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= 002308
(938 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 81/344 (23%), Positives = 144/344 (41%), Gaps = 62/344 (18%)
Query: 180 ISIVGMGGIGKTTLAQLAC-NHVEVKREFDKTL-WVCVSETFDEFRIAKAMLEALTGSTS 237
++I GM G GK+ LA A +H ++ F + WV V + D+ + + T
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQ 208
Query: 238 NLNALQSLLISIDESI---------AGKRFLLVLDDVWDGDYIKWEPFYRCLKKGLHGSK 288
+ + Q L ++I+E+ R LL+LDDVWD W LK +
Sbjct: 209 DESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAFDSQCQ 259
Query: 289 ILITTRKESIV-SMMRSTDIISIE-ELAEEECWVLFKRLAFFGRSTEECEKLEQIGQRIA 346
IL+TTR +S+ S+M ++ +E L +E+ + ++ L + I
Sbjct: 260 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD-----LPEQAHSII 314
Query: 347 RKCKGLPLAAKTMGSLMSS----------KKTEEEWKRILNSDLWKVEEIEKGVLTPLWL 396
++CKG PL +G+L+ + +++KRI S + E +++ + +
Sbjct: 315 KECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA----MSI 370
Query: 397 SYNDLPSRVKRCFSYCAVFPKDYNIKKDELITLWMAQGYLSAEAAEQDEEMETIGEEYFG 456
S L +K ++ ++ KD + L LW + EE+E I +E+
Sbjct: 371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMET----------EEVEDILQEFVN 420
Query: 457 ILASRSFFQEFKKSYDNRIIACKMHDMVHDLAQFVSENECFSLE 500
S F KS+ +HD+ D F++E C L+
Sbjct: 421 --KSLLFCDRNGKSF-----RYYLHDLQVD---FLTEKNCSQLQ 454
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 81/344 (23%), Positives = 145/344 (42%), Gaps = 62/344 (18%)
Query: 180 ISIVGMGGIGKTTLAQLAC-NHVEVKREFDKTL-WVCVSETFDEFRIAKAMLEALTGSTS 237
++I GM G GK+ LA A +H ++ F + WV V + D+ + + T
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQ 214
Query: 238 NLNALQSLLISIDESI---------AGKRFLLVLDDVWDGDYIKWEPFYRCLKKGLHGSK 288
+ + Q L ++I+E+ R LL+LDDVWD W LK +
Sbjct: 215 DESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAFDSQCQ 265
Query: 289 ILITTRKESIV-SMMRSTDIISIE-ELAEEECWVLFKRLAFFGRSTEECEKLEQIGQRIA 346
IL+TTR +S+ S+M ++ +E L +E+ + ++ L + I
Sbjct: 266 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA-----DLPEQAHSII 320
Query: 347 RKCKGLPLAAKTMGSLMSS----------KKTEEEWKRILNSDLWKVEEIEKGVLTPLWL 396
++CKG PL +G+L+ + +++KRI S + E +++ + +
Sbjct: 321 KECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA----MSI 376
Query: 397 SYNDLPSRVKRCFSYCAVFPKDYNIKKDELITLWMAQGYLSAEAAEQDEEMETIGEEYFG 456
S L +K ++ ++ KD + L LW + EE+E I +E+
Sbjct: 377 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMET----------EEVEDILQEF-- 424
Query: 457 ILASRSFFQEFKKSYDNRIIACKMHDMVHDLAQFVSENECFSLE 500
+ S F KS+ +HD+ D F++E C L+
Sbjct: 425 VNKSLLFCDRNGKSFRYY-----LHDLQVD---FLTEKNCSQLQ 460
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 47.0 bits (110), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 70/280 (25%), Positives = 115/280 (41%), Gaps = 54/280 (19%)
Query: 180 ISIVGMGGIGKTTLAQLACNHVEVKREFDKTLWVCVSETFDEFRIAKAMLEALTGSTSNL 239
++I GM G GK+ LA E R+ L C S I K L NL
Sbjct: 150 VTIYGMAGCGKSVLA------AEAVRDH-SLLEGCFSGGVHWVSIGKQDKSGLLMKLQNL 202
Query: 240 --------NALQSLLISIDESI---------AGKRFLLVLDDVWDGDYIKWEPFYRCLKK 282
+ Q L ++I+E+ R LL+LDDVWD P+ LK
Sbjct: 203 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD-------PW--VLKA 253
Query: 283 GLHGSKILITTRKESIV-SMMRSTDIISIEE-LAEEECWVLFKRLAFFGRSTEECEKLEQ 340
+ +IL+TTR +S+ S+M ++ +E L E+ + L+ F + E L
Sbjct: 254 FDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKG---LEILSLFVNMKK--EDLPA 308
Query: 341 IGQRIARKCKGLPLAAKTMGSLMSS----------KKTEEEWKRILNSDLWKVEEIEKGV 390
I ++CKG PL +G+L+ + +++KRI S + E +++
Sbjct: 309 EAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA- 367
Query: 391 LTPLWLSYNDLPSRVKRCFSYCAVFPKDYNIKKDELITLW 430
+ +S L +K ++ ++ KD + L LW
Sbjct: 368 ---MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW 404
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 69/280 (24%), Positives = 114/280 (40%), Gaps = 54/280 (19%)
Query: 180 ISIVGMGGIGKTTLAQLACNHVEVKREFDKTLWVCVSETFDEFRIAKAMLEALTGSTSNL 239
++I GM G GK+ LA E R+ L C S I K L NL
Sbjct: 157 VTIYGMAGCGKSVLA------AEAVRDH-SLLEGCFSGGVHWVSIGKQDKSGLLMKLQNL 209
Query: 240 --------NALQSLLISIDESI---------AGKRFLLVLDDVWDGDYIKWEPFYRCLKK 282
+ Q L ++I+E+ R LL+LDDVWD P+ LK
Sbjct: 210 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD-------PW--VLKA 260
Query: 283 GLHGSKILITTRKESIV-SMMRSTDIISIEE-LAEEECWVLFKRLAFFGRSTEECEKLEQ 340
+ +IL+TT +S+ S+M ++ +E L E+ + L+ F + E L
Sbjct: 261 FDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKG---LEILSLFVNMKK--EDLPA 315
Query: 341 IGQRIARKCKGLPLAAKTMGSLMSS----------KKTEEEWKRILNSDLWKVEEIEKGV 390
I ++CKG PL +G+L+ + +++KRI S + E +++
Sbjct: 316 EAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA- 374
Query: 391 LTPLWLSYNDLPSRVKRCFSYCAVFPKDYNIKKDELITLW 430
+ +S L +K ++ ++ KD + L LW
Sbjct: 375 ---MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW 411
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 41/153 (26%), Positives = 62/153 (40%), Gaps = 24/153 (15%)
Query: 520 LMLIMGKESTFPISTCRAKRIRSL-------LIEWPE-FGHSSLNGE-----ILEELFRE 566
L L P S R+R L L E PE + +GE L+ L E
Sbjct: 132 LTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLE 191
Query: 567 STSLRALDFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISGCS 626
T +R+L P +I L +L+ L + + + L + L LE+LD+ GC+
Sbjct: 192 WTGIRSL-----------PASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCT 240
Query: 627 DLRELPKGIGKLINMKHLLNSGTRSLRYMPVGI 659
LR P G +K L+ +L +P+ I
Sbjct: 241 ALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDI 273
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 565 RESTSLRALDFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISG 624
R + LR++ P F P +L HL++ + + +LP+T + LE L ++
Sbjct: 83 RVALELRSVPLPQF------PDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLAR 136
Query: 625 CSDLRELPKGIGKLINMKHL 644
+ LR LP I L ++ L
Sbjct: 137 -NPLRALPASIASLNRLREL 155
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 607 LPETLCELYNLEKLDISGCSDLRELPKGIGKL 638
LP + L LEKLD+ GC +L LP I +L
Sbjct: 269 LPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
Score = 29.3 bits (64), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 45/158 (28%), Positives = 64/158 (40%), Gaps = 29/158 (18%)
Query: 772 VFPSWMASLTNLKSLDLCFCENCEQLP-PLGKL-PSLEQLFISYMSSVKRVGDEFLGVES 829
P+ +ASL L+ L + C +LP PL S E + + S++ E+ G+ S
Sbjct: 141 ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL---EWTGIRS 197
Query: 830 DRHDXXXXXXVIIAFPKLKSL------------SIFEMEELEEWDY-GITRTGN---TFI 873
I LKSL +I + +LEE D G T N F
Sbjct: 198 -------LPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFG 250
Query: 874 NIMPRLSSLTINYCSKLKALPDHIHQTTTLKELRIGEC 911
P L L + CS L LP IH+ T L++L + C
Sbjct: 251 GRAP-LKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGC 287
>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 = 37.4 bits (85), Expect = 0.036, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 39/58 (67%), Gaps = 3/58 (5%)
Query: 589 EKLVHLRYLNLSDQKIKKLPETLCE-LYNLEKLDISGCSDLRELPKGI-GKLINMKHL 644
+KL +L YLNL+ +++ LP+ + + L NL +LD+S + L+ LP+G+ KL +K L
Sbjct: 130 DKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLS-YNQLQSLPEGVFDKLTQLKDL 186
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 560 LEELFRESTSLRALDFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIKKLPETLCE-LYNLE 618
L+EL+ S L AL F + L L L+L ++ LP + + L +L+
Sbjct: 66 LKELYLGSNQLGALPVGVF----------DSLTQLTVLDLGTNQLTVLPSAVFDRLVHLK 115
Query: 619 KLDISGCSDLRELPKGIGKLINMKHL 644
+L + C+ L ELP+GI +L ++ HL
Sbjct: 116 ELFMC-CNKLTELPRGIERLTHLTHL 140
Score = 32.7 bits (73), Expect = 0.91, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 583 EIPRNIEKLVHLRYLNLSDQKIKKLP 608
E+PR IE+L HL +L L ++K +P
Sbjct: 126 ELPRGIERLTHLTHLALDQNQLKSIP 151
Score = 30.4 bits (67), Expect = 4.4, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 580 LPLEIPRNIEKLVHLRYLNLSDQKIKKL-PETLCELYNLEKLDISGCSDLRELPKGIGKL 638
+P IP N + L L D +I KL P L NL++L + G + L LP G+
Sbjct: 34 VPAGIPTNAQ------ILYLHDNQITKLEPGVFDSLINLKELYL-GSNQLGALPVGVFDS 86
Query: 639 INMKHLLNSGTRSLRYMPVGI 659
+ +L+ GT L +P +
Sbjct: 87 LTQLTVLDLGTNQLTVLPSAV 107
>pdb|4ARN|A Chain A, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|B Chain B, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|C Chain C, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|D Chain D, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARR|A Chain A, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor With The Magic Triangle I3c
pdb|4ARR|B Chain B, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor With The Magic Triangle I3c
Length = 279
Score = 33.1 bits (74), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 579 YLPLEIPRNIEKLVHLRYLNLSDQKIKKLPETLCE-LYNLEKLDISGCSDLRELPKGI-G 636
++P + ++ L HL I+++P L + L NLE ++ G + LR++P+GI G
Sbjct: 137 HIPANLLTDMRNLSHLEL----RANIEEMPSHLFDDLENLESIEF-GSNKLRQMPRGIFG 191
Query: 637 KLINMKHLLNSGTRSLRYMPVGI 659
K+ +K LN + L+ +P GI
Sbjct: 192 KMPKLKQ-LNLASNQLKSVPDGI 213
>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 = 1.4, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 563 LFRESTSLRALDFPSFYLPLEIPRNI-EKLVHLRYLNLSDQKIKKLPETLCE-LYNLEKL 620
+F E TSL L L +P + KL L YLNLS +++ LP + + L L++L
Sbjct: 47 VFDELTSLTQLYLGGNKLQ-SLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKEL 105
Query: 621 DISGCSDLRELPKGI-GKLINMKHL 644
++ + L+ LP G+ KL +K L
Sbjct: 106 ALN-TNQLQSLPDGVFDKLTQLKDL 129
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 588 IEKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISG 624
E LV+LRYLNL +K +P L L LE+L++SG
Sbjct: 152 FEGLVNLRYLNLGMCNLKDIPN-LTALVRLEELELSG 187
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 588 IEKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISG 624
E LV+LRYLNL +K +P L L LE+L++SG
Sbjct: 152 FEGLVNLRYLNLGMCNLKDIP-NLTALVRLEELELSG 187
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 3/117 (2%)
Query: 545 IEWPEFGHSSLNGEILEELFRESTSLRALDFPSFYLPLEIPRNIEKLVHLRYLNLSDQKI 604
+E +F HS+L +F +L LD + + L L L ++
Sbjct: 398 LEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSF 457
Query: 605 KK--LPETLCELYNLEKLDISGCSDLRELPKGIGKLINMKHLLNSGTRSLRYMPVGI 659
++ LP+ EL NL LD+S C + P L +++ +LN + L+ +P GI
Sbjct: 458 QENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQ-VLNMASNQLKSVPDGI 513
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 102 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 150
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 151 LEHLDLSSNKIQSIYCTDLRVL 172
>pdb|1BY1|A Chain A, Dbl Homology Domain From Beta-Pix
Length = 209
Score = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 855 MEELEEWDYGITRTGNTFINIMPRLSSLTINYC----SKLKALPDH 896
+EE + R G F+N+MP++ +L + YC S + L +H
Sbjct: 75 LEECTKLPEAQQRVGGCFLNLMPQMKTLYLTYCANHPSAVNVLTEH 120
>pdb|1Y63|A Chain A, Initial Crystal Structural Analysis Of A Probable Kinase
From Leishmania Major Friedlin
Length = 184
Score = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 16/74 (21%)
Query: 170 SSEQQKGLHIISIVGMGGIGKTTLAQLAC------NHVEVKR---------EFDKTLWVC 214
S EQ KG++I+ I G G GKT++A++ H+EV + E+D L
Sbjct: 4 SMEQPKGINIL-ITGTPGTGKTSMAEMIAAELDGFQHLEVGKLVKENHFYTEYDTELDTH 62
Query: 215 VSETFDEFRIAKAM 228
+ E DE R+ M
Sbjct: 63 IIEEKDEDRLLDFM 76
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 589 EKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISG 624
E L +LRYLNL+ ++++P L L L++LD+SG
Sbjct: 182 EGLSNLRYLNLAMCNLREIPN-LTPLIKLDELDLSG 216
>pdb|2JQD|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of Lanp
Length = 169
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 589 EKLVHLRYLNLSDQKIKKLP--ETLCELYNLEKLDISGC--SDLRELPKGIGKLINMKHL 644
EK +L++LNLS KIK L E L +L NL+ LD+ C ++L + + KL+
Sbjct: 90 EKCPNLKHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNAYRENVFKLLPQVMY 149
Query: 645 LNSGTRSLRYMP 656
L+ R + P
Sbjct: 150 LDGYDRDNKEAP 161
>pdb|3ULA|A Chain A, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
pdb|3ULA|C Chain C, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
Length = 279
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 104 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 152
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 153 LEHLDLSSNKIQSIYCTDLRVL 174
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 103 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 151
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 152 LEHLDLSSNKIQSIYCTDLRVL 173
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 103 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 151
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 152 LEHLDLSSNKIQSIYCTDLRVL 173
>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 = 30.0 bits (66), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 126 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 174
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 175 LEHLDLSSNKIQSIYCTDLRVL 196
>pdb|2Z62|A Chain A, Crystal Structure Of The Tv3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z65|A Chain A, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
pdb|2Z65|B Chain B, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
Length = 276
Score = 30.0 bits (66), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 21/82 (25%)
Query: 560 LEELFRESTSLRAL-DFPSFYLPLEIPRNIEKLVHLRYLNLSDQKIK--KLPETLCELYN 616
L++L T+L +L +FP I L L+ LN++ I+ KLPE L N
Sbjct: 102 LQKLVAVETNLASLENFP-----------IGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 150
Query: 617 LEKLDISG-------CSDLREL 631
LE LD+S C+DLR L
Sbjct: 151 LEHLDLSSNKIQSIYCTDLRVL 172
>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 = 30.0 bits (66), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 588 IEKLVHLRYLNLSDQKIK--KLPETLCELYNLEKLDISG-------CSDLREL 631
I L L+ LN++ I+ KLPE L NLE LD+S C+DLR L
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVL 172
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 588 IEKLVHLRYLNLSDQKIK--KLPETLCELYNLEKLDISG-------CSDLREL 631
I L L+ LN++ I+ KLPE L NLE LD+S C+DLR L
Sbjct: 122 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVL 174
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 29.6 bits (65), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 588 IEKLVHLRYLNLSDQKIKKLPETLCELYNLEKLDISG 624
E L +L+YLNL IK +P L L LE+L++SG
Sbjct: 192 FEGLFNLKYLNLGMCNIKDMPN-LTPLVGLEELEMSG 227
>pdb|1IZ2|A Chain A, Interactions Causing The Kinetic Trap In Serpin Protein
Folding
Length = 394
Score = 29.6 bits (65), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 198 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 237
>pdb|1HP7|A Chain A, A 2.1 Angstrom Structure Of An Uncleaved
Alpha-1-Antitrypsin Shows Variability Of The Reactive
Center And Other Loops
Length = 394
Score = 29.6 bits (65), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 198 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 237
>pdb|1KCT|A Chain A, Alpha1-Antitrypsin
Length = 394
Score = 29.6 bits (65), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 198 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 237
>pdb|1QLP|A Chain A, 2.0 Angstrom Structure Of Intact Alpha-1-Antitrypsin: A
Canonical Template For Active Serpins
Length = 394
Score = 29.6 bits (65), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 198 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 237
>pdb|7API|A Chain A, The S Variant Of Human Alpha1-Antitrypsin, Structure And
Implications For Function And Metabolism
pdb|8API|A Chain A, The S Variant Of Human Alpha1-antitrypsin, Structure And
Implications For Function And Metabolism
pdb|9API|A Chain A, The S Variant Of Human Alpha1-Antitrypsin, Structure And
Implications For Function And Metabolism
Length = 347
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 187 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 226
>pdb|3DRU|A Chain A, Crystal Structure Of Gly117phe Alpha1-Antitrypsin
pdb|3DRU|B Chain B, Crystal Structure Of Gly117phe Alpha1-Antitrypsin
pdb|3DRU|C Chain C, Crystal Structure Of Gly117phe Alpha1-Antitrypsin
Length = 404
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 208 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 247
>pdb|3DRM|A Chain A, 2.2 Angstrom Crystal Structure Of Thr114phe Alpha1-
Antitrypsin
Length = 404
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 208 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 247
>pdb|3NE4|A Chain A, 1.8 Angstrom Structure Of Intact Native Wild-Type
Alpha-1-Antitrypsin
Length = 424
Score = 29.6 bits (65), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 228 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 267
>pdb|1QMB|A Chain A, Cleaved Alpha-1-Antitrypsin Polymer
Length = 326
Score = 29.3 bits (64), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 173 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 212
>pdb|1D5S|A Chain A, Crystal Structure Of Cleaved Antitrypsin Polymer
Length = 334
Score = 29.3 bits (64), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 179 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 218
>pdb|1EZX|A Chain A, Crystal Structure Of A Serpin:protease Complex
Length = 335
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 853 FEMEELEEWDYGITRTGNTFINIMPRLSSLTINYCSKLKA 892
FE+++ EE D+ + + + +M RL I +C KL +
Sbjct: 175 FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSS 214
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
0.320 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,296,146
Number of Sequences: 62578
Number of extensions: 975972
Number of successful extensions: 2321
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 2263
Number of HSP's gapped (non-prelim): 73
length of query: 938
length of database: 14,973,337
effective HSP length: 108
effective length of query: 830
effective length of database: 8,214,913
effective search space: 6818377790
effective search space used: 6818377790
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)