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= 043056
(559 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 = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 64/245 (26%), Positives = 105/245 (42%), Gaps = 53/245 (21%)
Query: 180 IYGMGGIGKTMLAEEVAR--KVKSDKLFDQVVFVEVSQNQD----IRKLQG--------- 224
I+GM G GK++LA E R + V +V V + QD + KLQ
Sbjct: 152 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK-QDKSGLLMKLQNLCTRLDQDE 210
Query: 225 EIADKLGLKFHEESESGRANSLFKRIKAEKKILIILDNIWENLDLRVVGIPHGDGHKDCK 284
+ +L L E + R L K ++ L+ILD++W++ L+ C+
Sbjct: 211 SFSQRLPLNIEEAKDRLRILMLRKHPRS----LLILDDVWDSWVLKAFD-------SQCQ 259
Query: 285 VLLTARSLDVLSGKMDSRPNFSIGV---LNEE---EAWNLFKKMAGDYIEGSEFQSVARD 338
+LLT R V M P + + V L +E E +LF M + ++ A
Sbjct: 260 ILLTTRDKSVTDSVMG--PKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHS 312
Query: 339 VAKECAGLPVSVVTIARALRNKRLF--EWKDALEQL--------RRPSSTNFKDIQQTAY 388
+ KEC G P+ V I LR+ F W+ L+QL R+ SS +++ + +
Sbjct: 313 IIKECKGSPLVVSLIGALLRD---FPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMS 369
Query: 389 KAIEL 393
++E+
Sbjct: 370 ISVEM 374
>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 = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 63/242 (26%), Positives = 102/242 (42%), Gaps = 47/242 (19%)
Query: 180 IYGMGGIGKTMLAEEVAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKLQGE- 225
I+GM G GK++LA E R + V +V V QN R Q E
Sbjct: 158 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDES 217
Query: 226 IADKLGLKFHEESESGRANSLFKRIKAEKKILIILDNIWENLDLRVVGIPHGDGHKDCKV 285
+ +L L E + R L K ++ L+ILD++W++ L+ C++
Sbjct: 218 FSQRLPLNIEEAKDRLRILMLRKHPRS----LLILDDVWDSWVLKAFD-------SQCQI 266
Query: 286 LLTARSLDVLSGKMDSRPNFSIGV---LNEE---EAWNLFKKMAGDYIEGSEFQSVARDV 339
LLT R V M P + + V L +E E +LF M + ++ A +
Sbjct: 267 LLTTRDKSVTDSVMG--PKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSI 319
Query: 340 AKECAGLPVSVVTIARALRNKRLFEWKDALEQL--------RRPSSTNFKDIQQTAYKAI 391
KEC G P+ V I LR+ W+ L+QL R+ SS +++ + + ++
Sbjct: 320 IKECKGSPLVVSLIGALLRDFP-NRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISV 378
Query: 392 EL 393
E+
Sbjct: 379 EM 380
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 61/240 (25%), Positives = 99/240 (41%), Gaps = 43/240 (17%)
Query: 180 IYGMGGIGKTMLAEEVAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKLQGE- 225
IYGM G GK++LA E R + V +V + QN +R Q E
Sbjct: 152 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 211
Query: 226 IADKLGLKFHEESESGRANSLFKRIKAEKKILIILDNIWENLDLRVVGIPHGDGHKDCKV 285
+ +L L E + R L K ++ L+ILD++W+ L+ C++
Sbjct: 212 FSQRLPLNIEEAKDRLRVLMLRKHPRS----LLILDDVWDPWVLKAFD-------NQCQI 260
Query: 286 LLTARSLDVLSGKMDSRPNFSI--GVLNEE--EAWNLFKKMAGDYIEGSEFQSVARDVAK 341
LLT R V M + + G+ E+ E +LF M + + + A + K
Sbjct: 261 LLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHSIIK 315
Query: 342 ECAGLPVSVVTIARALRNKRLFEWKDALEQL--------RRPSSTNFKDIQQTAYKAIEL 393
EC G P+ V I LR+ W L QL R+ SS +++ + + ++E+
Sbjct: 316 ECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEM 374
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 60/240 (25%), Positives = 98/240 (40%), Gaps = 43/240 (17%)
Query: 180 IYGMGGIGKTMLAEEVAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKLQGE- 225
IYGM G GK++LA E R + V +V + QN +R Q E
Sbjct: 159 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 218
Query: 226 IADKLGLKFHEESESGRANSLFKRIKAEKKILIILDNIWENLDLRVVGIPHGDGHKDCKV 285
+ +L L E + R L K ++ L+ILD++W+ L+ C++
Sbjct: 219 FSQRLPLNIEEAKDRLRVLMLRKHPRS----LLILDDVWDPWVLKAFD-------NQCQI 267
Query: 286 LLTARSLDVLSGKMDSRPNFSI--GVLNEE--EAWNLFKKMAGDYIEGSEFQSVARDVAK 341
LLT V M + + G+ E+ E +LF M + + + A + K
Sbjct: 268 LLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHSIIK 322
Query: 342 ECAGLPVSVVTIARALRNKRLFEWKDALEQL--------RRPSSTNFKDIQQTAYKAIEL 393
EC G P+ V I LR+ W L QL R+ SS +++ + + ++E+
Sbjct: 323 ECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEM 381
>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex
With Dna
Length = 387
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 35/133 (26%), Positives = 59/133 (44%), Gaps = 17/133 (12%)
Query: 146 RLIFNKDYLP--FESRMFTLRNILSAL------EDPDVNMLGIYGMGGIGKTMLAEEVAR 197
R + DY+P R LR + L E P +L YG+ G GKT +A V R
Sbjct: 9 RWVLLPDYVPDVLPHREAELRRLAEVLAPALRGEKPSNALL--YGLTGTGKTAVARLVLR 66
Query: 198 KVK----SDKLFDQVVFVEVSQNQDIRKLQGEIADKLGLK--FHEESESGRANSLFKRIK 251
+++ S + + ++V + ++ IA+ +G++ F S L KR+
Sbjct: 67 RLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLS 126
Query: 252 AEKKI-LIILDNI 263
+ I +I+LD I
Sbjct: 127 RLRGIYIIVLDEI 139
>pdb|4FIQ|A Chain A, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIQ|B Chain B, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIQ|C Chain C, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIQ|D Chain D, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIQ|E Chain E, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIQ|F Chain F, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus Horikoshii
pdb|4FIR|A Chain A, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
pdb|4FIR|B Chain B, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
pdb|4FIR|C Chain C, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
pdb|4FIR|D Chain D, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
pdb|4FIR|E Chain E, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
pdb|4FIR|F Chain F, Crystal Structure Of Pyridoxal Biosynthesis Lyase Pdxs
From Pyrococcus
Length = 335
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 40/147 (27%), Positives = 63/147 (42%), Gaps = 36/147 (24%)
Query: 310 LNEEEAWNLFKKMAGDYIEGSEFQSVARDVAKECAGLPVSVVTIARALRNKRLFEWKDAL 369
+ +EE + + +K A Y+ +A V KE +GLP R L N+ ++E
Sbjct: 183 MTDEEIYGVAEKFAEPYLR------LAFSV-KEISGLP------KRVLENEPIYE----- 224
Query: 370 EQLRRPSSTNFKDIQQTAYKAIELSYNKLEGEELKNIFLLIGYTAIASIDALLMCGMGL- 428
+++I + YK I L KL L + G A + DA LM MG+
Sbjct: 225 -------GFTYREIVEDIYK-ILLEIKKLG--RLPVVNFAAGGVATPA-DAALMMAMGMD 273
Query: 429 ------GLFQGVNKMEVARARVRTLVH 449
G+F+ N ++ARA V + H
Sbjct: 274 GVFVGSGIFKSSNPPKMARAIVEAVNH 300
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 172 DPDVNMLGIYGMGGIGKTMLAEEVARKVKSDKLFDQVVFVEVSQNQDIRKLQGE 225
DP +L +YG G GKTML + VA K+ F+ V+ ++ + K GE
Sbjct: 204 DPPRGVL-LYGPPGTGKTMLVKAVANSTKA-------AFIRVNGSEFVHKYLGE 249
>pdb|2QGZ|A Chain A, Crystal Structure Of A Putative Primosome Component From
Streptococcus Pyogenes Serotype M3. Northeast Structural
Genomics Target Dr58
Length = 308
Score = 29.6 bits (65), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 61/148 (41%), Gaps = 22/148 (14%)
Query: 68 EENVENWLARANNVIVEADKFTDDEATANKRCFKGLCPNLKTRRRL-------SKE-AER 119
+E + L++ N +VE K+ + + KG P L +KE E
Sbjct: 43 QEQINLSLSKFNQFLVERQKYQLKDPS---YIAKGYQPILAMNEGYADVSYLETKELVEA 99
Query: 120 QKEAAVKVREARRFDRISYCTAPEDIRLIFNKDY-LPFESRMFTLRNILSALED-PDVNM 177
QK+AA+ +RI + P+ R I D + SRM IL +E P
Sbjct: 100 QKQAAIS-------ERIQLVSLPKSYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQ 152
Query: 178 LGIYGMG--GIGKTMLAEEVARKVKSDK 203
G+Y G GIGK+ L +A ++ K
Sbjct: 153 KGLYLYGDMGIGKSYLLAAMAHELSEKK 180
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
0.319 0.134 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,147,429
Number of Sequences: 62578
Number of extensions: 603092
Number of successful extensions: 2137
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 2124
Number of HSP's gapped (non-prelim): 32
length of query: 559
length of database: 14,973,337
effective HSP length: 104
effective length of query: 455
effective length of database: 8,465,225
effective search space: 3851677375
effective search space used: 3851677375
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: 54 (25.4 bits)