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= 041612
(276 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 = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 48/187 (25%), Positives = 70/187 (37%), Gaps = 41/187 (21%)
Query: 118 IYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKIQEE- 163
IYGM G GK++LA E R + V +V + QN +R QEE
Sbjct: 152 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 211
Query: 164 IGDKLGLKFHEESESGRANSLFTHGHK------------------GCKVLLTARSQDVLS 205
+L L E + R L H C++LLT R + V
Sbjct: 212 FSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTD 271
Query: 206 GKMDSRPNFSI--GVLNEE--EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT 261
M + + G+ E+ E SLF M + + + A + KEC G P+ +
Sbjct: 272 SVMGPKHVVPVESGLGREKGLEILSLFVNM-----KKEDLPAEAHSIIKECKGSPLVVSL 326
Query: 262 IARALRN 268
I LR+
Sbjct: 327 IGALLRD 333
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 49/189 (25%), Positives = 70/189 (37%), Gaps = 45/189 (23%)
Query: 118 IYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKIQEE- 163
I+GM G GK++LA E R + V +V V QN R Q+E
Sbjct: 152 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDES 211
Query: 164 IGDKLGLKFHEESESGRANSLFTHGHK------------------GCKVLLTARSQDVLS 205
+L L E + R L H C++LLT R + V
Sbjct: 212 FSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTD 271
Query: 206 GKMDSRPNFSIGV---LNEE---EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI 259
M P + + V L +E E SLF M + ++ A + KEC G P+ +
Sbjct: 272 SVMG--PKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSIIKECKGSPLVV 324
Query: 260 VTIARALRN 268
I LR+
Sbjct: 325 SLIGALLRD 333
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 47/187 (25%), Positives = 69/187 (36%), Gaps = 41/187 (21%)
Query: 118 IYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKIQEE- 163
IYGM G GK++LA E R + V +V + QN +R QEE
Sbjct: 159 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 218
Query: 164 IGDKLGLKFHEESESGRANSLFTHGHK------------------GCKVLLTARSQDVLS 205
+L L E + R L H C++LLT + V
Sbjct: 219 FSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTSDKSVTD 278
Query: 206 GKMDSRPNFSI--GVLNEE--EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSIVT 261
M + + G+ E+ E SLF M + + + A + KEC G P+ +
Sbjct: 279 SVMGPKHVVPVESGLGREKGLEILSLFVNM-----KKEDLPAEAHSIIKECKGSPLVVSL 333
Query: 262 IARALRN 268
I LR+
Sbjct: 334 IGALLRD 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 = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 49/189 (25%), Positives = 70/189 (37%), Gaps = 45/189 (23%)
Query: 118 IYGMGGIGKTMLAEEIAR--KVKSDKLFDQVVFVEVS-----------QNQDIRKIQEE- 163
I+GM G GK++LA E R + V +V V QN R Q+E
Sbjct: 158 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDES 217
Query: 164 IGDKLGLKFHEESESGRANSLFTHGHK------------------GCKVLLTARSQDVLS 205
+L L E + R L H C++LLT R + V
Sbjct: 218 FSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTD 277
Query: 206 GKMDSRPNFSIGV---LNEE---EAWSLFKKMAGDYIEDSEFQSIARDVAKECAGLPVSI 259
M P + + V L +E E SLF M + ++ A + KEC G P+ +
Sbjct: 278 SVMG--PKYVVPVESSLGKEKGLEILSLFVNM-----KKADLPEQAHSIIKECKGSPLVV 330
Query: 260 VTIARALRN 268
I LR+
Sbjct: 331 SLIGALLRD 339
>pdb|1F48|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1IHU|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase In Complex With
Mg-Adp-Alf3
pdb|1II0|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II0|B Chain B, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II9|A Chain A, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
pdb|1II9|B Chain B, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
Length = 589
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 19/96 (19%)
Query: 105 LSALEDPDV-----NMLGIYGMGGIGKTMLAEEIARKVKSDKLF-------DQVVFVEVS 152
LSAL D D+ ++ + G GG+GKT +A IA ++ +D F D + ++
Sbjct: 315 LSALVD-DIARNEHGLIMLMGKGGVGKTTMAAAIAVRL-ADMGFDVHLTTSDPAAHLSMT 372
Query: 153 QNQDIRKIQEEIGDKLGLKFHEESESGRANSLFTHG 188
N + +Q D HEE+E R + L T G
Sbjct: 373 LNGSLNNLQVSRIDP-----HEETERYRQHVLETKG 403
>pdb|3LX2|A Chain A, Crystal Structure Analysis Of Pcna From Thermococcus
Kodakaraensis Tk0582
pdb|3LX2|B Chain B, Crystal Structure Analysis Of Pcna From Thermococcus
Kodakaraensis Tk0582
pdb|3LX2|C Chain C, Crystal Structure Analysis Of Pcna From Thermococcus
Kodakaraensis Tk0582
Length = 259
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 140 DKLFDQVVFVEVSQNQDIRKIQEE--------IGDKLGLKFHEESESGRANSLFTHGHKG 191
+K FD+ VF + +R I + + L K+ ESE A L +
Sbjct: 21 EKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDL----KRF 76
Query: 192 CKVLLTARSQDVLSGKMDSRPNFSIGVLNEEEAW 225
KVL ARS+D L + +G+L +E W
Sbjct: 77 LKVLKLARSRDTLVLRKGGENFLEVGLLGDENTW 110
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 107 ALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSD 140
A+E ++ + ++G G GKT LAE IAR +D
Sbjct: 44 AIEAGHLHSMILWGPPGTGKTTLAEVIARYANAD 77
>pdb|3RN2|A Chain A, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
pdb|3RN2|B Chain B, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
pdb|3RN5|A Chain A, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
pdb|3RN5|B Chain B, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
pdb|3RN5|C Chain C, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
pdb|3RN5|D Chain D, Structural Basis Of Cytosolic Dna Recognition By Innate
Immune Receptors
Length = 208
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 13/100 (13%)
Query: 104 ILSALEDPDVNMLGIYGMGGIGKTMLAEEIARKVKSDKLFD--------QVVFVEVSQNQ 155
I A E P +N L +G I + + + K + LFD +V+ V +N+
Sbjct: 104 IRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGV---RNE 160
Query: 156 DIRKIQEEIGDKLGLKFHEESESGRANSLFTHGHKGCKVL 195
D K +E GDK+ L F S++G L + H KV+
Sbjct: 161 DTMKCKE--GDKVRLTFFTLSKNGEKLQLTSGVHSTIKVI 198
>pdb|3S9L|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 2
pdb|3S9L|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 2
pdb|3S9M|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 1
pdb|3S9M|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 1
pdb|3S9N|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Room Temperature
pdb|3S9N|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Room Temperature
Length = 654
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 5/95 (5%)
Query: 183 SLFTHGHKGCKVLLTA-----RSQDVLSGKMDSRPNFSIGVLNEEEAWSLFKKMAGDYIE 237
S F H H G T + PN + ++ A LF M GD
Sbjct: 190 SFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPS 249
Query: 238 DSEFQSIARDVAKECAGLPVSIVTIARALRNKRLF 272
D + S R V E + +++ + + ++ +F
Sbjct: 250 DWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIF 284
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
0.315 0.132 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,464,147
Number of Sequences: 62578
Number of extensions: 291699
Number of successful extensions: 1164
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 1149
Number of HSP's gapped (non-prelim): 62
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)