I-TASSER results

I-TASSER results for job id Rv1907c

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

Input Sequence in FASTA format

>protein (215 residues)
MIGPARRSTTTRRSTPRADRLAGCWCLPGAICQTPRAWWSQARRDGDDETGMRRKGAEMC
WMCDHPEATAEEYLDEVYGIMLMHGWAVQHVECERRPFAYTVGLTRRGLPELVVTGLSPR
RGQRLLNIAARRALVGDLLTPGMQTTLPAGPLVETVQVTHPDAHLYCAIAIFGDKVTALQ
LVWADRRGRWPWAADFDEGRGTQPVLGMRATRRSA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIGPARRSTTTRRSTPRADRLAGCWCLPGAICQTPRAWWSQARRDGDDETGMRRKGAEMCWMCDHPEATAEEYLDEVYGIMLMHGWAVQHVECERRPFAYTVGLTRRGLPELVVTGLSPRRGQRLLNIAARRALVGDLLTPGMQTTLPAGPLVETVQVTHPDAHLYCAIAIFGDKVTALQLVWADRRGRWPWAADFDEGRGTQPVLGMRATRRSA
Prediction	CCCCCCCCCCCCCCCCCHHHCCCEEHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEHCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEHCCCCCCCEEEEEHCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCEEHCCCCCCEEEEEHCCCCHHHHHHHHHHHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	99887666655567875554444444566545787467777765555445666787643334689875577999999999999898899957899986688765578998799987998999999999999999899889986654567766899857887788888899878898689999968999998999998776668878889887899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MIGPARRSTTTRRSTPRADRLAGCWCLPGAICQTPRAWWSQARRDGDDETGMRRKGAEMCWMCDHPEATAEEYLDEVYGIMLMHGWAVQHVECERRPFAYTVGLTRRGLPELVVTGLSPRRGQRLLNIAARRALVGDLLTPGMQTTLPAGPLVETVQVTHPDAHLYCAIAIFGDKVTALQLVWADRRGRWPWAADFDEGRGTQPVLGMRATRRSA
Prediction	74344454444455344143101010112100521532155545546543334651131022154275434512540252046210001003476330000000253520000000034620130033005204756404444424116323033143633441011014124660300000001672300125616564221121235456568
	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

CCCCCCCCCCCCCCCCCHHHCCCEEHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEHCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEHCCCCCCCEEEEEHCCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCEEHCCCCCCEEEEEHCCCCHHHHHHHHHHHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MIGPARRSTTTRRSTPRADRLAGCWCLPGAICQTPRAWWSQARRDGDDETGMRRKGAEMCWMCDHPEATAEEYLDEVYGIMLMHGWAVQHVECERRPFAYTVGLTRRGLPELVVTGLSPRRGQRLLNIAARRALVGDLLTPGMQTTLPAGPLVETVQVTHPDAHLYCAIAIFGDKVTALQLVWADRRGRWPWAADFDEGRGTQPVLGMRATRRSA

2fmlA2

0.11

0.10

0.90

0.76

MUSTER

KEADQLKVLLIQRKGH---PFRNSWALPGGFVNRNESTEDSVLRETKEETGVVISQENIEQLHSRPDRDPRGWVVTVSYLAFIGEEPL--IAGDDAKEVHWFNLERHGQHITLSHE------VEITLDLKTAASLGKDTLAFDHSEIIIKAFNRVVDKEHEP----QVLQVLGKDFTITEAFL----GV--DYRSIDHSNFKKATQYFEELGEPS

3bnmB2

0.09

0.07

0.87

0.68

dPPAS

VLEARDRVGGRLQTVTGYQGIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYADYVIITVPQSVLNLSVQ--------PEKNLRGRIEFQPPLKPVIQDAFDKIDPVDMVVAMSNGQDSRIRFA-----------------GEHT--IMDGAGCAYGA

3hczA

0.21

0.10

0.47

0.63

wdPPAS

LLGKA--YTDTTGTYRYLYDVQA-QCGH---CQTPYDWWLKNRAKGERK------------------------DEEWLKFIRSKKWLNVRDSKNHTDFKYDI----YATPVLYVLKIGYENLDDFLVQYEKSLKTK-------------------------------------------------------------------------------

2wm1A

0.16

0.15

0.91

0.73

wMUSTER

WAKPEDTLNLCQVSYP--RRFVGLGTLP---MQAPELAVKEMERCV-KELGFP--GVQIGTHVNEWDLN-AQELFPVYAAAERLKCSLFVHPWDMQMICSMIGVFEK-FPKLVCFGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGS--FYTDALVHDPLSLKLLTDVIGKD----KVILTD----YPFPLGEEPGKLIESMEEFDEETKNK

4i6kA

0.13

0.12

0.88

0.64

wPPAS

MISTQDHSIETARYAPDVQSFHN---FTHGLVQPNQAMLNAIQQYPDQHTGI--VGVRLNLFGLNLPALNTPDWQKFLRNVESLNWQVELHAPPKVQLL----LNEYSFD-VVIFGRVDGIEDPDYQKFLSLLNVKQ--VSGFYRLGATPSNINIA-----QQAYNIFKEKGFLH----KLIW-D----WPHTQHESLITYEDAIIVFDKHEQCL

4hedA

0.26

0.07

0.25

0.79

dPPAS2

---PGVCFKVLTTKEPKA-NIKRCYNLPNRMCIDPNASWLAERLYRLKEKGVTCRGEA-------------------------------------------------------------------------------------------------------------------------------------------------------------

4i6kA

0.11

0.10

0.92

0.70

PPAS

VFSTQDHSIETARYAPDLDEHTHGVLVQPSFLGTNNQAMLNAIQQYPQHTTTFNVGVRLNLFGLNLPALNTPDWQKFLRNVESLNWQVELHAPPKYLVQLLPQLNEYSFDVVI-FGRVDGIEDPDYQKFLSLLNVKQ--VSGFYRLGATPSNINIA-----QQAYNIFKEKGFLH----KLIW-D----WPHTQHESLITYEDAIKAFKQIVFDK

1pjcA1

0.24

0.17

0.73

0.60

Env-PPAS

MIGPKEIKNQEFRLSPSVRTLAGHTVFTQAVVPSAKDAWSREKEPLPAEYDLMQKDQLLFTYLH------LAAARELTEQLMRVGL---TA------IAYTVELPNRSLP-LNMPGAVPWTATQALNNSTLPYVVK-----------LANQGLKALET---DDALAKGLNVQAHRLVAVQQVFPDL-A---------------------------

3h95A

0.13

0.09

0.69

0.71

MUSTER

VFDESTRKILVVQDRNK---LKNMWKFPGGLSEPEEDIGDTAVREVFEETGIKSEFRSVLSIRQQHDMY--------------IICRLKPYSFTINFCCLRCEWMD--LNDLAKTENTTPITSRVARLLLYGYREGFDLTVEELPAVYTGLFYKLYHKELPENYKTM------------------------------------------------

1kezA

0.13

0.12

0.91

0.63

dPPAS

FDGSDGFSLDLVDMADGPGEVT-VICCAGTAISGPHEFTRLAGALRGIARAVPQPGYE---EGEPLPSSMAAVAAVQADAVIRT--------QGDKPFGHSAGLLDRGHPGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDT--------RLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHVAVPGDHFTM

(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=-3.02

Estimated TM-score = 0.37±0.13

Estimated RMSD = 12.6±4.3Å

Download Model 2

C-score=-4.86

Download Model 3

C-score=-4.62

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	2wm1A	0.731	3.26	0.116	0.926
2	4infA	0.723	3.44	0.116	0.926
3	2hbxA	0.723	3.26	0.091	0.916
4	2dvtA	0.712	3.48	0.116	0.926
5	4l5pA	0.705	3.50	0.101	0.921
6	4dziA	0.695	3.73	0.106	0.921
7	3nurA	0.693	3.59	0.092	0.907
8	2f6kA	0.691	3.63	0.118	0.907
9	4hjwA	0.689	3.90	0.095	0.921
10	3ij6A	0.681	3.65	0.093	0.902

(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	9	3q4dC	ALA	Rep, Mult	24,27,58,60,89,116,157,186
2	0.05	2	5boeB	PEP	Rep, Mult	58,116,157,185,187,192
3	0.02	1	3qj1A	PEG	Rep, Mult	127,130
4	0.02	1	3arzA	I5I	Rep, Mult	86,185,192
5	0.02	1	3dr2B	CA	Rep, Mult	99,100,136
6	0.02	1	2bruB	NAP	Rep, Mult	126,144
7	0.02	1	1wkqA	IMD	Rep, Mult	39,100
8	0.02	1	3bo5A	ZN	Rep, Mult	24,32,60,63
9	0.02	1	2hbv0	III	Rep, Mult	65,99,126,132,157,160,163,164,167,194,195,198
10	0.02	1	1jkeA	ZN	Rep, Mult	71,75
11	0.02	1	3izrH	III	Rep, Mult	85,175
12	0.02	1	1rkuB	MG	Rep, Mult	29,185

	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	1v77A	0.540	3.83	0.048	0.735	3.1.26.5	NA
2	0.066	1wx0A	0.501	4.55	0.136	0.744	2.2.1.2	NA
3	0.066	3ngfA	0.580	4.21	0.074	0.823	5.3.1.22	54,183
4	0.060	2q01C	0.617	3.99	0.089	0.837	5.3.1.12	185,194
5	0.060	1qoxM	0.631	4.65	0.072	0.958	3.2.1.21	NA
6	0.060	2dgaA	0.632	4.73	0.043	0.963	3.2.1.21	NA
7	0.060	1ll6A	0.606	4.22	0.059	0.856	3.2.1.14	42
8	0.060	2z1sA	0.634	4.53	0.072	0.954	3.2.1.21	173,184
9	0.060	1wcgA	0.625	4.94	0.067	0.972	3.2.1.147	NA
10	0.060	1u22A	0.614	4.17	0.058	0.865	2.1.1.14	NA
11	0.060	2e3zA	0.623	4.53	0.074	0.930	3.2.1.21	NA
12	0.060	3cmjA	0.581	4.50	0.057	0.851	3.2.1.21	NA
13	0.060	1j5sA	0.608	4.11	0.090	0.828	5.3.1.12	NA
14	0.060	1qoxA	0.631	4.65	0.072	0.958	3.2.1.21	NA
15	0.060	1qw7A	0.607	4.26	0.119	0.870	3.1.8.1	185
16	0.060	2ftwA	0.606	3.93	0.050	0.823	3.5.2.2	NA
17	0.060	1tr1D	0.631	4.64	0.039	0.954	3.2.1.21	NA
18	0.060	2nq5A	0.615	4.19	0.057	0.870	2.1.1.14	58
19	0.060	3gnrA	0.636	4.41	0.054	0.930	3.2.1.21	NA
20	0.060	1edgA	0.602	4.47	0.036	0.884	3.2.1.4	NA
21	0.060	2e9lA	0.625	4.54	0.063	0.940	3.2.1.21	NA
22	0.060	2wm1A	0.731	3.26	0.116	0.926	4.1.1.45	173

(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	0.19	0.681	3.65	0.09	0.90	3ij6A	GO:0016787 GO:0046872
1	0.13	0.732	3.26	0.13	0.93	4ofcA	GO:0001760 GO:0005829 GO:0006568 GO:0006569 GO:0008270 GO:0016787 GO:0016829 GO:0016831 GO:0046872 GO:0046874 GO:0051259 GO:0070062 GO:1904984 GO:1905004 GO:1905012
2	0.13	0.724	3.44	0.12	0.93	4qrnA	GO:0016787 GO:0046872
3	0.13	0.713	3.46	0.10	0.93	4qroA	GO:0016787 GO:0046872
4	0.12	0.712	3.48	0.12	0.93	2dvtA	GO:0016787 GO:0046872
5	0.12	0.705	3.50	0.11	0.92	4icmA	GO:0016787 GO:0046872
6	0.12	0.694	3.65	0.07	0.91	2gwgA	GO:0016787 GO:0046872
7	0.12	0.696	3.65	0.11	0.92	2f6kA	GO:0016787 GO:0046872
8	0.12	0.691	3.97	0.10	0.93	4hjwC	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
9	0.11	0.701	3.59	0.09	0.92	3nurA	GO:0016787
10	0.10	0.693	3.74	0.11	0.92	4dziC	GO:0016787
11	0.10	0.693	3.85	0.10	0.92	4hk5D	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
12	0.07	0.518	4.73	0.05	0.78	3irsA	GO:0016787
13	0.07	0.613	3.72	0.07	0.82	3cjpA	GO:0016787 GO:0046872
14	0.07	0.725	3.25	0.09	0.92	4eraA	GO:0001760 GO:0006568 GO:0016787 GO:0046872 GO:1904984
15	0.07	0.578	4.48	0.08	0.85	2vunA	GO:0016787 GO:0016810 GO:0043792 GO:0046872 GO:0051187
16	0.06	0.401	6.23	0.04	0.75	1bxrA	GO:0000050 GO:0000166 GO:0003824 GO:0004087 GO:0004088 GO:0005524 GO:0005829 GO:0005951 GO:0006221 GO:0006526 GO:0006807 GO:0008652 GO:0016597 GO:0016874 GO:0019856 GO:0044205 GO:0046872
17	0.06	0.342	5.37	0.06	0.56	1g5bB	GO:0004721 GO:0006470 GO:0016787 GO:0046872
18	0.06	0.338	5.15	0.06	0.53	4wnrA	GO:0005525 GO:0005622 GO:0007264

Consensus prediction of GO terms

Molecular Function	GO:0016787	GO:0046872
GO-Score	0.54	0.54
Biological Processes	GO:0006569	GO:1904984	GO:1905004	GO:1905012	GO:0051259
GO-Score	0.13	0.13	0.13	0.13	0.13
Cellular Component	GO:0070062	GO:0005829
GO-Score	0.13	0.13

(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.