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= 001283
(1108 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WLT|A Chain A, The Crystal Structure Of Helicobacter Pylori
L-Asparaginase At 1.4 A Resolution
pdb|2WT4|A Chain A, Room Temperature Crystal Structure Of Helicobacter Pylori
L- Asparaginase At 1.8 A Resolution
Length = 332
Score = 37.4 bits (85), Expect = 0.048, Method: Composition-based stats.
Identities = 31/104 (29%), Positives = 48/104 (46%), Gaps = 17/104 (16%)
Query: 854 VGGENEPTSIGSFDRGRLIERE-----------SRVKSIDMEN-PSGRLREETLLTRAQR 901
+ G S+GS+ G L +E +R++ + N S + EE AQR
Sbjct: 17 IAGSGVDASLGSYKSGELGVKELLKAIPSLNKIARIQGEQVSNIGSQDMNEEIWFKLAQR 76
Query: 902 SSESYMKRKRSHGGIIDTNNVQMLEERRDIFYFLSFIVHNTKPV 945
+ E + R G +I T+ LEE YFL+ ++H+TKPV
Sbjct: 77 AQE-LLDDSRIQGVVI-THGTDTLEESA---YFLNLVLHSTKPV 115
>pdb|1Q3C|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-Viii
(Nei) From E. Coli: The E2a Mutant At 2.3 Resolution
Length = 262
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 1065 WWIFPAGLVLCKIFQSQLVNWHVANLEIQDRTL---YSNDFELF 1105
W+ FP K +QSQL+ HV ++E + + L +SND L+
Sbjct: 26 WFAFPQ----LKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLY 65
>pdb|1Q3B|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-Viii
(Nei) From E. Coli: The R252a Mutant At 2.05 Resolution.
pdb|2OPF|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-Viii
(Nei) From E. Coli (R252a) In Complex With Ap-Site
Containing Dna Substrate
Length = 262
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 1065 WWIFPAGLVLCKIFQSQLVNWHVANLEIQDRTL---YSNDFELF 1105
W+ FP K +QSQL+ HV ++E + + L +SND L+
Sbjct: 26 WFAFPQ----LKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLY 65
>pdb|2OQ4|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
pdb|2OQ4|B Chain B, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
Length = 262
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 1065 WWIFPAGLVLCKIFQSQLVNWHVANLEIQDRTL---YSNDFELF 1105
W+ FP K +QSQL+ HV ++E + + L +SND L+
Sbjct: 26 WFAFPQ----LKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLY 65
>pdb|1K3W|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of The
Dna Repair Enzyme Endonuclease Viii With Dna
pdb|1K3X|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of The
Dna Repair Enzyme Endonuclease Viii With Brominated-Dna
pdb|1Q39|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-Viii
(Nei) From E. Coli: The Wt Enzyme At 2.8 Resolution.
pdb|2EA0|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-viii
(nei) From E. Coli In Complex With Ap-site Containing Dna
Substrate
Length = 262
Score = 32.0 bits (71), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 1065 WWIFPAGLVLCKIFQSQLVNWHVANLEIQDRTL---YSNDFELF 1105
W+ FP K +QSQL+ HV ++E + + L +SND L+
Sbjct: 26 WFAFPQ----LKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLY 65
>pdb|3EHB|A Chain A, A D-Pathway Mutation Decouples The Paracoccus Denitrificans
Cytochrome C Oxidase By Altering The Side Chain
Orientation Of A Distant, Conserved Glutamate
Length = 558
Score = 31.2 bits (69), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 1008 PRRSVGLARVYALWNVTSLINVGVA-----FLCGYVHYSSGSSPNKKVPNFQPWNFSMDE 1062
PRR + +A WN S I ++ F G V Y+ + VPN+ WN D
Sbjct: 472 PRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNY--WNEHADT 529
Query: 1063 SEW 1065
EW
Sbjct: 530 LEW 532
>pdb|1AR1|A Chain A, Structure At 2.7 Angstrom Resolution Of The Paracoccus
Denitrificans Two-Subunit Cytochrome C Oxidase Complexed
With An Antibody Fv Fragment
pdb|3HB3|A Chain A, High Resolution Crystal Structure Of Paracoccus
Denitrificans Cytochrome C Oxidase
Length = 558
Score = 31.2 bits (69), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 1008 PRRSVGLARVYALWNVTSLINVGVA-----FLCGYVHYSSGSSPNKKVPNFQPWNFSMDE 1062
PRR + +A WN S I ++ F G V Y+ + VPN+ WN D
Sbjct: 472 PRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNY--WNEHADT 529
Query: 1063 SEW 1065
EW
Sbjct: 530 LEW 532
>pdb|1QLE|A Chain A, Cryo-structure Of The Paracoccus Denitrificans Four-subunit
Cytochrome C Oxidase In The Completely Oxidized State
Complexed With An Antibody Fv Fragment
Length = 538
Score = 30.8 bits (68), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 1008 PRRSVGLARVYALWNVTSLINVGVA-----FLCGYVHYSSGSSPNKKVPNFQPWNFSMDE 1062
PRR + +A WN S I ++ F G V Y+ + VPN+ WN D
Sbjct: 456 PRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNY--WNEHADT 513
Query: 1063 SEW 1065
EW
Sbjct: 514 LEW 516
>pdb|3QO4|A Chain A, The Crystal Structure Of Death Receptor 6
Length = 181
Score = 30.4 bits (67), Expect = 5.3, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 468 CEECPVGTY--KNVTGSDKSLCHQCPPQEFPHRAVYISVRGGIAETPCPYRCISE 520
C++CP GTY ++ T + +C CP F I + PCP+ I +
Sbjct: 30 CDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHENGIE-KCHDCSQPCPWPMIEK 83
>pdb|3U3P|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3Q|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3S|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3T|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3V|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
Length = 313
Score = 30.4 bits (67), Expect = 5.4, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 468 CEECPVGTY--KNVTGSDKSLCHQCPPQEFPHRAVYISVRGGIAETPCPYRCISE 520
C++CP GTY ++ T + +C CP F I + PCP+ I +
Sbjct: 26 CDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHENGIE-KCHDCSQPCPWPMIEK 79
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 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,690,542
Number of Sequences: 62578
Number of extensions: 1082738
Number of successful extensions: 2165
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2162
Number of HSP's gapped (non-prelim): 14
length of query: 1108
length of database: 14,973,337
effective HSP length: 109
effective length of query: 999
effective length of database: 8,152,335
effective search space: 8144182665
effective search space used: 8144182665
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: 57 (26.6 bits)