Mike Clark
"An antibody engineer who also enjoys the mountains."
mrc7@cam.ac.uk
Mike's home-page
© Mike Clark, PhD., Cambridge University, UK
Last updated on 23rd March 2000
TR_IMMUNO:CAA05416
!!AA_SEQUENCE 1.0
ID CAA05416 PRELIMINARY; PRT; 117 AA.
AC CAA05416;
DT 01-JUN-1998 (TrEMBLrel. 06, Created)
DT 01-JUN-1998 (TrEMBLrel. 06, Last sequence update)
DT 01-JUN-1998 (TrEMBLrel. 06, Last annotation update)
DE IGG HEAVY CHAIN (FRAGMENT).
GN VHDi62.
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=BALB/C; TISSUE=SPLEEN;
RA KUETTNER G.;
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP SEQUENCE FROM N.A.
RC STRAIN=BALB/C; TISSUE=SPLEEN;
RX MEDLINE; 95021314.
RA DOERING E., STIGLER R., GRUETZ G., VONBAEHR R., SCHNEIDER-MERGENER J.;
RT "Identification and characterization of a TNFalpha antagonist derived
RT from a monoclonal antibody.";
RL Mol. Immunol. 31:1059-1067(1994).
DR EMBL; AJ002433; CAA05416.1; -.
FT NON_TER 1 1
FT NON_TER 117 117
SQ SEQUENCE 117 AA; 13092 MW; 7712522A CRC32;
CAA05416 Length: 117 March 22, 2000 23:52 Type: P Check: 5134 ..
1 QIQLVQSGPE LKKPGETVKI SCKASGYTFT HYGMNWVKQA PGKGLKWMGW
51 INTYTGEPTY ADDFKEHFAF SLETSASTVF LQINNLKNED TATYFCARER
101 GDAMDYWGQG TSVTVSS
TR_IMMUNO:CAA05417
!!AA_SEQUENCE 1.0
ID CAA05417 PRELIMINARY; PRT; 107 AA.
AC CAA05417;
DT 01-JUN-1998 (TrEMBLrel. 06, Created)
DT 01-JUN-1998 (TrEMBLrel. 06, Last sequence update)
DT 01-JUN-1998 (TrEMBLrel. 06, Last annotation update)
DE IGG LIGHT CHAIN (FRAGMENT).
GN VLDi62.
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=BALB/C; TISSUE=SPLEEN;
RA KUETTNER G.;
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP SEQUENCE FROM N.A.
RC STRAIN=BALB/C; TISSUE=SPLEEN;
RX MEDLINE; 95021314.
RA DOERING E., STIGLER R., GRUETZ G., VONBAEHR R., SCHNEIDER-MERGENER J.;
RT "Identification and characterization of a TNFalpha antagonist derived
RT from a monoclonal antibody.";
RL Mol. Immunol. 31:1059-1067(1994).
DR EMBL; AJ002434; CAA05417.1; -.
FT NON_TER 1 1
FT NON_TER 107 107
SQ SEQUENCE 107 AA; 11900 MW; 3666731A CRC32;
CAA05417 Length: 107 March 22, 2000 23:56 Type: P Check: 7972 ..
1 SIVMTQTPKF LLVSAGDRVT ITCTASQSVS NDVVWYQQKP GQSPKMLMYS
51 AFNRYTGVPD RFTGRGYGTD FTFTISSVQA EDLAVYFCQQ DYNSPRTFGG
101 GTKLEIK
Date: Mon, 13 Mar 2000 19:21:54 +0000
TFASTA translates and searches a DNA sequence data bank
version 3.2t07 August 17, 1999
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
/tmp/.fasta3-search-5709881: 117 aa
>TNFalphaH
vs V-Base too library
searching /data/gcgblast/v-base 0 library
167083 residues in 638 sequences
Expectation_n fit: rho(ln(x))= 62.2772+/-0.0108; mu= -185.0027+/- 0.482;
mean_var=9708.3339+/-8019.782, 0's: 1 Z-trim: 0 B-trim: 0 in 0/21
Kolmogorov-Smirnov statistic: 0.1971 (N=25) at 56
TFASTA (3.27 August, 1999) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 36, gap-pen: -16/ -2, width: 16 reg.-scaled
Scan time: 0.290
The best scores are: initn init1 opt z-sc E(637)
VI-4-1B ( 296) [1] 497 497 508 84.4 4.4
DP-21_4D275A ( 296) [1] 494 494 505 84.1 4.5
YAC-10_1D37 ( 294) [1] 489 489 500 83.6 4.8
7A-4 ( 254) [1] 424 424 436 78.0 9.7
>>VI-4-1B (296 aa)
Frame: 1 initn: 497 init1: 497 opt: 508 Z-score: 84.4 expect() 4.4
72.449% identity in 98 aa overlap (1-98:1-294)
10 20 30 40 50 60
TNFalp QIQLVQSGPELKKPGETVKISCKASGYTFTHYGMNWVKQAPGKGLKWMGWINTYTGEPTY
:.:::::: :::::: .::.:::::::::: :.::::.::::.::.::::::: ::.:::
VI-4-1 QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAMNWVRQAPGQGLEWMGWINTNTGNPTY
10 40 70 100 130 160
70 80 90 100 110
TNFalp ADDFKEHFAFSLETSASTVFLQINNLKNEDTATYFCARERGDAMDYWGQGTSVTVSS
:. : .:.:::.::.::..:::..:: ::::.:.:::
VI-4-1 AQGFTGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCAR
190 220 250 280
>>DP-21_4D275A (296 aa)
Frame: 1 initn: 494 init1: 494 opt: 505 Z-score: 84.1 expect() 4.5
72.449% identity in 98 aa overlap (1-98:1-294)
10 20 30 40 50 60
TNFalp QIQLVQSGPELKKPGETVKISCKASGYTFTHYGMNWVKQAPGKGLKWMGWINTYTGEPTY
:.:::::: :::::: .::.:::::::::: :.::::.::::.::.::::::: ::.:::
DP-21_ QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAMNWVRQAPGQGLEWMGWINTNTGNPTY
10 40 70 100 130 160
70 80 90 100 110
TNFalp ADDFKEHFAFSLETSASTVFLQINNLKNEDTATYFCARERGDAMDYWGQGTSVTVSS
:. : .:.:::.::.::..::: .:: ::::.:.:::
DP-21_ AQGFTGRFVFSLDTSVSTAYLQICSLKAEDTAVYYCAR
190 220 250 280
>>YAC-10_1D37 (294 aa)
Frame: 1 initn: 489 init1: 489 opt: 500 Z-score: 83.6 expect() 4.8
69.388% identity in 98 aa overlap (1-98:1-294)
10 20 30 40 50 60
TNFalp QIQLVQSGPELKKPGETVKISCKASGYTFTHYGMNWVKQAPGKGLKWMGWINTYTGEPTY
:.:::::: :.:.:: .::.:::::::.:: :::::: ::::.::.::::.:::::.:::
YAC-10 QVQLVQSGHEVKQPGASVKVSCKASGYSFTTYGMNWVPQAPGQGLEWMGWFNTYTGNPTY
10 40 70 100 130 160
70 80 90 100 110
TNFalp ADDFKEHFAFSLETSASTVFLQINNLKNEDTATYFCARERGDAMDYWGQGTSVTVSS
:. : .:.::..:::::..:::..:: :: : :.:::
YAC-10 AQGFTGRFVFSMDTSASTAYLQISSLKAEDMAMYYCAR
190 220 250 280
>>7A-4 (254 aa)
Frame: 1 initn: 424 init1: 424 opt: 436 Z-score: 78.0 expect() 9.7
72.619% identity in 84 aa overlap (1-84:1-252)
10 20 30 40 50 60
TNFalp QIQLVQSGPELKKPGETVKISCKASGYTFTHYGMNWVKQAPGKGLKWMGWINTYTGEPTY
:.:::::: :::::: .::.:::::::::: :.::::.::::.::.::::::: ::.:::
7A-4 QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAMNWVRQAPGQGLEWMGWINTNTGNPTY
10 40 70 100 130 160
70 80 90 100 110
TNFalp ADDFKEHFAFSLETSASTVFLQINNLKNEDTATYFCARERGDAMDYWGQGTSVTVSS
:. : .:.:::.::.::..:::.
7A-4 AQGFTGRFVFSLDTSVSTAYLQIS
190 220 250
117 residues in 1 query sequences
167083 residues in 638 library sequences
Tcomplib (4 proc)[version 3.2t07 August 17, 1999]
start: Mon Mar 13 19:21:53 2000 done: Mon Mar 13 19:21:54 2000
Scan time: 0.290 Display time: 0.010
Function used was TFASTA
Date: Mon, 13 Mar 2000 19:29:25 +0000
TFASTA translates and searches a DNA sequence data bank
version 3.2t07 August 17, 1999
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
/tmp/.fasta3-search-5551776: 19 aa
>TNFalphaHJ
vs V-Base too library
searching /data/gcgblast/v-base 0 library
167083 residues in 638 sequences
Expectation_n fit: rho(ln(x))= 3.9368+/-0.00846; mu= 1.1446+/- 0.477;
mean_var=9.1655+/- 6.547, 0's: 4 Z-trim: 12 B-trim: 13 in 1/17
Kolmogorov-Smirnov statistic: 0.2943 (N=25) at 46
TFASTA (3.27 August, 1999) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 36, gap-pen: -16/ -2, width: 16 reg.-scaled
Scan time: 0.140
The best scores are: initn init1 opt z-sc E(622)
JH3B ( 50) [2] 86 86 86 279.4 5.8e-11
JH3A ( 50) [2] 86 86 86 279.4 5.8e-11
JH6A ( 63) [3] 84 84 84 269.8 2e-10
JH6B ( 63) [3] 84 84 84 269.8 2e-10
JH4B ( 48) [3] 81 81 81 263.4 4.5e-10
JH4A ( 48) [3] 81 81 81 263.4 4.5e-10
JH4D ( 48) [3] 81 81 81 263.4 4.5e-10
JH6C ( 63) [3] 79 79 79 253.3 1.7e-09
JH5A ( 51) [3] 65 65 71 229.6 3.5e-08
JH5B ( 51) [3] 65 65 70 226.3 5.3e-08
JH1 ( 52) [1] 65 65 67 216.1 1.9e-07
JH2 ( 53) [2] 59 59 66 212.6 3.1e-07
JHPSI2 ( 54) [2] 35 35 35 110.0 0.16
>>JH3B (50 aa)
Frame: 2 initn: 86 init1: 86 opt: 86 Z-score: 279.4 expect() 5.8e-11
81.250% identity in 16 aa overlap (4-19:2-49)
10
TNFalp ERGDAMDYWGQGTSVTVSS
::.: ::::: :::::
JH3B DAFDIWGQGTMVTVSS
20
>>JH3A (50 aa)
Frame: 2 initn: 86 init1: 86 opt: 86 Z-score: 279.4 expect() 5.8e-11
81.250% identity in 16 aa overlap (4-19:2-49)
10
TNFalp ERGDAMDYWGQGTSVTVSS
::.: ::::: :::::
JH3A DAFDVWGQGTMVTVSS
20
>>JH6A (63 aa)
Frame: 3 initn: 84 init1: 84 opt: 84 Z-score: 269.8 expect() 2e-10
85.714% identity in 14 aa overlap (6-19:21-62)
10
TNFalp ERGDAMDYWGQGTSVTVSS
:: :::::.:::::
JH6A YYYYYGMDVWGQGTTVTVSS
30 60
>>JH6B (63 aa)
Frame: 3 initn: 84 init1: 84 opt: 84 Z-score: 269.8 expect() 2e-10
85.714% identity in 14 aa overlap (6-19:21-62)
10
TNFalp ERGDAMDYWGQGTSVTVSS
:: :::::.:::::
JH6B YYYYYGMDVWGQGTTVTVSS
30 60
>>JH4B (48 aa)
Frame: 3 initn: 81 init1: 81 opt: 81 Z-score: 263.4 expect() 4.5e-10
92.308% identity in 13 aa overlap (7-19:9-47)
10
TNFalp ERGDAMDYWGQGTSVTVSS
::::::: :::::
JH4B YFDYWGQGTLVTVSS
30
>>JH4A (48 aa)
Frame: 3 initn: 81 init1: 81 opt: 81 Z-score: 263.4 expect() 4.5e-10
92.308% identity in 13 aa overlap (7-19:9-47)
10
TNFalp ERGDAMDYWGQGTSVTVSS
::::::: :::::
JH4A YFDYWGQGTLVTVSS
30
>>JH4D (48 aa)
Frame: 3 initn: 81 init1: 81 opt: 81 Z-score: 263.4 expect() 4.5e-10
92.308% identity in 13 aa overlap (7-19:9-47)
10
TNFalp ERGDAMDYWGQGTSVTVSS
::::::: :::::
JH4D YFDYWGQGTLVTVSS
30
>>JH6C (63 aa)
Frame: 3 initn: 79 init1: 79 opt: 79 Z-score: 253.3 expect() 1.7e-09
78.571% identity in 14 aa overlap (6-19:21-62)
10
TNFalp ERGDAMDYWGQGTSVTVSS
:: ::.::.:::::
JH6C YYYYYYMDVWGKGTTVTVSS
30 60
>>JH5A (51 aa)
Frame: 3 initn: 65 init1: 65 opt: 71 Z-score: 229.6 expect() 3.5e-08
84.615% identity in 13 aa overlap (7-19:12-50)
10
TNFalp ERGDAMDYWGQGTSVTVSS
: ::::: :::::
JH5A NWFDSWGQGTLVTVSS
30
>>JH5B (51 aa)
Frame: 3 initn: 65 init1: 65 opt: 70 Z-score: 226.3 expect() 5.3e-08
84.615% identity in 13 aa overlap (7-19:12-50)
10
TNFalp ERGDAMDYWGQGTSVTVSS
: ::::: :::::
JH5B NWFDPWGQGTLVTVSS
30
>>JH1 (52 aa)
Frame: 1 initn: 65 init1: 65 opt: 67 Z-score: 216.1 expect() 1.9e-07
83.333% identity in 12 aa overlap (8-19:16-51)
10
TNFalp ERGDAMDYWGQGTSVTVSS
.::::: :::::
JH1 AEYFQHWGQGTLVTVSS
10 40
>>JH2 (53 aa)
Frame: 2 initn: 59 init1: 59 opt: 66 Z-score: 212.6 expect() 3.1e-07
76.923% identity in 13 aa overlap (7-19:14-52)
10
TNFalp ERGDAMDYWGQGTSVTVSS
: ::.:: :::::
JH2 YWYFDLWGRGTLVTVSS
20 50
>>JHPSI2 (54 aa)
Frame: 2 initn: 35 init1: 35 opt: 35 Z-score: 110.0 expect() 0.16
66.667% identity in 9 aa overlap (10-18:23-49)
10
TNFalp ERGDAMDYWGQGTSVTVSS
:::. :::
JHPSI2 LQVLGALGQGSPDTVSL
20 50
19 residues in 1 query sequences
167083 residues in 638 library sequences
Tcomplib (4 proc)[version 3.2t07 August 17, 1999]
start: Mon Mar 13 19:29:25 2000 done: Mon Mar 13 19:29:25 2000
Scan time: 0.140 Display time: 0.020
Function used was TFASTA
Date: Mon, 13 Mar 2000 19:23:23 +0000
TFASTA translates and searches a DNA sequence data bank
version 3.2t07 August 17, 1999
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
/tmp/.fasta3-search-5494149: 107 aa
>TNFalphaL
vs V-Base too library
searching /data/gcgblast/v-base 0 library
167083 residues in 638 sequences
Expectation_n fit: rho(ln(x))= 42.7516+/-0.0106; mu= -125.6237+/- 0.479;
mean_var=8984.8252+/-7774.508, 0's: 1 Z-trim: 0 B-trim: 0 in 0/21
Kolmogorov-Smirnov statistic: 0.1126 (N=22) at 46
TFASTA (3.27 August, 1999) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 36, gap-pen: -16/ -2, width: 16 reg.-scaled
Scan time: 0.260
The best scores are: initn init1 opt z-sc E(637)
L10A ( 290) [1] 413 311 423 82.3 5.7
DPK3_L11 ( 287) [1] 410 410 421 82.1 5.8
DPK23_L25- ( 290) [1] 408 311 418 81.8 6.1
V268 ( 290) [1] 408 311 418 81.8 6.1
DPK1_O18- ( 287) [1] 407 407 417 81.7 6.1
L16_HUMKV31ES- ( 287) [1] 407 407 415 81.5 6.3
DPK21_HUMKV328H5 ( 287) [1] 407 407 415 81.5 6.3
V3B ( 287) [1] 395 395 414 81.4 6.3
DPK9_O12- ( 287) [1] 391 391 414 81.4 6.3
HUMKV329 ( 287) [1] 401 401 412 81.2 6.5
VH ( 290) [1] 390 288 410 80.9 6.7
VG_38K- ( 287) [1] 400 400 409 80.9 6.8
V108 ( 287) [1] 393 393 408 80.8 6.9
DPK24_VKIVKLOB- ( 305) [1] 391 299 406 80.3 7.3
3A7 ( 287) [1] 399 399 402 80.1 7.5
VG_13K11- ( 287) [1] 394 394 397 79.6 8
VE ( 287) [1] 380 380 397 79.6 8
VA ( 287) [1] 381 381 395 79.4 8.2
DPK4_A20 ( 287) [1] 384 384 395 79.4 8.2
DPK8_VD ( 287) [1] 386 386 394 79.3 8.3
>>L10A (290 aa)
Frame: 1 initn: 413 init1: 311 opt: 423 Z-score: 82.3 expect() 5.7
64.211% identity in 95 aa overlap (2-95:4-288)
10 20 30 40 50
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVV-WYQQKPGQSPKMLMYSAFNRYTGVP
:::::.: : .: :.:::..: ::::::.. . ::::::::.:..:.:.: .: ::.:
L10A EIVMTQSPPTLSLSPGERVTLSCRASQSVSSSYLSWYQQKPGQAPRLLIYGASTRATGIP
10 40 70 100 130 160
60 70 80 90 100
TNFalp DRFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:::.:::::: :
L10A ARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLP
190 220 250 280
>>DPK3_L11 (287 aa)
Frame: 1 initn: 410 init1: 410 opt: 421 Z-score: 82.1 expect() 5.8
62.105% identity in 95 aa overlap (1-95:1-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
.: :::.:. : .:.:::::::: :::.. ::. :::::::..::.:.:.: . .:::.
DPK3_L AIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.: :::: :
DPK3_L RFSGSGSGTDFTLTISSLQPEDFATYYCLQDYNYP
190 220 250 280
>>DPK23_L25- (290 aa)
Frame: 1 initn: 408 init1: 311 opt: 418 Z-score: 81.8 expect() 6.1
63.158% identity in 95 aa overlap (2-95:4-288)
10 20 30 40 50
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVV-WYQQKPGQSPKMLMYSAFNRYTGVP
:::::.: : .: :.:.:..: ::::::.. . ::::::::.:..:.:.: .: ::.:
DPK23_ EIVMTQSPATLSLSPGERATLSCRASQSVSSSYLSWYQQKPGQAPRLLIYGASTRATGIP
10 40 70 100 130 160
60 70 80 90 100
TNFalp DRFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:::.:::::: :
DPK23_ ARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLP
190 220 250 280
>>V268 (290 aa)
Frame: 1 initn: 408 init1: 311 opt: 418 Z-score: 81.8 expect() 6.1
63.158% identity in 95 aa overlap (2-95:4-288)
10 20 30 40 50
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVV-WYQQKPGQSPKMLMYSAFNRYTGVP
:::::.: : .: :.:.:..: ::::::.. . ::::::::.:..:.:.: .: ::.:
V268 EIVMTQSPATLSLSPGERATLSCRASQSVSSSYLSWYQQKPGQAPRLLIYGASTRATGIP
10 40 70 100 130 160
60 70 80 90 100
TNFalp DRFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:::.:::::: :
V268 ARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLP
190 220 250 280
>>DPK1_O18- (287 aa)
Frame: 1 initn: 407 init1: 407 opt: 417 Z-score: 81.7 expect() 6.1
64.894% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: :::.:. : .:.:::::::: :::..:: . :::::::..::.:.:.: : ::::.
DPK1_O DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : ::::::::::.: ::.:.:.::: : :
DPK1_O RFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLP
190 220 250 280
>>L16_HUMKV31ES- (287 aa)
Frame: 1 initn: 407 init1: 407 opt: 415 Z-score: 81.5 expect() 6.3
61.702% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
:::::.: : :: :.:.:..: ::::::....::::::::.:..:.:.: .: ::.:
L16_HU EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : ::.::.::::.:.::.:::.::: : :
L16_HU RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWP
190 220 250 280
>>DPK21_HUMKV328H5 (287 aa)
Frame: 1 initn: 407 init1: 407 opt: 415 Z-score: 81.5 expect() 6.3
61.702% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
:::::.: : :: :.:.:..: ::::::....::::::::.:..:.:.: .: ::.:
DPK21_ EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : ::.::.::::.:.::.:::.::: : :
DPK21_ RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWP
190 220 250 280
>>V3B (287 aa)
Frame: 1 initn: 395 init1: 395 opt: 414 Z-score: 81.4 expect() 6.3
61.702% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: :::.:.:: .:.:::::::: ::::.:. . :::::::..::.:.:.: . .:::.
V3B DIQMTQSPSFLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.:: :..:
V3B RFSGSGSGTDFTLTISSLQPEDFATYYCQCGYSTP
190 220 250 280
>>DPK9_O12- (287 aa)
Frame: 1 initn: 391 init1: 391 opt: 414 Z-score: 81.4 expect() 6.3
61.702% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: :::.:. : .:.:::::::: ::::.:. . :::::::..::.:.:.: . .:::.
DPK9_O DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.:::.:..:
DPK9_O RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTP
190 220 250 280
>>HUMKV329 (287 aa)
Frame: 1 initn: 401 init1: 401 opt: 412 Z-score: 81.2 expect() 6.5
60.638% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
::: :.: : :: :.:.:..: ::::::....::::::::.:..:.:.: .: ::.:
HUMKV3 EIVMMQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : ::.::.::::.:.::.:::.::: : :
HUMKV3 RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNXP
190 220 250 280
>>VH (290 aa)
Frame: 1 initn: 390 init1: 288 opt: 410 Z-score: 80.9 expect() 6.7
62.105% identity in 95 aa overlap (2-95:4-288)
10 20 30 40 50
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSND-VVWYQQKPGQSPKMLMYSAFNRYTGVP
:::::.: : .: :.:::..: ::::::.. ..::::::::.:..:.:.: .: :..:
VH EIVMTQSPPTLSLSPGERVTLSCRASQSVSSSYLTWYQQKPGQAPRLLIYGASTRATSIP
10 40 70 100 130 160
60 70 80 90 100
TNFalp DRFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:::.::::.: :
VH ARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDHNLP
190 220 250 280
>>VG_38K- (287 aa)
Frame: 1 initn: 400 init1: 400 opt: 409 Z-score: 80.9 expect() 6.8
60.638% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
::.::.: : .: :.:.:..: ::::::. ..::::::::.:..:.:.: :: ::.:
VG_38K EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.. ::.:::.::: : :
VG_38K RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWP
190 220 250 280
>>V108 (287 aa)
Frame: 1 initn: 393 init1: 393 opt: 408 Z-score: 80.8 expect() 6.9
60.638% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: .::.:. : .:.:::::::: :::..:: . ::::::::.: .:.:.: . .:::.
V108 DIQVTQSPSSLSASVGDRVTITCRASQGISNGLSWYQQKPGQAPTLLIYAASSLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.: :::..:
V108 RFSGSGSGTDFTLTISSLQPEDVATYYCLQDYTTP
190 220 250 280
>>DPK24_VKIVKLOB- (305 aa)
Frame: 1 initn: 391 init1: 299 opt: 406 Z-score: 80.3 expect() 7.3
62.000% identity in 100 aa overlap (2-95:4-303)
10 20 30 40 50
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSV------SNDVVWYQQKPGQSPKMLMYSAFNR
:::::.: : :: :.:.::.: .:::: .: ..:::::::: ::.:.: : .:
DPK24_ DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTR
10 40 70 100 130 160
60 70 80 90 100
TNFalp YTGVPDRFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
.::::::.: : :::::.::::.::::.:::.::: :..:
DPK24_ ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP
190 220 250 280
>>3A7 (287 aa)
Frame: 1 initn: 399 init1: 399 opt: 402 Z-score: 80.1 expect() 7.5
59.783% identity in 92 aa overlap (2-93:4-279)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
::.::.: : .: :.:.:..: :::.::....::::::::.:..:.:.: :: ::.:
3A7 EIVLTQSPATLSLSPGERATLSCRASQGVSSNLAWYQQKPGQAPRLLIYDASNRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.. ::.:::.::: :
3A7 RFSGSGPGTDFTLTISSLEPEDFAVYYCQQRSNWH
190 220 250 280
>>VG_13K11- (287 aa)
Frame: 1 initn: 394 init1: 394 opt: 397 Z-score: 79.6 expect() 8
59.783% identity in 92 aa overlap (2-93:4-279)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
::.::.: : .: :.:.:..: :::.::. ..::::::::.:..:.:.: :: ::.:
VG_13K EIVLTQSPATLSLSPGERATLSCRASQGVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.. ::.:::.::: :
VG_13K RFSGSGPGTDFTLTISSLEPEDFAVYYCQQRSNWH
190 220 250 280
>>VE (287 aa)
Frame: 1 initn: 380 init1: 380 opt: 397 Z-score: 79.6 expect() 8
57.895% identity in 95 aa overlap (1-95:1-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
.: :::.:. . .:.:::::::: :::..:. ..:::::::..::.:.:.: . .:::.
VE AIRMTQSPSSFSASTGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::: .:.::.:.:.::: :. :
VE RFSGSGSGTDFTLTISCLQSEDFATYYCQQYYSYP
190 220 250 280
>>VA (287 aa)
Frame: 1 initn: 381 init1: 381 opt: 395 Z-score: 79.4 expect() 8.2
58.947% identity in 95 aa overlap (1-95:1-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
.: .::.:. : .:.:::::::: :::..:. ..:::::::..::.:.:.: . .:::.
VA AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.::: : :
VA RFSGSGSGTDFTLTISSLQPEDFATYYCQQFNNYP
190 220 250 280
>>DPK4_A20 (287 aa)
Frame: 1 initn: 384 init1: 384 opt: 395 Z-score: 79.4 expect() 8.2
59.574% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: :::.:. : .:.:::::::: :::..:: ..:::::::. ::.:.:.: . .:::.
DPK4_A DIQMTQSPSSLSASVGDRVTITCRASQGISNYLAWYQQKPGKVPKLLIYAASTLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : :::::.::::.: ::.:.:.::. ..:
DPK4_A RFSGSGSGTDFTLTISSLQPEDVATYYCQKYNSAP
190 220 250 280
>>DPK8_VD (287 aa)
Frame: 1 initn: 386 init1: 386 opt: 394 Z-score: 79.3 expect() 8.3
58.511% identity in 94 aa overlap (2-95:4-285)
10 20 30 40 50 60
TNFalp SIVMTQTPKFLLVSAGDRVTITCTASQSVSNDVVWYQQKPGQSPKMLMYSAFNRYTGVPD
: .::.:.:: .:.:::::::: :::..:. ..:::::::..::.:.:.: . .:::.
DPK8_V DIQLTQSPSFLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASTLQSGVPS
10 40 70 100 130 160
70 80 90 100
TNFalp RFTGRGYGTDFTFTISSVQAEDLAVYFCQQDYNSPRTFGGGTKLEIK
::.: : ::.::.::::.: ::.:.:.::: . :
DPK8_V RFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYP
190 220 250 280
107 residues in 1 query sequences
167083 residues in 638 library sequences
Tcomplib (4 proc)[version 3.2t07 August 17, 1999]
start: Mon Mar 13 19:23:23 2000 done: Mon Mar 13 19:23:23 2000
Scan time: 0.260 Display time: 0.040
Function used was TFASTA
Date: Mon, 13 Mar 2000 19:27:19 +0000
TFASTA translates and searches a DNA sequence data bank
version 3.2t07 August 17, 1999
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
/tmp/.fasta3-search-5719990: 12 aa
>TNFalphaLJ
vs V-Base too library
searching /data/gcgblast/v-base 0 library
167083 residues in 638 sequences
Expectation_n fit: rho(ln(x))= 2.8016+/-0.00905; mu= 3.4844+/- 0.511;
mean_var=16.5738+/-13.191, 0's: 17 Z-trim: 8 B-trim: 6 in 1/18
Kolmogorov-Smirnov statistic: 0.2052 (N=23) at 42
TFASTA (3.27 August, 1999) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 36, gap-pen: -16/ -2, width: 16 reg.-scaled
Scan time: 0.150
The best scores are: initn init1 opt z-sc E(613)
JK4 ( 38) [2] 66 66 66 178.5 2.4e-05
JK2 ( 39) [3] 60 60 60 163.6 0.00016
JK5 ( 38) [2] 57 57 57 156.4 0.00041
JK1 ( 38) [2] 56 56 56 154.0 0.00056
JK3 ( 38) [2] 52 52 52 144.1 0.002
>>JK4 (38 aa)
Frame: 2 initn: 66 init1: 66 opt: 66 Z-score: 178.5 expect() 2.4e-05
90.909% identity in 11 aa overlap (2-12:5-37)
10
TNFalp RTFGGGTKLEIK
:::::::.:::
JK4 LTFGGGTKVEIK
20
>>JK2 (39 aa)
Frame: 3 initn: 60 init1: 60 opt: 60 Z-score: 163.6 expect() 0.00016
90.909% identity in 11 aa overlap (2-12:6-38)
10
TNFalp RTFGGGTKLEIK
::: :::::::
JK2 YTFGQGTKLEIK
30
>>JK5 (38 aa)
Frame: 2 initn: 57 init1: 57 opt: 57 Z-score: 156.4 expect() 0.00041
81.818% identity in 11 aa overlap (2-12:5-37)
10
TNFalp RTFGGGTKLEIK
::: ::.::::
JK5 ITFGQGTRLEIK
20
>>JK1 (38 aa)
Frame: 2 initn: 56 init1: 56 opt: 56 Z-score: 154.0 expect() 0.00056
81.818% identity in 11 aa overlap (2-12:5-37)
10
TNFalp RTFGGGTKLEIK
::: :::.:::
JK1 WTFGQGTKVEIK
20
>>JK3 (38 aa)
Frame: 2 initn: 52 init1: 52 opt: 52 Z-score: 144.1 expect() 0.002
72.727% identity in 11 aa overlap (2-12:5-37)
10
TNFalp RTFGGGTKLEIK
::: :::..::
JK3 FTFGPGTKVDIK
20
12 residues in 1 query sequences
167083 residues in 638 library sequences
Tcomplib (4 proc)[version 3.2t07 August 17, 1999]
start: Mon Mar 13 19:27:19 2000 done: Mon Mar 13 19:27:19 2000
Scan time: 0.150 Display time: 0.010
Function used was TFASTA
Mike Clark