D-I-TASSER PF04161

D-I-TASSER results for PF04161

Input Sequence in FASTA format

>PF04161 (216 residues)
ICIECRYPVKTLYTEYSGADDRSSGHGVRLTVCKNCGRFCDKYVEHDFVVLFIDLVLIKP
QVYRHLLHNTLMREHDQFDPSIIRLGILLLLFDVYLTWARIEKQTSNSANSSSDSNFLLL
AQQPIVFQYVFFLILCALSTLAFHLSIRFLTSSPFSPLVLFGFIPRYPRPNSVSTALLVS
SSTKLFPILMVIWEYDVPAAARSLGWAVVANNVEAL

Predicted Contact and Distance Map Used in D-I-TASSER

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure, top 2L) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact and distance maps, 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 a color scale represents a distance of 1-20+ angstroms.

Top 10 threading templates (target type: very hard)

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Threading
program

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Seq

ICIECRYPVKTLYTEYSGADDRSSGHGVRLTVCKNCGRFCDKYVEHDFVVLFIDLVLIKPQVYRHLLHNTLMREHDQFDPSIIRLGILLLLFDVYLTWARIEKQTSNSANSSSDSNFLLLAQQPIVFQYVFFLILCALSTLAFHLSIRFLTSSPFSPLVLFGFIPRYPRPNSVSTALLVSSSTKLFPILMVIWEYDVPAAARSLGWAVVANNVEAL

4k1cA1

0.05

0.03

0.54

0.75

DisCoVER

LASPLNFLLVFVLGLWGHFQLSHTLTFLFNF-LAII---PLAAI-----------LA----NA--TEELADKAGNTIGGLLNATFGNA---VELIVSIIA----------------------------------------------------------LKKGNPHHSL---SVKSSLVILLGTTVIISFCADFLVTINVVES--------------

3mk7A

0.10

0.07

0.73

0.83

DEthreader

-------------------------------------------VVRQFAIMTVVWG----IVGMGLGVFIALFGRP-HTNAVIFFGGCALFATSYYSVQRTCQTTL-FAP----KLAAFTFGVVAYAVFFNFGFAGFLGMSGLFYGMSTFEGMMVNALSHYTDWT-IGHV-HAGALGWAMVIGALYHLVPKVF-G-RE--QMHSIGLINTHFWLAI

3q8dA

0.10

0.98

0.59

CEthreader

AFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTLKGALQPFTPLLLRFGGRGEVKTLRSAEAV-----SLALPLSGITLYSGLYINELLSRVLEYETRFSELFFDYLHCIQSLAGVTGTPEPALRRFELALLGHLGYGVNFTHCAGSGEPVDDTMTYRYREEKGFIASVVIDNKTFTGRQLKALNAREFPDADTLRAAKRFTRMALKPYL

5vaiR

0.05

0.96

0.67

EigenThreader

FCNRDGAPGSFVNVSCPWYLPWASNVLQYRFCTAEGHWLPKDIKDAALKWMYSTAAQQHQWDGLLSYQDS--------LGCRLVFLLMQYCVAANYYWLLVEGAYLYTLLAFAVFSEQRIFKLYLSIGWGVPLLFVIPWGIVKYLYEIRVICIVVSKLKANLMCKTDIKCRLAKSTLTLIPLLGTHEVIFAFVRGTLRFVKLFTELSFTSFQGLMV

5tj5A

0.10

0.08

0.84

0.29

HHpred

----------ALSLVLNEKK-------INKM---KRGEIFDMAFTGRYIILLMGVF----SMYTGFLYNGTENALLFSNSYKMKLSILMMTYSYFFSLANHL---DIIG----NFIPGLLF---MQGIFGYLSVCIVYKWAVDWVLLNMLINMFLSPGTDDELYPHQAKVQVFLLLMALVCIPWLLLKPLHFKFDIMIQVIHTIEFCNCVSHTASY

6gykM

0.11

0.09

0.78

MRFsearch

-CPECKVYPPKIVERFS----------EGDVVCALCGLVLSKLVDVQAAFAKITMLCDAA----------------ELPKIVKDCAKEAYSIMAASILIGCRRAE-------VARTFKEIQSTKEFGKTLNIMKNILRKSQNLTYIPRFCSHLG-------------LPMQVTTSAEYTAKKCKSIYLNILLFQIPVTEGTIKSGYKILYEHRDKL

7by1A

0.14

0.12

0.85

0.52

FFAS-3D

-C-KCNG-----WKNPKPPPAANLSEL-----CRSCEHPLADHVSHDEINRLLGMVVDVENLFM-SVHKEEDTDTKQVYFYLFKLLRKCIIEQGVLNFVQYKFSHLAPRERQTMFELSKMFLLCLKVNYTRWLCYCHVTTHVFGRSLLRSIFTVTRRQLLEKFRVEKDKLVPEKRTLILTHFPKFLSMLEEIWESG--------------------

3wajA1

0.11

0.10

0.90

0.79

SPARKS-K

SIAGIIFSATSGESLRAVLAFIPAIGGVLAILPVYLLTREVFDKRAAVIAAFLIAIVPGQFLQRSILGFND----------HHIWEAFWQVSALGTFLLAYNRWKGHDLTAR---------QMAYPVIAGITIGLYVLSWGAGFIIAPIILAFMFFAFVLAGFVN--ADRKNLSLVAVVTFAVSALIYLPFAFNYPLLVLLGSAVIAAAFYQIEKW

4he8F

0.09

0.06

0.66

0.96

CNFpred

---------------------------------------------TPVSALIHAATMVTAGVYLIARSSFLYSVLPDVSYAIAVVGLLTAAYGALSAFGQT--------------DIKKIVAYSTISQLGYMFLAAGVGAYWVALFHVFTHAFF-------------KALLFLASGSVIHA-RWHALIGALALGGLPLLSGFWSKDAILAATLTYP

6vr4A

0.07

0.06

0.84

0.83

DEthreader

LSDITTLDVF---------------------KKTEFVQAYPSYSNRINFKSLELS-F-SQDKLNKVLRGG-TK------DHFIPETDKIVNAFTDHFVSEVNRKEAYQLEGKLFQNYNEPINGVSNEQKILIKQTINKVLNQRIKENIRYFKDQGLVIDTVNKKGFHFISHVVSDFTLNSIASIEYTKLFG-FGLVTPTYKV----HDPLYQLKKF

(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)	Threading program lists the threading program used to identify the template.
(f)	Template residues identical to query sequence are highlighted in color.

Top 5 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.55
	2	model2.pdb.gz
	3	model3.pdb.gz
	4	model4.pdb.gz
	5	model5.pdb.gz

(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, calculated based on significance of threading template alignments, contact satisfaction rate, mean absolute error between distnace of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. higher estimated TM-score signifies higher model confidence.

References:
1.	Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, S. M. Mortuza, Yang Zhang. "Deep-learning contact-map guided protein structure prediction in CASP13." Proteins: Structure, Function, and Bioinformatics, 87: 1149-1164 (2019).