1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
|
VNEAFETLKRC MyoD Vandromme M, PNAS 1995,(10):4646-50
experimental motif.
TLKRC 16 100 0 myf5_bovin,myod_brare,myf5_chick,myod_chick,myod_cotja,myf5_human,myod_human,myf5_mouse,myod_mouse,myf5_notvi,myo1_oncmy,myod_pig,myod_rat,cut1_schpo,myod_sheep,myf5_xenla nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
this motif occurs in more than one family
VNEAFE 18 100 0 myod_caebr,myod_caeel,myod_chick,myod_cotja,myog_chick,myog_cotja,myod_drome,myod_human,myog_human,sum1_lytva,myod_mouse,myog_mouse,myod_pig,myog_pig,myod_rat,myog_rat,myod_sheep,myod_xenla nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
is only found in myod family. Seems to be a well conserved part of seq
within the family.Probably not part of the NLS.
[DE][ST][PL]KR[STC] 16 93.75 6.25 myf5_bovin,myod_brare,myf5_chick,myod_chick,myod_cotja,dif_drome,myf5_human,myod_human,myf5_mouse,myod_mouse,myf5_notvi,myo1_oncmy,myod_pig,myod_rat,myod_sheep,myf5_xenla nuc,nuc,nuc,nuc,nuc,cyt,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
# /data/swissprot/current/d/dif_drome ANNOTATION IN SWISSPROT
#SUBCELLULAR LOCATION: CYTOPLASMIC; ACCUMULATES IN THE NUCLEUS UPON BACTERIAL INFECTION OF INJURY.
#KW Nuclear protein; DNA-binding; Transcription regulation; Activator;
look at mpi3_pig and mpi3_mouse seq id. Same family but different NLS's.
RRKx{3,5}R[DE]R{3,}?[PLV] 24 100 0 myf5_bovin,myod_brare,myf5_chick,myf6_chick,myod_caebr,myod_caeel,myod_chick,myod_cotja,myod_drome,myf5_human,myf6_human,myod_human,myf5_mouse,myf6_mouse,myod_mouse,myf5_notvi,myo1_oncmy,myo2_oncmy,myod_pig,myf6_rat,myod_rat,myod_sheep,myf5_xenla,myod_xenla nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
# CONSERVATION OF NLS AMONG families. Look at myod_chick and
# myod_xenla. 77% seq IDE.
[DE][ST][PL]KR[STCYFW] 21 76.1904761904762 23.8095238095238 if2_aquae,if2_bacst,myf5_bovin,myod_brare,myf5_chick,myod_chick,myod_cotja,dif_drome,aact_human,myf5_human,myod_human,myf5_mouse,myod_mouse,myf5_notvi,myo1_oncmy,myod_pig,myod_rat,myod_sheep,myf5_xenla,myod_xenla,sywc_yeast cyt,cyt,nuc,nuc,nuc,nuc,nuc,cyt,ext,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,cyt
# the addition of only Y also
[DE][ST][PL]KR[STCY] 18 88.8888888888889 11.1111111111111 if2_bacst,myf5_bovin,myod_brare,myf5_chick,myod_chick,myod_cotja,dif_drome,myf5_human,myod_human,myf5_mouse,myod_mouse,myf5_notvi,myo1_oncmy,myod_pig,myod_rat,myod_sheep,myf5_xenla,myod_xenla cyt,nuc,nuc,nuc,nuc,nuc,cyt,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
#-----------------------------------------------------------------------------------------------
REKKEKEQKEKCA prot.Hsc9 Nederlof PM, PNAS 1995,(26):12060-4
TEST: R[DE][KR][KR][DE][KR][DE][QM][KR][DE]K 2 0 100 prc9_human,prc9_rat cyt,cyt
TEKK[QG]KSILYDCA prot.Hsc3 Nederlof PM, PNAS 1995,(26):12060-4
SDKKVRSRLIECA Ta alpha Nederlof PM, PNAS 1995,(26):12060-4
None of these look like an NLS.
TEST: [DE]KK[QMGA]K[ST] 9 44.4444444444444 55.5555555555556 prc3_carau,t2fa_drome,prc3_human,prc3_mouse,prc3_rat,h1_tigca,b4_xenla,prc3_xenla,pr16_yeast cyt,nuc,cyt,cyt,cyt,nuc,nuc,cyt,nuc
#------------------------------------------------------------------------------------------------
/data/swissprot/current/h/tf2d_human has a 30 residue long stretch
of Q.
NLS Motifs hard to find.
2 putative: RIREPRT & RLXXRKXXRV
[QM][RK][VI][RK][DE][PL][RK][ST] 29 100 0 tf21_arath,tf22_arath,tf2d_acaca,tf2d_acecl,tf2d_artsf,tf2d_caeel,tf2d_canal,tf2d_chick,tf2d_dicdi,tf2d_drome,tf2d_emeni,tf2d_human,tf21_maize,tf22_maize,tf2d_mesau,tf2d_mescr,tf2d_mouse,tf2d_schpo,tf2d_soltu,tf2d_soybn,tf2d_spofr,tf2d_strpu,tf2d_tobac,tf2d_trifl,tf2d_triga,tf21_wheat,tf22_wheat,tf2d_xenla,tf2d_yeast nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
#but all from same family
R[PL]xx[KR]{2,}?xx[KR]V 25 100 0
hsp2_alose,prt1_clupa,prt2_clupa,tf2d_chick,hsp2_horse,hsp3_horse,tf2d_human,tf2d_mesau,tf2d_mouse,prt1_oncke,prt2_oncmy,prt5_oncmy,prt6_oncmy,prt7_oncmy,prt8_oncmy,prt9_oncmy,prta_oncmy,prt1_salir,prt2_salir,prt3_salir,tf2d_strpu,tf2d_trifl,tf2d_triga,tf2d_xenla,est1_yeast
nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
# has different fmilies.
#---------------------------------------------------------------------------------------------------
TKRSxxxM influenzaNP Wang P, J Virol 1997,(71):1850-6
found in only cha4_yeast; but this protein has a bipartite motif: [RK]{3,}?x{8,16}[RK]{4,}?
#---------------------------------------------------------------------------------------------------
LKRKLQR Pax-QNR Carriere C, Cell Gr Diff 1995,(6):1531-40
# results of db scan
[PL][KR]{3,}?[PL][QM]R 8 100 0 pax6_brare,pax6_chick,pax6_cotja,pax6_human,pax6_mouse,pax6_oryla,pax6_rat,pax6_xenla nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
# not found in any other families.
# Other putative motifs
#/data/swissprot/current/h/pax6_human AN INTERESTING EXAMPLE OF USE
# FOR OUR TOOL.
#pax6_human: NRRAKWRRE
R[RK]x[KR]x[RK]{2,}?[DE] 132 100 0 hxa5_ambme,hxb1_ambme,scr_apime,h114_brare,hox3_brafl,hx5l_brare,hxa1_brare,hxb4_brare,hxb5_brare,hxb6_brare,hxc5_brare,hxc6_brare,hxd4_brare,pax6_brare,ctcf_chick,hxa4_chick,hxa7_cotja,hxb1_chick,hxb1_cypca,hxb3_chick,hxb4_chick,hxb5_chick,hxb6_chick,hxd3_chick,hxd4_chick,hxd8_chick,pax6_chick,pax6_cotja,un30_caeel,brm_drome,croc_drome,hmdf_drome,hmft_drohy,hmft_drome,hmux_drome,hmz1_drome,scr_drome,sus_drome,t2d2_drome,hxb4_fugru,ak95_human,cg2f_human,chd3_human,ctcf_human,fre3_human,hxa1_human,hxa3_human,hxa4_human,hxa5_human,hxa6_human,hxa7_human,hxb1_human,hxb3_human,hxb4_human,hxb5_human,hxb6_human,hxb7_human,hxb8_human,hxc4_human,hxc5_human,hxc6_human,hxc8_human,hxd3_human,hxd4_human,hxd8_human,ipf1_human,pax6_human,cx10_mouse,fre3_mouse,gsh2_mouse,gshi_mouse,hxa1_mouse,hxa3_mouse,hxa4_mouse,hxa5_mouse,hxa6_mouse,hxa7_mouse,hxb1_mouse,hxb3_mouse,hxb4_mouse,hxb5_mouse,hxb6_mouse,hxb7_mouse,hxb8_mouse,hxc4_mouse,hxc5_mouse,hxc6_mouse,hxc8_mouse,hxd1_mouse,hxd3_mouse,hxd4_mouse,hxd8_mouse,ipf1_mesau,ipf1_mouse,pax6_mouse,hxc5_notvi,hxc6_notvi,pax6_oryla,dpod_plafk,hxb8_pig,ak95_rat,hxa4_rat,hxa5_rat,hxa7_rat,hxb7_rat,hxb8_rat,hxc4_rat,hxc8_rat,hxd3_rat,ipf1_rat,pax6_rat,h2b1_strpu,h2b2_strpu,hxa4_sheep,hxa5_salsa,hxa5_sheep,hxa7_sheep,hxc6_sheep,hb7a_xenla,hb7b_xenla,hm8_xenla,hxa1_xenla,hxa7_xenla,hxb3_xenla,hxb4_xenla,hxb5_xenla,hxb6_xenla,hxc5_xenla,hxc6_xenla,hxd1_xenla,pax6_xenla,snf2_yeast nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
#-------------------------------------------------------------------------------------------------
KRAAEDDEDDDVDTKKQK hProTalpha Rubstov YT, FEBS Let 1997,(413):135-41
#results of db scan
KRx{12}KKQK 4 100 0 thya_bovin,thya_human,thya_mouse,thya_rat nuc,nuc,nuc,nuc
#only in 1 family. probably not NLS.
[PL]K[DE]KK[DE] 5 100 0 thya_bovin,thya_human,scp1_mesau,thya_mouse,thya_rat nuc,nuc,nuc,nuc,nuc
[GA]E{8} 13 100 0 thya_bovin,cenb_crigr,cenb_human,irf5_human,thya_human,cenb_mouse,irf5_mouse,ku70_mouse,thya_mouse,thya_rat,cenb_sheep,nupl_xenla,leur_yeast nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
# CHECK IF DNA BINDING PROTEINS ARE RICH IN E
#--------------------------------------------------------------------------------------------
Look at /data/swissprot/current/h/vbp1_human location annotation.
Cytoplasmic but translocates to the nucleus when bound to C terminal
of vhl.
#---------------------------------------------------------------------------------------
3446 ebn2_ebv nuc euka NUCLEAR. ASSOCIATED WITH THE NUCLEAR MATRIX.
#-------------------------------------------------------------------------------------------------
All 3 cyt proteins have extremely long stretches of R.
fxr1_human cyt 621 RRRxRRRR,RRRRxRRR 502,501
fxr2_human cyt 673 RRRxRRRR,RRRRxRRR 544,543
fxr1_xenla cyt 648 RRRxRRRR,RRRRxRRR 531,530
x is S.
#------------------------------------------------------------------------------------------------
Non interchangeability of R and K.
KKKKKK 24 70.8333333333333 29.1666666666667 hs9a_chick,hs9a_crigr,sr72_canfa,ssrp_chick,no60_drome,t2d2_drome,chd4_human,gcf_human,hs9a_human,pwp1_human,rms1_human,sn24_human,sr72_human,t2fa_human,hs9a_mouse,phi1_myted,pls1_mouse,dpoa_oxyno,hs9a_pig,rpc1_plafa,top2_plafk,dkc1_rat,t2fa_xenla,top2_yeast cyt,cyt,cyt,nuc,nuc,nuc,nuc,nuc,cyt,nuc,nuc,nuc,cyt,nuc,cyt,nuc,nuc,nuc,cyt,nuc,nuc,nuc,nuc,nuc
RRRRRR 81 100 0 hsp1_alose,hsp1_antla,hsp1_antst,hsp1_antsw,prt_antgr,prta_acist,prtb_acigu,gatb_bommo,hsp1_bovin,hsp2_bovin,prt1_bufja,prt2_bufja,cdp_canfa,hsp1_caefu,hsp1_cavpo,hsp2_calja,hsp_chick,hsp_cotja,hsp1_dasro,hsp1_dasvi,hsp1_didma,hsp1_droau,ebn6_ebv,hsp1_gorgo,fre4_human,hsp1_horse,hsp1_human,hsp1_hylla,hsp2_horse,hsp3_horse,rev_hv2be,rev_hv2d1,ve2_hpv37,h2b2_lytpi,hsp1_macag,hsp1_maceu,hsp1_macgi,hsp1_macrg,hsp1_macru,hsp1_mouse,hsp1_murlo,hsp2_macmu,hsp2_macne,hsp1_notty,prt1_oncke,prt5_oncmy,prt6_oncmy,prt7_oncmy,prt8_oncmy,prt9_oncmy,h2b1_paran,h2b2_paran,h2b3_paran,hsp1_parbi,hsp1_phaci,hsp1_pig,hsp1_plagi,hsp1_plain,hsp1_plams,hsp1_plate,hsp1_psecu,hsp2_pig,hsp1_rabit,hsp1_rat,h2b1_strpu,h2b2_strpu,hsp1_sagim,hsp1_sarha,hsp1_sheep,prt1_salir,prt1_sepof,prt2_salir,prt2_scyca,prt2_sepof,prt3_salir,prt3_scyca,rev_sivs4,rev_sivsp,hsp1_tacac,hsp1_trivu,mcm2_yeast nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc
#---------------------------------------------------------------------------------------------------
Expt suggested NLS's for AMIDA
RGRRRRQR Amida Irie Y, J.Biol.Chem.2000(275):2647-53
RKRRR Amida Irie Y, J.Biol.Chem.2000(275):2647-53
Seq of Amida
TITLE:Molecular cloning and characterization of amida, a novel protein
which interacts with a neuron-specific immediate early gene product
arc, contains novel nuclear localization signals, and causes cell
death in cultured cells
SEQ: 1 meleqregtm aavgfeefsa ppgselalpp lfgghilese letevefvsg glggsglrer
61 deeeeaargr rrrqrelnrr kyqalgrrcr eieqvnervl nrlhqvqrit rrlqqerrfl
121 mrvldsygdd yrasqftivl edegsqgtda ptpgnaenep peketlsppr rtpappepgs
181 papgegpsgr krrrvprdgr ragnaltpel apvqikveed fgfeadeald sswvsrgpdk
241 llpyptlasp asd
results od db scan:
RKRRR 20 85 15 ht31_arath,mb11_copci,sdc3_caeel,chd3_human,sn22_human,ve2_hpv04,ve2_hpv07,ve2_hpv40,atf3_mouse,rms5_neucr,h2b_patgr,rpb1_plafd,fre6_rat,spm1_rat,leu3_salty,prt2_scyca,tat_sivmk,tat_sivml,leu3_theaq,yox1_yeast nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,nuc,mit,nuc,nuc,nuc,nuc,cyt,nuc,nuc,nuc,cyt,nuc
[RK][GA][RK]{4}[QMN][RK] 3 66.6666666666667 33.3333333333333 ctcf_chick,ctcf_human,apt_myctu nuc,nuc,cyt
#----------------------------------------------------------------------------------------------------
PPVKRERTS RanBP3 Welch K, Mol Cell Biol.1999(19):8400-11
#-----------------------------------------------------------------------------------------------------
# CONS OF NLS WITHIN FAMILY.
consider tala_povba and tala_bfdv. Sequence Identity is 37%, weighted
similarity 50%.
-------- tala_povaba has NLS: PKKKRKV
aligned segment of tala_bfdv: ENVSVPD
Not a well conserved part of sequence.
tala_bfdv has NLS: [KR][DE][KR][DE]xx[KR][KR][KR][KR]
|
