I-TASSER results for Example

Submitted Sequence

>your_protein MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNA SRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHI DILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLA SMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERM VDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD

User specified restraint

Predicted Secondary Structure

Sequence	20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                    MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD
Prediction	CCCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCSSSSSCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHCCCCCSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCHHHCCCCCCSSSSCCCSSSCCCCCCCCCCC
Conf.Score	9987889999999799998629999999999869989997273265555567777777888875220122136368640235741003422110344312449999999999999809987999888678545689355999999999999719999999999998647966999950101405787307889999999999999999857442808988850866661010258859999999854998898799999999999948754688886799789946236780125789

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                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                    |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |
							Sec.Str Seq	CCCCCCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCSSSSSCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHCCCCCSSSSCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCHHHCCCCCCSSSSCCCSSSCCCCCCCCCCC MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD
1	1enoA	0.65	0.64	0.99	2.44	Download		-LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLSHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNAPIQKTLTADEVGNAAAFLVSPLASAITGATIYVDNGLNSMGVAL-DSPVF
2	2o2sA	0.58	0.58	0.99	1.73	Download		--PIDLRGQTAFVAGVADSHGYGWAIAKHLASAGARVALGTWPPVLGLFQKSLQSGRLDEDRKLPDGSLIEFAGVYPLDAAFDKPEDVPQDIKDNKRYAGVDGYTIKEVAVKVKQDLGNIDILVHSLANGPEVTKPLLETSRKGYLAASSNSAYSFVSLLQHFGPIMNEGGSAVTLSYLAAERVVPGYGGGMSSAKAALESDTRTLAWEAGQKYGVRVNAISAGPLKSRAASAIGKSDYAIDYSYNNAPLRRDLHSDDVGGAALFLLSPLARAVSGVTLYVDNGLHAMGQAVRSMPP-
3	1enoA	0.65	0.64	0.99	2.38	Download		-LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLSHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNAPIQKTLTADEVGNAAAFLVSPLASAITGATIYVDNGLNSMGVA-LDSPK-
4	1jh2A	0.04	0.04	0.33	1.80	Download		-----AKVNIKPLEDKILVQANEAETTTASGLVIPDTAKEKPQEGTVVAVGPGRWDEDEKRIPLDVAEGDTVIYSKYGGTEIKYNGEEYLILSARDVLAVVK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
5	1enoA	0.64	0.64	1.00	2.55	Download		-LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLSHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNAPIQKTLTADEVGNAAAFLVSPLASAITGATIYVDNGLNSMGVALDSPVFK
6	2oosA	0.51	0.49	0.94	2.00	Download		-------EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAI-------EYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD-----
7	1enp	0.61	0.58	0.89	4.24	Download		-LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAA---LVGTWV-PALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANKPLLE-TS----RKGYLAAISASSYSFVSLLSHFLPI---GGASISLTYIASE-IIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAA----------KAIGFIDTMIEYSYADEVGNAAAFLVS-LASAITGATIYVDNGLNSMG---------
8	2oosA	0.51	0.49	0.94	2.16	Download		-------EDICFIAGIGDTNGYGWGIAKELSKRNVKIIFGIWPPVYNIFMKNYKNGKFDNDMIIDKDKKMNILDMLPFDASFDTANDIDEETKNNKRYNMLQNYTIEDVANLIHQKYGKINMLVHSLANAKEVQKDLLNTSRKGYLDALSKSSYSLISLCKYFVNIMKPQSSIISLTYHASQKVVPGYGGGMSSAKAALESDTRVLAYHLGRNYNIRINTISAGPLKSRAATAI-------EYSEKYAPLRQKLLSTDIGSVASFLLSRESRAITGQTIYVDNGLNIMFLPDD-----
9	1enoA	0.65	0.64	0.99	2.14	Download		-LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLSHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNAPIQKTLTADEVGNAAAFLVSPLASAITGATIYVDNGLNSMGVA-LDSPVF
10	2o2sA	0.58	0.58	0.99	2.23	Download		--PIDLRGQTAFVAGVADSHGYGWAIAKHLASAGARVALGTWPPVLGLFQKSLQSGRLDEDRKLPDGSLIEFAGVYPLDAAFDKPEDVPQDIKDNKRYAGVDGYTIKEVAVKVKQDLGNIDILVHSLANGPEVTKPLLETSRKGYLAASSNSAYSFVSLLQHFGPIMNEGGSAVTLSYLAAERVVPGYGGGMSSAKAALESDTRTLAWEAGQKYGVRVNAISAGPLKSRAASAIGKIDYAIDYSYNNAPLRRDLHSDDVGGAALFLLSPLARAVSGVTLYVDNGLHAMGQA-VDSRSM
(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 0.9841 0.79 0.64 1.00 1enoA Model1   2 0.9681 1.27 0.57 0.99 2o2sA Model1   3 0.8111 2.48 0.33 0.87 1jvfA Model1   4 0.7975 2.19 0.29 0.85 1qg6A Model1   5 0.7939 1.84 0.35 0.84 3ek2A Model1   6 0.7933 2.41 0.32 0.85 2qioA Model1   7 0.7929 1.99 0.34 0.84 2p91A Model1   8 0.7847 2.00 0.28 0.84 1enyA Model1   9 0.7716 2.71 0.20 0.87 2bgkA Model1   10 0.7686 2.41 0.24 0.85 2ae2A Model1

Structural alignment using TM-align   -LPIDLRGKRAFIAGIADDNGYGWAVAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYPLDAVFDNPEDVPEDVKANKRYAGSSNWTVQEAAECVRQDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLSHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKQNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNAPIQKTLTADEVGNAAAFLVSPLASAITGATIYVDNGLNSMGVALDSPVFK  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    --PIDLRGQTAFVAGVADSHGYGWAIAKHLASAGARVALGTWPPVLGLFQKSLQSGRLDEDRKLPDGSLIEFAGVYPLDAAFDKPEDVPQDIKDNKRYAGVDGYTIKEVAVKVKQDLGNIDILVHSLANGPEVTKPLLETSRKGYLAASSNSAYSFVSLLQHFGPIMNEGGSAVTLSYLAAERVVPGYGGGMSSAKAALESDTRTLAWEAGQKYGVRVNAISAGPLKSRAASAIGKS-GEKSFIDYAIDYSYNNAPLRRDLHSDDVGGAALFLLSPLARAVSGVTLYVDNGLHAMGQAVDSRSMPP  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLAS--RA-----GKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD-    ---GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVR-P----IA--Q------ELNSPYVYELDVSKE-E-------------------HFKSLYNSVKKDLGSLDFIVHSVAFAPKEALEGSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKYMAHYN-VMGLAKAALESAVRYLAVDLGK-HHIRVNALSAGPIRTLASSGIADFRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYHVMGMGAVEEKDNKATLLWDLHKEQ  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSP--EIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEM-F--PKD---------    ---GFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVE-E----FA--A------QLGSDIVLQCDVAEDA--------------------SIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYN-VMGLAKASLEANVRYMANAMGP-EGVRVNAISAGPIRTLAA--SGIKDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAM-NE-----  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSP-EIAK-PLL-DTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASR--AGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    --MGFLDGKRILLTGLLSNRSIAYGIAKACKREGAELAFTYVGDRFKDRIT-E----FA--A------EFGSELVFPCDVADDA--------------------QIDALFASLKTHWDSLDGLVHSIGFAPREAIAGDFLDGLTRENFRIAHDISAYSFPALAKAALPMLSDDASLLTLSYLGAERAIPNYN-TMGLAKAALEASVRYLAVSLGA-KGVRVNAISAGPI---S-G-IKSFGKILDFVESNSPLKRNVTIEQVGNAGAFLLSDLASGVTAEVMHVDSGFNAVVGG---M---  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSP--EIAKPLLD-TSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    --MELLQGKTFVVMGVANQRSIAWGIARSLHNAGAKLIFTYAGERLERNVR-E----LA-DTL-----EGQESLVLPCDVTNDE--------------------ELTACFETIKQEVGTIHGVAHCIAFANRDDLKGEFVDTSRDGFLLAQNISAFSLTAVAREAKKVMTEGGNILTLTYLGGERVVKNYN-VMGVAKASLEASVKYLANDLGQ-HGIRVNAISAGPIRTLSA---KGVGDFNSILREIEERAPLRRTTTQEEVGDTAVFLFSDLARGVTGENIHVDSGYHILG---------  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSP--EIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLAS---RAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    ---GLLEGKRALITGVANERSIAYGIAKSFHREGAQLAFTYATPKLEKRVR-E----IA--K------GFGSDLVVKCDVSLDE--------------------DIKNLKKFLEENWGSLDIIVHSIAYAPKEEFKGGVIDTSREGFKIAMDISVYSLIALTRELLPLMEGRNGAIVTLSYYGAEKVVPHYN-VMGIAKAALESTVRYLAYDIAK-HGHRINAISAGPVKTLA----AITGFHLLMEHTTKVNPFGKPITIEDVGDTAVFLCSDWARAITGEVVHVDNGYHIMGVF-------  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSP-EIAK-PLLDTSRKGYLAALSTSSYSFISLLSHFGPIMN-AGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLAS--RAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    --AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFD-RLRLIQRITD----R--L-------PAKAPLLELDVQN-EE-------------------HLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFD-PSRAMPAYN-WMTVAKSALESVNRFVAREAG-KYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQL-L-------  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHF-G--HIDILVHSLANSP-E-IA-KPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLAS--RAGKAI-------G-FIERMVDYYQDWAPLPSPM-EAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD    --TNRLQDKVAIITGGAG--GIGETTAKLFVRYGAKVVIADI--ADDHGQKVCN---N---I------GSPDVISFVHCDVTKDE--------------------DVRNLVDTTIAKHGKLDIMFGNVGVLSTTPYSILEAGNEDFKRVMDINVYGAFLVAKHAARVMIPAKKGSIVFTASISSFTAGEGVSHVYTATKHAVLGLTTSLCTELGE-YGIRVNCVSPYIVASPLLTDVFGVDSSRVEELAHQAANLKGTLLRAEDVADAVAYLAGDESKYVSGLNLVIDGGYTRTNPAFPTALKHGL  MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLT-FAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIM--NAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGK--AIGFIERMVDYYQDWAPLP-SPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD--    A-GRWNLEGCTALVTGGSR--GIGYGIVEELASLGASVYT-CSR-NQKELN-DCL-T--Q--WR----SKGFKVEASVCDLSSRS--------------------ERQELMNTVANHFHGKLNILVNNAGIV--IYKEAKDYTVEDYSLIMSINFEAAYHLSVLAHPFLKASERGNVVFISSVSGALAVPYEA-VYGATKGAMDQLTRCLAFEWAK-DNIRVNGVGPGVIATSLVEMTIQDPEQKENLNKLIDRCALRRMGEPKELAAMVAFLCFPAASYVTGQIIYVDGGLMANCG-F------  -MLKIDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFG-HIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIM--NAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLAS--RAGKAIG-FIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEMFPKD

(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	0.9655	1.58	0.65	0.99	2.5901	1cwuB	1.3.1.9
2	0.7056	1.88	0.62	0.75	1.8724	2ptgB	1.3.1.9
3	0.7385	1.50	0.53	0.76	1.7222	1nhdB	1.3.1.9
4	0.7468	2.10	0.26	0.81	1.1274	1ae1A	1.1.1.206
5	0.7393	2.47	0.25	0.82	1.0919	2p68A	1.1.1.100

(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	0.9843	0.77	0.64	1.00	1enpA	3.17	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0043229 GO:0044444
2	0.9429	0.91	0.57	0.96	2o50B	2.82	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394
3	0.9280	1.68	0.50	0.96	2o2yD	2.47	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394
4	0.7378	1.50	0.53	0.76	2nq8B	2.04	GO:0004318 GO:0005515 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394
5	0.5802	0.92	0.68	0.59	1enpA	1.92	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0043229 GO:0044444
6	0.7886	1.45	0.39	0.82	2yw9H	1.86	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394
7	0.5457	0.82	0.62	0.55	2o50B	1.71	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394
8	0.8094	2.49	0.33	0.87	2pd4D	1.71	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394 GO:0055114 GO:0005623 GO:0005886
9	0.7367	1.70	0.35	0.77	2p91D	1.64	GO:0004318 GO:0005488 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394 GO:0055114
10	0.7989	1.95	0.29	0.85	2fhsA	1.62	GO:0004318 GO:0005515 GO:0016631 GO:0006631 GO:0006633 GO:0009058 GO:0009987 GO:0032787 GO:0044249 GO:0046394 GO:0046677 GO:0055114 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0005886 GO:0043229 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:0005488 1.790    GO:0009987 1.505    GO:0005623 1.471 GO:0004318 1.362    GO:0009058 1.432    GO:0005737 1.240 GO:0016631 1.362    GO:0044249 1.432    GO:0005622 1.240 GO:0005515 0.256    GO:0032787 1.362    GO:0044444 1.240 GO:0016614 0.212    GO:0006631 1.362    GO:0043229 1.100 GO:0016616 0.212    GO:0006633 1.362    GO:0005739 0.585 GO:0000149 0.072    GO:0046394 1.362    GO:0016020 0.501 GO:0051117 0.072    GO:0055114 0.873    GO:0009536 0.382 GO:0019899 0.072    GO:0046677 0.239    GO:0009507 0.382 GO:0050356 0.071    GO:0050896 0.239    GO:0005886 0.306

(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, in preparation).
(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.