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= 020131
(330 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GD1|Y Chain Y, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 183
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 180 LPPWMIKQGMNLTKEQRGEVKQES------KMDGSSATGGLSDDKKSTVEDDKAS----- 228
LPP ++ +LTK RGE +Q + D + L DK+ + +DD+ S
Sbjct: 102 LPPLTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQ 161
Query: 229 -LQDEYIRAYYAALLKKQQEL 248
L D I+ AAL K+ EL
Sbjct: 162 KLTDAAIKKIEAALADKEAEL 182
>pdb|1YC5|A Chain A, Sir2-P53 Peptide-Nicotinamide
pdb|2H4F|A Chain A, Sir2-P53 Peptide-Nad+
pdb|2H4J|A Chain A, Sir2-Deacetylated Peptide (From Enzymatic Turnover In
Crystal)
pdb|2H2D|A Chain A, The Structural Basis For Sirtuin Substrate Affinity
pdb|2H2F|A Chain A, The Structural Basis For Sirtuin Substrate Affinity
pdb|2H2G|A Chain A, The Structural Basis Of Sirtuin Substrate Affinity
pdb|2H2H|A Chain A, The Structural Basis Of Sirtuin Substrate Specificity
pdb|2H2I|A Chain A, The Structural Basis Of Sirtuin Substrate Affinity
pdb|3D4B|A Chain A, Crystal Structure Of Sir2tm In Complex With Acetyl P53
Peptide And Dadme-Nad+
pdb|3D81|A Chain A, Sir2-S-Alkylamidate Complex Crystal Structure
pdb|3PDH|A Chain A, Structure Of Sir2tm Bound To A Propionylated Peptide
Length = 246
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 6 KDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49
K +E V+EY C C+++Y D ++ + D C++CN
Sbjct: 110 KKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPL-CDDCN 152
>pdb|1EK8|A Chain A, Crystal Structure Of The Ribosome Recycling Factor (Rrf)
From Escherichia Coli
pdb|1ZN0|A Chain A, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The
50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf
pdb|1ZN1|A Chain A, Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 70s
Post- Termination Complex
pdb|2RDO|8 Chain 8, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|4GAS|Y Chain Y, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 185
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 180 LPPWMIKQGMNLTKEQRGEVKQES------KMDGSSATGGLSDDKKSTVEDDKAS----- 228
LPP ++ +LTK RGE +Q + D + L DK+ + +DD+ S
Sbjct: 102 LPPLTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQ 161
Query: 229 -LQDEYIRAYYAALLKKQQEL 248
L D I+ AAL K+ EL
Sbjct: 162 KLTDAAIKKIEAALADKEAEL 182
>pdb|2H59|A Chain A, Sir2 H116a-Deacetylated P53 Peptide-3'-O-Acetyl Adp Ribose
pdb|2H59|B Chain B, Sir2 H116a-Deacetylated P53 Peptide-3'-O-Acetyl Adp Ribose
pdb|3JR3|A Chain A, Sir2 Bound To Acetylated Peptide
Length = 246
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 6 KDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49
K +E V+EY C C+++Y D ++ + D C++CN
Sbjct: 110 KKVIELAGNVEEYYCVRCEKKYTVEDVIKKLESSDVPL-CDDCN 152
>pdb|2H4H|A Chain A, Sir2 H116y Mutant-P53 Peptide-Nad
Length = 246
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 6 KDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49
K +E V+EY C C+++Y D ++ + D C++CN
Sbjct: 110 KKVIELYGNVEEYYCVRCEKKYTVEDVIKKLESSDVPL-CDDCN 152
>pdb|1ISE|A Chain A, Crystal Structure Of A Mutant Of Ribosome Recycling Factor
From Escherichia Coli, Arg132gly
Length = 185
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 180 LPPWMIKQGMNLTKEQRGEVKQESKM------DGSSATGGLSDDKKSTVEDDKAS----- 228
LPP ++ +LTK RGE +Q D + L DK+ + +DD+ S
Sbjct: 102 LPPLTEERRKDLTKIVRGEAEQARVAVRNVGRDANDKVKALLKDKEISEDDDRRSQDDVQ 161
Query: 229 -LQDEYIRAYYAALLKKQQEL 248
L D I+ AAL K+ EL
Sbjct: 162 KLTDAAIKKIEAALADKEAEL 182
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
0.309 0.127 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,366,631
Number of Sequences: 62578
Number of extensions: 244079
Number of successful extensions: 570
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 563
Number of HSP's gapped (non-prelim): 14
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 52 (24.6 bits)