I-TASSER results for job id S34187

Submitted Sequence

>SOP PAGGYYQNYQGYSGYQQGGYQQYNPDAGYQQQYNPQGGYQQYNPQGGYQQQFNPQGG

Predicted Secondary Structure

Sequence	20                  40                    |                   |                   PAGGYYQNYQGYSGYQQGGYQQYNPDAGYQQQYNPQGGYQQYNPQGGYQQQFNPQGG
Prediction	CCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	986433354664331446603416886513132687650124678762334478889

Top 5 Models predicted by I-TASSER

Top 10 templates used by I-TASSER

Rank	PDB Hit	Iden1	Iden2	Cov.	Norm. Z-score	Download Align.		20                  40                    |                   |
							Sec.Str Seq	CCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC PAGGYYQNYQGYSGYQQGGYQQYNPDAGYQQQYNPQGGYQQYNPQGGYQQQFNPQGG
1	1c51A	0.23	0.23	1.00	0.90	Download		GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2	2z5nA	0.27	0.07	0.26	0.69	Download		----------------------------------------KVSRRGGHQNSYKPY--
3	2ra2A	0.22	0.21	0.89	0.86	Download		--PNYVHTNDGRSIVTDGKPQTDNDTGSY---KDANGNKQQINRTDVKEVALENLE-
4	1zvoC	0.04	0.10	0.98	0.62	Download		AQASSVPTAQPQAEGSLAKATTAPATTRNTGRGGEEKKKEKEKEEQEERETKTPE-C
5	1zvoC	0.10	0.10	0.91	1.10	Download		-----AQASSVPTAQPQAEGSLAKATTAPATTRNTGRGGEEKKKEKEKEEQEERETK
6	1fvgA	0.29	0.30	0.72	0.76	Download		PTQG-RQGNDHGSQYRSAIYPTFYYAEDYHQQYLSK------D-PDGYC--------
7	3dw8B	0.02	0.12	0.96	0.71	Download		RNTKRDITLEASRENNKPR--TVLKPRKVCASGKRKKDEISVDSLDFLHTAWHPKEN
8	1qwyA	0.18	0.33	0.98	0.77	Download		-YSYTFVDAQGHTHYFYNCYPKNANANGSGQTYVNTAGDNNDSQSQQHINQYGYQSN
9	2ra2A	0.24	0.21	0.89	0.61	Download		P--NYVHTNDGRSIVTDGKPQTDNDTGSY---KDANGNKQQINRTDVKEVALENLE-
10	1w0rA	0.12	0.21	1.00	0.84	Download		PQHGGPFCAGDATRTHICNTAVPCPVDGEWDSWGEWSPCIRRNMKSISCQEIPGQQS
(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)

Rank TM-score RMSDa IDENa Cov. PDB Hit 1 0.5637 2.43 0.06 0.91 1u0rA Model1   2 0.5495 2.69 0.06 0.88 1b34B Model1   3 0.5417 2.39 0.08 0.86 1yt5A Model1   4 0.5340 2.89 0.10 0.88 1n9rA Model1   5 0.5268 2.64 0.04 0.86 1d3bB Model1   6 0.5258 2.51 0.04 0.82 3bw1A Model1   7 0.5208 2.63 0.06 0.86 1y96A Model1   8 0.5201 2.43 0.02 0.84 1z0sA Model1   9 0.5199 2.35 0.04 0.86 1suwA Model1   10 0.5130 2.66 0.04 0.82 1ljoA Model1

Structural alignment using TM-align   HRSVLLVVHTATETARRVEKVLGDNKIALRVLSAEAVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGV-VVEIDGRPV-SAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPM-VTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWR  --------------------------------------------------------------------------------------------------------------------------------------------------PAGGYYQNY--QGYSGYQQGGYQQYNP---------------------DAGYQQQYNPQG-GYQQYNPQ--GGYQQQFNPQGG-------------------------------------------------------    TGPLSVLTQSVKNNTQVLINCRNNKK-LLG--RVKAFDRHCNM-V-LENVKEMDRYISKMF-LRGDSVIVVLRNP-LIAGK  ------------PAGGYYQNYQ--GYSGYQQGGYQQYNPDAGYQQQYNP-------QGGYQQYNPQGGYQQQFNPQGG---    FREETRWFIQIESELGNHLALNDVTLERDLSGKMVEI-EVEVEHHSSMW-FFADGV-VISTPTGSTAYSLSIGGPIIFPECEVLEI-S-PIAPQFFLTRSV-VIPSNFKVVV-E-SQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRR  ---------------------------P------AGGYYQNY--QGYSGYQQG-GYQQYNP---------------------DAGYQQQY-NPQ--GGYQQYNPQ--GGYQQQFNPQGG------------------------------------------------    LKGLVNHR-VGVKLKFNSTEYR-GTLVSTDNYFNL-Q-LNEAEEFVAGVSHGTLGEIF-IRCNNVLYIREL-PN-  -----PAGGYYQNYQG-YSGYQQGGYQQYNPDAGYQQQYNP-----------Q-GGYQQYNPQGGYQQQFNPQGG    SKMLQHIDYR-MRCILQDGRIF-IG-TFKAFDKHMNL-I-LCDCDEFRKIKPKNSKQAEREEKRVLGLVL-LRGENLVSMTVEG--PPP  -------PAGGYYQNYQ-GYSGYQQGGYQQYNPDAGYQQQYNPQ----------------------GGYQQYNPQGGYQQQFNPQGG--    HHMETPLDLLKLNLDER-VYIKLRGAR-TL-VG-TLQAFDSHCNI-V-LSDAVETIYQLNNEELSESERRCEMVF-IRGDTVTLISTP-SAVEI--  --------------PAGGYYQNYQ--GYSGYQQGGYQQYNPDAGYQQQYNP-------------------QGGYQQYNPQGGYQQQFNPQ----GG    MSEWMKKGPLEWQDYIYKE-VRVT-ASEKN-EYKG--WVLTTDPVSANI-V-LVNFLEDGSMSVT-GIMGHAVQTVETMN-EGDHRVREKLMHLF  ----------------PAGGYYQNYQ---GYSGYQQGGYQQYNP-DAGYQQQYNP-Q-----GGYQQYNPQGGYQQQFNPQGG------------    PR-V-SCSA--MPDVLALNEI-AVLSRKPAKMIDVALRVDGVEVDRIRCDGFIVATQIGSTGYAFSAGGPVVEPYLECFILIPIAPFRFGWKPYVVSMERKIEVIAEKAIV-V-AD--GQKS-VDFDGEI-TIEK-S--  PAGGYYQNYQGYSGYQQG-GYQQYN--------------------------------------------------------------------------------PD-AGYQQQYNPQGGYQQYNPQGGYQQQFNPQGG    MRAAVVYKTDGHVKRIEEALKRLEVEVELFNQPSEELENFDFIVSVGGDGTILRILQKLKRCPPIFGINTGRVGLLTHASPENFEVELKKAVEKFEVERFPRVSCSAMPDVLALNEIAVLSRKPAKMI-DVAL-RVDGVEVDR-IRCDGF-IVATQIGSTGYAFSAGGPVVEPYLECFIL-I-PIAPFRFGWKPYVVSMERKI-EVIAEKAIVVADGQKSVDFDGEITIEKSEFPAVFFKNEKRFRNLFGKVRSIG--  ------------------------------------------------------------------------------------------------------------------------------PAGGYYQNY---QGYSGYQQG-GYQQYNP---------------------DAGYQQQY--NPQ-GGYQQYNP--QGGYQQQFNPQ---------------------------------------------GG    GAMVLPNQMVKSMVGKI-IRVEMKGEENQLVG-KLEGVDDYMNL-Y-LTNAMECKGEEKVRSLGEIV-LRGNNVVLIQP-Q---  --------------PAGGYYQNYQ-GYSGYQQGGYQQYNPDAGYQQQYNP------------QGGYQQYNPQGGYQQQFNPQGG

(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

Rank	TM-score	RMSDa	IDENa	Cov.	EC-Score	PDB Hit	EC No.
1	0.3790	3.31	0.19	0.74	0.6305	1qx4B	1.6.2.2
2	0.3019	3.99	0.23	0.67	0.6237	1hniA	2.7.7.7
3	0.4431	3.60	0.14	0.82	0.5872	1ps9A	1.3.1.34
4	0.3972	3.99	0.14	0.86	0.5805	1pbhA	3.4.22.1
5	0.4647	3.17	0.12	0.86	0.5771	2de0X	2.4.1.68

(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

Rank	TMscore	RMSDa	IDENa	Cov.	PDB Hit	Fh-Score	Associated GO Terms
1	0.3996	3.58	0.19	0.81	1pvjD	0.69	GO:0008234 GO:0006508 GO:0009405 GO:0009987 GO:0034960 GO:0043283 GO:0044237 GO:0005576
2	0.4909	2.82	0.16	0.81	1qc6B	0.67	GO:0003779 GO:0005522 GO:0017124 GO:0001775 GO:0006810 GO:0006928 GO:0007275 GO:0009605 GO:0009611 GO:0009653 GO:0010926 GO:0019222 GO:0022607 GO:0030029 GO:0030030 GO:0030154 GO:0043283 GO:0043933 GO:0044087 GO:0044237 GO:0044238 GO:0048519 GO:0048856 GO:0050794 GO:0050817 GO:0050878 GO:0051641 GO:0060255 GO:0065008 GO:0005622 GO:0005623 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005925 GO:0016323 GO:0030027 GO:0031252 GO:0043229
3	0.4075	3.01	0.19	0.75	1s1hH	0.66	GO:0003735 GO:0006412 GO:0009058 GO:0009987 GO:0010467 GO:0034960 GO:0034961 GO:0043283 GO:0043284 GO:0044249 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0022626 GO:0022627 GO:0030529 GO:0043229 GO:0044445
4	0.4599	3.47	0.15	0.84	2z0lH	0.65	GO:0003677 GO:0006139 GO:0009058 GO:0009889 GO:0009987 GO:0043283 GO:0044249 GO:0044260 GO:0050794 GO:0060255 GO:0065007 GO:0005622 GO:0005623 GO:0005634 GO:0043229 GO:0044424
5	0.4388	3.37	0.17	0.79	1ps9A	0.64	GO:0005506 GO:0008670 GO:0010181 GO:0043169 GO:0050660 GO:0050662 GO:0051539 GO:0055114
6	0.3790	3.31	0.19	0.74	1qx4B	0.63	GO:0004128 GO:0009055 GO:0006066 GO:0006695 GO:0008203 GO:0009058 GO:0009987 GO:0044249 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0005740 GO:0005741 GO:0005783 GO:0005789 GO:0012505 GO:0019867 GO:0031966 GO:0031975 GO:0042175 GO:0043229 GO:0044429 GO:0044432 GO:0044444
7	0.3935	3.45	0.18	0.75	1w18B	0.62	GO:0050053 GO:0007587 GO:0005576
8	0.3827	4.39	0.15	0.88	1m1jE	0.61	GO:0005102 GO:0030674 GO:0001775 GO:0007154 GO:0007165 GO:0007599 GO:0009605 GO:0010926 GO:0022607 GO:0030168 GO:0034621 GO:0034622 GO:0050817 GO:0051258 GO:0065008 GO:0070271 GO:0005576 GO:0005577 GO:0005615
9	0.3599	3.47	0.19	0.72	1umkA	0.61	GO:0004128 GO:0009055 GO:0006066 GO:0006695 GO:0008015 GO:0008203 GO:0009058 GO:0009987 GO:0044249 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0005740 GO:0005741 GO:0005743 GO:0005783 GO:0005789 GO:0005829 GO:0005833 GO:0012505 GO:0019867 GO:0031966 GO:0031975 GO:0042175 GO:0043229 GO:0044429 GO:0044432 GO:0044445
10	0.3651	3.28	0.19	0.70	1ndhA	0.60	GO:0004128 GO:0009055 GO:0050660 GO:0050662 GO:0006066 GO:0006636 GO:0006695 GO:0008203 GO:0009058 GO:0009987 GO:0017144 GO:0030497 GO:0032787 GO:0033559 GO:0044249 GO:0046394 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0005740 GO:0005741 GO:0005783 GO:0005789 GO:0012505 GO:0019867 GO:0031966 GO:0031975 GO:0042175 GO:0043229 GO:0044429 GO:0044432 GO:0044444

Consensus Prediction of Gene Ontology terms
Molecular Function    Biological Process   Cellular Location GO term GO-Score    GO term GO-Score   GO term GO-Score GO:0003824 0.380    GO:0008152 0.515    GO:0044424 0.442 GO:0005488 0.318    GO:0009987 0.512    GO:0005623 0.442 GO:0016491 0.248    GO:0044237 0.451    GO:0044464 0.442 GO:0009055 0.184    GO:0044238 0.451    GO:0005622 0.442 GO:0004128 0.184    GO:0009058 0.315    GO:0043229 0.442 GO:0016651 0.184    GO:0044249 0.315    GO:0043226 0.442 GO:0016653 0.184    GO:0043170 0.267    GO:0005737 0.317 GO:0005515 0.128    GO:0043283 0.267    GO:0043227 0.309 GO:0050660 0.125    GO:0044260 0.265    GO:0043231 0.309 GO:0030554 0.125    GO:0032501 0.251    GO:0016020 0.251

(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: PRO: 1    GLN: 17    GLY: 18    GLY: 19    TYR: 20    GLN: 21    GLN: 22    GLN: 31    GLN: 32    TYR: 33    ASN: 34    PRO: 35    GLN: 36    GLY: 37    GLY: 38    TYR: 39

Identified analogs with similar binding site: Rank PDB Hit TM-score RMSDa IDENa Cov. BS-score Download Complex Binding site residues on the predicted model 1 1umkA 0.3599 3.47 0.19 0.75 0.13 Download 1,17,18,19,20,21,22,31,32,33,34,35,36,37,38,39 (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.