I-TASSER results

I-TASSER results for job id Rv3749c

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

Input Sequence in FASTA format

>protein (169 residues)
MPCCGSLTRAPIGLCGRRTSWPRLGEPWSTASTSAPNGLTTAFAFGYNDLIAAMNNHYKD
RHVLAAAVRERAEVIVTTNLKHFPDDALKPYQIKALHPDDFLLDQLDLYEEATKAVILGM
VDAYIDPPFTPHSLLDALGEQVPQFAAKARRLFPSGSPFGLGVLLPFDQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPCCGSLTRAPIGLCGRRTSWPRLGEPWSTASTSAPNGLTTAFAFGYNDLIAAMNNHYKDRHVLAAAVRERAEVIVTTNLKHFPDDALKPYQIKALHPDDFLLDQLDLYEEATKAVILGMVDAYIDPPFTPHSLLDALGEQVPQFAAKARRLFPSGSPFGLGVLLPFDQ
Prediction	CCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCEEEHCCCCCCCHHHHHHHCCEEHCHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Conf.Score	9877665444445555556665789999999999999856654667567776479998768999999998997999767789998888766989988899999999969999999999999998689999999999999987999999999975678888777888789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPCCGSLTRAPIGLCGRRTSWPRLGEPWSTASTSAPNGLTTAFAFGYNDLIAAMNNHYKDRHVLAAAVRERAEVIVTTNLKHFPDDALKPYQIKALHPDDFLLDQLDLYEEATKAVILGMVDAYIDPPFTPHSLLDALGEQVPQFAAKARRLFPSGSPFGLGVLLPFDQ
Prediction	6511331331322133346335524541541252045103403154154016404234512000000130402000022254135730562504223023002301433152014004400642554643054005204520450053037217544434345435478
	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

CCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCEEEHCCCCCCCHHHHHHHCCEEHCHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
MPCCGSLTRAPIGLCGRRTSWPRLGEPWSTASTSAPNGLTTAFAFGYNDLIAAMNNHYKDRHVLAAAVRERAEVIVTTNLKHFPDDALKPYQIKALHPDDFLLDQLDLYEEATKAVILGMVDAYIDPPFTPHSLLDALGEQVPQFAAKARRLFPSGSPFGLGVLLPFDQ

5cwmA1

0.15

0.10

0.67

1.16

dPPAS2

-------------------DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAE------KEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAA---RLAKRVLELAEKQG---------------------------

1t33A

0.05

0.87

1.02

dPPAS2

DFLGEKFRPHAEKAERLFSQPAPDRDAIRELILLACKNMIMLLTQEDTVNLSKFSPTSAYQLVHEQVIDPLHTHLT--------RLVAAYTGCDANDTRMILHTHALLGEVLAFRLGKETILLRTGWPQFDEEKAELIYQTVTCHIDLILHGLTQ--------------

3w3tA

0.09

0.08

0.96

0.69

MUSTER

VQVQGKHIAIHTSVLDD---KVSAMELLQSYATLLRGQFAVYVKEVMEEIALPSLDFYLHDGVRAAGATLIPILLSCLLA---ATEELVLL-WHKASSKLIGGLMSEPMPEITQVYHNSLVNGIKVDNCLSEDQLAAFTKGVSANLTDTYERMQDRDEYNEFTDEDLLD

5cwdA

0.10

0.09

0.96

0.66

dPPAS

TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQATKEAARSFCEAAARAAAESNDEEVAKIAAKACLEV---AKQAGMPTKEAARS----FCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESNDEEVACKEVAKQAGMPWLE

1veiA

0.15

0.13

0.87

0.57

wdPPAS

MT---SFTIPGL-----------SDKKASDVADLLQKQLSTYNDPNFIGVHEMI-----DPQVELVRGYA-AERIATGTPGAI-DRTWDDYSVERDTVQAHLAALDLV-YNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAGGQLTHEGQSTEK

5cwfA

0.11

0.10

0.94

0.65

wMUSTER

KKVMEAL--KKAVELAKKNNDDEVAREIERAAKEIVEALRENNSDEMAKVMLAL-----AKAVLLAAKNNDDEVAIVEALRENNSDEMAKV---MLALAKAVLLAAKNNDDEVAREIARAAAEIVEAENNSDEMAKKMLELAKRVLDAAKNDDETAREIARQAAEEVEA

1ihcA

0.12

0.09

0.82

0.65

wPPAS

I--VGVL----VSDSCFRNLAE-------RSGINLKDLVQDPSLLGGTISAYKIVPD--EIEEIKETLID-LNLILT-APRDVTPEATKEV-IERE-ALAMLMGSLNVTPLGMLSPVCGIRGK---PKKGSQECFQFILPALPHAIDLLRDAIVKVKE--------HD-

4cj9A9

0.10

0.04

0.43

1.01

dPPAS2

-------------------------------------------------------------------------------------ERLGERGF---SRADIVNVAGNNGGAQALKAVLEHEATLNERGFSRADIVKIAGNGGAQALKAVLEHEATLDERGF--------

5cwdA

0.10

0.09

0.96

0.73

PPAS

TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQATKEAARSFCEAAARAAAESNDEEVAKIAAKACLEV---AKQAGMPTKEAARS----FCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESNDEEVACKEVAKQAGMPWLE

1o8oB

0.10

0.09

0.88

0.78

Env-PPAS

PEYVAILT-----VSDTVSAGAGPDRSGPRAVSVVDSSS--EKLGGAKVVATAVVPDEVKDILQKWSDVDEMDLILTLTPRDVTPEATKKVIERETPGLLFVMMQESLKITPFAMLSRSAAGIRGSTPGNPNAVAECMEALLPALKHALKQIKGD--------------

(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=-3.32

Estimated TM-score = 0.35±0.12

Estimated RMSD = 12.7±4.3Å

Download Model 2

C-score=-3.76

Download Model 3

C-score=-3.80

Download Model 4

C-score=-4.43

Download Model 5

C-score=-4.25

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	5cwbA	0.673	3.45	0.084	0.911
2	4by6A	0.621	4.19	0.044	0.923
3	4c0dA2	0.618	4.19	0.115	0.917
4	5t8vA	0.612	4.17	0.093	0.888
5	5cwdA	0.605	3.94	0.099	0.899
6	5cwlA	0.591	4.16	0.060	0.888
7	3tj1A	0.587	3.61	0.051	0.817
8	3feyA2	0.577	4.16	0.081	0.870
9	2km4A	0.570	3.74	0.066	0.793
10	4c0eA	0.568	3.99	0.092	0.840

(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	0.15	8	4hw3E	19G	Rep, Mult	32,46,50,54,63,66,67,70,71,96
2	0.10	5	1e7fA	DAO	Rep, Mult	61,65
3	0.04	2	5e8gA	CO	Rep, Mult	60,62
4	0.04	2	3d9pB	III	Rep, Mult	25,29,69,72,73
5	0.02	1	3d9pA	III	Rep, Mult	20,25,66,69,70
6	0.02	1	1h2u0	III	Rep, Mult	36,40,41
7	0.02	1	1o7dC	MAN	Rep, Mult	132,136
8	0.02	1	3g4fA	MG	Rep, Mult	107,111
9	0.02	1	1cviC	UUU	Rep, Mult	77,79
10	0.02	1	3a0bM	MGE	Rep, Mult	98,101,102
11	0.02	1	1szaB	III	Rep, Mult	21,25,65,68,69,72,73,118,121
12	0.02	1	2yl8A	MN	Rep, Mult	48,60
13	0.02	1	3h8fB	MN	Rep, Mult	60,104,107

	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	1j0mA	0.506	5.16	0.057	0.858	4.2.2.12	NA
2	0.060	2cqsA	0.510	4.98	0.082	0.834	2.4.1.20	NA
3	0.060	3ihyC	0.525	4.26	0.067	0.799	2.7.1.137	97,100,103
4	0.060	1e1cA	0.509	4.41	0.062	0.781	5.4.99.2	97
5	0.060	2x0sA	0.545	4.74	0.074	0.864	2.7.9.1	NA
6	0.060	1l2aE	0.426	5.74	0.025	0.781	3.2.1.4	35
7	0.060	1vbgA	0.524	4.65	0.041	0.823	2.7.9.1	NA
8	0.060	1w0cA	0.505	4.88	0.072	0.799	1.5.1.33	91
9	0.060	1gowA	0.519	4.41	0.056	0.793	3.2.1.23	NA
10	0.060	3btaA	0.524	5.37	0.061	0.905	3.4.24.69	NA
11	0.060	1kc7A	0.553	4.74	0.074	0.864	2.7.9.1	NA
12	0.060	3h8eA	0.533	3.96	0.092	0.757	3.4.11.1	95,114
13	0.060	3hfwA	0.558	4.24	0.026	0.864	3.2.2.19	NA
14	0.060	1gytA	0.527	4.04	0.077	0.763	3.4.11.1	NA
15	0.060	3c5wA	0.501	3.97	0.048	0.722	3.1.3.16	54,62
16	0.060	1vjzA	0.507	4.43	0.056	0.775	3.2.1.4	NA
17	0.060	1reqA	0.518	4.30	0.054	0.781	5.4.99.2	NA
18	0.060	1ojnA	0.509	5.21	0.075	0.876	4.2.2.1	48
19	0.060	1ujkB	0.529	4.06	0.052	0.781	3.4.23.46	50,52

(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	0.21	0.547	3.82	0.03	0.80	2diwA	GO:0000166 GO:0003676 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0006397 GO:0008380 GO:0016363 GO:0043175
1	0.08	0.554	3.84	0.07	0.78	4nacA	GO:0005654 GO:0016591 GO:0042795 GO:0070940
2	0.08	0.570	3.74	0.07	0.79	2km4A	GO:0000790 GO:0000993 GO:0003677 GO:0005634 GO:0006351 GO:0006355 GO:0010526 GO:0031124 GO:0035861 GO:0042769
3	0.07	0.621	4.19	0.04	0.92	4by6A	GO:0046872
4	0.07	0.546	3.54	0.09	0.76	4flbA	GO:0005654 GO:0016591 GO:0042795
5	0.07	0.605	4.20	0.12	0.89	5fu7A	GO:0000122 GO:0000289 GO:0000932 GO:0004535 GO:0005615 GO:0005634 GO:0005737 GO:0005778 GO:0005829 GO:0006351 GO:0006355 GO:0006417 GO:0006977 GO:0007275 GO:0010606 GO:0016020 GO:0017148 GO:0019904 GO:0030014 GO:0030015 GO:0030331 GO:0031047 GO:0032947 GO:0033147 GO:0035195 GO:0042974 GO:0043231 GO:0044822 GO:0048387 GO:0060213 GO:0061014 GO:0070016 GO:0090503 GO:1900153 GO:2000036
6	0.07	0.449	4.33	0.13	0.71	5et1A	GO:0003779 GO:0005737 GO:0005856 GO:0005902 GO:0005903 GO:0007605 GO:0007626 GO:0015629 GO:0017124 GO:0030046 GO:0030054 GO:0031941 GO:0032420 GO:0032421 GO:0032426 GO:0042995 GO:0043197 GO:0051015 GO:0051017 GO:0051491 GO:0051494 GO:0051639
7	0.07	0.442	4.74	0.01	0.73	1s70B	GO:0005737 GO:0007165 GO:0019208 GO:0019901 GO:0030018 GO:0030155 GO:0031672 GO:0035507 GO:0071889 GO:0072357
8	0.07	0.457	4.29	0.07	0.69	4rlvA	GO:0002027 GO:0003283 GO:0005200 GO:0005622 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0006874 GO:0006888 GO:0007165 GO:0007399 GO:0008093 GO:0010628 GO:0010881 GO:0010882 GO:0014704 GO:0016020 GO:0016323 GO:0016324 GO:0019899 GO:0019901 GO:0030018 GO:0030054 GO:0030315 GO:0030507 GO:0030674 GO:0030913 GO:0031430 GO:0031647 GO:0031672 GO:0033292 GO:0033365 GO:0034394 GO:0034613 GO:0036309 GO:0036371 GO:0042383 GO:0043005 GO:0043034 GO:0043268 GO:0044325 GO:0045121 GO:0045202 GO:0045211 GO:0050821 GO:0051117 GO:0051279 GO:0051597 GO:0051924 GO:0051928 GO:0055117 GO:0060307 GO:0070296 GO:0070972 GO:0072659 GO:0072661 GO:0086004 GO:0086005 GO:0086014 GO:0086015 GO:0086046 GO:0086066 GO:0086070 GO:0086091 GO:0098907 GO:0098910 GO:1901018 GO:1901019 GO:1901021 GO:2001259
9	0.06	0.434	5.05	0.04	0.74	2bklB	GO:0004252 GO:0006508 GO:0008236 GO:0070008
10	0.06	0.395	4.81	0.06	0.64	4otkA	GO:0005618 GO:0005886 GO:0016491 GO:0040007 GO:0055114
11	0.06	0.358	5.58	0.01	0.67	4p3lA	GO:0006810 GO:0008643 GO:0030288 GO:0042597
12	0.06	0.354	4.88	0.06	0.56	4wjiA	GO:0000166 GO:0004665 GO:0006571 GO:0008977 GO:0055114
13	0.06	0.347	3.39	0.06	0.47	2zgdA
14	0.06	0.367	4.66	0.07	0.57	3wpnA	GO:0000166 GO:0000922 GO:0003777 GO:0005524 GO:0005737 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0005876 GO:0006890 GO:0007018 GO:0007049 GO:0007051 GO:0007052 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008574 GO:0016020 GO:0019886 GO:0019901 GO:0032403 GO:0046602 GO:0051225 GO:0051301 GO:0090307
15	0.06	0.370	4.85	0.07	0.61	4x0tA	GO:0004029 GO:0004043 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0006081 GO:0006554 GO:0007605 GO:0008152 GO:0008802 GO:0016491 GO:0016620 GO:0019285 GO:0042426 GO:0055114 GO:0070062
16	0.06	0.311	4.32	0.05	0.48	3h7mA	GO:0000155 GO:0000160 GO:0000166 GO:0005524 GO:0005622 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0023014
17	0.06	0.434	5.22	0.08	0.70	1v4vA	GO:0008761 GO:0016853
18	0.06	0.277	5.83	0.03	0.53	3j7y7	GO:0000002 GO:0000166 GO:0003723 GO:0004827 GO:0005739 GO:0005743 GO:0005761 GO:0005840 GO:0006418 GO:0006433 GO:0016876 GO:0030529 GO:0044822 GO:0070125 GO:0070126
19	0.06	0.282	3.74	0.06	0.41	2ktbB	GO:0000228 GO:0003677 GO:0003682 GO:0005634 GO:0005654 GO:0006338 GO:0006351 GO:0006355 GO:0007067 GO:0008285 GO:0016568 GO:0090544
20	0.06	0.287	4.33	0.06	0.43	1eq1A	GO:0005576 GO:0006810 GO:0006869 GO:0008289
21	0.06	0.284	4.67	0.03	0.44	3kf9A	GO:0005509 GO:0007049 GO:0007067 GO:0046872 GO:0051301
22	0.06	0.269	4.99	0.06	0.43	3idoA	GO:0004725 GO:0006470 GO:0035335

Consensus prediction of GO terms

Molecular Function	GO:0070063	GO:1901265	GO:0036094
GO-Score	0.42	0.42	0.42
Biological Processes	GO:0016071	GO:0006396
GO-Score	0.42	0.42
Cellular Component	GO:0030529	GO:0034399	GO:0005654
GO-Score	0.42	0.42	0.32

(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.