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= 038448
(385 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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/105 (32%), Positives = 50/105 (47%), Gaps = 8/105 (7%)
Query: 239 SRLFEAGAPGSKIVFTTRNLGVAEK-MGPLPAYPLKE-LSNDDCLSVFSPHSLGEKDFST 296
S + +A +I+ TTR+ V + MGP P++ L + L + S +K
Sbjct: 254 SWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK---- 309
Query: 297 HPSLKEIGEKIVKKCNGLPLVAKSLGGLLRGFLNH-ESDKKQMEN 340
L E I+K+C G PLV +G LLR F N E KQ++N
Sbjct: 310 -ADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQN 353
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/105 (32%), Positives = 50/105 (47%), Gaps = 8/105 (7%)
Query: 239 SRLFEAGAPGSKIVFTTRNLGVAEK-MGPLPAYPLKE-LSNDDCLSVFSPHSLGEKDFST 296
S + +A +I+ TTR+ V + MGP P++ L + L + S +K
Sbjct: 248 SWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK---- 303
Query: 297 HPSLKEIGEKIVKKCNGLPLVAKSLGGLLRGFLNH-ESDKKQMEN 340
L E I+K+C G PLV +G LLR F N E KQ++N
Sbjct: 304 -ADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQN 347
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 250 KIVFTTRNLGVAEK-MGPLPAYPLKE-LSNDDCLSVFSPHSLGEKDFSTHPSLKEIGEKI 307
+I+ TTR+ V + MGP P++ L + L + S +K+ L I
Sbjct: 259 QILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHSI 313
Query: 308 VKKCNGLPLVAKSLGGLLRGFLN 330
+K+C G PLV +G LLR F N
Sbjct: 314 IKECKGSPLVVSLIGALLRDFPN 336
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 250 KIVFTTRNLGVAEK-MGPLPAYPLKE-LSNDDCLSVFSPHSLGEKDFSTHPSLKEIGEKI 307
+I+ TT + V + MGP P++ L + L + S +K+ L I
Sbjct: 266 QILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE-----DLPAEAHSI 320
Query: 308 VKKCNGLPLVAKSLGGLLRGFLN 330
+K+C G PLV +G LLR F N
Sbjct: 321 IKECKGSPLVVSLIGALLRDFPN 343
>pdb|4GE0|A Chain A, Schizosaccharomyces Pombe Dj-1 T114p Mutant
pdb|4GE0|B Chain B, Schizosaccharomyces Pombe Dj-1 T114p Mutant
pdb|4GE0|C Chain C, Schizosaccharomyces Pombe Dj-1 T114p Mutant
pdb|4GE0|D Chain D, Schizosaccharomyces Pombe Dj-1 T114p Mutant
Length = 194
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 281 LSVFSPHSLGEKDFSTHPSLKEIGEKIVKKCN---GL----PLVAKSLGGLLRGFLNHES 333
+++ LG K ST P ++++ ++ KK N G+ PL AK+ G + H S
Sbjct: 76 IAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIXAGPLTAKTSGLPNKQITGHPS 135
Query: 334 DKKQMENLGRKYFQE 348
+ Q+E G KY +
Sbjct: 136 VRGQLEEGGYKYLDQ 150
>pdb|1E6Y|C Chain C, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
pdb|1E6Y|F Chain F, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
Length = 247
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 247 PGSKIVFTTRNLGVAEKMGPLPAYPLKELSNDDCLSVFSPHSLGEKDFSTHPSLKEIGE 305
PG+ V R ++ K+ L+E+S++D +V + G STHP L E+GE
Sbjct: 8 PGATSVAANRRKHMSGKL-----EKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGE 61
>pdb|2VPI|A Chain A, Human Gmp Synthetase - Glutaminase Domain
pdb|2VPI|B Chain B, Human Gmp Synthetase - Glutaminase Domain
Length = 218
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 241 LFEAGAPGSKIV-FTTRNLGVAEKMGPL--PAYPLKELSNDDCLSVFSPHSLGEKDFS-T 296
+ +AGA K++ R L V ++ PL PA+ +KE + P+S+ +D
Sbjct: 29 ILDAGAQYGKVIDRRVRELFVQSEIFPLETPAFAIKEQGFRAIIISGGPNSVYAEDAPWF 88
Query: 297 HPSLKEIGEKIVKKCNGLPLVAKSLGGLLR 326
P++ IG+ ++ C G+ ++ K GG +
Sbjct: 89 DPAIFTIGKPVLGICYGMQMMNKVFGGTVH 118
>pdb|2VXO|A Chain A, Human Gmp Synthetase In Complex With Xmp
pdb|2VXO|B Chain B, Human Gmp Synthetase In Complex With Xmp
Length = 697
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 4/96 (4%)
Query: 232 YNDWTNRSRLFEAGAPGSKIV-FTTRNLGVAEKMGPL--PAYPLKELSNDDCLSVFSPHS 288
++ + + +AGA K++ R L V ++ PL PA+ +KE + P+S
Sbjct: 25 HHHYEGAVVILDAGAQYGKVIDRRVRELFVQSEIFPLETPAFAIKEQGFRAIIISGGPNS 84
Query: 289 LGEKDFS-THPSLKEIGEKIVKKCNGLPLVAKSLGG 323
+ +D P++ IG+ ++ C G+ ++ K GG
Sbjct: 85 VYAEDAPWFDPAIFTIGKPVLGICYGMQMMNKVFGG 120
>pdb|3POT|C Chain C, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
pdb|3POT|F Chain F, Structural Analysis Of A Ni(Iii)-Methyl Species In
Methyl-Coenzyme M Reductase From Methanothermobacter
Marburgensis
Length = 249
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 272 LKELSNDDCLSVFSPHSLGEKDFSTHPSLKEIGE 305
L+E+S++D + + + GE+ S HP L+E+ E
Sbjct: 28 LREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 61
>pdb|1HBM|C Chain C, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBM|F Chain F, Methyl-Coenzyme M Reductase Enzyme Product Complex
pdb|1HBN|C Chain C, Methyl-Coenzyme M Reductase
pdb|1HBN|F Chain F, Methyl-Coenzyme M Reductase
pdb|1HBO|C Chain C, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBO|F Chain F, Methyl-Coenzyme M Reductase Mcr-Red1-Silent
pdb|1HBU|C Chain C, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|1HBU|F Chain F, Methyl-Coenzyme M Reductase In The Mcr-Red1-Silent State
In Complex With Coenzyme M
pdb|3M1V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M1V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2R|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2U|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M2V|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M30|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|C Chain C, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
pdb|3M32|F Chain F, Structural Insight Into Methyl-Coenzyme M Reductase
Chemistry Using Coenzyme B Analogues
Length = 248
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 272 LKELSNDDCLSVFSPHSLGEKDFSTHPSLKEIGE 305
L+E+S++D + + + GE+ S HP L+E+ E
Sbjct: 27 LREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 60
>pdb|1MRO|C Chain C, Methyl-Coenzyme M Reductase
pdb|1MRO|F Chain F, Methyl-Coenzyme M Reductase
Length = 247
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 272 LKELSNDDCLSVFSPHSLGEKDFSTHPSLKEIGE 305
L+E+S++D + + + GE+ S HP L+E+ E
Sbjct: 27 LREISDEDVVKILGHRAPGEEYPSVHPPLEEMDE 60
>pdb|4GDH|A Chain A, Schizosaccharomyces Pombe Dj-1
pdb|4GDH|B Chain B, Schizosaccharomyces Pombe Dj-1
pdb|4GDH|C Chain C, Schizosaccharomyces Pombe Dj-1
pdb|4GDH|D Chain D, Schizosaccharomyces Pombe Dj-1
Length = 194
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 281 LSVFSPHSLGEKDFSTHPSLKEIGEKIVKKCN---GL----PLVAKSLGGLLRGFLNHES 333
+++ LG K ST P ++++ ++ KK N G+ L AK+ G + H S
Sbjct: 76 IAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIXAGTLTAKTSGLPNKQITGHPS 135
Query: 334 DKKQMENLGRKYFQE 348
+ Q+E G KY +
Sbjct: 136 VRGQLEEGGYKYLDQ 150
>pdb|4GE3|A Chain A, Schizosaccharomyces Pombe Dj-1 T114v Mutant
pdb|4GE3|B Chain B, Schizosaccharomyces Pombe Dj-1 T114v Mutant
pdb|4GE3|C Chain C, Schizosaccharomyces Pombe Dj-1 T114v Mutant
pdb|4GE3|D Chain D, Schizosaccharomyces Pombe Dj-1 T114v Mutant
Length = 194
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 281 LSVFSPHSLGEKDFSTHPSLKEIGEKIVKKCN--------GLPLVAKSLGGLLRGFLNHE 332
+++ LG K ST P ++++ ++ KK N G+ L AK+ G + H
Sbjct: 76 IAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIXAGV-LTAKTSGLPNKQITGHP 134
Query: 333 SDKKQMENLGRKYFQE 348
S + Q+E G KY +
Sbjct: 135 SVRGQLEEGGYKYLDQ 150
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 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,792,185
Number of Sequences: 62578
Number of extensions: 363648
Number of successful extensions: 906
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 894
Number of HSP's gapped (non-prelim): 19
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
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)