02	1	1kj4B	III	Rep, Mult	118,121

	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	2zxqA	0.441	5.30	0.046	0.760	3.2.1.97	NA
2	0.060	2ouyA	0.448	5.23	0.038	0.766	3.1.4.17	90,147
3	0.060	3cf4A	0.480	4.80	0.043	0.807	1.2.99.2	81
4	0.060	1r18A	0.443	4.77	0.049	0.731	2.1.1.77	NA
5	0.060	2nvrA	0.451	5.27	0.053	0.801	3.5.1.98	NA
6	0.060	1mhyB	0.443	5.05	0.048	0.731	1.14.13.25	18,44,149
7	0.060	1hxgA	0.442	5.58	0.044	0.801	4.2.3.9,4.1.99.7	99
8	0.060	2fpqA	0.455	3.89	0.050	0.649	3.4.24.69	NA
9	0.060	1yq2A	0.444	5.42	0.046	0.801	3.2.1.23	112
10	0.060	2cqsA	0.456	4.89	0.075	0.754	2.4.1.20	NA
11	0.060	1kl7A	0.450	5.39	0.043	0.807	4.2.3.1	NA
12	0.060	2z8yP	0.444	4.93	0.040	0.743	2.3.1.169	98
13	0.060	2iu4B	0.451	5.16	0.041	0.760	2.7.1.2	NA
14	0.060	3lmdA	0.442	5.15	0.066	0.754	2.5.1.30	25
15	0.060	2vqjA	0.441	5.10	0.094	0.766	3.5.1.98	29
16	0.060	5r1rA	0.451	5.10	0.060	0.784	1.17.4.1	NA
17	0.060	1zefA	0.450	4.77	0.075	0.725	3.1.3.1	NA
18	0.060	3e2dA	0.449	4.63	0.065	0.714	3.1.3.1	NA
19	0.060	1rqiA	0.448	5.09	0.060	0.743	2.5.1.10	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	0.06	0.461	5.23	0.07	0.80	4dnrA	GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
1	0.06	0.492	4.74	0.07	0.79	3aqpA	GO:0005622 GO:0005886 GO:0006810 GO:0006886 GO:0015031 GO:0015450 GO:0016020 GO:0016021 GO:0071806
2	0.06	0.478	5.12	0.06	0.80	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
3	0.06	0.490	4.89	0.09	0.80	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
4	0.06	0.312	6.09	0.04	0.64	4iixA	GO:0016787 GO:0030153
5	0.06	0.346	4.90	0.07	0.57	4ni5B	GO:0016491 GO:0055114
6	0.06	0.350	5.44	0.07	0.64	3u0oB	GO:0000166 GO:0000287 GO:0004756 GO:0005524 GO:0005829 GO:0016260 GO:0016301 GO:0016310 GO:0016740 GO:0070329
7	0.06	0.377	5.25	0.03	0.67	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
8	0.06	0.330	6.05	0.06	0.65	3w9iF	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
9	0.06	0.320	5.97	0.07	0.64	4r86B	GO:0005215 GO:0006810 GO:0016020 GO:0016021
10	0.06	0.350	5.81	0.05	0.67	3c7aA	GO:0000166 GO:0016491 GO:0047830 GO:0050662 GO:0055114
11	0.06	0.325	5.47	0.06	0.56	1zmrA	GO:0000166 GO:0004618 GO:0005524 GO:0005737 GO:0005829 GO:0006096 GO:0016301 GO:0016310 GO:0016740
12	0.06	0.317	5.44	0.04	0.58	3ihtA	GO:0046872 GO:0051536 GO:0051539
13	0.06	0.320	5.53	0.06	0.57	2r8bA	GO:0016787
14	0.06	0.311	5.03	0.07	0.51	4l0jA	GO:0000746 GO:0003677 GO:0003678 GO:0004386 GO:0005524 GO:0016818 GO:0032508
15	0.06	0.453	5.20	0.08	0.81	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
16	0.06	0.283	5.51	0.05	0.53	3axgA	GO:0016787
17	0.06	0.475	5.05	0.05	0.80	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
18	0.06	0.465	4.94	0.06	0.77	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655

Consensus prediction of GO terms

Molecular Function	GO:0005507	GO:0015450	GO:0005375	GO:0015080	GO:0015307	GO:0042802	GO:0016787
GO-Score	0.07	0.07	0.07	0.07	0.06	0.06	0.06
Biological Processes	GO:0051234
GO-Score	0.47
Cellular Component	GO:0031224	GO:0071944
GO-Score	0.37	0.36

(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.