INSERM EBGM U436

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Homology with Neq data

1JBBA and pdb protein have 34 % sequence identity. 
	>1JBBA
	MASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGI
	FELELYLPDDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIR
	TVLLSIQALLASPNPNDPLANDVAEDWIKNEQGAKAKAREWTKLYAKKKPE


	________mdffppccbfbghiafdlffklpacdcddfebjkhpfklgopa
	cmmmdpgfipcfkbgciacdddddbehfklnopacfdldfnhfpfklopmm
	mmmmmklmmdpfbgkbccggklkfkmmmmmnopanmmmmmmmm________


	>unknwon-Neq
	________4566644534100012233443334533222214542243321
	444453234223344465445446432343212234446555443234455
	3333323455434122333665554434442122543333312________
Simple prediction of 1JBBA. 

1JBBA           -MASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLP
2AAK            MSTPARKRLMRDFKRLQQDPPAGISGAPQDNNIMLWNAVIFGPDDTPWDGGTFKLSLQFS
                  :.  **:::: ::* .** .**:. *:*:*:  ::..* **:::*::.* *:*.* :.
2AAK-PB		ZZfklmmmmmmmmmmmmmgcehiacdddfklckbccddddddehifkgoiacdddddddf
1JBBA-pred	 ________mdffppccbfbghiafdlffklpacdcddfebjkhpfklgopacmmmdpgf
1JBBA-pred	 ________456664453410001223344333453322221454224332144445323

1JBBA           DDYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPND
2AAK            EDYPNKPPTVRFVSRMFHPNIYADGSICLDILQNQWSPIYDVAAILTSIQSLLCDPNPNS
                :*** :.*.***:::::****   * ****:*:.:***  :: ::* ***:**..****.
2AAK-PB		kbckbccddddfbdcddfklcfkopacdfklmmmpcfklcfklmmmmmmmmmmopcfklp
1JBBA-pred	ipcfkbgciacdddddbehfklnopacfdldfnhfpfklopmmmmmmmklmmdpfbgkbc
1JBBA-pred	422334446544544643234321223444655544323445533333234554341223

1JBBA           PLANDVAEDWIKNEQGAKAKAREWTKLYAKKKPE
2AAK            PANSEAARMYSESKREYNRRVRDVVEQSWT----
                *  .:.*. : :.::  : :.*: .:   .    
2AAK-PB		fblmlmmmmmmmmmlmmmmmmmmmmmmmZZ
1JBBA-pred	cggklkfkmmmmmnopanmmmmmmmm________
1JBBA-pred	33665554434442122543333312________
Simple prediction of 1JBBA aligned with 2aak sequence (CLUSTALW), the traduction of 2aak in terms of Protein Blocks, and the prediction of 1JBBA. 
DPVPGI
DPPAGI
** .**
gcehia
fbghia
410001
Exemple of an intersting part of 1JBBA: in a conserved sequence, the Neq is strong, so PB series hia could be well-predict, the N-ter is less defined, but succession ghia is well coherent and PBs e and g are found in closest states. 
FQVTIEGPEQ
WNAVIFGPDD
::..* **::
cddddddehi
cddfebjkhp
3322221454
An other intersting exemple: the succession seems to be really coming from a beta-sheet , i.e. PB's series d, but in 1JBBA, the repetitive structure seems to be shorter.
The rasmol script allow to look at the real 3D structures with the Neq inforamtion. rasmol script

2aak colored

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Last modif : 25 April 2004