I-TASSER results

I-TASSER results for job id Rv1428c

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

Input Sequence in FASTA format

>protein (275 residues)
MSETDSPGNGDDAGIGDIGKFDPGLTQRLISVLRPVLKTYHRSQVHGLDSFPPGGALVVA
NHSGGMFPMDVPVFSVDFYDKFGYDRPVYTLSHDILFMGLTGDLFRRTGYIRATRENAAK
ALRSGGVVVVFPGGDYDAYRPTFAENVIDFNGRKGYVSTAVEAGVPIVPAVSIGGQESQL
YLSRGTWLARRLGLKRLLRSDILPISFGFPFGFSAAIPPNLPLPAKIVMQVLDPINLTKQ
FGEDPDVDAVDEHVRSVMQQALNDLAAKRRFPILG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSETDSPGNGDDAGIGDIGKFDPGLTQRLISVLRPVLKTYHRSQVHGLDSFPPGGALVVANHSGGMFPMDVPVFSVDFYDKFGYDRPVYTLSHDILFMGLTGDLFRRTGYIRATRENAAKALRSGGVVVVFPGGDYDAYRPTFAENVIDFNGRKGYVSTAVEAGVPIVPAVSIGGQESQLYLSRGTWLARRLGLKRLLRSDILPISFGFPFGFSAAIPPNLPLPAKIVMQVLDPINLTKQFGEDPDVDAVDEHVRSVMQQALNDLAAKRRFPILG
Prediction	CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEHCHCCCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEHCHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHCCEEEEHCCCCCCCCCCCCCCCEEHCCCCCHHHHHHHHHCCCEEEEEEHCCCHHHCCCCCCCHHHHHHCCHHHHCCCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	98766788888888887666798999999999999999874859998555899987999858887656899999999999859985687763456645679999999898668999999999989989998698545666788886566479855899999989988889986875444446788567777665444335555555677666566788888999758999889855787788899999999999999999999999996888899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSETDSPGNGDDAGIGDIGKFDPGLTQRLISVLRPVLKTYHRSQVHGLDSFPPGGALVVANHSGGMFPMDVPVFSVDFYDKFGYDRPVYTLSHDILFMGLTGDLFRRTGYIRATRENAAKALRSGGVVVVFPGGDYDAYRPTFAENVIDFNGRKGYVSTAVEAGVPIVPAVSIGGQESQLYLSRGTWLARRLGLKRLLRSDILPISFGFPFGFSAAIPPNLPLPAKIVMQVLDPINLTKQFGEDPDVDAVDEHVRSVMQQALNDLAAKRRFPILG
Prediction	76636436645515444145222400300222022202301203033114026631322212200210310000000013424341101000243132211222022010010137203400641200000001022134334453213146120000001417020000000003201321452430232242433332300101213322233231130233230100003104156344664225302630252025005501752634247
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEHCHCCCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEHCHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHCCEEEEHCCCCCCCCCCCCCCCEEHCCCCCHHHHHHHHHCCCEEEEEEHCCCHHHCCCCCCCHHHHHHCCHHHHCCCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
MSETDSPGNGDDAGIGDIGKFDPGLTQRLISVLRPVLKTYHRSQVHGLDSFPPGGALVVANHSGGMFPMDVPVFSVDFYDKFGYDRPVYTLSHDILFMGLTGDLFRRTGYIRATRENAAKALRSGGVVVVFPGGDYDAYRPTFAENVIDFNGRKGYVSTAVEAGVPIVPAVSIGGQESQLYLSRGTWLARRLGLKRLLRSDILPISFGFPFGFSAAIPPNLPLPAKIVMQVLDPINLTKQFGEDPDVDAVDEHVRSVMQQALNDLAAKRRFPILG

1k30A2

0.14

0.12

0.81

1.61

wdPPAS

-----SSHKAIREPFD--------YYIFGQNYIRPLIDFG--SFVGNLEKLQQG-VVLISNHQTE---ADPAIISLLLEKTNPAENTIFVAGDRVLADPLCKPFSIGRNLICVSLKEMALLLRGGQLIWIAPSGGRDRPDPSTGEWYPA-SSVDNMRRLIQHSDVPLFPLALLC----HDIMPPPSQVEIEIRV----------------------------AFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISG

1k30A2

0.14

0.12

0.81

1.39

wPPAS

-----SSHKAIREPFD--------YYIFGQNYIRPLIDFG-NSFVGNLEKLQQGNVVLISNHQT----ADPAIISLLLEKTNPAENTIFVAGDRVLADPLCKPFSIGRNLICVSLKEMALLLRGGQLIWIAPSGGRD--RPDPSTGEWYPSSVDNMRRLIQHSDVPLFPLALLC----HDIMPPPSQVEIEI----------------------------VIAFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISG

3ihbA2

0.14

0.05

0.37

1.58

dPPAS2

LTDLRT---GAEKPGTGWDAAVYPRWQEAAADRAALSAAT------------------------GGGAVHEAAAAAARDENDGPIRTVVLNLA---RVDRIDDVGRRL-----IAEGVRRLQADGVRVEVEPERILPL-----------------------------------------------------------------------------------------------------------------------------------------

1k30A2

0.14

0.12

0.83

1.02

Env-PPAS

----------SSHHKAIREPFD--YYIFGQNYIRPLIDFG-NSFVGNLSLFKDHNVVLISNHQTEADPAIISLLLEKTNPYI-AENTIFVAGDRVLADPLCKPFSIGRNLICVSLKEMALLLRGGQLIWIAPSGGRD--RPDPSTGEWYPAPFDNMRRLIQHSDVPLFPLALL----CHDIMPPPSQVEIEIRV-----------IAFNG----------------AGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISG

1k30A

0.14

0.12

0.86

1.24

wdPPAS

LLDVEDPFVFSSHHKAIREPFD--YYIFGQNYIRPLIDFG--SFVGNLEKLQQG-VVLISNHQTEADPAIISLLLEKTNPYI-AENTIFVAGDRVLADPLCKPFSIGRNLICVSLKEMALLLRGGQLIWIAPSGGRDRPDPSTGEWYPA-SSVDNMRRLIQHSDVPLFPLALLC----HDIMPPPSQVEIEIRV----------------------------AFNGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISG

1k30A

0.15

0.12

0.85

1.00

wPPAS

LLDVEDPFVFSSHHKAIREPFD--YYIFGQNYIRPLID-FGNSFVGNLEKLQQGNVVLISNHQT----ADPAIISLLLEKTNPAENTIFVAGDRVLADPLCKPFSIGRNLICVSLKEMALLLRGGQLIWIAPSGGRD--RPDPSTGEWY-SSVDNMRRLIQHSDVPLFPLALLC----HDIMPPPSQVEIEI---------------------------VIAF-NGAGLSVAPEISFEEIAATHKNPEEVREAYSKALFDSVAMQYNVLKTAISG

5croA

0.17

0.03

0.17

1.19

dPPAS2

---------------------------------------------------------------------------------------------------MLKDYAMRFGDLGVYQSAINKAIHAGRFLTINADGSAEEVKPFPSN----------------------------------------------------------------------------------------------------------------------------------

2pijB

0.18

0.04

0.20

1.15

dPPAS2

--------------------------------------------------------------------------------------KKIPLSKYLEEHGTQSALAAALGVN----QSAISQVRAGREITLYEDGRVEANEIRPIPA---------------------------------------------------------------------------------------------------------------------------------

4ltyC

0.13

0.07

0.56

1.12

dPPAS2

-------------------------------------------------------------------------------------------------IEREAEHQAFL------DWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYN----RFVVNLQQTGCHLVVLA--GNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRP-----------RDIITSQEKQQHLLAAITDYYQQHYADACKLRGDQPLP

1lvaA2

0.14

0.03

0.21

1.06

dPPAS2

------------------------------------------------------------------FSETQKKLLKDLEDKY---------RVSRWQPPSFKEVAGSFNLDPSEEELLHYLVREGVLVKINDE----------------------------------------------------------------------------------------------------------------------------------------------

(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=-1.65

Estimated TM-score = 0.51±0.15

Estimated RMSD = 9.7±4.6Å

Download Model 2

C-score=-3.13

Download Model 3

C-score=-3.70

Download Model 4

C-score=-2.34

Download Model 5

C-score=-4.95

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	1k30A	0.789	2.12	0.134	0.866
2	5hm8A	0.513	5.11	0.063	0.785
3	3ondA	0.510	5.43	0.082	0.815
4	3h9uC	0.506	5.38	0.084	0.785
5	3ce6A	0.498	5.22	0.041	0.774
6	1v8bA	0.495	5.32	0.104	0.767
7	3glqA	0.493	5.30	0.050	0.771
8	3n58A	0.489	5.25	0.046	0.753
9	3gvpA	0.487	5.46	0.067	0.764
10	5kf6A	0.479	6.09	0.088	0.818

(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	0.05	2	1iuqA	GOL	Rep, Mult	149,150,252,255,256,259
2	0.05	2	1kzuE	BCL	Rep, Mult	262,265
3	0.05	2	2e18A	ZN	Rep, Mult	70,177
4	0.05	2	1brrC	ARC	Rep, Mult	59,258,262
5	0.02	1	2wse1	CLA	Rep, Mult	163,164
6	0.02	1	3npyA	ZN	Rep, Mult	177,255
7	0.02	1	3zukB	CA	Rep, Mult	246,248
8	0.02	1	3jzmF	MG	Rep, Mult	63,65
9	0.02	1	3wu2h	CLA	Rep, Mult	254,258
10	0.02	1	3ovnA	MPV	Rep, Mult	164,168
11	0.02	1	1pznA	IMD	Rep, Mult	154,155
12	0.02	1	1sumB	FE	Rep, Mult	248,252
13	0.02	1	1d4fA	NAD	Rep, Mult	96,101,118
14	0.02	1	5ddlB	5AU	Rep, Mult	264,268
15	0.02	1	5ezmA	MPG	Rep, Mult	171,266
16	0.02	1	2o011	CLA	Rep, Mult	163,164,165,168,169,184
17	0.02	1	1fipA	III	Rep, Mult	234,235
18	0.02	1	3a0bK	CLA	Rep, Mult	166,167,169

	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	1k30A	0.789	2.12	0.134	0.866	2.3.1.15	62
2	0.060	2vz8A	0.428	5.70	0.108	0.673	2.3.1.85	62
3	0.060	3g1uC	0.503	5.37	0.071	0.782	3.3.1.1	NA
4	0.060	3n58A	0.489	5.25	0.046	0.753	3.3.1.1	94,133
5	0.060	2ve5H	0.429	5.87	0.057	0.706	1.2.1.8	92,133
6	0.060	1wndA	0.428	5.79	0.056	0.706	1.2.1.19	184
7	0.060	2jfdA	0.251	6.25	0.038	0.436	2.3.1.85	265
8	0.060	1o9jA	0.403	5.74	0.040	0.636	1.2.1.3	NA
9	0.060	1bxsA	0.431	5.77	0.065	0.702	1.2.1.36	NA
10	0.060	2d4eC	0.433	5.61	0.045	0.691	1.2.1.60	NA
11	0.060	3gvpA	0.487	5.46	0.067	0.764	3.3.1.1	NA
12	0.060	2w8oA	0.429	5.86	0.077	0.702	1.2.1.24	67,94
13	0.060	1kzhB	0.436	5.53	0.062	0.684	2.7.1.90	65
14	0.060	2vz9B	0.437	5.74	0.101	0.687	2.3.1.85	62
15	0.060	2o2pA	0.435	5.77	0.028	0.702	1.5.1.6	NA
16	0.060	1o01C	0.435	5.62	0.053	0.698	1.2.1.3	NA
17	0.060	3ce6A	0.498	5.22	0.041	0.774	3.3.1.1	133,150
18	0.060	2ve5A	0.281	6.80	0.040	0.513	1.2.1.8	NA
19	0.060	1v8bC	0.495	5.35	0.104	0.771	3.3.1.1	233

(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	0.14	0.789	2.12	0.13	0.87	1k30A	GO:0004366 GO:0006629 GO:0006650 GO:0008152 GO:0008654 GO:0009507 GO:0009536 GO:0009570 GO:0016024 GO:0016740 GO:0016746
1	0.07	0.512	5.06	0.06	0.78	5jpiA	GO:0004013 GO:0006730 GO:0016787
2	0.07	0.502	5.36	0.07	0.79	3ondB	GO:0004013 GO:0006730 GO:0016787
3	0.07	0.498	5.22	0.04	0.77	3ce6A	GO:0004013 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006730 GO:0009087 GO:0016787 GO:0033353 GO:0040007 GO:0046085 GO:0070403
4	0.07	0.499	5.33	0.07	0.78	3n58B	GO:0004013 GO:0005737 GO:0006730 GO:0016787
5	0.07	0.503	5.37	0.07	0.78	3g1uC	GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
6	0.07	0.487	5.46	0.07	0.76	3gvpA	GO:0004013 GO:0005737 GO:0005783 GO:0005829 GO:0006730 GO:0016787 GO:0033353 GO:0043005 GO:0043231
7	0.07	0.495	5.32	0.10	0.77	1v8bA	GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
8	0.07	0.506	5.38	0.08	0.79	3h9uC	GO:0000166 GO:0004013 GO:0005829 GO:0006730 GO:0016787 GO:0033353
9	0.07	0.492	5.44	0.09	0.77	1a7aA	GO:0000096 GO:0001666 GO:0002439 GO:0004013 GO:0005634 GO:0005737 GO:0005829 GO:0006730 GO:0007584 GO:0016787 GO:0019510 GO:0030554 GO:0032259 GO:0033353 GO:0042470 GO:0042745 GO:0042802 GO:0043005 GO:0051287 GO:0070062 GO:0071268
10	0.07	0.496	5.50	0.08	0.79	3d64A	GO:0004013 GO:0005737 GO:0006730 GO:0016787
11	0.07	0.456	5.27	0.11	0.71	3x2fA	GO:0004013 GO:0005737 GO:0005829 GO:0006730 GO:0016787 GO:0033353
12	0.06	0.381	5.18	0.07	0.57	4k26A	GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524
13	0.06	0.391	5.31	0.05	0.59	3awdA	GO:0016491 GO:0055114
14	0.06	0.381	5.18	0.07	0.57	4ijuB	GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0006704 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524
15	0.06	0.387	4.86	0.07	0.57	4iboD	GO:0016491 GO:0055114
16	0.06	0.363	5.19	0.08	0.55	4wecA	GO:0000166
17	0.06	0.345	5.37	0.03	0.53	3vpxB	GO:0006520 GO:0016491 GO:0016639 GO:0055114
18	0.06	0.378	5.28	0.07	0.58	3dwfB	GO:0003845 GO:0005783 GO:0005789 GO:0006629 GO:0008202 GO:0016020 GO:0016021 GO:0016491 GO:0030324 GO:0055114 GO:0070524

Consensus prediction of GO terms

Molecular Function	GO:0016802
GO-Score	0.48
Biological Processes	GO:0044281	GO:0044763	GO:0044237
GO-Score	0.48	0.48	0.40
Cellular Component	GO:0009570	GO:0005886	GO:0005618	GO:0005576	GO:0005829
GO-Score	0.14	0.07	0.07	0.07	0.07

(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.