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= 042806
(390 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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 59/212 (27%), Positives = 87/212 (41%), Gaps = 38/212 (17%)
Query: 172 NPDVNMLGIYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG- 224
N + + IYGM G K+ LA E R + E F V +V + K QD + K+Q
Sbjct: 144 NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-QDKSGLLMKLQNL 202
Query: 225 --------EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPH 276
+ +L L + E D R LR K L+ILD++W +A
Sbjct: 203 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLR----KHPRSLLILDDVWDPWVLKAF---- 254
Query: 277 GDDRKGCKVLLTARSLDVLSRKMDSQQNFSV----GVLKEDEAWSLFKKMAGDYIEGSEF 332
D++ C++LLT R V M + V G K E SLF M + +
Sbjct: 255 -DNQ--CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAE-- 309
Query: 333 KWVAKDVARECAGLPVSIVTVARALGTRDYLN 364
A + +EC G P+ + + L RD+ N
Sbjct: 310 ---AHSIIKECKGSPLVVSLIGALL--RDFPN 336
>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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 57/204 (27%), Positives = 84/204 (41%), Gaps = 38/204 (18%)
Query: 180 IYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG--------- 224
I+GM G K+ LA E R + E F V +V V K QD + K+Q
Sbjct: 152 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK-QDKSGLLMKLQNLCTRLDQDE 210
Query: 225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCK 284
+ +L L + E D R LR K L+ILD++W + +A C+
Sbjct: 211 SFSQRLPLNIEEAKDRLRILMLR----KHPRSLLILDDVWDSWVLKAFD-------SQCQ 259
Query: 285 VLLTARSLDVLSRKMDSQQ----NFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVA 340
+LLT R V M + S+G K E SLF M + ++ A +
Sbjct: 260 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSII 314
Query: 341 RECAGLPVSIVTVARALGTRDYLN 364
+EC G P+ + + L RD+ N
Sbjct: 315 KECKGSPLVVSLIGALL--RDFPN 336
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 58/212 (27%), Positives = 86/212 (40%), Gaps = 38/212 (17%)
Query: 172 NPDVNMLGIYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG- 224
N + + IYGM G K+ LA E R + E F V +V + K QD + K+Q
Sbjct: 151 NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK-QDKSGLLMKLQNL 209
Query: 225 --------EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPH 276
+ +L L + E D R LR K L+ILD++W +A
Sbjct: 210 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLR----KHPRSLLILDDVWDPWVLKAF---- 261
Query: 277 GDDRKGCKVLLTARSLDVLSRKMDSQQNFSV----GVLKEDEAWSLFKKMAGDYIEGSEF 332
D++ C++LLT V M + V G K E SLF M + +
Sbjct: 262 -DNQ--CQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAE-- 316
Query: 333 KWVAKDVARECAGLPVSIVTVARALGTRDYLN 364
A + +EC G P+ + + L RD+ N
Sbjct: 317 ---AHSIIKECKGSPLVVSLIGALL--RDFPN 343
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 57/204 (27%), Positives = 84/204 (41%), Gaps = 38/204 (18%)
Query: 180 IYGMGGIVKTTLAKEVAR-KAETEKLFD-QVIFVEVSKIQD----IRKIQG--------- 224
I+GM G K+ LA E R + E F V +V V K QD + K+Q
Sbjct: 158 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK-QDKSGLLMKLQNLCTRLDQDE 216
Query: 225 EIADKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCK 284
+ +L L + E D R LR K L+ILD++W + +A C+
Sbjct: 217 SFSQRLPLNIEEAKDRLRILMLR----KHPRSLLILDDVWDSWVLKAFD-------SQCQ 265
Query: 285 VLLTARSLDVLSRKMDSQQ----NFSVGVLKEDEAWSLFKKMAGDYIEGSEFKWVAKDVA 340
+LLT R V M + S+G K E SLF M + ++ A +
Sbjct: 266 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSII 320
Query: 341 RECAGLPVSIVTVARALGTRDYLN 364
+EC G P+ + + L RD+ N
Sbjct: 321 KECKGSPLVVSLIGALL--RDFPN 342
>pdb|2Q9U|A Chain A, Crystal Structure Of The Flavodiiron Protein From Giardia
Intestinalis
pdb|2Q9U|B Chain B, Crystal Structure Of The Flavodiiron Protein From Giardia
Intestinalis
Length = 414
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 34/179 (18%), Positives = 69/179 (38%), Gaps = 30/179 (16%)
Query: 137 SYNIIPDDTLLLS---IKDYEACESRMST---LNDILDALKNPDVNMLGIYGMGGIVKTT 190
++ P+D +L S + A R + ++ ++ K N+LG++
Sbjct: 157 TFTYCPEDKILFSNDGFGQHYATSRRWADECDVSHVMHLFKEYTANILGLF--------- 207
Query: 191 LAKEVARKAETEKLFDQVIFVEVSKIQDIRKIQGEIADKLGLTLHEESDSGRARSLRNRL 250
A+ K + VE+ I + D +GL + E + +
Sbjct: 208 -------SAQMRKALEVASTVEIKYILSAHGVSWR-GDAMGLAIAEYDRWSKGQHC---- 255
Query: 251 KKEKTILVILDNIWGNLDFQAVGIPHGDDRKGCK-VLLTARSLDVLSRKMDSQQNFSVG 308
+K + V+LD+++G A+ + G GC+ VLL S D+ + + + +V
Sbjct: 256 --QKKVTVVLDSMYGTTHRMALALLDGARSTGCETVLLEMTSSDITKVALHTYDSGAVA 312
>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 68/163 (41%), Gaps = 38/163 (23%)
Query: 180 IYGMGGIVKTTLAKEVARKAETEKLFDQVIFVEVSK---------IQDIRKIQGEIA--- 227
+YG G KT LAK VA +T F +++ E+ + + I K+ GE A
Sbjct: 221 LYGAPGTGKTLLAKAVAN--QTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSI 278
Query: 228 ------DKLGLTLHEESDSGRARSLRNRLKKEKTILVILDNIWGNLDFQAVGIPHGDDRK 281
D +G T +S+SG R + ++T+L +L+ + G DDR
Sbjct: 279 VFIDEIDAIG-TKRYDSNSGGEREI------QRTMLELLNQLDGF-----------DDRG 320
Query: 282 GCKVLLTARSLDVLSRKMDSQQNFSVGVLKEDEAWSLFKKMAG 324
KV++ ++ L + +L E+ S KK+ G
Sbjct: 321 DVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILG 363
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
0.318 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,972,952
Number of Sequences: 62578
Number of extensions: 436712
Number of successful extensions: 1247
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1242
Number of HSP's gapped (non-prelim): 22
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)