D-I-TASSER P57073-D2

D-I-TASSER results for P57073-D2

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

Input Sequence in FASTA format

>P57073 (276 residues)
YQPRRRKSAKAGHSDSDSGAELGPHPGGGAVYKAEAGLGDGHHHGDHTGQTHGPPTPPTT
PKTELQQAGAKPELKLEGRRPVDSGRQNIDFSNVDISELSSEVMGTMDAFDVHEFDQYLP
LGGPAPPEPGQAYGGAYFHAGASPVWAHKSAPSASASPTETGPPRPHIKTEQPSPGHYGD
QPRGSPDYGSCSGQSSATPAAPAGPFAGSQGDYGDLQASSYYGAYPGYAPGLYQYPCFHS
PRRPYASPLLNGLALPPAHSPTSHWDQPVYTTLTRP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| YQPRRRKSAKAGHSDSDSGAELGPHPGGGAVYKAEAGLGDGHHHGDHTGQTHGPPTPPTTPKTELQQAGAKPELKLEGRRPVDSGRQNIDFSNVDISELSSEVMGTMDAFDVHEFDQYLPLGGPAPPEPGQAYGGAYFHAGASPVWAHKSAPSASASPTETGPPRPHIKTEQPSPGHYGDQPRGSPDYGSCSGQSSATPAAPAGPFAGSQGDYGDLQASSYYGAYPGYAPGLYQYPCFHSPRRPYASPLLNGLALPPAHSPTSHWDQPVYTTLTRP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	998664567788888888765577777775445788887888888888878999889889998867798887777788887878888877777777777865334678877788788888889888888888888788888788877888888899988888888877888889998888899999888888788888888888888889998888888888889998999888888899989988888898899988899888889855147899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| YQPRRRKSAKAGHSDSDSGAELGPHPGGGAVYKAEAGLGDGHHHGDHTGQTHGPPTPPTTPKTELQQAGAKPELKLEGRRPVDSGRQNIDFSNVDISELSSEVMGTMDAFDVHEFDQYLPLGGPAPPEPGQAYGGAYFHAGASPVWAHKSAPSASASPTETGPPRPHIKTEQPSPGHYGDQPRGSPDYGSCSGQSSATPAAPAGPFAGSQGDYGDLQASSYYGAYPGYAPGLYQYPCFHSPRRPYASPLLNGLALPPAHSPTSHWDQPVYTTLTRP
Prediction	843444554442524465445454335644244454344444334534344434544444452545445454544464444674544414144242442445234424424354264344444344443443232223323223333444444444445554444443446444343445434443434334334344333334434444242453444442333334433333333223443132323344443445212564253122242658
	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

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
YQPRRRKSAKAGHSDSDSGAELGPHPGGGAVYKAEAGLGDGHHHGDHTGQTHGPPTPPTTPKTELQQAGAKPELKLEGRRPVDSGRQNIDFSNVDISELSSEVMGTMDAFDVHEFDQYLPLGGPAPPEPGQAYGGAYFHAGASPVWAHKSAPSASASPTETGPPRPHIKTEQPSPGHYGDQPRGSPDYGSCSGQSSATPAAPAGPFAGSQGDYGDLQASSYYGAYPGYAPGLYQYPCFHSPRRPYASPLLNGLALPPAHSPTSHWDQPVYTTLTRP

5b4xB

0.07

2.96

0.64

CEthreader

SLIFTNRHEVRRIDLVKRNYSRLIPMLKNVVALDVEVATNRIYWCDLSYRKIYSAYMDKASDPKEQEVLIDEQLHSPEGLAVDWVHKHIYWTDSGNKTISVATVDGGRRRTLFSRNLSEPRAIAVDPLRGFMYWSDWGDQAKIEKSGLNGVDRQTLVSDNIEWPNVDSKLHQLSSIDFSGGNRKTLISSTDFLSHPFGIAVFEDKVFWTDLENEAIFSANRLNGLEISILAENLNNPHDIVIFHELKQPRAPDACELSVQPNGGCEYLCLPAPQIS

6vbu8

0.06

2.57

0.62

EigenThreader

EHSQYKDWWWKVQIGKCYYRLGLYREAEKQFKSALKQQEMVDTFLYLAKVYISLDQPLTALNLFKPGEVTLLCGIAATEYYKEVLKQDNTHVEAIACIGSNHFYTDQPEVALRFYRRLLQMGVYNCQLFNNLGLCCFYAQQYDMTLTSFERALSLAENEEEVADVWYNLGHVAVGTGDTNLAHQCFRLALVSNNQHAEAYNNLAVLEMRRGHVEQAKALLQTASSLAPHMYEPHFNFATISDKIGDLQRSYAAAKKSEAAFPDHVDTQHLIKQLEQ

2xd8A

0.09

3.30

0.56

FFAS-3D

-NQVATGTGYGGATDKYALLKLFSGEMFKGFQHETIARDLVTKRTLKNGKSLQFIYTGRMTSSFHT----------PGTPILGNADKAPPVAEKTI-VMDDLLISSAFVYDLDETLAHYELRGEISKKIGYALARGARSASPVSATNFVEPGGTQIRVGSGTNESDAFTASALVNAFYDADEKGVSSQGRCAVLNPRQYYALIQDIGSNGLVNRDVQGSALQS--GNGVIEIAGIHIYKSMNIPFLGKYGVKYGGTTGETSPGNLGSHIGPTPENA

4btgA3

0.12

0.11

3.99

1.23

SPARKS-K

SARGLTQAFAIGELKNQLSGALQLPLQFTRTFSASMT-SELLWEAYVYRVGRTATYPPSTPKELLRNTNGIDQLRSRGRAEVIFSDEELSSTIIPI-----EAMSEVSPFKLRPINETTSYIGQTSAIDHMGQP--SHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEPLAPSNGAEMTLGFPSVVERALRTGIVDESLEARASNAVMHYAVAHNPEVHQGVAAEQGSLYLVWNVRTERIPVGYNAIEGGSIRTPEP----LEAIAYNKPIQP

5yz0A

0.07

0.06

2.50

0.83

DEthreader

--G-NAESASWAGYLTAIFTCCMHDFKVTIYLHILVVQQVYIMTTVFSMLDHLQWRHKQALAE-DSMVSTVDYEDYQSVTRFLD---QDLASFAHFSFIKKQNI-QE--HL--GFLQ-K-LYAAMHIHGVKSMLGLGAWKVWSVLQEYVKERLLLNKRPDYNECQSARYVERANETPPENLGRAMLL---------------DAESRRELHAYCSTAMSRILFCRLTHNMVNGMGPMG--GLFRRACEVTMHVHLIQEATD---------------

6r5kA

0.07

0.06

2.45

0.97

MapAlign

--------EITAISFDEKANLIWSGDSYGCISSYDPTFQLYTRYRGHIGGNSV------------------------KDILSHRDGILSISEDSLHFANRRGVTKLNLTSIDIAAFSELNTMCYSPHSLKNNIYCGGDNTNWGIASIDLNRGCLDSLLNYSSKVKLMCSNNKVLSIGRQTGTVDLLDPTSNRTIKSFNAHSASISAMDLRDNTLVTVGKSKRADPFVNVYDLDFVQLHPLLPTVMIVASSSGSFDFIDLSNPTLRTQYVHPCQSI-

2atyA

0.08

3.14

0.85

MUSTER

VDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNMWGPTRLPTCVSVFPLEGSIEGRGGSELADPEVPRDCGCKPCICTVPEVSSVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWVEVHTAQTQPREEQFNSTFRSVSELPIMHQDWLNGNSAAFPAPIEKTISKTKGRPKAPQLYTIPPPKEQMAKDKVS-MITDFFPEDITVEWQWAENYKNTQPIMNTNESYFVYSQKSNWEA-TFTEGLHN

5eyiA1

0.16

0.05

1.82

0.46

HHsearch

--------------SGS-SSPLPKVAHNLGFY----------FSP------------------DLTQ---FAKLPVELAPHVVTTQNNEKWPDR----L---VASL------RP----IHKYSRACIGAG-YMVGPSVTPGVVSYYLTKFVKGEA-QLLPE-------------------------------------------------------------------------------------------------------------------

6wteA

0.08

3.15

0.54

CEthreader

RRLTDAPVVGGGIGFSTMPFALVEYFGIEYGVKGPGEKILGLIRNTERGAVRVPPAVLTVRHGKTQPAEPTGQFEPRVWQVDQLSVYRRRSGVPRKVDNLEYYRRGGLGSIVDEMESLAAQGILDQHTTDSEFNLSIAHAKNLLREIVRRRHADPDNPLNRLRLWVYCQPSPFDEEFADLLAAAGCRGVNVGSYTFEDTERLVRLCRERGILTMVEALFGFMALDATVTGFSLGLRLFPYTPMGIEIAEQCAGVRTAPGLQSNTADGPIVLKPLRM

6bk8T

0.04

2.07

0.60

EigenThreader

NRLDMGQWIRYAQFEIEQHDMRRARSIFERALLVDSSFIPLWIRYIDAELKVKCINHARNLMNRAISTLPRVDKLWYKYLIVEESLNNVEIVRSLYTKWCSL---EPGVNAWNSFVDFEIRQKNNSIEETISYKRKMEYETILSNYDTWWLYLDLISEFPKQIMQTFEKAIVDSKNVQWKRYIYLWMRYICYVELESLLEEELFQRLIDDIFSKIWLMYAKFLIRDVPKARKILGKAIGTFKGYIELEVKLEFDRVRKIYEKFIEFQDLQIWSQYG

(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	0.4216

(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	1n7qA	0.43	6.59	0.060	0.772	model1_1n7qA.pdb.gz
2	3wkyA	0.43	6.82	0.040	0.801	model1_3wkyA.pdb.gz
3	4yzwA	0.42	6.86	0.059	0.797	model1_4yzwA.pdb.gz
4	1j0nA	0.42	6.54	0.045	0.746	model1_1j0nA.pdb.gz
5	3ixvM	0.42	6.84	0.048	0.797	model1_3ixvM.pdb.gz
6	1llaA	0.42	6.76	0.073	0.768	model1_1llaA.pdb.gz
7	1hcyA	0.42	6.85	0.040	0.775	model1_1hcyA.pdb.gz
8	3hhsA	0.42	6.74	0.032	0.768	model1_3hhsA.pdb.gz
9	6kz8A2	0.41	6.21	0.063	0.703	model1_6kz8A2.pdb.gz
10	1rw9A	0.41	6.53	0.058	0.743	model1_1rw9A.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:0003676	0.82	nucleic acid binding
GO:0003677	0.80	DNA binding
GO:0044212	0.74	transcription regulatory region DNA binding
GO:0000976	0.73	transcription regulatory region sequence-specific DNA binding
GO:0001046	0.60	core promoter sequence-specific DNA binding
GO:0003700	0.53	transcription factor activity, sequence-specific DNA binding
GO:0044877	0.50	macromolecular complex binding
GO:0000981	0.50	RNA polymerase II transcription factor activity, 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:0032502	1.00	developmental process
GO:0048869	0.98	cellular developmental process
GO:0044767	0.98	single-organism developmental process
GO:0009653	0.91	anatomical structure morphogenesis
GO:0048856	0.89	anatomical structure development
GO:0030154	0.82	cell differentiation
GO:0065007	0.80	biological regulation
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0060255	0.77	regulation of macromolecule metabolic process
GO:0048646	0.77	anatomical structure formation involved in morphogenesis
GO:0048513	0.76	animal organ development
GO:0048518	0.74	positive regulation of biological process
GO:0010604	0.73	positive regulation of macromolecule metabolic process
GO:0010556	0.73	regulation of macromolecule biosynthetic process
GO:0010468	0.73	regulation of gene expression
GO:0080090	0.71	regulation of primary metabolic process
GO:0051171	0.71	regulation of nitrogen compound metabolic process
GO:0031326	0.71	regulation of cellular biosynthetic process
GO:0010628	0.70	positive regulation of gene expression
GO:0010557	0.70	positive regulation of macromolecule biosynthetic process
GO:0006355	0.70	regulation of transcription, DNA-templated
GO:0031325	0.68	positive regulation of cellular metabolic process
GO:0045893	0.67	positive regulation of transcription, DNA-templated
GO:0048731	0.64	system development
GO:0048523	0.62	negative regulation of cellular process
GO:0048729	0.60	tissue morphogenesis
GO:2000026	0.59	regulation of multicellular organismal development
GO:0002009	0.58	morphogenesis of an epithelium
GO:0044707	0.57	single-multicellular organism process
GO:0006357	0.57	regulation of transcription from RNA polymerase II promoter
GO:0061138	0.55	morphogenesis of a branching epithelium
GO:0060041	0.55	retina development in camera-type eye
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0051094	0.55	positive regulation of developmental process
GO:0050767	0.55	regulation of neurogenesis
GO:0045944	0.53	positive regulation of transcription from RNA polymerase II promoter
GO:0031324	0.53	negative regulation of cellular metabolic process
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:0051093	0.52	negative regulation of developmental process
GO:0045892	0.52	negative regulation of transcription, DNA-templated
GO:0045597	0.52	positive regulation of cell differentiation
GO:0043066	0.52	negative regulation of apoptotic process
GO:0008284	0.52	positive regulation of cell proliferation
GO:0022414	0.51	reproductive process
GO:2000027	0.50	regulation of organ morphogenesis
GO:0065008	0.50	regulation of biological quality
GO:0044702	0.50	single organism reproductive process
GO:0003006	0.50	developmental process involved in reproduction

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:0043231	0.89	intracellular membrane-bounded organelle
GO:0005634	0.88	nucleus
GO:0005737	0.56	cytoplasm
GO:0032991	0.50	macromolecular 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

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	1a1qA	0.223	5.49	0.053	0.348	3.4.21.98	NA
2	0.060	1p8jA	0.399	6.21	0.050	0.685	3.4.21.75	NA
3	0.060	1l5jA	0.387	6.32	0.063	0.677	4.2.1.3	211,244,247
4	0.060	3b9jC	0.391	6.80	0.052	0.725	1.17.3.2 1.17.1.4	NA
5	0.060	1j0mA	0.419	6.46	0.065	0.732	4.2.2.12	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

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	2ckjC	0.355	6.38	0.065	0.616	0.79	FES	complex1.pdb.gz	225,226,227,229,233,234,235
2	0.01	1fiqA	0.239	5.75	0.044	0.388	0.73	FES	complex2.pdb.gz	225,226,227,235,236
3	0.01	2ckjD	0.358	6.31	0.061	0.612	0.71	FES	complex3.pdb.gz	217,218,220,221,222,223
4	0.01	1fiqA	0.239	5.75	0.044	0.388	0.72	FES	complex4.pdb.gz	198,204,222,223,259,261

	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.