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I-TASSER results for job id S34328

  Submitted Sequence

>LTP2
AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSS
CGIALPTCH

  Predicted Secondary Structure

Sequence                  20                  40                  60
                   |                   |                   |          
AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
PredictionCCCCHHHHCCCHHHHHCCCCCCHHHHHHHHHCCHHHHHHHCCCCHHHHCCCHHHHHHHHHCCCCCCCCC
Conf.Score998777613038889669999899999899614587778448409875288989999998599998889

  Top 5 Models predicted by I-TASSER

Download Model 1
C-score= 1.38
 
Estimated accuracy of Model1: 0.91±0.06 (TM-score)    0.8±0.8Å (RMSD)    (Read more about C-score of generated models)

  Top 10 templates used by I-TASSER

RankPDB
Hit		Iden1Iden2Cov.Norm.
Z-score		Download
Align.		                   20                  40                  60
                   |                   |                   |         
Sec.Str
Seq		CCCCHHHHCCCHHHHHCCCCCCHHHHHHHHHCCHHHHHHHCCCCHHHHCCCHHHHHHHHHCCCCCCCCC
AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
11l6hA 1.00 1.00 1.00 4.46Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
21l6hA 1.00 1.00 0.99 6.57Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTC-
31l6hA 1.00 1.00 1.00 3.60Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
41l6hA 1.00 1.00 1.00 1.64Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
51n89A 0.60 0.58 0.97 7.43Download -ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-
61l6hA 1.00 1.00 1.00 6.64Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
71l6hA 1.00 1.00 1.00 3.59Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
81l6hA 1.00 1.00 1.00 5.70Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
91l6hA 1.00 1.00 1.00 3.26Download AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
101n89A 0.60 0.58 0.97 4.38Download -ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-
(a)All the residues are colored in black; however, those residues in template which are identical to the residue in the query sequence are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade. (more about the colors used)
(b)Rank of templates represents the top ten threading templates used by I-TASSER.
(c)Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence.
(d)Ident2 is the percentage sequence identity of the whole template chains with query sequence.
(e)Cov. represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein.
(f)Norm. Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa.
(g)Download Align. provides the 3D structure of the aligned regions of the threading templates.
(h)The top 10 alignments reported above (in order of their ranking) are from the following threading programs:
       1: MUSTER   2: HHSEARCH   3: SP3   4: PROSPECT2   5: PPA-I   6: HHSEARCH I   7: FUGUE   8: HHSEARCH II   9: SPARKS   10: MUSTER   

  10 proteins in PDB which are structurally closest to the first I-TASSER model (identified by TM-align)

RankTM-scoreRMSDaIDENaCov.PDB
Hit
10.7272 2.41 0.27 0.972algA
Model1
 
20.7050 2.12 0.28 0.931fk5A
Model1
 
30.6881 2.51 0.24 0.961siyA
Model1
 
40.6701 2.13 0.52 0.941n89A
Model1
 
50.6581 2.59 0.19 0.931t12A
Model1
 
60.6560 2.40 0.24 0.942rknA
Model1
 
70.6424 2.53 0.23 0.941be2A
Model1
 
80.6190 3.30 0.10 0.991hssA
Model1
 
90.6008 2.97 0.15 0.941beaA
Model1
 
100.5895 2.69 0.07 0.861jdhA
Model1
 
Structural alignment using TM-align
 
MITCGQVSSSLAPCIPYVRGGGAVPPACCNGIRNVNNLARTTPDRQAA-CNCLKQLSASVPGV-NPNNAAALPGKCGVSIPYKISASTNCATVK 
-AGCN--AGQLTVCTGAIAGGARPTAACCSSLRAQQ--------G--CFCQFAKDP-RYGR-YVNSPNARKAVSSCGIALPT-------C-H-- 
 
AISCGQVASAIAPCISYARGQGSGPSAGCCSGVRSLNNAARTTADRRAA-CNCLK-N--AAAGVSGLN-AGNAASIPSKCGVSIPYTISTSTDCSRVN 
-AGCN--AGQLTVCTGAIAGGA-RPTAACCSSLRAQQ--------G--CFCQ-FAKDPRYGR-Y--V-NSPNARKAVSSCGIALPT-------C--H- 
 
MTCGQVQGNLAQCIGFLQKGGVVPPSCCTGVKNILNSSRTTADRRAV-CSCL-KA-AAGAVRGINPNNAEALPGKCGVNIPYKISTSTNCNSIN 
AGCN-AGQ-LTVCTGAIAGGARPTAACCSSLRAQQ--------G--CFCQ-FAKDPRYGRY--VNSPNARKAVSSCGIALPT-----CH----- 
 
-ACQASQLAVCASAILSGAKPSGE-CCGNLRAQQGCFCQYAKDPT-YGQYIRSPHARDTLTSCGLAVP-HC 
AGCNAGQLTVCTGAIA-GGARPTAACCSSLRAQQGCFCQFA-KDPRYGRYVNSPNARKAVSSCGIALPTCH 
 
AITCGQVTSNLAPCLAYLRNTGPLG-RCCGGVKALVNSARTTEDRQIA-CTCLK-S--AAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSKVQ 
-AGCN--AGQLTVCTGAIAGGARPTAACCSSLRAQQ--G--------CFCQF-AKDPRYGR-Y--VNSPNARKAVSSCGIAL-PT-----CH---- 
 
AI-DLCGMSQDELNECKPAVSKENPTSPSQPCCTALQHADFACLCGYKNSPWL-GSFGVDP-ELASALPKQCGLANAPTC- 
--AGC--NAG-QLTVCTGAIA--GGARPTAACCSSLRAQQG-CFCQFAKDPRYGR---YVNSPNARKAVSSCGI-ALPTCH 
 
LNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTV-CNCLK-G--IARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY 
AGC-N-AGQLTVCTGAIAGGARPTAACCSSLRAQQ--------G--CFCQ-FAKDPRYGR-Y-VNSP-NARKAVSSCGI-ALP------TCH--- 
 
MCYPGQAFQVPALPACRPLLRLQCNGSQVPEAVLRDCCQQLAHISEWCRCGALYSMLDSMYKEHGAFPRCRREV-VKLTAASITAVCRLPIVVDASGDGAYVCKDVAAYPDA 
-----AGCNAGQLTVCTGAIAGG----AR---PTAACCSSLRAQQ--GCFCQFAKDPRYGR----Y--------VNSPNARKAVSSCGIALPTC----------H------- 
 
SCVPGWAIPHN-PLPSCRWYVTSRTCGIGPRLPWPELKR-RCCRELADIPAYCRCTALS-ILMDGAIPPGPDAQLEGRLEDLPGCPREVQRGF-AATLVTEAECNLATISGVAECPWILG 
--AG---C-NAGQLTVCTGAIAGG---------AR--PTAACCSSLR-A---QQ-GCFCQF-AKDP----------RYG-------RY-VNSPNARKAVS--SCGI------ALP-TC-H 
 
AVVNLIRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGL-LGTLVQLL----GSDDINVVTCAAGILSNLTCNN-YKNKMM---VCQV--G--GIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQFVEGVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRMS 
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCNA-GQL-TVCTGAIAGGAR--P--TAACCSSLRAQQ-GCFCQF-AKDPRYGRYVNSPNARK-AV-SS------------CGI--ALP-T-CH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
 
(a)Residue pairs that are structurally aligned by TM-align program are highlighted in color. Coloring scheme is based on the property of amino acids, where polar are brightly coloured while non-polar residues are colored in dark shade.(more about the colors used)
(b)Ranking of proteins is based on TM-score of the structural alignment between Model1 and the PDB structures in our template library.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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 model.

  Function Prediction

  Predicted EC Numbers

RankTM-scoreRMSDaIDENaCov.EC-ScorePDB
Hit		EC No.
10.5235 2.71 0.16 0.811.07013eneA 2.7.1.153
 
20.5195 2.71 0.16 0.811.06642a4zA 2.7.1.153
 
30.4954 3.19 0.17 0.831.06641j0mA 4.2.2.12
 
40.5085 2.81 0.16 0.801.04781e7uA 2.7.1.153
 
50.4927 3.40 0.17 0.831.03553bjtA 2.7.1.40
 
(a)Ranking is based on EC-score, which is a confidence score for the Enzyme Classification (EC) Number prediction.
(b)RMSDa is the RMSD between models and the PDB structure in the structurally aligned regions by TM-align.
(c)IDENa is percentage sequence identity in the structurally aligned region.
(d)Cov. represents the coverage of the alignment and is equal to the number of structurally aligned residues divided by length of model.
(e)EC-Score is defined based on the C-score of the structure prediction and similarity of the model with known enzyme structures, as identified using both global and local structural alignment programs. The global similarity score uses TM-score, IDENa,RMSDa and Cov. of the structural alignment by TM-align, while the local match compares the structural and chemical similarity of local spatial motifs in the model with known catalytic site of enzymes. A prediction with a EC-score >1.1 signifies a prediction with high confidence (upto 3 digit numbers of EC) and vice versa (For details, see Ambrish, Kucukural and Zhang,Large scale benchmarking of protein function prediction using predicted protein structures, 2009, submitted).

  Predicted GO terms

RankTMscoreRMSDaIDENaCov.PDB
Hit		Fh-ScoreAssociated GO Terms
10.8961 0.90 0.60 0.971tukA 3.02 GO:0008289 GO:0006869
20.5443 2.72 0.67 0.861l6hA 2.42 GO:0008289 GO:0006869
30.7159 2.24 0.35 0.961uvcB 1.92 GO:0008289 GO:0006869
40.7391 1.88 0.28 0.942b5sB 1.76 GO:0008289 GO:0006869
50.7123 2.23 0.27 0.961midA 1.70 GO:0008289 GO:0006869
60.7012 2.15 0.28 0.931mzmA 1.68 GO:0008289 GO:0006869
70.6318 2.41 0.27 0.941gh1A 1.60 GO:0008289 GO:0006869
80.6881 2.51 0.24 0.961siyA 1.57 GO:0005215 GO:0008289 GO:0006805 GO:0006869 GO:0009617 GO:0009620 GO:0009987 GO:0044237 GO:0050830 GO:0050832 GO:0051704
90.6581 2.59 0.19 0.931t12A 1.36 GO:0008289 GO:0006869 GO:0006952 GO:0009607
100.5544 3.31 0.21 0.941hypA 1.31 GO:0006869

Consensus Prediction of Gene Ontology terms 
Molecular Function  Biological Process Cellular Location
GO termGO-Score  GO termGO-Score GO termGO-Score
GO:00082891.072  GO:00068690.918  GO:00057370.940
GO:00038240.222  GO:00508960.421  GO:00056230.940
GO:00431690.220  GO:00081520.412  GO:00056220.940
GO:00055440.220  GO:00650070.387  GO:00058290.512
GO:00431670.220  GO:00508780.330  GO:00329910.362
GO:00055430.220  GO:00069500.311  GO:00432340.362
GO:00468720.220  GO:00507890.276  GO:00432270.313
GO:00055090.220  GO:00325010.275  GO:00432290.313
GO:00167400.168  GO:00442370.245  GO:00432310.313
GO:00052150.136  GO:00099870.245  GO:00432260.313

(a)Ranking in the first table is based on a function prediction score (Fh-score), which is calculated based on the C-score of the structure prediction and the TM-score, IDENa, RMSDa and Cov. of the structural alignment by TM-align between the predicted model and the PDB structures (For details, see Ambrish, Kucukural and Zhang,Large scale benchmarking of protein function prediction using predicted protein structures, 2009, submitted).
(b)RMSDa is the RMSD between models and the PDB structure in the structurally aligned regions by TM-align.
(c)IDENa is the percentage sequence identity in the structurally aligned region.
(d)Cov. represents the coverage of the alignment and is equal to the number of structurally aligned residues divided by length of model.
(e)A consensus prediction of GO terms is derived from the structural analogs that have an Fh-score of >=1.0. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on the Fh-score of the template from which the GO term is derived. A prediction with a GO-score >0.5 signifies a prediction with high confidence and vice versa.


  Predicted Binding Site


Binding site residues in the model:
ALA:5  GLY:6  LEU:8  THR:9  THR:12  ILE:15  GLN:32  
PHE:36  PHE:39  TYR:45  VAL:49  ASN:50  SER:51  ALA:54  
ARG:55  VAL:58  LEU:65  
Identified analogs with similar binding site:

RankPDB
Hit		TM-scoreRMSDaIDENaCov.BS-scoreDownload
Complex		Binding site residues on the predicted model
11n89A0.6701 2.13 0.52 0.96 0.64Download5,6,8,9,12,15,32,36,39,45,49,50,51,54,55,58,65
21fk3A0.7053 2.13 0.28 0.94 0.60Download8,11,15,29,32,33,34,35,36,37,39,48,49,54,58,66
31be2_0.6424 2.53 0.23 0.96 0.58Download7,8,9,10,11,12,14,15,25,28,29,30,31,32,33,34,35,36,37,38,39,49,54,57,58,61,63,66,67,68
42rknA0.6560 2.40 0.24 0.96 0.58Download4,5,6,8,36,39,40,45,49,50,54,55
51hdoA0.4846 3.72 0.15 0.85 0.50Download5,8,12,15,16,39,41,42,43,44,45,46,48
62gcgA0.4000 3.48 0.22 0.75 0.13Download1,2,3,4,5,6,8,35,38,39,41,42,45

(a)Ranking of the analogs in the table is based on their BS-score. BS-score is calculated by first finding the structural analogs of the predicted model based on their TM-score, IDENa and Cov. of the structural alignment. The ligand(s) in the analog structure are then transferred onto the model and the fitness of the ligand-model complex (BS-score) is calculated by comparing the local structure and sequence similarity in the binding site region. (For detail, see Kucukural, Szilagyi, Ambrish, and Zhang, Template based ligand binding site prediction on modeled protein structure, 2009, in preparation).
(b) A BS-score of >0.5 signifies a binding site prediction with high confidence and vice-versa.
(c)RMSDa the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa 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 model.
(f)The image shows the ligand-protein complex with the best BS-score. The ligand is depicted in magenta colored ball & stick, the predicted binding site residues interacting with the ligand are shown as transparent green spheres, while the N & C terminus in the model are marked by blue and red spheres respectively.



 Please cite following articles when you use the I-TASSER server:
1.Yang Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9:40 (2008).
2.Yang Zhang. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, 8: 108-117 (2007).
3.Sitao Wu, Jeffrey Skolnick, Yang Zhang. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology, 5:17 (2007).