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= psy4541
(309 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PNU|H Chain H, Crystal Structure Of A Streptomycin Dependent Ribosome
From Escherichia Coli, 50s Subunit Of 70s Ribosome. This
File, 1pnu, Contains Only Molecules Of The 50s Ribosomal
Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site
Trna Are In The Pdb File 1pns.
pdb|1PNY|H Chain H, Crystal Structure Of The Wild Type Ribosome From E. Coli,
50s Subunit Of 70s Ribosome. This File, 1pny, Contains
Only Molecules Of The 50s Ribosomal Subunit. The 30s
Subunit Is In The Pdb File 1pnx.
pdb|1VOR|K Chain K, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOU|K Chain K, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOW|K Chain K, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOY|K Chain K, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VP0|K Chain K, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400
Length = 143
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 250 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 284
K +IPK D N V++D SG PLG R+ I S +R
Sbjct: 2 KTYIPKNDEQNWVVVDASGVPLG-RLATLIASRIR 35
>pdb|1NKW|H Chain H, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
pdb|1NWX|H Chain H, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Abt-773
pdb|1NWY|H Chain H, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Azithromycin
pdb|1SM1|H Chain H, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Quinupristin And Dalfopristin
pdb|1XBP|H Chain H, Inhibition Of Peptide Bond Formation By Pleuromutilins:
The Structure Of The 50s Ribosomal Subunit From
Deinococcus Radiodurans In Complex With Tiamulin
pdb|2ZJP|G Chain G, Thiopeptide Antibiotic Nosiheptide Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|2ZJQ|G Chain G, Interaction Of L7 With L11 Induced By Microccocin Binding
To The Deinococcus Radiodurans 50s Subunit
pdb|2ZJR|G Chain G, Refined Native Structure Of The Large Ribosomal Subunit
(50s) From Deinococcus Radiodurans
pdb|3CF5|G Chain G, Thiopeptide Antibiotic Thiostrepton Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|3DLL|G Chain G, The Oxazolidinone Antibiotics Perturb The Ribosomal
Peptidyl-Transferase Center And Effect Trna Positioning
pdb|3PIO|G Chain G, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
pdb|3PIP|G Chain G, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
Length = 174
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 250 KPHIPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 284
K +IPK D N V++D SG PLG R+ I S +R
Sbjct: 30 KTYIPKNDEQNWVVVDASGVPLG-RLATLIASRIR 63
>pdb|3P5P|A Chain A, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
13-Aza-13,14-Dihydrocopalyl Diphosphate
pdb|3P5R|A Chain A, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
2-Fluorogeranylgeranyl Diphosphate
pdb|3P5R|B Chain B, Crystal Structure Of Taxadiene Synthase From Pacific Yew
(Taxus Brevifolia) In Complex With Mg2+ And
2-Fluorogeranylgeranyl Diphosphate
Length = 764
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 29 PCLHHIKLLTRLRVVDNCE---IGRQAMAE--GKPPRVIAIYNQTHIGTIGDKVL 78
PC++ I LL RL +VDN E IGR E G V +++ IG D ++
Sbjct: 239 PCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLV 293
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 105 PCLHHIKLLTRLRVVDNCE---IGRQAMAE--GKPPRVIAIYNQTHIGTIGDKVL 154
PC++ I LL RL +VDN E IGR E G V +++ IG D ++
Sbjct: 239 PCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLV 293
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 181 PCLHHIKLLTRLRVVDNCE---IGRQAMAE--GKPPRVIAIYNQTHIGTIGDKVL 230
PC++ I LL RL +VDN E IGR E G V +++ IG D ++
Sbjct: 239 PCMYSIDLLERLSLVDNIEHLGIGRHFKQEIKGALDYVYRHWSERGIGWGRDSLV 293
>pdb|1PNU|I Chain I, Crystal Structure Of A Streptomycin Dependent Ribosome
From Escherichia Coli, 50s Subunit Of 70s Ribosome. This
File, 1pnu, Contains Only Molecules Of The 50s Ribosomal
Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site
Trna Are In The Pdb File 1pns.
pdb|1PNY|I Chain I, Crystal Structure Of The Wild Type Ribosome From E. Coli,
50s Subunit Of 70s Ribosome. This File, 1pny, Contains
Only Molecules Of The 50s Ribosomal Subunit. The 30s
Subunit Is In The Pdb File 1pnx.
pdb|1VOR|L Chain L, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOU|L Chain L, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOW|L Chain L, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOY|L Chain L, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VP0|L Chain L, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400
Length = 132
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 255 KTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 284
+ D N V+I++ G P GTR+ P+ LR
Sbjct: 89 RFDRNAAVIINNQGEPRGTRVFGPVARELR 118
>pdb|1NKW|I Chain I, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
pdb|1NWX|I Chain I, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Abt-773
pdb|1NWY|I Chain I, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Azithromycin
pdb|1SM1|I Chain I, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Quinupristin And Dalfopristin
pdb|1XBP|I Chain I, Inhibition Of Peptide Bond Formation By Pleuromutilins:
The Structure Of The 50s Ribosomal Subunit From
Deinococcus Radiodurans In Complex With Tiamulin
pdb|2ZJP|H Chain H, Thiopeptide Antibiotic Nosiheptide Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|2ZJQ|H Chain H, Interaction Of L7 With L11 Induced By Microccocin Binding
To The Deinococcus Radiodurans 50s Subunit
pdb|2ZJR|H Chain H, Refined Native Structure Of The Large Ribosomal Subunit
(50s) From Deinococcus Radiodurans
pdb|3CF5|H Chain H, Thiopeptide Antibiotic Thiostrepton Bound To The Large
Ribosomal Subunit Of Deinococcus Radiodurans
pdb|3DLL|H Chain H, The Oxazolidinone Antibiotics Perturb The Ribosomal
Peptidyl-Transferase Center And Effect Trna Positioning
pdb|3PIO|H Chain H, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
pdb|3PIP|H Chain H, Crystal Structure Of The Synergistic Antibiotic Pair
Lankamycin And Lankacidin In Complex With The Large
Ribosomal Subunit
Length = 134
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 255 KTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 284
+ D N V+I++ G P GTR+ P+ LR
Sbjct: 90 RFDRNAAVIINNQGEPRGTRVFGPVARELR 119
>pdb|3BBO|M Chain M, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 121
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 253 IPKTDTNNVVLIDDSGTPLGTRIHVPIPSMLR 284
I + D N V+ID G P GTRI I LR
Sbjct: 76 IIRYDDNAAVIIDQEGNPKGTRIFGAIARELR 107
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
0.321 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,876,975
Number of Sequences: 62578
Number of extensions: 345404
Number of successful extensions: 602
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 11
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)