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= 002044
(976 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 = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 85/205 (41%), Gaps = 37/205 (18%)
Query: 204 ISLVGMGGIGKTTLAQFAYNDEDVI------------------SNFEKRMWNCESIIEAL 245
+++ GM G GK+ LA A D ++ S ++ N + ++
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 209
Query: 246 EGFAPNLG---ELNSLLLRIDAFIARKKFLLILDDVWTDDYSKWEPFRRCLINGHRESRI 302
E F+ L E LRI + LLILDDVW W L + +I
Sbjct: 210 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW----DSW-----VLKAFDSQCQI 260
Query: 303 LVTTRKETVA-RMMESTDVIFIKE-LSEQECWALFKRFACFGRSLSECEQLEEIGKKIVG 360
L+TTR ++V +M V+ ++ L +++ + F ++ L E I+
Sbjct: 261 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA-----DLPEQAHSIIK 315
Query: 361 KCKGLPLAAKTIGSLLRFKRTREEW 385
+CKG PL IG+LLR R E+
Sbjct: 316 ECKGSPLVVSLIGALLRDFPNRWEY 340
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 85/205 (41%), Gaps = 37/205 (18%)
Query: 204 ISLVGMGGIGKTTLAQFAYNDEDVI------------------SNFEKRMWNCESIIEAL 245
+++ GM G GK+ LA A D ++ S ++ N + ++
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 215
Query: 246 EGFAPNLG---ELNSLLLRIDAFIARKKFLLILDDVWTDDYSKWEPFRRCLINGHRESRI 302
E F+ L E LRI + LLILDDVW W L + +I
Sbjct: 216 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW----DSW-----VLKAFDSQCQI 266
Query: 303 LVTTRKETVA-RMMESTDVIFIKE-LSEQECWALFKRFACFGRSLSECEQLEEIGKKIVG 360
L+TTR ++V +M V+ ++ L +++ + F ++ L E I+
Sbjct: 267 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA-----DLPEQAHSIIK 321
Query: 361 KCKGLPLAAKTIGSLLRFKRTREEW 385
+CKG PL IG+LLR R E+
Sbjct: 322 ECKGSPLVVSLIGALLRDFPNRWEY 346
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 50/197 (25%), Positives = 83/197 (42%), Gaps = 37/197 (18%)
Query: 204 ISLVGMGGIGKTTLAQFAYNDEDVI------------------SNFEKRMWNCESIIEAL 245
+++ GM G GK+ LA A D ++ S ++ N ++
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 209
Query: 246 EGFAPNLG-ELNSLLLRIDAFIARK--KFLLILDDVWTDDYSKWEPFRRCLINGHRESRI 302
E F+ L + R+ + RK + LLILDDVW +P+ L + +I
Sbjct: 210 ESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW-------DPW--VLKAFDNQCQI 260
Query: 303 LVTTRKETVA-RMMESTDVIFIKE-LSEQECWALFKRFACFGRSLSECEQLEEIGKKIVG 360
L+TTR ++V +M V+ ++ L ++ + F + E L I+
Sbjct: 261 LLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK-----EDLPAEAHSIIK 315
Query: 361 KCKGLPLAAKTIGSLLR 377
+CKG PL IG+LLR
Sbjct: 316 ECKGSPLVVSLIGALLR 332
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 38.5 bits (88), Expect = 0.017, Method: Composition-based stats.
Identities = 34/108 (31%), Positives = 52/108 (48%), Gaps = 30/108 (27%)
Query: 574 GLFDQLTGLRVLRIEGMKSLIGSGTNEIPKGIXXXXXXXXXXXXXVEKLPETCCE-LLNL 632
G+FD LT L VL + GTN++ LP + L++L
Sbjct: 82 GVFDSLTQLTVLDL---------GTNQL------------------TVLPSAVFDRLVHL 114
Query: 633 QTLNMCGSPGLKRLPQGIGKLINLRHLMFEVDYLEYMPKG-IERLTSL 679
+ L MC + L LP+GI +L +L HL + + L+ +P G +RL+SL
Sbjct: 115 KELFMCCNK-LTELPRGIERLTHLTHLALDQNQLKSIPHGAFDRLSSL 161
Score = 32.7 bits (73), Expect = 1.0, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 629 LLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKGIERLTSLRTLS 683
L L L++ G+ L LP + +L++L+ L + L +P+GIERLT L L+
Sbjct: 87 LTQLTVLDL-GTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLA 141
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 37.7 bits (86), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 49/197 (24%), Positives = 82/197 (41%), Gaps = 37/197 (18%)
Query: 204 ISLVGMGGIGKTTLAQFAYNDEDVI------------------SNFEKRMWNCESIIEAL 245
+++ GM G GK+ LA A D ++ S ++ N ++
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 216
Query: 246 EGFAPNLG-ELNSLLLRIDAFIARK--KFLLILDDVWTDDYSKWEPFRRCLINGHRESRI 302
E F+ L + R+ + RK + LLILDDVW +P+ L + +I
Sbjct: 217 ESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW-------DPW--VLKAFDNQCQI 267
Query: 303 LVTTRKETVA-RMMESTDVIFIKE-LSEQECWALFKRFACFGRSLSECEQLEEIGKKIVG 360
L+TT ++V +M V+ ++ L ++ + F + E L I+
Sbjct: 268 LLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK-----EDLPAEAHSIIK 322
Query: 361 KCKGLPLAAKTIGSLLR 377
+CKG PL IG+LLR
Sbjct: 323 ECKGSPLVVSLIGALLR 339
>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 = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 597 GTNEIPKGIXXXXXXXXXXXXXVEKLPETCCELLNLQTLNMCGSPGLKRLPQGI-GKLIN 655
G +P GI ++ LP + L T G L+ LP G+ KL +
Sbjct: 18 GRTSVPTGIPAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTS 77
Query: 656 LRHLMFEVDYLEYMPKGI-ERLTSLRTLS 683
L +L + L+ +P G+ ++LT L+ L+
Sbjct: 78 LTYLNLSTNQLQSLPNGVFDKLTQLKELA 106
Score = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 29/126 (23%)
Query: 559 SYNTLNQKASAQVLQGLFDQLTGLRVLRIEGMKSLIGSGTNEIPKGIXXXXXXXXXXXXX 618
+Y L + + G+FD+LT L L + G K +P G+
Sbjct: 31 TYLDLETNSLKSLPNGVFDELTSLTQLYLGGNK------LQSLPNGV------------- 71
Query: 619 VEKLPETCCELLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKGI-ERL 676
KL T LNL T L+ LP G+ KL L+ L + L+ +P G+ ++L
Sbjct: 72 FNKL--TSLTYLNLSTNQ------LQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKL 123
Query: 677 TSLRTL 682
T L+ L
Sbjct: 124 TQLKDL 129
>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 = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 34/127 (26%), Positives = 57/127 (44%), Gaps = 29/127 (22%)
Query: 558 LSYNTLNQKASAQVLQGLFDQLTGLRVLRIEGMKSLIGSGTNEIPKGIXXXXXXXXXXXX 617
L+Y L + G+FD+LT L+ L L+ + +P G+
Sbjct: 87 LTYLILTGNQLQSLPNGVFDKLTNLKEL------VLVENQLQSLPDGVFD---------- 130
Query: 618 XVEKLPETCCELLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKGI-ER 675
+L NL LN+ + L+ LP+G+ KL NL L + L+ +P+G+ ++
Sbjct: 131 ----------KLTNLTYLNLAHNQ-LQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDK 179
Query: 676 LTSLRTL 682
LT L+ L
Sbjct: 180 LTQLKDL 186
Score = 32.7 bits (73), Expect = 0.91, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 3/58 (5%)
Query: 628 ELLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKGI-ERLTSLRTLS 683
EL NL L + G+ L+ LP G+ KL NL+ L+ + L+ +P G+ ++LT+L L+
Sbjct: 83 ELTNLTYLILTGNQ-LQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLN 139
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 34.7 bits (78), Expect = 0.29, Method: Composition-based stats.
Identities = 35/128 (27%), Positives = 60/128 (46%), Gaps = 13/128 (10%)
Query: 558 LSYNTLNQKASAQVLQGLFDQLTGLRVLRIEGMKSLIGSGTNEIPKGIXXXXXXXXXXXX 617
L+Y L + G+FD+LT L+ L L+ + +P G+
Sbjct: 87 LTYLILTGNQLQSLPNGVFDKLTNLKEL------VLVENQLQSLPDGVFDKLTNLTYLYL 140
Query: 618 ---XVEKLPETCCE-LLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKG 672
++ LP+ + L NL L++ + L+ LP+G+ KL L+ L + L+ +P G
Sbjct: 141 YHNQLQSLPKGVFDKLTNLTRLDL-DNNQLQSLPEGVFDKLTQLKQLSLNDNQLKSVPDG 199
Query: 673 I-ERLTSL 679
+ +RLTSL
Sbjct: 200 VFDRLTSL 207
Score = 32.7 bits (73), Expect = 0.92, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 628 ELLNLQTLNMCGSPGLKRLPQGI-GKLINLRHLMFEVDYLEYMPKGI-ERLTSLRTL 682
EL NL L + G+ L+ LP G+ KL NL+ L+ + L+ +P G+ ++LT+L L
Sbjct: 83 ELTNLTYLILTGNQ-LQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYL 138
>pdb|2A5Y|B Chain B, Structure Of A Ced-4CED-9 Complex
pdb|2A5Y|C Chain C, Structure Of A Ced-4CED-9 Complex
pdb|3LQQ|A Chain A, Structure Of The Ced-4 Apoptosome
pdb|3LQQ|B Chain B, Structure Of The Ced-4 Apoptosome
pdb|3LQR|A Chain A, Structure Of Ced-4:ced-3 Complex
pdb|3LQR|B Chain B, Structure Of Ced-4:ced-3 Complex
Length = 549
Score = 33.9 bits (76), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 72/185 (38%), Gaps = 35/185 (18%)
Query: 206 LVGMGGIGKTTLAQFAYNDEDVIS--NFEKRMWNCESIIEALEGFA-------------- 249
L G G GK+ +A A + D + N++ +W +S F
Sbjct: 157 LHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDD 216
Query: 250 ----PNLGELNSLLLR---IDAFIARKKFLLILDDVWTDDYSKWEPFRRCLINGHRESRI 302
P++ + S++L+ +A I R L + DDV ++ +W R R
Sbjct: 217 LLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRL--------RC 268
Query: 303 LVTTRKETVARMMEST-DVIFIKELSEQECWALFKRFACFGRSLSECEQLEEIGKKIVGK 361
LVTTR ++ T + I + L EC+ + +G + E+ E++ K +
Sbjct: 269 LVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLE---AYGMPMPVGEKEEDVLNKTIEL 325
Query: 362 CKGLP 366
G P
Sbjct: 326 SSGNP 330
>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 = 33.5 bits (75), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 54/101 (53%), Gaps = 15/101 (14%)
Query: 4 AIVSVVLQQLISVAVEETKGGVRLVTGVGTEVKRLQDNLEAIQAVLV---DAERRQLEEL 60
A +S ++ +L + EE K L GV ++ L LE+ A L+ + R QL+
Sbjct: 1 AAISNLIPKLGELLTEEFK----LHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQ 56
Query: 61 PVRLWLEKLKEASYDMEDMLDEWNTARLKLQIEGV--DDEN 99
+LW ++++E SY +ED++D + +Q++G+ DD N
Sbjct: 57 D-KLWADEVRELSYVIEDVVD-----KFLVQVDGIKSDDNN 91
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 41/156 (26%), Positives = 68/156 (43%), Gaps = 33/156 (21%)
Query: 529 KLRHLMLVLGYKNSFPVSIFYARKLRSLMLSYNTLNQKASAQVLQGLFDQLTGLRVLRIE 588
KLR L L + P IF ++L++L + T N+ + + G+FDQL L LR++
Sbjct: 62 KLRLLYLNDNKLQTLPAGIF--KELKNLETLWVTDNKLQALPI--GVFDQLVNLAELRLD 117
Query: 589 GMKSLIGSGTNEIPKGIXXXXXXXXXXXXXVEKLPETCCELLNLQTLNMCGSPGLKRLPQ 648
++ LP + L T G L+ LP+
Sbjct: 118 ---------------------------RNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPK 150
Query: 649 GI-GKLINLRHLMFEVDYLEYMPKG-IERLTSLRTL 682
G+ KL +L+ L + L+ +P+G ++LT L+TL
Sbjct: 151 GVFDKLTSLKELRLYNNQLKRVPEGAFDKLTELKTL 186
>pdb|3QF4|B Chain B, Crystal Structure Of A Heterodimeric Abc Transporter In
Its Inward- Facing Conformation
Length = 598
Score = 29.6 bits (65), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 171 IDLSEVRGRVEEKNAL-----KSKLLCKSSEQTNAVQIISLVGMGGIGKTTLAQFAYNDE 225
++L EVRG +E KN K +L + Q ++LVG G GKTT+
Sbjct: 346 VELREVRGEIEFKNVWFSYDKKKPVLKDITFHIKPGQKVALVGPTGSGKTTIVNLLMRFY 405
Query: 226 DV 227
DV
Sbjct: 406 DV 407
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
0.321 0.138 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,009,017
Number of Sequences: 62578
Number of extensions: 1077784
Number of successful extensions: 2734
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2718
Number of HSP's gapped (non-prelim): 22
length of query: 976
length of database: 14,973,337
effective HSP length: 108
effective length of query: 868
effective length of database: 8,214,913
effective search space: 7130544484
effective search space used: 7130544484
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)