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PR00057

Identifier
NFKBTNSCPFCT  [View Relations]  [View Alignment]  
Accession
PR00057
No. of Motifs
5
Creation Date
07-FEB-1994  (UPDATE 21-JUN-1999)
Title
Transcription factor NF-KB signature
Database References

PROSITE; PS01204 REL
PFAM; PF00554 RHD
INTERPRO; IPR000451
Literature References
1. SEN, R. AND BALTIMORE, D. 
Multiple nuclear factors interact with the immunoglobulin enhancer sequences.
CELL 46(5) 705-716(1986). 
 
2. BAEUERLE, P.A.
The inducible transcription activator NF-kappa-B - regulation by
distinct protein subunits.
BIOCHIM.BIOPHYS.ACTA 1072(1) 63-80 (1991).
 
3. GHOSH, G., VAN DUYNE, G., GHOSH, S. AND SIGLER, P.B.
Structure of NF-kB p50 homodimer bound to a kB site.
NATURE 373 303-317 (1995).

Documentation
The transcription factor NF-kB was first identified as a DNA-binding 
protein specific for the 10-base pair kB site in the immunoglobulin k 
light-chain enhancer of B lymphocytes [1]. It is now known to be a member
of a highly similar family of transcription factors, which share a 300 
amino acid `rel homology region' (RHR) [2]: members include p50, p52, 
p65, c-Rel, v-Rrel, RelB, and the Drosophila proteins, Dorsal and Dif. 
These proteins exist as homo- and heterodimers that bind to kB sites in
the enhancer regions of several target genes, most of which are involved
in cellular defence mechanisms and differentiation.
 
The RHR, which is located N-terminally, is responsible for protein
dimerisation, DNA binding and nuclear localisation. The more variable
C-terminal domains (not found in p50 or p52) may be responsible for
transactivation. DNA binding requires the entire RHR, by contrast with
other eukaryotic and prokaryotic transcription factors, where much
smaller DNA-binding domains confer full specificity and binding
affinity for the target [3].
 
The structure of the transcription factor NF-kB p50 homodimer bound to
a palindromic kB site shows the RHR to fold into 2 distinct domains,
similar to the beta-sandwich structure of the immunoglobulins [3]. The 
p50 dimer envelops an undistorted B-DNA helix, making specific contacts
along the 10bp kB recognition site, mainly through loops connecting
secondary structure elements in both domains. The C-terminal domains
form a dimerisation interface between beta-sheets using residues that
are strongly conserved in the Rel family.
 
NFKBTNSCPFCT is a 5-element fingerprint that provides a signature for
NF-kB transcription factors and releated RHR sequences. The fingerprint
was derived from an initial alignment of 7 sequences: the motifs were 
drawn from conserved regions spanning the full RHR. Two iterations on 
OWL25.1 were required to reach convergence, at which point a true set 
comprising 27 sequences was identified.
 
An update on SPTR37_9f identified a true set of 23 sequences, and 3
partial matches.
Summary Information
  23 codes involving  5 elements
2 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
52323232323
421221
300000
200110
12345
True Positives
DIF_DROME     DORS_DROME    KBF1_CHICK    KBF1_HUMAN    
KBF1_MOUSE KBF2_CHICK KBF2_HUMAN KBF3_HUMAN
O13075 O73630 O77088 Q91833
RELB_HUMAN RELB_MOUSE RELB_XENLA REL_AVIRE
REL_CHICK REL_HUMAN REL_MOUSE TF65_CHICK
TF65_HUMAN TF65_MOUSE TF65_XENLA
True Positive Partials
Codes involving 4 elements
O73789 Q17034
Codes involving 2 elements
Q94527
Sequence Titles
DIF_DROME   DORSAL-RELATED IMMUNITY FACTOR DIF - DROSOPHILA MELANOGASTER (FRUIT FLY). 
DORS_DROME EMBRYONIC POLARITY DORSAL PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
KBF1_CHICK NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT [CONTAINS: NUCLEAR FACTOR NF- KAPPA-B P50 SUBUNIT] - GALLUS GALLUS (CHICKEN).
KBF1_HUMAN NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT] - HOMO SAPIENS (HUMAN).
KBF1_MOUSE NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT (DNA-BINDING FACTOR KBF1) (EBP- 1) (NF-KAPPA-B1 P84/NF-KAPPA-B1 P98) [CONTAINS: NUCLEAR FACTOR NF- KAPPA-B P50 SUBUNIT] - MUS MUSCULUS (MOUSE).
KBF2_CHICK NUCLEAR FACTOR NF-KAPPA-B P100 SUBUNIT [CONTAINS: NUCLEAR FACTOR NF- KAPPA-B P52 SUBUNIT] - GALLUS GALLUS (CHICKEN).
KBF2_HUMAN NUCLEAR FACTOR NF-KAPPA-B P100 SUBUNIT (H2TF1) (ONCOGENE LYT-10) (LYT10) [CONTAINS: NUCLEAR FACTOR NF-KAPPA-B P52 SUBUNIT] - Homo sapiens (Human).
KBF3_HUMAN NUCLEAR FACTOR NF-KAPPA-B P49 SUBUNIT - HOMO SAPIENS (HUMAN).
O13075 NUCLEAR FACTOR NF-KB1 - GALLUS GALLUS (CHICKEN).
O73630 P100-NFKAPPAB2 - Xenopus laevis (African clawed frog).
O77088 DORSAL B - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q91833 XREL2 PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
RELB_HUMAN TRANSCRIPTION FACTOR RELB (I-REL) - HOMO SAPIENS (HUMAN).
RELB_MOUSE TRANSCRIPTION FACTOR RELB - MUS MUSCULUS (MOUSE).
RELB_XENLA TRANSCRIPTION FACTOR RELB HOMOLOG - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
REL_AVIRE REL TRANSFORMING PROTEIN (P58 V-REL) - AVIAN RETICULOENDOTHELIOSIS VIRUS.
REL_CHICK C-REL PROTO-ONCOGENE PROTEIN (C-REL PROTEIN) (P68) - GALLUS GALLUS (CHICKEN).
REL_HUMAN C-REL PROTO-ONCOGENE PROTEIN (C-REL PROTEIN) - HOMO SAPIENS (HUMAN).
REL_MOUSE C-REL PROTO-ONCOGENE PROTEIN (C-REL PROTEIN) - MUS MUSCULUS (MOUSE).
TF65_CHICK TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT) - GALLUS GALLUS (CHICKEN).
TF65_HUMAN TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT) - HOMO SAPIENS (HUMAN).
TF65_MOUSE TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT) - MUS MUSCULUS (MOUSE).
TF65_XENLA PUTATIVE TRANSCRIPTION FACTOR P65 HOMOLOG (XREL1) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).

O73789 REL-RELATED EMBRYONIC ONCOPROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q17034 IMMUNE FACTOR - ANOPHELES GAMBIAE (AFRICAN MALARIA MOSQUITO).

Q94527 REL/NF-KAPPA B HOMOLOG - DROSOPHILA MELANOGASTER (FRUIT FLY).
Scan History
OWL25_1    2  50   NSINGLE    
OWL26_0 1 100 NSINGLE
SPTR37_9f 1 100 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
EQPKQRGFRFRYGCEGPS KBF3_HUMAN 44 44 -
EQPKQRGFRFRYGCEGPS KBF2_HUMAN 44 44 -
EQPKQRGMPFRYECEGRS RELB_HUMAN 131 131 -
EQPAGKALRFRYECEGRS DORS_DROME 53 53 -
EQPKQRGMRFRYKCEGRS REL_XENLA 24 24 -
EQPRQRGMRFRYKCEGRS REL_CHICK 13 13 -
EQPKQRGFRFRYVCEGPS KBF1_HUMAN 49 49 -

Motif 2 width=15
Element Seqn Id St Int Rpt
LKPVTSQPIHDSKSP KBF3_HUMAN 209 147 -
MDPVLSEPVYDKKST RELB_HUMAN 284 135 -
LPFVVSQPIYDNRAP REL_XENLA 175 133 -
LPPVVSEPIFDKKAM DORS_DROME 208 137 -
LPPLISNPIYDNRAP REL_CHICK 166 135 -
LEPVVSDAIYDSKAP KBF1_HUMAN 232 165 -
LKPVTSQPIHDSKSP KBF2_HUMAN 209 147 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GGDEIFILCDKVQKDDIEVRF REL_CHICK 199 18 -
GGDEIFLLCDKVQKEDIEVIF REL_XENLA 208 18 -
GGEEIYLLCDKVQKDDIQIRF KBF1_HUMAN 265 18 -
GGDEVYLLCDKVQKDDIEVRF KBF3_HUMAN 242 18 -
GGDEVYLLCDKVQKDDIEVRF KBF2_HUMAN 242 18 -
GGEELYLLCDKVQKEDISVVF RELB_HUMAN 317 18 -
GNTQIILLCEKVAKEDISVRF DORS_DROME 239 16 -

Motif 4 width=19
Element Seqn Id St Int Rpt
FQHTDVHKQTAITFKTPRY DORS_DROME 275 15 -
FSQADVHRQVAIVFRTPPF REL_CHICK 230 10 -
FSPTDVHRQFAIVFKTPKY KBF1_HUMAN 301 15 -
FSQADVHRQVAIVFRTPAF REL_XENLA 239 10 -
FSPTDVHKQYAIVFRTPPY KBF3_HUMAN 276 13 -
FSPTDVHKQYAIVFRTPPY KBF2_HUMAN 276 13 -
FSQADVHRQIAIVFKTPPY RELB_HUMAN 348 10 -

Motif 5 width=15
Element Seqn Id St Int Rpt
VSDSKQFTYYPLVED KBF2_HUMAN 317 22 -
TSEALPFEYVPMDSD DORS_DROME 316 22 -
VSEPMDFRYLPDEKD REL_CHICK 270 21 -
VSEPMEFQYLPDEGD REL_XENLA 280 22 -
TSEPKPFLYYPEIKD KBF1_HUMAN 342 22 -
VSDSKQFTYYPLVED KBF3_HUMAN 317 22 -
CSEPLPFTYLPRDHD RELB_HUMAN 389 22 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
EQPRQRGMRFRYKCEGRS REL_HUMAN 14 14 -
EQPRQRGMRFRYKCEGRS REL_MOUSE 14 14 -
EQPRQRGMRFRYKCEGRS REL_CHICK 13 13 -
EQPRQRGTRFRYKCEGRS REL_AVIRE 22 22 -
EQPKQRGMRFRYKCEGRS TF65_XENLA 24 24 -
EQPKQRGMRFRYKCEGRS TF65_MOUSE 25 25 -
EQPKQRGMRFRYKCEGRS TF65_HUMAN 25 25 -
EQPKQRGMRFRYKCEGRS TF65_CHICK 31 31 -
EQPKQRGFRFRYVCEGPS KBF1_MOUSE 46 46 -
EQPKQRGFRFRYVCEGPS KBF1_HUMAN 49 49 -
EQPKQRGFRFRYVCEGPS KBF1_CHICK 53 53 -
EQPKQRGFRFRYVCEGPS O13075 74 74 -
EQPKQRGFRFRYVCEGPS KBF2_CHICK 43 43 -
EQPKQRGFRFRYGCEGPS KBF3_HUMAN 44 44 -
EQPKQRGFRFRYGCEGPS KBF2_HUMAN 44 44 -
EQPRQRGMRYRYKCEGRC Q91833 28 28 -
EQPKQRGFRFRYVCEGPS O73630 49 49 -
EQPKQRGMRFRYECEGRS RELB_MOUSE 109 109 -
EQPKQRGMPFRYECEGRS RELB_HUMAN 131 131 -
EQPKQRGMRFRYQCEGRS RELB_XENLA 84 84 -
EQPAGKALRFRYECEGRS DORS_DROME 53 53 -
EQPAGKALRFRYECEGRS O77088 53 53 -
EEPTSNIIRFRYKCEGRT DIF_DROME 84 84 -

Motif 2 width=15
Element Seqn Id St Int Rpt
LPPVVSNPIYDNRAP REL_HUMAN 167 135 -
LPPIVSNPIYDNRAP REL_MOUSE 167 135 -
LPPLISNPIYDNRAP REL_CHICK 166 135 -
LPPLISNPIYDNRAP REL_AVIRE 175 135 -
LPFVVSQPIYDNRAP TF65_XENLA 175 133 -
LTPVLSHPIFDNRAP TF65_MOUSE 175 132 -
LPPVLPHPIFDNRAP TF65_HUMAN 175 132 -
LPPVLSQPIYDNRAP TF65_CHICK 180 131 -
LEPVVSDAIYDSKAP KBF1_MOUSE 229 165 -
LEPVVSDAIYDSKAP KBF1_HUMAN 232 165 -
LDPVISDAIYDSKAP KBF1_CHICK 236 165 -
LDPVISDAIYDSKAP O13075 257 165 -
LQPVISDPIHDSKSP KBF2_CHICK 208 147 -
LKPVTSQPIHDSKSP KBF3_HUMAN 209 147 -
LKPVTSQPIHDSKSP KBF2_HUMAN 209 147 -
LGPVVSNPIYDNRAP Q91833 181 135 -
LPPVISDPIHDSKSP O73630 215 148 -
MDPILSEPVYDKKST RELB_MOUSE 262 135 -
MDPVLSEPVYDKKST RELB_HUMAN 284 135 -
IPPVLSDPIYDKKST RELB_XENLA 237 135 -
LPPVVSEPIFDKKAM DORS_DROME 208 137 -
LPPVVSEPIFDKKAM O77088 208 137 -
LDPIVSSPIYGKSSE DIF_DROME 240 138 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GGDEIFLLCDKVQKDDIEVRF REL_HUMAN 200 18 -
GGDEIFLLCDKVQKDDIEVRF REL_MOUSE 200 18 -
GGDEIFILCDKVQKDDIEVRF REL_CHICK 199 18 -
GGDEIFLLCDKVQKDDIEVRF REL_AVIRE 208 18 -
GGDEIFLLCDKVQKEDIEVIF TF65_XENLA 208 18 -
GGDEIFLLCDKVQKEDIEVYF TF65_MOUSE 208 18 -
GGDEIFLLCDKVQKEDIEVYF TF65_HUMAN 208 18 -
GGDEIFLLCDKVQKEDIEVRF TF65_CHICK 213 18 -
GGEEIYLLCDKVQKDDIQIRF KBF1_MOUSE 262 18 -
GGEEIYLLCDKVQKDDIQIRF KBF1_HUMAN 265 18 -
GGEEIYLLCDKVQKDDIQIRF KBF1_CHICK 269 18 -
GGEEIYLLCDKVQKDDIQIRF O13075 290 18 -
GGDEVYLLCDKVQKDDIEVRF KBF2_CHICK 241 18 -
GGDEVYLLCDKVQKDDIEVRF KBF3_HUMAN 242 18 -
GGDEVYLLCDKVQKDDIEVRF KBF2_HUMAN 242 18 -
GGDEIFLLCDKVQKDDIEVRF Q91833 214 18 -
GGDEVYLLCDKVQKDDIEVQF O73630 248 18 -
GGEELYLLCDKVQKEDISVVF RELB_MOUSE 295 18 -
GGEELYLLCDKVQKEDISVVF RELB_HUMAN 317 18 -
GGEEVYILCDKVQKEDILVIF RELB_XENLA 270 18 -
GNTQIILLCEKVAKEDISVRF DORS_DROME 239 16 -
GNTQIILLCEKVAKEDISVRF O77088 239 16 -
GGDEIIMLCEKIAKDDIEVRF DIF_DROME 269 14 -

Motif 4 width=19
Element Seqn Id St Int Rpt
FSQADVHRQVAIVFKTPPY REL_HUMAN 231 10 -
FSQADVHRQVAIVFKTPPY REL_MOUSE 231 10 -
FSQADVHRQVAIVFRTPPF REL_CHICK 230 10 -
FSQADVHRQVAIVFRTPPF REL_AVIRE 239 10 -
FSQADVHRQVAIVFRTPAF TF65_XENLA 239 10 -
FSQADVHRQVAIVFRTPPY TF65_MOUSE 239 10 -
FSQADVHRQVAIVFRTPPY TF65_HUMAN 239 10 -
FAAADVHRQVAIVFRTPPF TF65_CHICK 244 10 -
FSPTDVHRQFAIVFKTPKY KBF1_MOUSE 298 15 -
FSPTDVHRQFAIVFKTPKY KBF1_HUMAN 301 15 -
FSPTDVHRQFAIVFKTPKY KBF1_CHICK 305 15 -
FSPTDVHRQFAIVFKTPKY O13075 326 15 -
FSPTDVHKQYAIVFRTPPY KBF2_CHICK 275 13 -
FSPTDVHKQYAIVFRTPPY KBF3_HUMAN 276 13 -
FSPTDVHKQYAIVFRTPPY KBF2_HUMAN 276 13 -
FGQADVHRQVAIVFKTPPF Q91833 245 10 -
FAPTDVHKQYAIVFRTPPY O73630 282 13 -
FSQADVHRQIAIVFKTPPY RELB_MOUSE 326 10 -
FSQADVHRQIAIVFKTPPY RELB_HUMAN 348 10 -
FSQADVHRQIAIVLKTPPY RELB_XENLA 301 10 -
FQHTDVHKQTAITFKTPRY DORS_DROME 275 15 -
FQHTDVHKQTAITFKTPRY O77088 275 15 -
FQPTDVFKQMAIAFKTPRY DIF_DROME 306 16 -

Motif 5 width=15
Element Seqn Id St Int Rpt
VSESMDFRYLPDEKD REL_HUMAN 271 21 -
VSESMDFRYLPDEKD REL_MOUSE 271 21 -
VSEPMDFRYLPDEKD REL_CHICK 270 21 -
VSEPVDFRYLPDEED REL_AVIRE 279 21 -
VSEPMEFQYLPDEGD TF65_XENLA 280 22 -
LSEPMEFQYLPDTDD TF65_MOUSE 280 22 -
LSEPMEFQYLPDTDD TF65_HUMAN 280 22 -
RSPPLDFRYLPHQGD TF65_CHICK 285 22 -
TSEPKPFLYYPEIKD KBF1_MOUSE 339 22 -
TSEPKPFLYYPEIKD KBF1_HUMAN 342 22 -
TSEPKPFLYYPEIKD KBF1_CHICK 346 22 -
TSEPKPFLYYPEIKD O13075 367 22 -
VSDSKQFTYYPVVED KBF2_CHICK 316 22 -
VSDSKQFTYYPLVED KBF3_HUMAN 317 22 -
VSDSKQFTYYPLVED KBF2_HUMAN 317 22 -
VSEPMDFRYLPDPED Q91833 285 21 -
VSDSKQFTYYPLEQD O73630 323 22 -
CSEPLPFTYLPRDHD RELB_MOUSE 367 22 -
CSEPLPFTYLPRDHD RELB_HUMAN 389 22 -
RSEGMPFVYMPRVKD RELB_XENLA 342 22 -
TSEALPFEYVPMDSD DORS_DROME 316 22 -
TSEALPFEYVPMDSG O77088 316 22 -
TSAPLPFEYYPNPEL DIF_DROME 347 22 -