D-I-TASSER P23771-D1

D-I-TASSER results for P23771-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P23771 (443 residues)
MEVTADQPRWVSHHHPAVLNGQHPDTHHPGLSHSYMDAAQYPLPEEVDVLFNIDGQGNHV
PPYYGNSVRATVQRYPPTHHGSQVCRPPLLHGSLPWLDGGKALGSHHTASPWNLSPFSKT
SIHHGSPGPLSVYPPASSSSLSGGHASPHLFTFPPTPPKDVSPDPSLSTPGSAGSARQDE
KECLKYQVPLPDSMKLESSHSRGSMTALGGASSSTHHPITTYPPYVPEYSSGLFPPSSLL
GGSPTGFGCKSRPKARSSTGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPL
IKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEG
IQTRNRKMSSKSKKCKKVHDSLEDFPKNSSFNPAALSRHMSSLSHISPFSHSSHMLTTPT
PMHPPSSLSFGPHHPSSMVTAMG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MEVTADQPRWVSHHHPAVLNGQHPDTHHPGLSHSYMDAAQYPLPEEVDVLFNIDGQGNHVPPYYGNSVRATVQRYPPTHHGSQVCRPPLLHGSLPWLDGGKALGSHHTASPWNLSPFSKTSIHHGSPGPLSVYPPASSSSLSGGHASPHLFTFPPTPPKDVSPDPSLSTPGSAGSARQDEKECLKYQVPLPDSMKLESSHSRGSMTALGGASSSTHHPITTYPPYVPEYSSGLFPPSSLLGGSPTGFGCKSRPKARSSTGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRNRKMSSKSKKCKKVHDSLEDFPKNSSFNPAALSRHMSSLSHISPFSHSSHMLTTPTPMHPPSSLSFGPHHPSSMVTAMG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98888898655788876678889888899876677787678998777777788877888888888887777777788878998868998889888878888888888889887898888988889998888889988878888988987787899998778899888887778888889988877888877778888888898888889888888888777877778878888888777789998877666555665556667787875787521289987245565555556665555667766666666666544667888898612389998344664212554398888666777776666777887777777777777888878888877788888877888888888888898988999988889998976677899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MEVTADQPRWVSHHHPAVLNGQHPDTHHPGLSHSYMDAAQYPLPEEVDVLFNIDGQGNHVPPYYGNSVRATVQRYPPTHHGSQVCRPPLLHGSLPWLDGGKALGSHHTASPWNLSPFSKTSIHHGSPGPLSVYPPASSSSLSGGHASPHLFTFPPTPPKDVSPDPSLSTPGSAGSARQDEKECLKYQVPLPDSMKLESSHSRGSMTALGGASSSTHHPITTYPPYVPEYSSGLFPPSSLLGGSPTGFGCKSRPKARSSTGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRNRKMSSKSKKCKKVHDSLEDFPKNSSFNPAALSRHMSSLSHISPFSHSSHMLTTPTPMHPPSSLSFGPHHPSSMVTAMG
Prediction	67545543211123222223243243432122221332331334542421132343344343322231233334334433533221122222321213444434332321233322233133334242222323222322233121112222121212233234332323213333334343224243212333434322233332223222112211122222221322122112221333333333242233233244324341313413123345544322331222432433344332433433434443434431424512021334654312120101233443412341467415424344656555455455445535554445544344534444434444455443444443544443444333212334358
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380                 400                 420                 440

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MEVTADQPRWVSHHHPAVLNGQHPDTHHPGLSHSYMDAAQYPLPEEVDVLFNIDGQGNHVPPYYGNSVRATVQRYPPTHHGSQVCRPPLLHGSLPWLDGGKALGSHHTASPWNLSPFSKTSIHHGSPGPLSVYPPASSSSLSGGHASPHLFTFPPTPPKDVSPDPSLSTPGSAGSARQDEKECLKYQVPLPDSMKLESSHSRGSMTALGGASSSTHHPITTYPPYVPEYSSGLFPPSSLLGGSPTGFGCKSRPKARSSTGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRNRKMSSKSKKCKKVHDSLEDFPKNSSFNPAALSRHMSSLSHISPFSHSSHMLTTPTPMHPPSSLSFGPHHPSSMVTAMG

6f1tg

0.08

0.07

2.72

1.37

SPARKS-K

ILHSEEFLSFFDHSTRIVERALSEQINKLSLNRQFFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVNMKYKKTTPEYVFHCQSATFAKFHPNLVVGGTYSGWDNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHG-SKAGISEMFEGHQGPITGIHCHA------AVGAVDFSHLFVTSSFDWTVKLWSTKNNKPLYSFEDNAGYVYDVM--WSPTHPA------------------LFACVDGMGRLDLWNLN---------------------------------------NDTEVPTASISV---EGNPALNRVRWTHSGREIAVGDS-EGQIVIYDV------GEQIAVPRNDEWARFGRTL

4hc7A

0.98

0.24

6.70

3.72

CNFpred

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HMGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN------------------------------------------------------------------------------

2pffB

0.08

3.26

1.76

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGADNHFKDTYGFSILDIVINNPVNIVDGKLKTEKIRSEKGLLSATQFTQPALTLMEKAAFEDLKAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGK

3chnA

0.11

3.88

1.04

MUSTER

------QVKLLEQSGAEVKKPGASKASGYSFTSYGLHWVRQAPGQRLEWMGWISAGTGNTKY---SQKFRGRVTFTRDTSATTA---YMGLSSLRPEDTAVDPYGGGKSEFDYWGQGTLVTVSSASPTSPKVFPLSLCSTQPDGNVV-LVQGFFPQEPLSVTSGQGVTARNFPPSQDASGDLYTTSSQLTLPATQCLAGKSVTCHVKHYTNPSQDVTVPCPVPSTPPTPSPSTPPTPSPSCCHPRLSLHRPALEDLLLGSEANLTCTLTGLRTWTPSSGKSAVQG--PPERDLCGCYSVSSVLPGCAEPWNHGKTTCESKTPLTATLSKSGNTFRPEVHLLPPPSEELALNELVTLT-RGFSPKDVLVR---LQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAAEDWKALPLAFTQKTIDRLAGKPTHNVSVVMAEV

4hc7A

0.98

0.24

6.70

5.93

HHsearch

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HMGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRN------------------------------------------------------------------------------

6w1sK

0.08

3.09

1.28

SPARKS-K

VGSQVEGDPIVALHNGVKLALHVEKSGASSFGEKFVKFSPSLTLKPMEGWIAVTVSGL-VTVSLLKPVLTSTESLCRLRGRVALADIAFTGGGNIVVAAADGSSASPVKFYVVSEKCIDTEILPSDPNRKDRFPAITHLKFLARDMSEQVLLCATSSLVECWSLRKEGLPVNNIFQQQPMILKWRILSATNDLDRVSAVALPTNTDLKVASDTQFYPGLGLALAFQDGSVHMVHR-----LSLQTMAVFYSK----------AMQLSWTSLALVGIDNHGKL--SMLRISPSLGH---PLEPKLALQHLLFLLEYCMTGYDWWDILLHVQPGMVQSLVRILAMKASLCKLSRVLMAITSTLKSLLRPHFLNTPDKSPGDRLAEICAKITDVKTEEFVLDMNTLQALQQLLQVLYLLVSLPNQGSPLRPGHSFLRDGTSLGMLR

3vd6C

0.88

0.19

5.33

3.32

CNFpred

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPL--------------TQCTNCQTTTTTLWRRNASGDPVCNACGLYFKLHQVNRPLTMRKDGIQTRNRKAS--------------------------------------------------------------------------

1gjqA

0.06

2.51

1.58

MapAlign

MSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVYAVHISRMSASGRYLLVIGRDARIDMIDL--------WAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKV--------LLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAAKVAVIDSKDRRLSALVD-------------VGKTPHPGRGANFVHPKYGPVWSTLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSV--

2atyA

0.10

0.08

3.09

1.04

MUSTER

---------------------DISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGT--DKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPTCVSVFP-----LEGSIEGRGGSELADPEVPRDCGCKPCICTVPEVSSVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTAQTQPREEQFNSTFRSVSE-------PIMHQDWLNG-KEFKCRVNSAAFPAPIEKTISKTKGRPKAP-----------QLYTIPPPKEQMAKDKVCMITDFF--------PEDIT---VEQWNGQPAENYKNTQPIMN-----TNESYFVYSKLNVQKSNWEAGNTFTSVLHEGLHNHHTEKSLSHSPGK-----------

3gatA

0.77

0.12

3.26

2.89

HHsearch

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KRAGTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNRPLTMRKDGIQTRNRKVSSKGKKRR-------------------------------------------------------------------

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 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 and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.3764

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

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FileManager.getAtomSetCollectionFromFile(model1_6x6aA.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P23771/P23771-D1/model1_6x6aA.pdb.gz

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The Resolver thinks Pdb

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/jmol//j2s/J/shape/Mesh.js

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Time for openFile(model1_6x6aA.pdb.gz): 3111 ms

reading 13431 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

13431 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

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SpinHigh qualityWhite background

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6x6aA	0.46	6.79	0.038	0.729	model1_6x6aA.pdb.gz
2	6eooA	0.44	6.90	0.048	0.711	model1_6eooA.pdb.gz
3	6rc9A	0.44	6.84	0.043	0.698	model1_6rc9A.pdb.gz
4	3h7nA	0.43	6.38	0.036	0.655	model1_3h7nA.pdb.gz
5	6rutB	0.43	6.95	0.050	0.698	model1_6rutB.pdb.gz
6	6zcvA	0.43	6.75	0.023	0.675	model1_6zcvA.pdb.gz
7	3g0bB	0.43	6.69	0.032	0.666	model1_3g0bB.pdb.gz
8	6damA	0.43	6.78	0.054	0.682	model1_6damA.pdb.gz
9	1z68A	0.43	6.76	0.038	0.668	model1_1z68A.pdb.gz
10	2j5wA	0.42	7.23	0.038	0.711	model1_2j5wA.pdb.gz

(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 Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003677	0.98	DNA binding
GO:0003700	0.97	transcription factor activity, sequence-specific DNA binding
GO:0044212	0.95	transcription regulatory region DNA binding
GO:0043565	0.95	sequence-specific DNA binding
GO:0000981	0.95	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000976	0.94	transcription regulatory region sequence-specific DNA binding
GO:0003682	0.90	chromatin binding
GO:0001228	0.90	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001085	0.90	RNA polymerase II transcription factor binding
GO:0000977	0.90	RNA polymerase II regulatory region sequence-specific DNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044699	0.99	single-organism process
GO:0009987	0.99	cellular process
GO:0048869	0.97	cellular developmental process
GO:0048856	0.88	anatomical structure development
GO:0044767	0.87	single-organism developmental process
GO:0048513	0.85	animal organ development
GO:0009653	0.83	anatomical structure morphogenesis
GO:0035295	0.78	tube development
GO:0048646	0.77	anatomical structure formation involved in morphogenesis
GO:0048565	0.76	digestive tract development
GO:0009888	0.74	tissue development
GO:0045165	0.73	cell fate commitment
GO:0009887	0.73	organ morphogenesis
GO:0007507	0.72	heart development
GO:0048468	0.71	cell development
GO:0065007	0.59	biological regulation
GO:0050789	0.58	regulation of biological process
GO:0050794	0.55	regulation of cellular process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0005634	1.00	nucleus
GO:0032991	0.95	macromolecular complex
GO:0005667	0.92	transcription factor complex

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

script 1 started

FileManager.getAtomSetCollectionFromFile(model1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P23771/P23771-D1/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 805 ms

reading 6615 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

6615 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

6615 atoms selected

14 atoms selected

1 atoms selected

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spinY = 10

Script completed

Jmol script terminated

JSmol exec jmolApplet3 start applet null

Jmol JavaScript applet jmolApplet3__771976477962634__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet3__771976477962634__)

vwrOptions:

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setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/P23771/P23771-D1/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

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Jmol getValue emulate null

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Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

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Jmol applet jmolApplet3__771976477962634__ ready

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Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1l2aE	0.381	7.08	0.041	0.623	3.2.1.4	386
2	0.060	1z4zA	0.381	7.04	0.063	0.619	3.2.1.18	NA
3	0.060	1yiqA	0.422	6.84	0.040	0.682	1.1.99.-	NA
4	0.060	1lrwA	0.428	6.84	0.045	0.684	1.1.99.8	384
5	0.060	1gjqA	0.385	6.90	0.041	0.614	1.7.99.1 1.7.2.1	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (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.

Predicted Ligand Binding Sites

JSmol exec jmolApplet0 start applet null

/jmol//j2s/core/core.z.js

-- required by ClazzNode ajax=true async=false

/jmol//j2s/java/util/Hashtable.js

-- required by ClazzNode ajax=true async=false

JSmol exec jmolApplet1 start applet null

Jmol JavaScript applet jmolApplet1__771976477962634__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1__771976477962634__)

vwrOptions:

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setting document base to "https://zhanglab.comp.nus.edu.sg/HPmod/data/P23771/P23771-D1/"

Jmol Version: 14.2.13_2015.03.07 2015-03-07 10:45

java.vendor: Java2Script (HTML5)

java.version: 2015-03-01 07:13:29 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

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Jmol getValue emulate null

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Jmol getValue boxbgcolor null

Jmol getValue bgcolor #000000

backgroundColor = "#000000"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

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Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1__771976477962634__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/P23771/P23771-D1/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 554 ms

reading 6639 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

6639 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

6639 atoms selected

24 atoms selected

solventProbeRadius = 1.0

ambientPercent = 40

14 atoms selected

1 atoms selected

12 atoms selected

1 atoms selected

16 atoms selected

1 atoms selected

11 atoms selected

1 atoms selected

spinX = 10

spinY = 10

Script completed

Jmol script terminated

13431 atoms selected

6816 atoms selected

6615 atoms selected

ambientPercent = 40

Script completed

Jmol script terminated

/jmol//j2s/J/g3d/HermiteRenderer.js

-- required by ClazzNode ajax=true async=false

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Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1tkrB	0.428	6.68	0.041	0.668	0.42	UUU	complex1.pdb.gz	331,335,337,338
	2	0.01	1x70A	0.425	6.69	0.038	0.664	0.58	UUU	complex2.pdb.gz	327,337,361,362,363

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.