BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 041723
(228 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 46/118 (38%), Positives = 62/118 (52%), Gaps = 9/118 (7%)
Query: 82 PSLGNLTKLNDLYLFGNDFSGKVPDSLGDL-------LQLNYLTGEILVEIRKLTQLHIL 134
P+L N ++L L+L N SG +P SLG L L LN L GEI E+ + L L
Sbjct: 409 PTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETL 468
Query: 135 RLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
L N L G +PS + NL + LS+N L TG++ + LE+L L LS+N S
Sbjct: 469 ILDFNDLTGEIPSGLSNCTNLNWISLSNNRL--TGEIPKWIGRLENLAILKLSNNSFS 524
Score = 57.0 bits (136), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 43/123 (34%), Positives = 66/123 (53%), Gaps = 14/123 (11%)
Query: 82 PSLGNLTK-----LNDLYLFGNDFSGKVPDSLGDL-------LQLNYLTGEILVEIRKLT 129
P L NL + L +LYL N F+GK+P +L + L NYL+G I + L+
Sbjct: 380 PILPNLCQNPKNTLQELYLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLS 439
Query: 130 QLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
+L L+L N LEG +P + ++ L L L N+L TG++ L N +L + LS+N
Sbjct: 440 KLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDL--TGEIPSGLSNCTNLNWISLSNN 497
Query: 190 KLS 192
+L+
Sbjct: 498 RLT 500
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/114 (37%), Positives = 62/114 (54%), Gaps = 9/114 (7%)
Query: 83 SLGNLTKLNDLYLFGNDFSGKVPDSLGD-------LLQLNYLTGEILVEIRKLTQLHILR 135
SLG+L+KL DL L+ N G++P L +L N LTGEI + T L+ +
Sbjct: 434 SLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWIS 493
Query: 136 LAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
L+ N+L G +P I L NL L LS+N+ S G++ L + SL L L++N
Sbjct: 494 LSNNRLTGEIPKWIGRLENLAILKLSNNSFS--GNIPAELGDCRSLIWLDLNTN 545
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 112 LQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDL 171
+ N L+G I EI + L IL L N + GS+P + +LR L LDLS N L G
Sbjct: 636 MSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQ 695
Query: 172 NMVLLNLESLTALVLSSNKLS 192
M L + LT + LS+N LS
Sbjct: 696 AMSALTM--LTEIDLSNNNLS 714
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 18/89 (20%)
Query: 80 FLP-SLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAE 138
++P +G++ L L L ND SG +PD +GDL LN IL L+
Sbjct: 644 YIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLN-----------------ILDLSS 686
Query: 139 NQLEGSVPSSIFELRNLRALDLSDNNLSG 167
N+L+G +P ++ L L +DLS+NNLSG
Sbjct: 687 NKLDGRIPQAMSALTMLTEIDLSNNNLSG 715
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 41/142 (28%), Positives = 65/142 (45%), Gaps = 38/142 (26%)
Query: 98 NDFSGKVPDSLGDL----------------------------------LQLNYLTGEILV 123
N+FSG++P+SL +L LQ N TG+I
Sbjct: 350 NEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNGFTGKIPP 409
Query: 124 EIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTA 183
+ ++L L L+ N L G++PSS+ L LR L L N L G++ L+ +++L
Sbjct: 410 TLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLE--GEIPQELMYVKTLET 467
Query: 184 LVLSSNKLS--LLAGTTVNTNL 203
L+L N L+ + +G + TNL
Sbjct: 468 LILDFNDLTGEIPSGLSNCTNL 489
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 33/100 (33%), Positives = 51/100 (51%), Gaps = 13/100 (13%)
Query: 98 NDFSGKVPDSLGDLLQL-------NYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIF 150
N+FS +P LGD L N L+G+ I T+L +L ++ NQ G +P
Sbjct: 207 NNFSTGIP-FLGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFVGPIPP--L 263
Query: 151 ELRNLRALDLSDNNLSGTGDLNMVLLN-LESLTALVLSSN 189
L++L+ L L++N TG++ L ++LT L LS N
Sbjct: 264 PLKSLQYLSLAENKF--TGEIPDFLSGACDTLTGLDLSGN 301
Score = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 41/116 (35%), Positives = 55/116 (47%), Gaps = 12/116 (10%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSL--------GDLLQLNYLTGEILVEIRKLTQLHILRLAE 138
L L L L N F+G++PD L G L N+ G + + L L L+
Sbjct: 265 LKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSS 324
Query: 139 NQLEGSVP-SSIFELRNLRALDLSDNNLSGTGDLNMVLLNLE-SLTALVLSSNKLS 192
N G +P ++ ++R L+ LDLS N S G+L L NL SL L LSSN S
Sbjct: 325 NNFSGELPMDTLLKMRGLKVLDLSFNEFS--GELPESLTNLSASLLTLDLSSNNFS 378
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 17/71 (23%)
Query: 98 NDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELR-NLR 156
N+FSG++P + + K+ L +L L+ N+ G +P S+ L +L
Sbjct: 325 NNFSGELP----------------MDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASLL 368
Query: 157 ALDLSDNNLSG 167
LDLS NN SG
Sbjct: 369 TLDLSSNNFSG 379
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 6/86 (6%)
Query: 112 LQLNYLTGEI--LVEIRKLTQLHILRLAENQLE--GSVPSSIFELRNLRALDLSDNNLSG 167
L N L+G + L + + L L ++ N L+ G V S +L +L LDLS N++SG
Sbjct: 104 LSRNSLSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKV-SGGLKLNSLEVLDLSANSISG 162
Query: 168 TGDLNMVLLN-LESLTALVLSSNKLS 192
+ VL + L L +S NK+S
Sbjct: 163 ANVVGWVLSDGCGELKHLAISGNKIS 188
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 46/118 (38%), Positives = 62/118 (52%), Gaps = 9/118 (7%)
Query: 82 PSLGNLTKLNDLYLFGNDFSGKVPDSLGDL-------LQLNYLTGEILVEIRKLTQLHIL 134
P+L N ++L L+L N SG +P SLG L L LN L GEI E+ + L L
Sbjct: 412 PTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETL 471
Query: 135 RLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
L N L G +PS + NL + LS+N L TG++ + LE+L L LS+N S
Sbjct: 472 ILDFNDLTGEIPSGLSNCTNLNWISLSNNRL--TGEIPKWIGRLENLAILKLSNNSFS 527
Score = 57.0 bits (136), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 43/123 (34%), Positives = 66/123 (53%), Gaps = 14/123 (11%)
Query: 82 PSLGNLTK-----LNDLYLFGNDFSGKVPDSLGDL-------LQLNYLTGEILVEIRKLT 129
P L NL + L +LYL N F+GK+P +L + L NYL+G I + L+
Sbjct: 383 PILPNLCQNPKNTLQELYLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLS 442
Query: 130 QLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
+L L+L N LEG +P + ++ L L L N+L TG++ L N +L + LS+N
Sbjct: 443 KLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDL--TGEIPSGLSNCTNLNWISLSNN 500
Query: 190 KLS 192
+L+
Sbjct: 501 RLT 503
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 43/114 (37%), Positives = 62/114 (54%), Gaps = 9/114 (7%)
Query: 83 SLGNLTKLNDLYLFGNDFSGKVPDSLGD-------LLQLNYLTGEILVEIRKLTQLHILR 135
SLG+L+KL DL L+ N G++P L +L N LTGEI + T L+ +
Sbjct: 437 SLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWIS 496
Query: 136 LAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
L+ N+L G +P I L NL L LS+N+ S G++ L + SL L L++N
Sbjct: 497 LSNNRLTGEIPKWIGRLENLAILKLSNNSFS--GNIPAELGDCRSLIWLDLNTN 548
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 112 LQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDL 171
+ N L+G I EI + L IL L N + GS+P + +LR L LDLS N L G
Sbjct: 639 MSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQ 698
Query: 172 NMVLLNLESLTALVLSSNKLS 192
M L + LT + LS+N LS
Sbjct: 699 AMSALTM--LTEIDLSNNNLS 717
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 18/89 (20%)
Query: 80 FLP-SLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAE 138
++P +G++ L L L ND SG +PD +GDL LN IL L+
Sbjct: 647 YIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLN-----------------ILDLSS 689
Query: 139 NQLEGSVPSSIFELRNLRALDLSDNNLSG 167
N+L+G +P ++ L L +DLS+NNLSG
Sbjct: 690 NKLDGRIPQAMSALTMLTEIDLSNNNLSG 718
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 41/142 (28%), Positives = 65/142 (45%), Gaps = 38/142 (26%)
Query: 98 NDFSGKVPDSLGDL----------------------------------LQLNYLTGEILV 123
N+FSG++P+SL +L LQ N TG+I
Sbjct: 353 NEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNGFTGKIPP 412
Query: 124 EIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTA 183
+ ++L L L+ N L G++PSS+ L LR L L N L G++ L+ +++L
Sbjct: 413 TLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLE--GEIPQELMYVKTLET 470
Query: 184 LVLSSNKLS--LLAGTTVNTNL 203
L+L N L+ + +G + TNL
Sbjct: 471 LILDFNDLTGEIPSGLSNCTNL 492
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 33/100 (33%), Positives = 51/100 (51%), Gaps = 13/100 (13%)
Query: 98 NDFSGKVPDSLGDLLQL-------NYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIF 150
N+FS +P LGD L N L+G+ I T+L +L ++ NQ G +P
Sbjct: 210 NNFSTGIP-FLGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFVGPIPP--L 266
Query: 151 ELRNLRALDLSDNNLSGTGDLNMVLLN-LESLTALVLSSN 189
L++L+ L L++N TG++ L ++LT L LS N
Sbjct: 267 PLKSLQYLSLAENKF--TGEIPDFLSGACDTLTGLDLSGN 304
Score = 34.3 bits (77), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 41/116 (35%), Positives = 55/116 (47%), Gaps = 12/116 (10%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSL--------GDLLQLNYLTGEILVEIRKLTQLHILRLAE 138
L L L L N F+G++PD L G L N+ G + + L L L+
Sbjct: 268 LKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSS 327
Query: 139 NQLEGSVP-SSIFELRNLRALDLSDNNLSGTGDLNMVLLNLE-SLTALVLSSNKLS 192
N G +P ++ ++R L+ LDLS N S G+L L NL SL L LSSN S
Sbjct: 328 NNFSGELPMDTLLKMRGLKVLDLSFNEFS--GELPESLTNLSASLLTLDLSSNNFS 381
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 17/71 (23%)
Query: 98 NDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELR-NLR 156
N+FSG++P + + K+ L +L L+ N+ G +P S+ L +L
Sbjct: 328 NNFSGELP----------------MDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASLL 371
Query: 157 ALDLSDNNLSG 167
LDLS NN SG
Sbjct: 372 TLDLSSNNFSG 382
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 6/86 (6%)
Query: 112 LQLNYLTGEI--LVEIRKLTQLHILRLAENQLE--GSVPSSIFELRNLRALDLSDNNLSG 167
L N L+G + L + + L L ++ N L+ G V S +L +L LDLS N++SG
Sbjct: 107 LSRNSLSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKV-SGGLKLNSLEVLDLSANSISG 165
Query: 168 TGDLNMVLLN-LESLTALVLSSNKLS 192
+ VL + L L +S NK+S
Sbjct: 166 ANVVGWVLSDGCGELKHLAISGNKIS 191
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 37/110 (33%), Positives = 53/110 (48%), Gaps = 18/110 (16%)
Query: 83 SLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLE 142
SL NL LN LY+ G +N L G I I KLTQLH L + +
Sbjct: 71 SLANLPYLNFLYIGG----------------INNLVGPIPPAIAKLTQLHYLYITHTNVS 114
Query: 143 GSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
G++P + +++ L LD S N LSGT L + +L +L + N++S
Sbjct: 115 GAIPDFLSQIKTLVTLDFSYNALSGT--LPPSISSLPNLVGITFDGNRIS 162
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 40/132 (30%), Positives = 63/132 (47%), Gaps = 15/132 (11%)
Query: 82 PSLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQL-------NYLTGEILVEIRKLTQLHIL 134
P++ LT+L+ LY+ + SG +PD L + L N L+G + I L L +
Sbjct: 95 PAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGI 154
Query: 135 RLAENQLEGSVPSSIFELRNL-RALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKL-- 191
N++ G++P S L ++ +S N L TG + NL +L + LS N L
Sbjct: 155 TFDGNRISGAIPDSYGSFSKLFTSMTISRNRL--TGKIPPTFANL-NLAFVDLSRNMLEG 211
Query: 192 --SLLAGTTVNT 201
S+L G+ NT
Sbjct: 212 DASVLFGSDKNT 223
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 59/141 (41%), Gaps = 34/141 (24%)
Query: 82 PSLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQL--------NYLTGEILVEIRKLTQLHI 133
PS+ +L L + GN SG +PDS G +L N LTG+I L L
Sbjct: 143 PSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANL-NLAF 201
Query: 134 LRLAENQLEGSVP-----------------SSIFEL------RNLRALDLSDNNLSGTGD 170
+ L+ N LEG S F+L +NL LDL +N + GT
Sbjct: 202 VDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGT-- 259
Query: 171 LNMVLLNLESLTALVLSSNKL 191
L L L+ L +L +S N L
Sbjct: 260 LPQGLTQLKFLHSLNVSFNNL 280
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 44/120 (36%), Positives = 56/120 (46%), Gaps = 17/120 (14%)
Query: 83 SLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVE----------IRKLTQLH 132
+L LT L L L GN +P+ + D +L L +LVE KLT L
Sbjct: 80 ALKELTNLTYLILTGNQLQS-LPNGVFD--KLTNLKELVLVENQLQSLPDGVFDKLTNLT 136
Query: 133 ILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKL 191
L LA NQL+ S+P +F+ L NL LDLS N L + V L L L L N+L
Sbjct: 137 YLNLAHNQLQ-SLPKGVFDKLTNLTELDLSYNQLQSLPE--GVFDKLTQLKDLRLYQNQL 193
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 127 KLTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGT 168
KLTQL LRL +NQL+ SVP +F+ L +L+ + L DN T
Sbjct: 179 KLTQLKDLRLYQNQLK-SVPDGVFDRLTSLQYIWLHDNPWDCT 220
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 38/115 (33%), Positives = 49/115 (42%), Gaps = 19/115 (16%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSLGDLL-----------QLNYLTGEILVEIRKLTQLHILR 135
LT L +L L N +PD + D L QL L + KLT L L
Sbjct: 108 LTNLKELVLVENQLQS-LPDGVFDKLTNLTYLNLAHNQLQSLPKGVF---DKLTNLTELD 163
Query: 136 LAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
L+ NQL+ S+P +F+ L L+ L L N L D V L SL + L N
Sbjct: 164 LSYNQLQ-SLPEGVFDKLTQLKDLRLYQNQLKSVPD--GVFDRLTSLQYIWLHDN 215
>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
Length = 251
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 19/80 (23%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVP 146
LT+L+ LYL GN +P + D +LT+L LRL NQL+ S+P
Sbjct: 106 LTQLDKLYLGGNQLK-SLPSGVFD----------------RLTKLKELRLNTNQLQ-SIP 147
Query: 147 SSIFE-LRNLRALDLSDNNL 165
+ F+ L NL+ L LS N L
Sbjct: 148 AGAFDKLTNLQTLSLSTNQL 167
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 19/80 (23%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVP 146
LT+L+ LYL GN +P + D +LT+L LRL NQL+ S+P
Sbjct: 106 LTQLDKLYLGGNQLK-SLPSGVFD----------------RLTKLKELRLNTNQLQ-SIP 147
Query: 147 SSIFE-LRNLRALDLSDNNL 165
+ F+ L NL+ L LS N L
Sbjct: 148 AGAFDKLTNLQTLSLSTNQL 167
>pdb|3V47|A Chain A, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
pdb|3V47|B Chain B, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
Length = 455
Score = 33.5 bits (75), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 128 LTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVL 186
LT L L L++N L GS+ S +FE L L LDLS N++ GD L L +L L L
Sbjct: 322 LTHLLKLNLSQNFL-GSIDSRMFENLDKLEVLDLSYNHIRALGD--QSFLGLPNLKELAL 378
Query: 187 SSNKL 191
+N+L
Sbjct: 379 DTNQL 383
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 42/120 (35%), Positives = 56/120 (46%), Gaps = 17/120 (14%)
Query: 83 SLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVE----------IRKLTQLH 132
+L LT L L L GN +P+ + D +L L +LVE KLT L
Sbjct: 80 ALKELTNLTYLILTGNQLQS-LPNGVFD--KLTNLKELVLVENQLQSLPDGVFDKLTNLT 136
Query: 133 ILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKL 191
L L NQL+ S+P +F+ L NL LDL +N L + V L L L L+ N+L
Sbjct: 137 YLYLYHNQLQ-SLPKGVFDKLTNLTRLDLDNNQLQSLPE--GVFDKLTQLKQLSLNDNQL 193
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 40/115 (34%), Positives = 52/115 (45%), Gaps = 19/115 (16%)
Query: 87 LTKLNDLYLFGNDFSGKVPDSLGDLL-----------QLNYLTGEILVEIRKLTQLHILR 135
LT L +L L N +PD + D L QL L + KLT L L
Sbjct: 108 LTNLKELVLVENQLQS-LPDGVFDKLTNLTYLYLYHNQLQSLPKGVF---DKLTNLTRLD 163
Query: 136 LAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
L NQL+ S+P +F+ L L+ L L+DN L D V L SLT + L +N
Sbjct: 164 LDNNQLQ-SLPEGVFDKLTQLKQLSLNDNQLKSVPD--GVFDRLTSLTHIWLLNN 215
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 127 KLTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGT 168
KLTQL LRL +NQL+ SVP +F+ L +L+ + L DN T
Sbjct: 122 KLTQLKDLRLYQNQLK-SVPDGVFDRLTSLQYIWLHDNPWDCT 163
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 40/111 (36%), Positives = 49/111 (44%), Gaps = 11/111 (9%)
Query: 87 LTKLNDLYLFGNDFSG---KVPDSLGDLLQLNYLTGEILV----EIRKLTQLHILRLAEN 139
LT L LYL GN V + L L LN T ++ KLTQL L L N
Sbjct: 51 LTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTN 110
Query: 140 QLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
QL+ S+P +F+ L L+ L L N L D V L SL + L N
Sbjct: 111 QLQ-SLPDGVFDKLTQLKDLRLYQNQLKSVPD--GVFDRLTSLQYIWLHDN 158
>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 306
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 109 GDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNL 165
G+ Q N+L +I E+R LT L L++ QLE P++ L +L+ L++S NN
Sbjct: 159 GNSFQENFLP-DIFTELRNLT---FLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNF 211
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 112 LQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIF-ELRNLRALDLSDNNLSG 167
LQ N L+ +LT+L +L L +N+L+ ++P+ IF EL+NL L ++DN L
Sbjct: 44 LQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQ-TLPAGIFKELKNLETLWVTDNKLQA 99
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 127 KLTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALV 185
KLT L LRL NQL+ VP F+ L L+ L L +N L + +LE L L
Sbjct: 155 KLTSLKELRLYNNQLK-RVPEGAFDKLTELKTLKLDNNQLKRVPE--GAFDSLEKLKMLQ 211
Query: 186 LSSN 189
L N
Sbjct: 212 LQEN 215
>pdb|2XOT|A Chain A, Crystal Structure Of Neuronal Leucine Rich Repeat Protein
Amigo-1
pdb|2XOT|B Chain B, Crystal Structure Of Neuronal Leucine Rich Repeat Protein
Amigo-1
Length = 361
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 104 VPDSLGDLLQLNYLTGEILVEIR------KLTQLHILRLAENQLEGSVPSSIFELRNLRA 157
VP SL L L+ L +R +LT LH L L+ N L + + NLR
Sbjct: 33 VPQSLPSYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRY 92
Query: 158 LDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKL 191
LDLS N+L + + +L++L L+L +N +
Sbjct: 93 LDLSSNHLHTLDEF--LFSDLQALEVLLLYNNHI 124
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 109 GDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNL 165
G+ Q N+L +I E+R LT L L++ QLE P++ L +L+ L++S NN
Sbjct: 478 GNSFQENFLP-DIFTELRNLT---FLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNF 530
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 109 GDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNL 165
G+ Q N+L +I E+R LT L L++ QLE P++ L +L+ L++S NN
Sbjct: 454 GNSFQENFLP-DIFTELRNLT---FLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNF 506
>pdb|2V9S|A Chain A, Second Lrr Domain Of Human Slit2
pdb|2V9S|B Chain B, Second Lrr Domain Of Human Slit2
pdb|2V9S|C Chain C, Second Lrr Domain Of Human Slit2
pdb|2V9S|D Chain D, Second Lrr Domain Of Human Slit2
Length = 220
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 134 LRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSL 193
+RL +N ++ P + + LR +DLS+N +S L SL +LVL NK++
Sbjct: 37 IRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAP--DAFQGLRSLNSLVLYGNKITE 94
Query: 194 LAGT 197
L +
Sbjct: 95 LPKS 98
>pdb|2V9T|B Chain B, Complex Between The Second Lrr Domain Of Slit2 And The
First Ig Domain From Robo1
Length = 220
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 134 LRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSL 193
+RL +N ++ P + + LR +DLS+N +S L SL +LVL NK++
Sbjct: 37 IRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAP--DAFQGLRSLNSLVLYGNKITE 94
Query: 194 LAGT 197
L +
Sbjct: 95 LPKS 98
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 30.4 bits (67), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 127 KLTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALV 185
KLTQL L L++NQ++ S+P +F+ L L L L +N L N V L L L
Sbjct: 50 KLTQLTKLSLSQNQIQ-SLPDGVFDKLTKLTILYLHENKLQSLP--NGVFDKLTQLKELA 106
Query: 186 LSSNKL 191
L +N+L
Sbjct: 107 LDTNQL 112
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 127 KLTQLHILRLAENQLEGSVPSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALV 185
KLT+L IL L EN+L+ S+P+ +F+ L L+ L L N L D + L SL +
Sbjct: 74 KLTKLTILYLHENKLQ-SLPNGVFDKLTQLKELALDTNQLKSVPD--GIFDRLTSLQKIW 130
Query: 186 LSSN 189
L +N
Sbjct: 131 LHTN 134
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 37/107 (34%), Positives = 53/107 (49%), Gaps = 12/107 (11%)
Query: 93 LYLFGNDFSGKVP---DSLGDLLQL----NYLTGEILVEIRKLTQLHILRLAENQLEGSV 145
LYL N + P DSL +L +L N L + LTQL +L L NQL +
Sbjct: 45 LYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLT-VL 103
Query: 146 PSSIFE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKL 191
PS++F+ L +L+ L + N L+ +L + L LT L L N+L
Sbjct: 104 PSAVFDRLVHLKELFMCCNKLT---ELPRGIERLTHLTHLALDQNQL 147
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 128 LTQLHILRLAENQLEGSVPSSIF-ELRNLRALDLSDNNLSGTGDLNMVLLN-LESLTALV 185
L+ L +L++A N + + IF ELRNL LDLS L L+ N L SL L
Sbjct: 444 LSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLE---QLSPTAFNSLSSLQVLN 500
Query: 186 LSSNKL 191
++SN+L
Sbjct: 501 MASNQL 506
>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX
Length = 462
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 38/112 (33%), Positives = 60/112 (53%), Gaps = 9/112 (8%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVP-DSLGDLLQLNYLTGEI--LVEIRKLTQLHILRLAENQ 140
L NLTKL D+ + N + P +L +L L +I + ++ LT L+ L L+ N
Sbjct: 81 LKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNT 140
Query: 141 LEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
+ S S++ L +L+ L+ S N ++ DL L NL +L L +SSNK+S
Sbjct: 141 I--SDISALSGLTSLQQLNFSSNQVT---DL-KPLANLTTLERLDISSNKVS 186
>pdb|1P9A|G Chain G, Crystal Structure Of N-terminal Domain Of Human Platelet
Receptor Glycoprotein Ib-alpha At 1.7 Angstrom
Resolution
pdb|1QYY|A Chain A, Crystal Structure Of N-Terminal Domain Of Human Platelet
Receptor Glycoprotein Ib-Alpha At 2.8 Angstrom
Resolution
pdb|1QYY|G Chain G, Crystal Structure Of N-Terminal Domain Of Human Platelet
Receptor Glycoprotein Ib-Alpha At 2.8 Angstrom
Resolution
Length = 290
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++NNL+ +L
Sbjct: 109 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLT---ELPA 165
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 166 GLLNGLENLDTLLLQENSL 184
>pdb|1GWB|B Chain B, Structure Of Glycoprotein 1b
pdb|1GWB|A Chain A, Structure Of Glycoprotein 1b
Length = 281
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++NNL+ +L
Sbjct: 110 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLT---ELPA 166
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 167 GLLNGLENLDTLLLQENSL 185
>pdb|1P8V|A Chain A, Crystal Structure Of The Complex Of Platelet Receptor
Gpib-alpha And Alpha-thrombin At 2.6a
Length = 279
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++NNL+ +L
Sbjct: 109 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLT---ELPA 165
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 166 GLLNGLENLDTLLLQENSL 184
>pdb|3CIG|A Chain A, Crystal Structure Of Mouse Tlr3 Ectodomain
pdb|3CIY|A Chain A, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
Double-Stranded Rna
pdb|3CIY|B Chain B, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
Double-Stranded Rna
Length = 697
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 125 IRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTAL 184
+ L +L + R+A ++ S PS LRNL LDLS+NN++ + +L LE+L L
Sbjct: 453 VPSLQRLMLRRVALKNVDIS-PSPFRPLRNLTILDLSNNNIANINE--DLLEGLENLEIL 509
Query: 185 VLSSNKLSLL 194
N L+ L
Sbjct: 510 DFQHNNLARL 519
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 37/107 (34%), Positives = 50/107 (46%), Gaps = 13/107 (12%)
Query: 99 DFSGKVPDSLGDLL-------QLN-YLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIF 150
+FS ++G L QLN +LT ++ E+ T + L LA NQL + S+
Sbjct: 185 EFSPGCFQTIGKLFALLLNNAQLNPHLTEKLCWELSN-TSIQNLSLANNQLLATSESTFS 243
Query: 151 ELR--NLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSLLA 195
L+ NL LDLS NNL G N L SL L L N + L+
Sbjct: 244 GLKWTNLTQLDLSYNNLHDVG--NGSFSYLPSLRYLSLEYNNIQRLS 288
>pdb|1OOK|G Chain G, Crystal Structure Of The Complex Of Platelet Receptor
Gpib-alpha And Human Alpha-thrombin
Length = 290
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++NNL+ +L
Sbjct: 109 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLT---ELPA 165
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 166 GLLNGLENLDTLLLQENSL 184
>pdb|3PMH|G Chain G, Mechanism Of Sulfotyrosine-Mediated Glycoprotein Ib
Interaction With Two Distinct Alpha-Thrombin Sites
Length = 290
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++NNL+ +L
Sbjct: 109 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLT---ELPA 165
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 166 GLLNGLENLDTLLLQENSL 184
>pdb|3G3B|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|C Chain C, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|E Chain E, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|G Chain G, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
Length = 170
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 47/101 (46%), Gaps = 13/101 (12%)
Query: 99 DFSGK----VPDSLGDLLQLNYLTGEILVEIR-----KLTQLHILRLAENQLEGSVPSSI 149
D SGK VP + Q+ YL + ++ +LTQL L L NQL +P+ +
Sbjct: 15 DCSGKSLASVPTGIPTTTQVLYLYDNRITKLEPGVFDRLTQLTRLDLDNNQLT-VLPAGV 73
Query: 150 FE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
F+ L L L L+DN L NL SLT + L +N
Sbjct: 74 FDKLTQLTQLSLNDNQLKSIP--RGAFDNLRSLTHIWLLNN 112
>pdb|3G39|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor
Length = 170
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 48/101 (47%), Gaps = 13/101 (12%)
Query: 99 DFSGK----VPDSLGDLLQLNYLTGEILVEIR-----KLTQLHILRLAENQLEGSVPSSI 149
D SGK VP + Q+ YL + ++ +LTQL L L NQL +P+ +
Sbjct: 15 DCSGKSLASVPTGIPTTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLT-VLPAGV 73
Query: 150 FE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
F+ L L L L+DN L NL+SLT + L +N
Sbjct: 74 FDKLTQLTQLSLNDNQLKSIP--RGAFDNLKSLTHIWLLNN 112
>pdb|3TWI|D Chain D, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
pdb|3TWI|E Chain E, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
pdb|3TWI|F Chain F, Variable Lymphocyte Receptor Recognition Of The
Immunodominant Glycoprotein Of Bacillus Anthracis Spores
Length = 179
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 12/92 (13%)
Query: 76 CKENFLPSL--GNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYL-------TGEILVEIR 126
C+E L S+ G T L+L+ N + P L QL YL T +
Sbjct: 26 CQERSLASVPAGIPTTTQVLHLYINQITKLEPGVFDSLTQLTYLNLAVNQLTALPVGVFD 85
Query: 127 KLTQLHILRLAENQLEGSVPSSIFELRNLRAL 158
KLT+L L L NQL+ S+P +F+ NL++L
Sbjct: 86 KLTKLTHLALHINQLK-SIPMGVFD--NLKSL 114
>pdb|3G3A|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|C Chain C, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|E Chain E, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
pdb|3G3A|G Chain G, Structure Of A Lamprey Variable Lymphocyte Receptor In
Complex With A Protein Antigen
Length = 178
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 48/101 (47%), Gaps = 13/101 (12%)
Query: 99 DFSGK----VPDSLGDLLQLNYLTGEILVEIR-----KLTQLHILRLAENQLEGSVPSSI 149
D SGK VP + Q+ YL + ++ +LTQL L L NQL +P+ +
Sbjct: 23 DCSGKSLASVPTGIPTTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLT-VLPAGV 81
Query: 150 FE-LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSN 189
F+ L L L L+DN L NL+SLT + L +N
Sbjct: 82 FDKLTQLTQLSLNDNQLKSIP--RGAFDNLKSLTHIWLLNN 120
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 24/39 (61%)
Query: 152 LRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNK 190
L NLR LDLS +++ + N+ L NL L +L LS N+
Sbjct: 349 LENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNE 387
>pdb|2OMU|A Chain A, Crystal Structure Of Inla G194s+s Y369s/hec1 Complex
Length = 462
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 38/112 (33%), Positives = 59/112 (52%), Gaps = 9/112 (8%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVP-DSLGDLLQLNYLTGEI--LVEIRKLTQLHILRLAENQ 140
L NLTKL D+ + N + P +L +L L +I + ++ LT L+ L L+ N
Sbjct: 81 LKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNT 140
Query: 141 LEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
+ S S++ L +L+ L S N ++ DL L NL +L L +SSNK+S
Sbjct: 141 I--SDISALSGLTSLQQLSFSSNQVT---DL-KPLANLTTLERLDISSNKVS 186
>pdb|2OMT|A Chain A, Crystal Structure Of Inla G194s+sHEC1 COMPLEX
Length = 462
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 38/112 (33%), Positives = 59/112 (52%), Gaps = 9/112 (8%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVP-DSLGDLLQLNYLTGEI--LVEIRKLTQLHILRLAENQ 140
L NLTKL D+ + N + P +L +L L +I + ++ LT L+ L L+ N
Sbjct: 81 LKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNT 140
Query: 141 LEGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLS 192
+ S S++ L +L+ L S N ++ DL L NL +L L +SSNK+S
Sbjct: 141 I--SDISALSGLTSLQQLSFSSNQVT---DL-KPLANLTTLERLDISSNKVS 186
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 73 IAYCKENFLPSLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYL 117
+A C +P+L L KL++L L GN S P S L+ L L
Sbjct: 192 LAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQGLMHLQKL 236
>pdb|1W8A|A Chain A, Third Lrr Domain Of Drosophila Slit
Length = 192
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 2/88 (2%)
Query: 102 GKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLS 161
G++P + L+ N LTG + + L+L EN+++ L L+ L+L
Sbjct: 51 GRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLY 110
Query: 162 DNNLSGTGDLNMVLLNLESLTALVLSSN 189
DN +S + +L SLT+L L+SN
Sbjct: 111 DNQISCV--MPGSFEHLNSLTSLNLASN 136
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 104 VPDSLGDLLQLNY----LTGEILVEIRKLTQLHILRLAENQLE--GSVPSSIFELRNLRA 157
P + L L++ LT + LT+L L L NQL+ + ++++L+
Sbjct: 319 CPSKISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQ 378
Query: 158 LDLSDNNLS---GTGDLNMVLLNLESLTALVLSSNKLS 192
LD+S N++S GD + +SL +L +SSN L+
Sbjct: 379 LDISQNSVSYDEKKGDCSWT----KSLLSLNMSSNILT 412
>pdb|3DXI|A Chain A, Crystal Structure Of The N-Terminal Domain Of A Putative
Aldolase (Bvu_2661) From Bacteroides Vulgatus
pdb|3DXI|B Chain B, Crystal Structure Of The N-Terminal Domain Of A Putative
Aldolase (Bvu_2661) From Bacteroides Vulgatus
Length = 320
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 12/90 (13%)
Query: 80 FLPSLGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAEN 139
FL L + K+ DL+ + F G P + +LL+ E+RK T + + +
Sbjct: 146 FLSKLKAIDKIADLFCXVDSFGGITPKEVKNLLK----------EVRKYTHVPVGFHGHD 195
Query: 140 QLEGSVPSSIFELRNLRALDLSDNNLSGTG 169
L+ + +SI + + +D D ++G G
Sbjct: 196 NLQLGLINSITAIDD--GIDFIDATITGXG 223
>pdb|1SQ0|B Chain B, Crystal Structure Of The Complex Of The Wild-Type Von
Willebrand Factor A1 Domain And Glycoprotein Ib Alpha At
2.6 Angstrom Resolution
Length = 288
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LNYLTGEILVEIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTGDLNM 173
N LT L +R L +L L L N+L+ P + L L L++N+L+ +L
Sbjct: 109 FNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNDLT---ELPA 165
Query: 174 VLLN-LESLTALVLSSNKL 191
LLN LE+L L+L N L
Sbjct: 166 GLLNGLENLDTLLLQENSL 184
>pdb|2WFH|A Chain A, The Human Slit 2 Dimerization Domain D4
pdb|2WFH|B Chain B, The Human Slit 2 Dimerization Domain D4
Length = 193
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 52/111 (46%), Gaps = 14/111 (12%)
Query: 90 LNDLYLFGNDFSGKVPDSLGDLLQL-------NYLTGEILVEIRKLTQLHILRLAENQLE 142
+ +LYL GN F+ VP L + L N ++ +TQL L L+ N+L
Sbjct: 33 VTELYLDGNQFT-LVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNRLR 91
Query: 143 GSVPSSIFELRNLRALDLSDNNLS--GTGDLNMVLLNLESLTALVLSSNKL 191
P + L++LR L L N++S G N +L +L+ L + +N L
Sbjct: 92 CIPPRTFDGLKSLRLLSLHGNDISVVPEGAFN----DLSALSHLAIGANPL 138
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 28.1 bits (61), Expect = 4.7, Method: Composition-based stats.
Identities = 27/115 (23%), Positives = 55/115 (47%), Gaps = 8/115 (6%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQL-- 141
GN+ K+ + +L N FS + D++ D + +T E + E +K L + + A+ L
Sbjct: 646 FGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREIT-ETIAEAKKKV-LDVTKEAQANLLT 703
Query: 142 --EGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSLL 194
G FE +R L+ + + ++N L +L ++ +V++ +K S +
Sbjct: 704 AKHGMTLRESFEDNVVRFLNEARDKAGRLAEVN--LKDLNNVKQMVMAGSKGSFI 756
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 27/115 (23%), Positives = 55/115 (47%), Gaps = 8/115 (6%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQL-- 141
GN+ K+ + +L N FS + D++ D + +T E + E +K L + + A+ L
Sbjct: 646 FGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREIT-ETIAEAKKKV-LDVTKEAQANLLT 703
Query: 142 --EGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSLL 194
G FE +R L+ + + ++N L +L ++ +V++ +K S +
Sbjct: 704 AKHGMTLRESFEDNVVRFLNEARDKAGRLAEVN--LKDLNNVKQMVMAGSKGSFI 756
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 27/115 (23%), Positives = 55/115 (47%), Gaps = 8/115 (6%)
Query: 84 LGNLTKLNDLYLFGNDFSGKVPDSLGDLLQLNYLTGEILVEIRKLTQLHILRLAENQL-- 141
GN+ K+ + +L N FS + D++ D + +T E + E +K L + + A+ L
Sbjct: 646 FGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREIT-ETIAEAKKKV-LDVTKEAQANLLT 703
Query: 142 --EGSVPSSIFELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNKLSLL 194
G FE +R L+ + + ++N L +L ++ +V++ +K S +
Sbjct: 704 AKHGMTLRESFEDNVVRFLNEARDKAGRLAEVN--LKDLNNVKQMVMAGSKGSFI 756
>pdb|2V50|A Chain A, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|B Chain B, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|C Chain C, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|D Chain D, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|E Chain E, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
pdb|2V50|F Chain F, The Missing Part Of The Bacterial Mexab-Oprm System:
Structural Determination Of The Multidrug Exporter Mexb
Length = 1052
Score = 27.3 bits (59), Expect = 7.8, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 124 EIRKLTQLHILRLAENQLEGSVPSSIFELRNLRALDLSDNNLSGTG 169
E+ K Q+H + + P S+ EL N DL + +G G
Sbjct: 646 ELAKRAQMHFFSFKDAMVFAFAPPSVLELGNATGFDLFLQDQAGVG 691
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 151 ELRNLRALDLSDNNLSGTGDLNMVLLNLESLTALVLSSNK 190
+L NL+ LDLS +++ + N+ L NL L L LS N+
Sbjct: 347 KLENLQKLDLSHSDIEASDCCNLQLKNLRHLQYLNLSYNE 386
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.132 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,374,649
Number of Sequences: 62578
Number of extensions: 176804
Number of successful extensions: 622
Number of sequences better than 100.0: 81
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 436
Number of HSP's gapped (non-prelim): 186
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)