D-I-TASSER P38435-D2

D-I-TASSER results for P38435-D2

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

Input Sequence in FASTA format

>P38435 (348 residues)
RPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMY
LVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDA
NHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHW
LFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSI
GMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKP
GLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| RPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVH
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCSCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSCCCCC
Confidence	999827899999999999999999996145313453376435664312330666412999999999999999981157999999999999999983512356658999999999999548981602354255545775764999999999999999999997262015871798998533346522344221699999999999999999999987768999999999999999998723589999999998616879999999971455531244445676664211246655544566612369999999999999999888741478877555532331012249
	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 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| RPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVH
Prediction	853322000000022021001000200110203310142321020100100312311201111111021110023133011001121221120001122311001100012112000000221000002135535442012000000120103002200211032202112001000313223202120123302121211210230332132123333332001101321220131231331011020000000226004300420353143214244433443533454454544443423320000001111220121031000042311015300200000037
	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 DeepPotential. 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

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

SS
Seq

CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCSCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCSCCCCC
RPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVH

7ccsB

0.09

0.08

3.15

1.15

SPARKS-K

GPLPAFLRGWNELLIIRPASTAVISLAFGNYILEPFFPT------------CEPPELAIKLLAAVGILLLTVLNSARVQDFFTAAKLLALLIIIVPGVVQLGQTQNPLAFYSGLYAYVGWDYLNFVTEEVNPEKNIPLAIVISMPIVTVAYVLTNVAYFTT-LSPEELLNAVAVTFGERLSWAVPIFVALSCFGSLNGSLFAMSRLFYVAARELPKRHTPLPALIVSGPLTAIMLFLGDL--FSLINFMSFGTWLFYGLVVAGLIYLRYK--------------------KPDLHRPIKVPLFIPILFLLTCLFLVAVSLYSDPVNCGIGFVIILTGVPVYFLFVYWD

3rkoB

0.09

0.07

2.85

1.51

CNFpred

LVLDGLSLTMLSVVTGVGFLIHMYASWY-EGYSRFFAY-TNLFIASMVVLVLADNLLLMYLGWEGVGLCSYLLIG-VVTRVGDVFLAFALFILYNELGTLN-LMWATLMLLGGAVGKSAQLPTWLADAMA--------GPTPVSALIHAATMVTAGVYLIARTHGLFLMTEVLHLVGIVGAVTLLLAGFAAQTDIKRVLAYSTMSQIGYMFLALGVQAWDAAIFHLMTHAFFKALLFLASGSVYLCFLVGGAALSATAGFFSKDEILAGAMAN---------------------------GHINLMVAGLVGAFMTSLYTFRMIFIVFHG------------------

3nz4A

0.09

3.48

0.54

CEthreader

VNGTSFATALASTVMYDANVLLLLVETLCGFCEVIFGREEFAHPLIHKVKPHPGQIESAELLEWLLRSSPFQDLSREYYSIDKLKKPKQDRYALRSSPQWLAPLVQTIRDATTTVETEVNSANDNDHANDRALHGANFQGSAVGFYMDYVRIAVAGLGKLLFAQFTELMIEYYSNGLPGNLSLGPDLSVDYGLKGLDIAMAAYSSELQYLANPVTTHVHSALALISARKTDEALDILKLIASHLTAMCQAVDLRQLEEALVKVVENVVSTLADECGLPNDTKARLLYVAKAVPVYTYLESPCDPTLPLLLGLKQSCFGSILALHKETDTLVDRLAEFEKRLSDRLENE

6xkwn

0.06

2.51

0.80

EigenThreader

KDEYFDGVIRAGVIATTFWGIVGFLVAVIIAFQLAFPALNLEFGNG------MLNFGRLRPLHTSAVIFAYVVQRTSAFVFWGWQLIIVTAATSYLLGGSQGKEHLDILVAIVWVAYLIAFLGTIFKANWFYLSFIVTIAMLHIVNNVQDAMTQWWYGHNAVGFFLT--AGFLGMMYYFVPERPV-----YSYKLSIVHFWALIFLYIWAGPHHLHYTASTLGMVMSVILMINGLMTLSGAWFYGMSTFEGPMMSIKAVNSLSHIGHVHSGALGWNGMITFGMLYFLTPRLWGRSGLYSLKLVSWHFWLATIGIVLYASSMWVSGIMEGLMWREVDAQGFLVNGFADT

6sp2A

0.09

0.08

2.97

0.79

FFAS-3D

-PSCTNASSS-RFMYAFILLVGTV-------LGAIALSPGLQDTLKKMPFCINSSLQVDCEYALGYMAV-------YRVCFGMACFFALMSLIMLPRSHIQNNKFLICFGAAIGAIFIPDGSFGPAMMWV----------GLIGGLAFILVQLVIIVDFAHSLAENWIE--------SAENSRGYYYALA----GVTLLCYILSLTGITLLYIYFTTGINKFFISINLIFCLAISVISHSGLLQSSLVTLYTVYL---TWSAVANNPEKECNPGMFGHTTRVTFDTTLYNCISSAVETEGVTYSWSMFHLVFVCASLYVMMTLTNWYKPHSEIWVKIVSSYGWSLAA-

6f2gA

0.10

0.09

3.48

1.10

SPARKS-K

AAGAPGLGLLAWFVAGIITIAGGLTVAEIGTIYP---QTGGMMIYLE----KVYGRWLGFLVGWAQMVFATQFVNLFTIVPTAILTSIFLMGVNFPLVVIIVAGLTSFGSALIATLFAYDGWINVGTLAGEMKNPGKMLPKVIIGGLSIVMAVYLLTNIAYLFVLDSSQLAPAALVASHLFEGGSKLVTIGILISVFGGINGYIISGLRVPYALATQNLPINGGLVMLGIAIVMILTGQ-----FNQLTDLIVFVIWFFITLTFIAVIILRKTQ--------PDIERPYRVPF-------YPVIPLIAIIGGLYIIFNTLIVQPKNAFIGILLTLIGIPIYFYCKKKY

3rkoC

0.11

0.08

2.99

1.47

CNFpred

------GLSLLMVVLTGLLGVLAVLCSWKEIE------------KYQGFFH----LNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHKASQASGLVMLIAILALVFVHY-VWTFNYEELLNTPM------GVEYLLMLGFFIAFAVKMPVVPL-HGWLPDA--------HSQAPTAGSVDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSVSHMG---FVLIAIYTGS-------------------------------QLAYQGAVIQMIAHGLSAAGLFILCGQL--------------------

2yevA

0.08

0.05

2.16

0.83

DEthreader

---E-YNQILTLHGATMLFFFIIQAGLTGFGNFVVPLMLGARD--------VAL-PRVNAFSYWAFLGAIVLALMSDFYLAAILLLGFSSLLGNANFVVVFAASLNLSLAGLTAATLLVLLER---K---------NPDPVLFQQFFWFYSHPVYILGALIAVPTGVKLFNIIGTLWLQMKTPLYWV-LG----FI-FNFLLGGITGVMLSMTPLDYQFHSFVVAHFHNVLMAGSGFGAFAG-----F------G--MPRRYYTYN---------------------------YHSSWQNLWTAAFFTIV--------------------------------------

5tqqA1

0.07

0.06

2.56

0.82

MapAlign

LGVLMALISTVYPVALVSFSSGFSQSI----TPFSGGSGIPELKTILSGVVLEDYLDIKNFGAKAVGLTCTLASKVGPFVHLSVMIAAYLGRVRAKATGESE--NKSKRNEMLVAGAAVGVATVFSGVLFCGFFAATCGMLGAICGVASCAYLFCQRKFLGPPGAGRFMASRLYLDSLLDHNSWALLTNLW---FEWFGTLALVMKFWMLILATTYFMPIFIFGAAIGRLLGEALSVIMPGGYALAGAAAFSGAVTSTALLAFELT---------------------------------GQIVHALPVLMAVLAANAIAQSCQPSFYDGTIIVLPWIRGR--------

6eznF

0.10

0.09

3.44

0.75

MUSTER

LPIDIRNVCVFAPLFSGVTAWATYEFTKEDASAGLLA---IVPGYISRSVAGSYDNEAIAITLLMVTFMFWIKAQKTGSIMHATCAALFYFYMVSA----WGGYVFITNLIPLHVFLL---------ILMGRYSSKLYSAYTTWYAIGTVASMQIPFVGFLPISNDHMAALGVFGLIQIVAFGDFVKGQISTPAFFFDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVLTLTPVICVSAAVALSKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVVLPSQTKLALIDDFREAYYWLRMNVAWDYGYQILVDNNTWNNTHIAIVGKAMAS

(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

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6668

(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 DeepPotential, 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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2yevA	0.46	5.79	0.052	0.695	model1_2yevA.pdb.gz
2	3dbyT	0.45	4.45	0.069	0.592	model1_3dbyT.pdb.gz
3	6o84A	0.44	5.16	0.085	0.612	model1_6o84A.pdb.gz
4	1xmeA	0.44	5.82	0.073	0.675	model1_1xmeA.pdb.gz
5	1m56A	0.44	5.63	0.068	0.655	model1_1m56A.pdb.gz
6	3mk7A	0.42	5.68	0.039	0.624	model1_3mk7A.pdb.gz
7	3capA	0.35	6.37	0.048	0.560	model1_3capA.pdb.gz
8	3o0rB	0.35	6.32	0.068	0.557	model1_3o0rB.pdb.gz
9	1ocrN2	0.33	5.44	0.081	0.474	model1_1ocrN2.pdb.gz
10	1oczC	0.29	6.02	0.052	0.448	model1_1oczC.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:0008488	1.00	gamma-glutamyl carboxylase activity

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:0017187	1.00	peptidyl-glutamic acid carboxylation
GO:0044699	0.77	single-organism process
GO:0044707	0.68	single-multicellular organism process
GO:0065007	0.57	biological regulation

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:0044424	1.00	intracellular part
GO:0016020	0.67	membrane
GO:0044444	0.65	cytoplasmic part
GO:0044446	0.62	intracellular organelle part
GO:0044425	0.61	membrane part
GO:0005789	0.58	endoplasmic reticulum membrane
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0031224	0.55	intrinsic component of membrane
GO:0016021	0.54	integral component of membrane

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

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	3f0nA	0.370	5.91	0.029	0.555	4.1.1.33	203,211
2	0.060	1gw6A	0.392	6.44	0.073	0.644	3.3.2.6	NA
3	0.060	1qleA	0.393	5.35	0.081	0.578	1.9.3.1	NA
4	0.060	1w07B	0.377	5.96	0.050	0.566	1.3.3.6	NA
5	0.060	3k92A	0.368	6.69	0.062	0.615	1.4.1.2	203

	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

Template proteins with similar binding site:

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	3s8gA	0.438	5.82	0.073	0.675	1.03	OLC	complex1.pdb.gz	152,156,211,212
2	0.01	3dtuC	0.390	6.31	0.051	0.624	1.20	DXC	complex2.pdb.gz	151,154,155,158,207,211
3	0.01	3dtuA	0.369	6.05	0.043	0.557	0.85	TRD	complex3.pdb.gz	159,161,200,203,207

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.