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= 002115
(965 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 = 60.1 bits (144), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 90/364 (24%), Positives = 147/364 (40%), Gaps = 63/364 (17%)
Query: 187 KNELVNRLLCESSKEQKGPCIISLVGMGGIGKTTLAQFAYNNDGVKRN-FEKRI-WVCVS 244
+ +LVN + + SK + P +++ GM G GK+ LA A + + F + WV V
Sbjct: 129 RKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG 188
Query: 245 EPFDEFRIARAIIESLTGSASNFGEFQSLMQHIQECVEGKK-------------FLLVLD 291
+ + ++ L + + +S Q + +E K LL+LD
Sbjct: 189 K-----QDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILD 243
Query: 292 DLWNEVYYKWEPFYKCLKNGLHESKILITTRKEIVARCMRSTNVIYVNVLSEIECWSVFE 351
D+W+ W LK + +IL+TTR + V + + V V S + E
Sbjct: 244 DVWD----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYV-VPVESSLGKEKGLE 293
Query: 352 QLAFFGRSMEECEKLENMGRQIVRKCKGLPLAAKTIASLLQSRNTEKEWQNXXXXXXXXX 411
L+ F +M++ + L I+++CKG PL I +LL R+ W+
Sbjct: 294 ILSLF-VNMKKAD-LPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQNKQ 349
Query: 412 XXXXR--------GLLAPLLLSYNELPSKIKQCFTYCAIFPKDYQIQKKELINLWMAQGY 463
R L + +S L IK +T +I KD ++ K L LW +
Sbjct: 350 FKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-- 407
Query: 464 LSKKGTKEMEDIGEEYFN--ILASRSFFQDFRRYGLGENYVCKMHDIVHDFAQFLCRNEC 521
T+E+EDI +E+ N +L + FR Y +HD+ D FL C
Sbjct: 408 -----TEEVEDILQEFVNKSLLFCDRNGKSFRYY---------LHDLQVD---FLTEKNC 450
Query: 522 FALQ 525
LQ
Sbjct: 451 SQLQ 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 = 57.0 bits (136), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 90/364 (24%), Positives = 147/364 (40%), Gaps = 63/364 (17%)
Query: 187 KNELVNRLLCESSKEQKGPCIISLVGMGGIGKTTLAQFAYNNDGVKRN-FEKRI-WVCVS 244
+ +LVN + + SK + P +++ GM G GK+ LA A + + F + WV V
Sbjct: 135 RKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG 194
Query: 245 EPFDEFRIARAIIESLTGSASNFGEFQSLMQHIQECVEGKK-------------FLLVLD 291
+ + ++ L + + +S Q + +E K LL+LD
Sbjct: 195 K-----QDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILD 249
Query: 292 DLWNEVYYKWEPFYKCLKNGLHESKILITTRKEIVARCMRSTNVIYVNVLSEIECWSVFE 351
D+W+ W LK + +IL+TTR + V + + V V S + E
Sbjct: 250 DVWD----SW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYV-VPVESSLGKEKGLE 299
Query: 352 QLAFFGRSMEECEKLENMGRQIVRKCKGLPLAAKTIASLLQSRNTEKEWQNXXXXXXXXX 411
L+ F +M++ + L I+++CKG PL I +LL R+ W+
Sbjct: 300 ILSLF-VNMKKAD-LPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYLKQLQNKQ 355
Query: 412 XXXXR--------GLLAPLLLSYNELPSKIKQCFTYCAIFPKDYQIQKKELINLWMAQGY 463
R L + +S L IK +T +I KD ++ K L LW +
Sbjct: 356 FKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-- 413
Query: 464 LSKKGTKEMEDIGEEYFN--ILASRSFFQDFRRYGLGENYVCKMHDIVHDFAQFLCRNEC 521
T+E+EDI +E+ N +L + FR Y +HD+ D FL C
Sbjct: 414 -----TEEVEDILQEFVNKSLLFCDRNGKSFRYY---------LHDLQVD---FLTEKNC 456
Query: 522 FALQ 525
LQ
Sbjct: 457 SQLQ 460
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 80/332 (24%), Positives = 132/332 (39%), Gaps = 58/332 (17%)
Query: 205 PCIISLVGMGGIGKTTLAQFAYNNDGVKRN-FEKRI-WVCVSEPFDEFRIARAIIESLTG 262
P +++ GM G GK+ LA A + + F + WV + + + ++ L
Sbjct: 147 PGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-----QDKSGLLMKLQN 201
Query: 263 SASNFGEFQSLMQHIQECVEGKK-------------FLLVLDDLWNEVYYKWEPFYKCLK 309
+ +S Q + +E K LL+LDD+W +P+ LK
Sbjct: 202 LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW-------DPW--VLK 252
Query: 310 NGLHESKILITTR-KEIVARCMRSTNVIYVNVLSEIECWSVFEQLAFFGRSMEECEKLEN 368
++ +IL+TTR K + M +V+ V S + E L+ F +E L
Sbjct: 253 AFDNQCQILLTTRDKSVTDSVMGPKHVVPVE--SGLGREKGLEILSLFVNMKKE--DLPA 308
Query: 369 MGRQIVRKCKGLPLAAKTIASLLQSRNTEKEWQNXXXXXXXXXXXXXR--------GLLA 420
I+++CKG PL I +LL R+ W R L
Sbjct: 309 EAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDE 366
Query: 421 PLLLSYNELPSKIKQCFTYCAIFPKDYQIQKKELINLWMAQGYLSKKGTKEMEDIGEEYF 480
+ +S L IK +T +I KD ++ K L LW + T+E+EDI +E+
Sbjct: 367 AMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEFV 419
Query: 481 NILASRSFFQDFRRYGLGENYVCKMHDIVHDF 512
N +S R G+++ +HD+ DF
Sbjct: 420 N----KSLLFCNRN---GKSFCYYLHDLQVDF 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 47.0 bits (110), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 79/332 (23%), Positives = 131/332 (39%), Gaps = 58/332 (17%)
Query: 205 PCIISLVGMGGIGKTTLAQFAYNNDGVKRN-FEKRI-WVCVSEPFDEFRIARAIIESLTG 262
P +++ GM G GK+ LA A + + F + WV + + + ++ L
Sbjct: 154 PGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-----QDKSGLLMKLQN 208
Query: 263 SASNFGEFQSLMQHIQECVEGKK-------------FLLVLDDLWNEVYYKWEPFYKCLK 309
+ +S Q + +E K LL+LDD+W +P+ LK
Sbjct: 209 LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW-------DPW--VLK 259
Query: 310 NGLHESKILITTR-KEIVARCMRSTNVIYVNVLSEIECWSVFEQLAFFGRSMEECEKLEN 368
++ +IL+TT K + M +V+ V S + E L+ F +E L
Sbjct: 260 AFDNQCQILLTTSDKSVTDSVMGPKHVVPVE--SGLGREKGLEILSLFVNMKKE--DLPA 315
Query: 369 MGRQIVRKCKGLPLAAKTIASLLQSRNTEKEWQNXXXXXXXXXXXXXR--------GLLA 420
I+++CKG PL I +LL R+ W R L
Sbjct: 316 EAHSIIKECKGSPLVVSLIGALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDE 373
Query: 421 PLLLSYNELPSKIKQCFTYCAIFPKDYQIQKKELINLWMAQGYLSKKGTKEMEDIGEEYF 480
+ +S L IK +T +I KD ++ K L LW + T+E+EDI +E+
Sbjct: 374 AMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEFV 426
Query: 481 NILASRSFFQDFRRYGLGENYVCKMHDIVHDF 512
N +S R G+++ +HD+ DF
Sbjct: 427 N----KSLLFCNRN---GKSFCYYLHDLQVDF 451
>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 = 46.2 bits (108), Expect = 9e-05, Method: Composition-based stats.
Identities = 38/108 (35%), Positives = 61/108 (56%), Gaps = 15/108 (13%)
Query: 586 LFDKLTCLRALTLGVHSLRLCENCIKEVRTNI-ENLLHLKYLNLAHQREIEKLPETLCE- 643
+FDKLT L+ L L EN ++ + + + L +L YLNLAH +++ LP+ + +
Sbjct: 104 VFDKLTNLKELV-------LVENQLQSLPDGVFDKLTNLTYLNLAHN-QLQSLPKGVFDK 155
Query: 644 LYNLEHLDISYCRNLRELPQGIGKLRKLMYLENDGTY--SLRYLPVGI 689
L NL LD+SY L+ LP+G+ KL L++ Y L+ +P G+
Sbjct: 156 LTNLTELDLSY-NQLQSLPEGV--FDKLTQLKDLRLYQNQLKSVPDGV 200
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 37.7 bits (86), Expect = 0.034, Method: Composition-based stats.
Identities = 40/131 (30%), Positives = 69/131 (52%), Gaps = 16/131 (12%)
Query: 586 LFDKLTCLRALTLGVHSLRLCENCIKEVRTNI-ENLLHLKYLNLAHQREIEKLPETLCE- 643
+FDKLT L+ L L EN ++ + + + L +L YL L H +++ LP+ + +
Sbjct: 104 VFDKLTNLKELV-------LVENQLQSLPDGVFDKLTNLTYLYLYHN-QLQSLPKGVFDK 155
Query: 644 LYNLEHLDISYCRNLRELPQGI-GKLRKLMYLE-NDGTYSLRYLPVGIGELIRLRIVKEF 701
L NL LD+ L+ LP+G+ KL +L L ND L+ +P G+ + + + +
Sbjct: 156 LTNLTRLDLDN-NQLQSLPEGVFDKLTQLKQLSLNDN--QLKSVPDGVFDRLT-SLTHIW 211
Query: 702 VVGGGYDRACS 712
++ +D ACS
Sbjct: 212 LLNNPWDCACS 222
>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 = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 43/87 (49%), Gaps = 16/87 (18%)
Query: 593 LRALTLGVHSLRLCENCIKEVRTNIENLLH--------LKYLNLAHQR-EIEKLPETLCE 643
+++L LG S + V TN+ +L + LK LN+AH + KLPE
Sbjct: 112 IQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 171
Query: 644 LYNLEHLDIS-------YCRNLRELPQ 663
L NLEHLD+S YC +LR L Q
Sbjct: 172 LTNLEHLDLSSNKIQSIYCTDLRVLHQ 198
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 617 IENLLHLKYLNLAHQR-EIEKLPETLCELYNLEHLDIS-------YCRNLRELPQ 663
I +L LK LN+AH + KLPE L NLEHLD+S YC +LR L Q
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 637 LPETLCELYNLEHLDISYCRNLRELPQGIGKLRKLMYLENDGTYSLRYLPVGI 689
LP+ EL NL LD+S C+ + P L L L N + L+ +P GI
Sbjct: 462 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVL-NMASNQLKSVPDGI 513
>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 = 37.0 bits (84), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 617 IENLLHLKYLNLAHQR-EIEKLPETLCELYNLEHLDIS-------YCRNLRELPQ 663
I +L LK LN+AH + KLPE L NLEHLD+S YC +LR L Q
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 37.0 bits (84), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 43/87 (49%), Gaps = 16/87 (18%)
Query: 593 LRALTLGVHSLRLCENCIKEVRTNIENLLH--------LKYLNLAHQR-EIEKLPETLCE 643
+++L LG S + V TN+ +L + LK LN+AH + KLPE
Sbjct: 89 IQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 148
Query: 644 LYNLEHLDIS-------YCRNLRELPQ 663
L NLEHLD+S YC +LR L Q
Sbjct: 149 LTNLEHLDLSSNKIQSIYCTDLRVLHQ 175
>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 = 36.6 bits (83), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 43/87 (49%), Gaps = 16/87 (18%)
Query: 593 LRALTLGVHSLRLCENCIKEVRTNIENLLH--------LKYLNLAHQR-EIEKLPETLCE 643
+++L LG S + V TN+ +L + LK LN+AH + KLPE
Sbjct: 90 IQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 149
Query: 644 LYNLEHLDIS-------YCRNLRELPQ 663
L NLEHLD+S YC +LR L Q
Sbjct: 150 LTNLEHLDLSSNKIQSIYCTDLRVLHQ 176
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 36.6 bits (83), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 617 IENLLHLKYLNLAHQR-EIEKLPETLCELYNLEHLDIS-------YCRNLRELPQ 663
I +L LK LN+AH + KLPE L NLEHLD+S YC +LR L Q
Sbjct: 122 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 176
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 36.6 bits (83), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 43/87 (49%), Gaps = 16/87 (18%)
Query: 593 LRALTLGVHSLRLCENCIKEVRTNIENLLH--------LKYLNLAHQR-EIEKLPETLCE 643
+++L LG S + V TN+ +L + LK LN+AH + KLPE
Sbjct: 89 IQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 148
Query: 644 LYNLEHLDIS-------YCRNLRELPQ 663
L NLEHLD+S YC +LR L Q
Sbjct: 149 LTNLEHLDLSSNKIQSIYCTDLRVLHQ 175
>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 = 36.6 bits (83), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 43/87 (49%), Gaps = 16/87 (18%)
Query: 593 LRALTLGVHSLRLCENCIKEVRTNIENLLH--------LKYLNLAHQR-EIEKLPETLCE 643
+++L LG S + V TN+ +L + LK LN+AH + KLPE
Sbjct: 88 IQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 147
Query: 644 LYNLEHLDIS-------YCRNLRELPQ 663
L NLEHLD+S YC +LR L Q
Sbjct: 148 LTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 36.6 bits (83), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 52/102 (50%), Gaps = 15/102 (14%)
Query: 5 AIISPLLQQLTAMAAAETKEQVKLVTGVGKEVKKLNSNLRAIQAVL---HDAEKRQVKEE 61
A IS L+ +L + E+ KL GV K ++ L L + A L + + Q+ +
Sbjct: 1 AAISNLIPKLGELLT----EEFKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQ 56
Query: 62 TVRLWLDQLRDACYDIEDVLGEWNTARLKLQIDGV--DDHEN 101
+LW D++R+ Y IEDV+ + +Q+DG+ DD+ N
Sbjct: 57 D-KLWADEVRELSYVIEDVVD-----KFLVQVDGIKSDDNNN 92
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 33.5 bits (75), Expect = 0.54, Method: Composition-based stats.
Identities = 35/129 (27%), Positives = 60/129 (46%), Gaps = 11/129 (8%)
Query: 584 PQLFDKLTCLRALTLGVHSLRLCENCIKEVRTNIENLLHLKYLNLAHQREIEKLPETLCE 643
P +FD L L+ L LG + L + ++L L L+L ++ LP + +
Sbjct: 57 PGVFDSLINLKELYLGSNQLGALPVGV------FDSLTQLTVLDLG-TNQLTVLPSAVFD 109
Query: 644 -LYNLEHLDISYCRNLRELPQGIGKLRKLMYLENDGTYSLRYLPVGIGELIRLRIVKEFV 702
L +L+ L + C L ELP+GI +L L +L D L+ +P G + + + ++
Sbjct: 110 RLVHLKELFMC-CNKLTELPRGIERLTHLTHLALDQN-QLKSIPHGAFDRLS-SLTHAYL 166
Query: 703 VGGGYDRAC 711
G +D C
Sbjct: 167 FGNPWDCEC 175
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 33.1 bits (74), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 44/98 (44%), Gaps = 1/98 (1%)
Query: 598 LGVHSLRLCENCIKEVRTNIENLLHLKYLNLAHQREIEKLPETLCELYNLEHLDISYCRN 657
+ + SLRL I+ + +I NL +LK L + + + L + L LE LD+ C
Sbjct: 183 VNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNS-PLSALGPAIHHLPKLEELDLRGCTA 241
Query: 658 LRELPQGIGKLRKLMYLENDGTYSLRYLPVGIGELIRL 695
LR P G L L +L LP+ I L +L
Sbjct: 242 LRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQL 279
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 56/129 (43%), Gaps = 12/129 (9%)
Query: 811 ITSLTNLRVLSLFECRNCEHLP-PLGKLPSIEVLEIYGVQSVKRVGNEFLGVESDTDGSS 869
I SL LR LS+ C LP PL + E G+ +++ + E+ G+ S +S
Sbjct: 146 IASLNRLRELSIRACPELTELPEPLAS--TDASGEHQGLVNLQSLRLEWTGIRSLP--AS 201
Query: 870 VIAFPKLKQLRFDEMDVLEEWDFGTAINGEIMIMPRLSSLSIRRCPKLKALPDRLLQKTT 929
+ LK L+ + +A+ I +P+L L +R C L+ P +
Sbjct: 202 IANLQNLKSLKIRNSPL-------SALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAP 254
Query: 930 LQALTIGEC 938
L+ L + +C
Sbjct: 255 LKRLILKDC 263
>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 = 32.7 bits (73), Expect = 0.89, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 35/88 (39%)
Query: 608 NCIKEVRTNIENLLHLKYLNLAHQREIEKLPETLCELYNLEHLDISYCRNLRELPQGIGK 667
N + + I L L YL + H +P+ L ++ L LD SY LP I
Sbjct: 88 NLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISS 147
Query: 668 LRKLMYLENDGTYSLRYLPVGIGELIRL 695
L L+ + DG +P G +L
Sbjct: 148 LPNLVGITFDGNRISGAIPDSYGSFSKL 175
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 603 LRLCENCIKEVRTNIENLLHLKYLNLAHQREIEKLPETLCELYNLEHLDISYCRNLRELP 662
L L N + E+ I+NL +L+ L+L+H R + LP L + L++ + + LP
Sbjct: 252 LYLNGNSLTELPAEIKNLSNLRVLDLSHNR-LTSLPAELGSCFQLKYFYF-FDNMVTTLP 309
Query: 663 QGIGKLRKLMYLENDG 678
G L L +L +G
Sbjct: 310 WEFGNLCNLQFLGVEG 325
>pdb|1FTS|A Chain A, Signal Recognition Particle Receptor From E. Coli
Length = 295
Score = 31.2 bits (69), Expect = 2.8, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 176 DESEIFGR-EEEKNELVNRLLCESSKEQKGPCIISLVGMGGIGK-TTLAQFAYNNDGVKR 233
D ++G +EE E++ ++ + E K P +I +VG+ G+GK TT+ + A R
Sbjct: 63 DAEALYGLLKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLA-------R 115
Query: 234 NFEKRIWVCVSEPFDEFRIA 253
FE++ + D FR A
Sbjct: 116 QFEQQGKSVMLAAGDTFRAA 135
>pdb|2XXA|B Chain B, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
pdb|2XXA|D Chain D, The Crystal Structure Of The Signal Recognition Particle
(Srp) In Complex With Its Receptor(Sr)
Length = 302
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 176 DESEIFGR-EEEKNELVNRLLCESSKEQKGPCIISLVGMGGIGK-TTLAQFAYNNDGVKR 233
D ++G +EE E++ ++ + E K P +I +VG+ G+GK TT+ + A R
Sbjct: 68 DAEALYGLLKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLA-------R 120
Query: 234 NFEKRIWVCVSEPFDEFRIA 253
FE++ + D FR A
Sbjct: 121 QFEQQGKSVMLAAGDTFRAA 140
>pdb|2QY9|A Chain A, Structure Of The Ng+1 Construct Of The E. Coli Srp
Receptor Ftsy
Length = 309
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 9/80 (11%)
Query: 176 DESEIFGR-EEEKNELVNRLLCESSKEQKGPCIISLVGMGGIGK-TTLAQFAYNNDGVKR 233
D ++G +EE E++ ++ + E K P +I +VG+ G+GK TT+ + A R
Sbjct: 69 DAEALYGLLKEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLA-------R 121
Query: 234 NFEKRIWVCVSEPFDEFRIA 253
FE++ + D FR A
Sbjct: 122 QFEQQGKSVMLAAGDTFRAA 141
>pdb|1Z81|A Chain A, Crystal Structure Of Cyclophilin From Plasmodium Yoelii
Length = 229
Score = 30.8 bits (68), Expect = 4.0, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 678 GTYSLRYLPVGIGELIRLRIVKEFVVGGG 706
G Y + LPVG I R++KEF++ GG
Sbjct: 98 GEYKVNNLPVGYKNTIFHRVIKEFMIQGG 126
>pdb|2YHS|A Chain A, Structure Of The E. Coli Srp Receptor Ftsy
Length = 503
Score = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 185 EEKNELVNRLLCESSKEQKGPCIISLVGMGGIGK-TTLAQFAYNNDGVKRNFEKRIWVCV 243
EE E++ ++ + E K P +I +VG+ G+GK TT+ + A R FE++ +
Sbjct: 273 EEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLA-------RQFEQQGKSVM 325
Query: 244 SEPFDEFRIA 253
D FR A
Sbjct: 326 LAAGDTFRAA 335
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
Length = 322
Score = 30.4 bits (67), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 11/82 (13%)
Query: 170 PSISSIDESEIFGREEEKNELVNRLLCESSKEQKGPCIISLVGMGGIGKTTLAQFAYN-- 227
PSI IDE + +NE E+++ K ++ + G+G L A N
Sbjct: 106 PSIIFIDEIDSLCGSRSENE------SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIP 159
Query: 228 ---NDGVKRNFEKRIWVCVSEP 246
+ ++R FEKRI++ + EP
Sbjct: 160 WVLDSAIRRRFEKRIYIPLPEP 181
>pdb|3EJW|A Chain A, Crystal Structure Of The Sinorhizobium Meliloti Ai-2
Receptor, Smlsrb
pdb|3EJW|B Chain B, Crystal Structure Of The Sinorhizobium Meliloti Ai-2
Receptor, Smlsrb
Length = 315
Score = 30.0 bits (66), Expect = 6.5, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 789 PNLKELRIYQYRGRRNVVPKIWITSLTNLRVLSLFECRNCEHLPPLGKLPSIEVLEIYGV 848
PN+ +R Y RG + + + +T +S+F +H+ G + E LEI GV
Sbjct: 223 PNV--MRPYIERG---TIQRFGLWDVTQQGKISVFVA---DHVLKNGPMKVGEKLEIPGV 274
Query: 849 QSVKRVGNEFLGVESDTDGSSVIAFPK 875
+V+ N+ G + + DG+ +I P+
Sbjct: 275 GTVEVSANKVQGYDYEADGNGIILLPE 301
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 61/138 (44%), Gaps = 16/138 (11%)
Query: 599 GVHSLRLCENCIKEVRT-NIENLLHLKYLNLAHQREIEKLPETLCELYNLEHLDISYCRN 657
G+ LRL I +R + + L LK L ++H ++ + NL L I++C N
Sbjct: 177 GLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHC-N 235
Query: 658 LRELPQGIGKLRKLMYLENDGTYSLRYLPVG------IGELIRLRIVKEFVVGGGYDRAC 711
L +P +R L+YL +L Y P+ + EL+RL +E + GG
Sbjct: 236 LTAVP--YLAVRHLVYLR---FLNLSYNPISTIEGSMLHELLRL---QEIQLVGGQLAVV 287
Query: 712 SLGSLKKLNLLRYCRIHG 729
+ + LN LR + G
Sbjct: 288 EPYAFRGLNYLRVLNVSG 305
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 30.0 bits (66), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 179 EIFGREEEKNELVNRLLCESSKEQKGPC-IISLVGMGGIGKTTLAQFAYNNDGVKRNFEK 237
E G+E K +L R+ E++K +K P + L G G+GKTTLA + GV N
Sbjct: 13 EYIGQERLKQKL--RVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV--NLRV 68
Query: 238 RIWVCVSEPFD 248
+ +P D
Sbjct: 69 TSGPAIEKPGD 79
>pdb|1GVI|A Chain A, Thermus Maltogenic Amylase In Complex With Beta-Cd
pdb|1GVI|B Chain B, Thermus Maltogenic Amylase In Complex With Beta-Cd
Length = 588
Score = 30.0 bits (66), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 266 NFGEFQSLMQHIQECVEGKKFLLVLDDLWNEVYYKWEPFYKCLKNG 311
+FG+ ++L ++ C E K ++LD ++N Y++ PF LKNG
Sbjct: 218 HFGDKETLKTLVKRCHE-KGIRVMLDAVFNHCGYEFAPFQDVLKNG 262
>pdb|1SMA|A Chain A, Crystal Structure Of A Maltogenic Amylase
pdb|1SMA|B Chain B, Crystal Structure Of A Maltogenic Amylase
Length = 588
Score = 30.0 bits (66), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 266 NFGEFQSLMQHIQECVEGKKFLLVLDDLWNEVYYKWEPFYKCLKNG 311
+FG+ ++L ++ C E K ++LD ++N Y++ PF LKNG
Sbjct: 218 HFGDKETLKTLVKRCHE-KGIRVMLDAVFNHCGYEFAPFQDVLKNG 262
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
0.322 0.139 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,685,577
Number of Sequences: 62578
Number of extensions: 1066668
Number of successful extensions: 2763
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 2730
Number of HSP's gapped (non-prelim): 64
length of query: 965
length of database: 14,973,337
effective HSP length: 108
effective length of query: 857
effective length of database: 8,214,913
effective search space: 7040180441
effective search space used: 7040180441
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)