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= 003773
(796 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 54/204 (26%), Positives = 86/204 (42%), Gaps = 40/204 (19%)
Query: 40 ISLFGLGGIGKTTLAQLAFNNEGVKRKFDIVIWVCVSDAFEEIRIAK----AILEVLDKS 95
++++G+ G GK+ LA A + + C S + I K +L L
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEG-------CFSGGVHWVSIGKQDKSGLLMKLQNL 202
Query: 96 ASSLGEFQSLMQQTQESI-------------RGKKFFLVLDDVWDGDFKKWDPFFSCLKN 142
L + +S Q+ +I + + L+LDDVWD P+ LK
Sbjct: 203 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD-------PWV--LKA 253
Query: 143 GHHESKILITTRDRSVALQ-MGSIDIISVKE-LGEEECWSLFKQVAFLGRSFEDCEKLEP 200
++ +IL+TTRD+SV MG ++ V+ LG E+ + + + E L
Sbjct: 254 FDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK-----EDLPA 308
Query: 201 IGRKIACKCKGLPLAAKVIGNLLR 224
I +CKG PL +IG LLR
Sbjct: 309 EAHSIIKECKGSPLVVSLIGALLR 332
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 53/204 (25%), Positives = 85/204 (41%), Gaps = 40/204 (19%)
Query: 40 ISLFGLGGIGKTTLAQLAFNNEGVKRKFDIVIWVCVSDAFEEIRIAK----AILEVLDKS 95
++++G+ G GK+ LA A + + C S + I K +L L
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEG-------CFSGGVHWVSIGKQDKSGLLMKLQNL 209
Query: 96 ASSLGEFQSLMQQTQESI-------------RGKKFFLVLDDVWDGDFKKWDPFFSCLKN 142
L + +S Q+ +I + + L+LDDVWD P+ LK
Sbjct: 210 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD-------PWV--LKA 260
Query: 143 GHHESKILITTRDRSVALQ-MGSIDIISVKE-LGEEECWSLFKQVAFLGRSFEDCEKLEP 200
++ +IL+TT D+SV MG ++ V+ LG E+ + + + E L
Sbjct: 261 FDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKK-----EDLPA 315
Query: 201 IGRKIACKCKGLPLAAKVIGNLLR 224
I +CKG PL +IG LLR
Sbjct: 316 EAHSIIKECKGSPLVVSLIGALLR 339
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 52/197 (26%), Positives = 86/197 (43%), Gaps = 26/197 (13%)
Query: 40 ISLFGLGGIGKTTLAQLAFNNEGVKRKF--DIVIWVCVSDAFEEIRIAK--AILEVLDKS 95
+++ G+ G GK+ LA A + + V WV V + + K + LD+
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 209
Query: 96 ASSLGEFQSLMQQTQESIR------GKKFFLVLDDVWDGDFKKWDPFFSCLKNGHHESKI 149
S +++ ++ +R + L+LDDVWD W LK + +I
Sbjct: 210 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAFDSQCQI 260
Query: 150 LITTRDRSVALQ-MGSIDIISVKE-LGEEECWSLFKQVAFLGRSFEDCEKLEPIGRKIAC 207
L+TTRD+SV MG ++ V+ LG+E+ + + ++ L I
Sbjct: 261 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA-----DLPEQAHSIIK 315
Query: 208 KCKGLPLAAKVIGNLLR 224
+CKG PL +IG LLR
Sbjct: 316 ECKGSPLVVSLIGALLR 332
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 61/152 (40%), Gaps = 13/152 (8%)
Query: 387 SFPMSTPEFNRLRTLLIYDLSPYSPSLNGSILVELFSKVACLRALVIRQWFVPLDDQNF- 445
+ P S NRLR L I L EL +A A Q V L
Sbjct: 141 ALPASIASLNRLRELSIRACP---------ELTELPEPLASTDASGEHQGLVNLQSLRLE 191
Query: 446 ---IREIPENIGKLIHLKYLNLSELCIERLPETLCELYNLQKLAVRWCTNLRELPAGIGK 502
IR +P +I L +LK L + + L + L L++L +R CT LR P G
Sbjct: 192 WTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG 251
Query: 503 LMNMRSLMNGQTEKLKYLPIGISRLTSLRTLE 534
++ L+ L LP+ I RLT L L+
Sbjct: 252 RAPLKRLILKDCSNLLTLPLDIHRLTQLEKLD 283
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 8/101 (7%)
Query: 442 DQNFIREIPENIGKLIHLKYLNLSELCIERLPETLCELYNLQKLAVRWCTNLRELP---A 498
D + E+P+ + L+ L L+ + LP ++ L L++L++R C L ELP A
Sbjct: 112 DAAGLXELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLA 171
Query: 499 GIGKLMNMRSLMNGQTEKLKY-----LPIGISRLTSLRTLE 534
+ L+N Q+ +L++ LP I+ L +L++L+
Sbjct: 172 STDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLK 212
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 36/144 (25%), Positives = 63/144 (43%), Gaps = 12/144 (8%)
Query: 448 EIPENIGKLIHLKYLNLSELCIERLPETLCELYNLQKLAVRWCTNLRELPAGIGKLMNMR 507
+ P+ +L HL++ + + LP+T + L+ L + LR LPA I L +R
Sbjct: 95 QFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLR 153
Query: 508 SLMNGQTEKLKYLPIGISR---------LTSLRTLEKFVVGGGVDGGSTCRLESLKNLQL 558
L +L LP ++ L +L++L G S L++LK+L+
Sbjct: 154 ELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLK- 212
Query: 559 LRECRVEGL-SNVSHVDEAERLQL 581
+R + L + H+ + E L L
Sbjct: 213 IRNSPLSALGPAIHHLPKLEELDL 236
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 52/197 (26%), Positives = 86/197 (43%), Gaps = 26/197 (13%)
Query: 40 ISLFGLGGIGKTTLAQLAFNNEGVKRKF--DIVIWVCVSDAFEEIRIAK--AILEVLDKS 95
+++ G+ G GK+ LA A + + V WV V + + K + LD+
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQD 215
Query: 96 ASSLGEFQSLMQQTQESIR------GKKFFLVLDDVWDGDFKKWDPFFSCLKNGHHESKI 149
S +++ ++ +R + L+LDDVWD W LK + +I
Sbjct: 216 ESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----W-----VLKAFDSQCQI 266
Query: 150 LITTRDRSVALQ-MGSIDIISVKE-LGEEECWSLFKQVAFLGRSFEDCEKLEPIGRKIAC 207
L+TTRD+SV MG ++ V+ LG+E+ + + ++ L I
Sbjct: 267 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKA-----DLPEQAHSIIK 321
Query: 208 KCKGLPLAAKVIGNLLR 224
+CKG PL +IG LLR
Sbjct: 322 ECKGSPLVVSLIGALLR 338
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/115 (32%), Positives = 65/115 (56%), Gaps = 14/115 (12%)
Query: 421 LFSKVACLRALVIRQWFVPLDDQNFIREIPENI-GKLIHLKYLNLSELCIERLPETLCE- 478
+F K+ L+ LV+ + N ++ +P+ + KL +L YLNL+ ++ LP+ + +
Sbjct: 104 VFDKLTNLKELVLVE--------NQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDK 155
Query: 479 LYNLQKLAVRWCTNLRELPAGI-GKLMNMRSLMNGQTEKLKYLPIGI-SRLTSLR 531
L NL +L + + L+ LP G+ KL ++ L Q + LK +P G+ RLTSL+
Sbjct: 156 LTNLTELDLSY-NQLQSLPEGVFDKLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQ 208
>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 = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 33/92 (35%), Positives = 52/92 (56%), Gaps = 6/92 (6%)
Query: 444 NFIREIPENI-GKLIHLKYLNLSELCIERLPETLCE-LYNLQKLAVRWCTNLRELPAGI- 500
N ++ +P + KL L YLNLS ++ LP + + L L++LA+ L+ LP G+
Sbjct: 62 NKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALN-TNQLQSLPDGVF 120
Query: 501 GKLMNMRSLMNGQTEKLKYLPIGI-SRLTSLR 531
KL ++ L Q + LK +P G+ RLTSL+
Sbjct: 121 DKLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQ 151
>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 516
Score = 35.4 bits (80), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 49/105 (46%), Gaps = 9/105 (8%)
Query: 24 NTLALASSEQQKGLRIISLFGLGGIGKTTLAQLAFNNEGVKRKFDIVIWVCVSDAFEEIR 83
N+ A + R L+G GIGKTT A L G +DI + SD +
Sbjct: 64 NSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----YDI-LEQNASDVRSKTL 118
Query: 84 IAKAILEVLDKSASSLGEFQSLMQQTQESIRGKKFFLVLDDVWDG 128
+ + LD + S +G F+ + +++ GK F +++D+V DG
Sbjct: 119 LNAGVKNALD-NMSVVGYFKH--NEEAQNLNGKHFVIIMDEV-DG 159
>pdb|2XHL|B Chain B, Structure Of A Functional Derivative Of Clostridium
Botulinum Neurotoxin Type B
Length = 433
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 361 NSRKESVINSFGEKVRHLGLNFEGGASFPMSTPEFNRLRTLLIYDLSPYSPSLNGSILVE 420
N+ K++++N E +L G A + S L+T++ +DLS Y+ N +IL+E
Sbjct: 362 NTLKKNLLNYIDENKLYLI----GSAEYEKSKVN-KYLKTIMPFDLSIYT---NDTILIE 413
Query: 421 LFSKVACLRALV 432
+F+K L AL
Sbjct: 414 MFNKYNSLEALA 425
>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 = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 413 LNGSILVELFSKVACLRALVIRQWFVPLD-DQNFIREIPENIGKLIHLKYLNLSELCIER 471
LNG+ L EL +++ L L + LD N + +P +G LKY + +
Sbjct: 254 LNGNSLTELPAEIKNLSNLRV------LDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTT 307
Query: 472 LPETLCELYNLQKLAV 487
LP L NLQ L V
Sbjct: 308 LPWEFGNLCNLQFLGV 323
>pdb|3ZUQ|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type B-Derivative, Lc-B-Gs-Hn-B
Length = 906
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%), Gaps = 3/35 (8%)
Query: 398 LRTLLIYDLSPYSPSLNGSILVELFSKVACLRALV 432
L+T++ +DLS Y+ N +IL+E+F+K L AL
Sbjct: 867 LKTIMPFDLSIYT---NDTILIEMFNKYNSLEALA 898
>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 = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 56/94 (59%), Gaps = 11/94 (11%)
Query: 446 IREIPENIGKLIHLKYLNLSEL--CIERLPETLCE-LYNLQKLAVRWCTN-LRELPAGI- 500
+ IP N+ L ++ L+ EL IE +P L + L NL+ ++ + +N LR++P GI
Sbjct: 135 LTHIPANL--LTDMRNLSHLELRANIEEMPSHLFDDLENLE--SIEFGSNKLRQMPRGIF 190
Query: 501 GKLMNMRSLMNGQTEKLKYLPIGI-SRLTSLRTL 533
GK+ ++ L N + +LK +P GI RLTSL+ +
Sbjct: 191 GKMPKLKQL-NLASNQLKSVPDGIFDRLTSLQKI 223
>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 = 3.8, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 456 LIHLKYLNLSELCIERLPETLCE-LYNLQKLAVRWCTNLRELPAGIGKLMNMRSLMNGQT 514
L L L+L + LP + + L +L++L + C L ELP GI +L ++ L Q
Sbjct: 87 LTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFM-CCNKLTELPRGIERLTHLTHLALDQN 145
Query: 515 EKLKYLPIG-ISRLTSL 530
+ LK +P G RL+SL
Sbjct: 146 Q-LKSIPHGAFDRLSSL 161
>pdb|2P14|A Chain A, Crystal Structure Of Small Subunit (r.bspd6i2) Of The
Heterodimeric Restriction Endonuclease R.bspd6i
Length = 192
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 375 VRHLGLNFEGGASFPMSTPEFNRLRTLLIYDLSPYSPSLNGSILVEL 421
RH+G N E P++ +F +L T L D ++P+ IL++L
Sbjct: 118 ARHIGFNKESEPVIPLTVDQFKKLVTQLKGDGEHFNPNKLKEILIKL 164
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: 20,838,078
Number of Sequences: 62578
Number of extensions: 772375
Number of successful extensions: 1653
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1630
Number of HSP's gapped (non-prelim): 27
length of query: 796
length of database: 14,973,337
effective HSP length: 107
effective length of query: 689
effective length of database: 8,277,491
effective search space: 5703191299
effective search space used: 5703191299
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: 55 (25.8 bits)