HOMEWORK5





1.The accession number of mouse LEF-1 and TCF-1 in SWISS-PROT

LEF-1:P27782......
TCF-1:Q00417......


2.The name and the residue number of the same DNA-binding domain corresponding to the full-length protein

Name:HMG BOX
LEF-1:297-365......
TCF-1:188-256......


3.The AA seequence of this DNA-binding domain of each protein

LEF-1: the DNA-binding domain is colored by green 
     MPQLSGGGGG GDPELCATDE MIPFKDEGDP QKEKIFAEIS HPEEEGDLAD IKSSLVNESE
     IIPASNGHEV VRQAPSSQEP YHDKAREHPD EGKHPDGGLY NKGPSYSSYS GYIMMPNMNS
     DPYMSNGSLS PPIPRTSNKV PVVQPSHAVH PLTPLITYSD EHFSPGSHPS HIPSDVNSKQ
     GMSRHPPAPE IPTFYPLSPG GVGQITPPIG WQGQPVYPIT GGFRQPYPSS LSGDTSMSRF
     SHHMIPGPPG PHTTGIPHPA IVTPQVKQEH PHTDSDLMHV KPQHEQRKEQ EPKRPHIKKP
     LNAFMLYMKE MRANVVAECT LKESAAINQI LGRRWHALSR EEQAKYYELA RKERQLHMQL
     YPGWSARDNY GKKKKRKREK LQESTSGTGP RMTAAYI.........................

TCF-1:the DNA-binding domain is colored by blue 
     MYKETVYSAF NLLMPYPPAS GAGQHPQPQP PLHNKPGQPP HGVPQLSPLY EHFSSPHPTP
     APADISQKQG VHRPLQTPDL SGFYSLTSGS MGQLPHTVSW PSPPLYPLSP SCGYRQHFPA
     PTAAPGAPYP RFTHPSLMLG SGVPGHPAAI PHPAIVPSSG KQELQPYDRN LKTQAEPKAE
     KEAKKPVIKK PLNAFMLYMK EMRAKVIAEC TLKESAAINQ ILGRRWHALS REEQAKYYEL
       ARKERQLHMQ LYPGWSARDN YGKKKRRSRE KHQESTTGGK RNAFGTYPEK AAAPAPFLPMTVL


4.The pI/Mw and the predicted secondary of this DNA-binding domain of LEF-1(from ProtParam) 

Molecular weight:8239.6
    
Theoretical pI:9.66

The predicted secondary is alpha-helix


5.The hydropathicity of this DNA-binding domain of TCF-1(from ProtScale)

Using the scale Hphob. / Kyte & Doolittle, the individual values for the 20 amino acids are: 

Ala:  1.800  Arg: -4.500  Asn: -3.500  Asp: -3.500  Cys:  2.500  Gln: -3.500  
Glu: -3.500  Gly: -0.400  His: -3.200  Ile:  4.500  Leu:  3.800  Lys: -3.900  
Met:  1.900  Phe:  2.800  Pro: -1.600  Ser: -0.800  Thr: -0.700  Trp: -0.900  
Tyr: -1.300  Val:  4.200  Asx: -3.500  Glx: -3.500  Xaa: -0.490  ...........



Weights for window positions 1,..,9, using linear weight variation model:

   1     2     3     4     5     6     7     8     9    
 1.00  1.00  1.00  1.00  1.00  1.00  1.00  1.00  1.00 
 edge                   center                   edge


6.The chymotrypsin cleavage of TCF-1(from PeptideMass) 

You have selected TCF1_MOUSE from SWISS-PROT:

T-CELL-SPECIFIC TRANSCRIPTION FACTOR 1 (TCF-1) (T-CELL FACTOR 1)
(TRANSCRIPTION FACTOR-7).

     [Theoretical pI: 9.79 / Mw (average mass): 33608.54 / Mw (monoisotopic mass): 33587.19]
massposition #MCpeptide sequence
3987.117
262-297
1
 GKKKRRSREKHQESTTGGKR NAFGTYPEKAAAPAPF
3456.738
14-46
1
 MPYPPASGAGQHPQPQPPLH NKPGQPPHGVPQL
3392.775
256-284
1
 SARDNYGKKKRRSREKHQES TTGGKRNAF
2874.486
54-80
1
 SSPHPTPAPADISQKQGVHR PLQTPDL
2859.678
168-192
1
 DRNLKTQAEPKAEKEAKKPV IKKPL
2791.453
140-167
1
 GSGVPGHPAAIPHPAIVPSS GKQELQPY
2733.386
51-75
1
 EHFSSPHPTPAPADISQKQG VHRPL
2693.571
172-195
1
 KTQAEPKAEKEAKKPVIKKP LNAF
2686.472
262-284
0
 GKKKRRSREKHQESTTGGKR NAF
2575.230
109-132
1
 SPSCGYRQHFPAPTAAPGAP YPRF
2516.362
139-164
1
 LGSGVPGHPAAIPHPAIVPS SGKQEL
2516.295
115-137
1
 RQHFPAPTAAPGAPYPRFTH PSL
2403.278
140-164
0
 GSGVPGHPAAIPHPAIVPSS GKQEL
2361.423
172-192
0
 KTQAEPKAEKEAKKPVIKKP L
2320.216
54-75
0
 SSPHPTPAPADISQKQGVHR PL
2171.222
202-222
1
 RAKVIAECTLKESAAINQIL
2083.043
13-32
1
 LMPYPPASGAGQHPQPQPPL
1981.019
115-132
0
 RQHFPAPTAAPGAPYPRF
1978.969
87-105
1
 TSGSMGQLPHTVSWPSPPL
1969.959
14-32
0
 MPYPPASGAGQHPQPQPPL
1888.996
92-108
1
 GQLPHTVSWPSPPLYPL
1802.966
33-49
1
 HNKPGQPPHGVPQLSPL
1660.840
285-300
1
 GTYPEKAAAPAPFLPM
1641.918
213-226
1
 KESAAINQILGRRW
1515.795
92-105
0
 GQLPHTVSWPSPPL
1505.797
33-46
0
 HNKPGQPPHGVPQL
1491.802
200-212
1
 KEMRAKVIAECTL
1331.670
227-237
1
 HALSREEQAKY
1319.663
285-297
0
 GTYPEKAAAPAPF
1228.538
252-261
1
 YPGWSARDNY
1173.553
230-238
1
 SREEQAKYY
1168.637
241-249
1
 ARKERQLHM
1142.664
239-247
1
 ELARKERQL
1103.624
203-212
0
 RAKVIAECTL
1086.615
213-222
0
 KESAAINQIL
1010.490
230-237
0
 SREEQAKY


7.The Prosite scanning of LEF-1 

[1] PDOC00001 PS00001  ASN_GLYCOSYLATION
N-glycosylation site

Number of matches: 2
                            1      57-60 NESE                                                        
                            2    126-129 NGSL                                                        




[2] PDOC00005 PS00005  PKC_PHOSPHO_SITE
Protein kinase C phosphorylation site

Number of matches: 3
                            1    137-139 SNK                                                         
                            2    320-322 TLK                                                         
                            3    365-367 SAR                                                         




[3] PDOC00006 PS00006  CK2_PHOSPHO_SITE
Casein kinase II phosphorylation site

Number of matches: 7
                            1      40-43 SHPE                                                        
                            2      76-79 SSQE                                                        
                            3    157-160 TYSD                                                        
                            4    273-276 TDSD                                                        
                            5    320-323 TLKE                                                        
                            6    339-342 SREE                                                        
                            7    365-368 SARD                                                        




[4] PDOC00007 PS00007  TYR_PHOSPHO_SITE
Tyrosine kinase phosphorylation site

                            93-100 KHPDGGLY                                                    




[5] PDOC00008 PS00008  MYRISTYL
N-myristoylation site

Number of matches: 4
                            1       6-11 GGGGGG                                                      
                            2       7-12 GGGGGD                                                      
                            3     97-102 GGLYNK                                                      
                            4    166-171 GSHPSH                                                      




[6] PDOC00009 PS00009  AMIDATION
Amidation site

Number of matches: 2
                            1    331-334 LGRR                                                        
                            2    370-373 YGKK
¦^­º­¶ .................................... ......................................................................... ...........
NEXT HOMEWORK