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= 003317
(831 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 43/160 (26%), Positives = 74/160 (46%), Gaps = 27/160 (16%)
Query: 245 DKAVDIFRVLSKKKF---VLLLDDMWKRVDLTQLGVPLPSPTTASKVVFTTRFVEVCGAM 301
++A D R+L +K +L+LDD+W L + + +++ TTR V ++
Sbjct: 227 EEAKDRLRILMLRKHPRSLLILDDVWD-------SWVLKAFDSQCQILLTTRDKSVTDSV 279
Query: 302 KAHEYF-KVEC-LAHEKAWILFQEHVERQTLESHPDIPELAETVTKECGGLPLALITIGR 359
+Y VE L EK + V + D+PE A ++ KEC G PL + IG
Sbjct: 280 MGPKYVVPVESSLGKEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGA 335
Query: 360 AMACKKQPEDWKYAIQVL--------RRSAS-EFPGMDEV 390
+ + P W+Y ++ L R+S+S ++ +DE
Sbjct: 336 LL--RDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 373
>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 = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 43/160 (26%), Positives = 74/160 (46%), Gaps = 27/160 (16%)
Query: 245 DKAVDIFRVLSKKKF---VLLLDDMWKRVDLTQLGVPLPSPTTASKVVFTTRFVEVCGAM 301
++A D R+L +K +L+LDD+W L + + +++ TTR V ++
Sbjct: 221 EEAKDRLRILMLRKHPRSLLILDDVWD-------SWVLKAFDSQCQILLTTRDKSVTDSV 273
Query: 302 KAHEYF-KVEC-LAHEKAWILFQEHVERQTLESHPDIPELAETVTKECGGLPLALITIGR 359
+Y VE L EK + V + D+PE A ++ KEC G PL + IG
Sbjct: 274 MGPKYVVPVESSLGKEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGA 329
Query: 360 AMACKKQPEDWKYAIQVL--------RRSAS-EFPGMDEV 390
+ + P W+Y ++ L R+S+S ++ +DE
Sbjct: 330 LL--RDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 367
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 35.8 bits (81), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 70/162 (43%), Gaps = 31/162 (19%)
Query: 245 DKAVDIFRVLSKKKF---VLLLDDMWKRVDLTQLGVP--LPSPTTASKVVFTTRFVEVCG 299
++A D RVL +K +L+LDD+W P L + +++ TTR V
Sbjct: 221 EEAKDRLRVLMLRKHPRSLLILDDVWD---------PWVLKAFDNQCQILLTTRDKSVTD 271
Query: 300 A-MKAHEYFKVEC-LAHEKAWILFQEHVERQTLESHPDIPELAETVTKECGGLPLALITI 357
+ M VE L EK + V + D+P A ++ KEC G PL + I
Sbjct: 272 SVMGPKHVVPVESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLI 327
Query: 358 GRAMACKKQPEDWKYAIQVL--------RRSAS-EFPGMDEV 390
G + + P W Y ++ L R+S+S ++ +DE
Sbjct: 328 GALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA 367
>pdb|4AW4|A Chain A, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|B Chain B, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|C Chain C, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
Length = 311
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 500 AGLTEVQVLQGIERWKGVRKISLMQNQIRNLPFTPICPDLQTLFLKGINELPRELKALVN 559
A ++++ +QGI+ + ++L NQI ++ P++ LFL G N+L ++K L N
Sbjct: 51 ANNSDIKSVQGIQYLPNLTSLNLSNNQITDISPIQYLPNVTKLFLNG-NKL-TDIKPLAN 108
Query: 560 LKYL 563
LK L
Sbjct: 109 LKNL 112
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 33.5 bits (75), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 69/162 (42%), Gaps = 31/162 (19%)
Query: 245 DKAVDIFRVLSKKKF---VLLLDDMWKRVDLTQLGVP--LPSPTTASKVVFTTRFVEVCG 299
++A D RVL +K +L+LDD+W P L + +++ TT V
Sbjct: 228 EEAKDRLRVLMLRKHPRSLLILDDVWD---------PWVLKAFDNQCQILLTTSDKSVTD 278
Query: 300 A-MKAHEYFKVEC-LAHEKAWILFQEHVERQTLESHPDIPELAETVTKECGGLPLALITI 357
+ M VE L EK + V + D+P A ++ KEC G PL + I
Sbjct: 279 SVMGPKHVVPVESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLI 334
Query: 358 GRAMACKKQPEDWKYAIQVL--------RRSAS-EFPGMDEV 390
G + + P W Y ++ L R+S+S ++ +DE
Sbjct: 335 GALL--RDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA 374
>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 = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 539 LQTLFLKG--INELPRELKALVNLKYLNLDHTTFLHPIPSPLISSFSM 584
L L+L G + ELP E+K L NL+ L+L H L +P+ L S F +
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNR-LTSLPAELGSCFQL 295
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 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,711,097
Number of Sequences: 62578
Number of extensions: 945886
Number of successful extensions: 1973
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1951
Number of HSP's gapped (non-prelim): 32
length of query: 831
length of database: 14,973,337
effective HSP length: 107
effective length of query: 724
effective length of database: 8,277,491
effective search space: 5992903484
effective search space used: 5992903484
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)