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= psy13246
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKQ|HH Chain h, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 130
Score = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 44/53 (83%), Positives = 49/53 (92%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVI 53
MVR+NVL+DALKSINNAEKRGKRQVLIRPCSKVIV+FLTVMMKHG + E +I
Sbjct: 1 MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEII 53
>pdb|3IZ6|H Chain H, Localization Of The Small Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 130
Score = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 37/49 (75%), Positives = 43/49 (87%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPE 49
MVRV+VL+DALK++ NAEKRGKRQVLIRP SKVI+KFL VM KHG + E
Sbjct: 1 MVRVSVLNDALKTMYNAEKRGKRQVLIRPSSKVIIKFLIVMQKHGYIGE 49
>pdb|3IZB|H Chain H, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O30|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 130
Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 37/58 (63%), Positives = 43/58 (74%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRT 58
M R +VL+DAL +INNAEK GKRQVLIRP SKVI+KFL VM KHG + E I R+
Sbjct: 1 MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRS 58
>pdb|1S1H|H Chain H, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex
From Yeast Obtained By Docking Atomic Models For Rna
And Protein Components Into A 11.7 A Cryo-Em Map. This
File, 1s1h, Contains 40s Subunit. The 60s Ribosomal
Subunit Is In File 1s1i
Length = 129
Score = 71.6 bits (174), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 36/56 (64%), Positives = 42/56 (75%)
Query: 3 RVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRT 58
R +VL+DAL +INNAEK GKRQVLIRP SKVI+KFL VM KHG + E I R+
Sbjct: 2 RSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRS 57
>pdb|3JYV|H Chain H, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 125
Score = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 34/53 (64%), Positives = 40/53 (75%)
Query: 6 VLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRT 58
+L+DAL +INNAEK GKRQVLIRP SKVI+KFL VM KHG + E I R+
Sbjct: 1 LLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRS 53
>pdb|3ZEY|J Chain J, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 130
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/53 (58%), Positives = 41/53 (77%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVI 53
M ++VL++AL+ I AE+RGKRQVLIRP SKV+VKFL VM KHG + E ++
Sbjct: 1 MTMMSVLANALRCIAGAERRGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIV 53
>pdb|2XZM|H Chain H, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 1
pdb|2XZN|H Chain H, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 2
Length = 130
Score = 62.4 bits (150), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 44/58 (75%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRT 58
MV+VN+L++ LK + NAEK GK+QVL+RP SKV++KFL +M K+G + E VI R+
Sbjct: 1 MVKVNILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRS 58
>pdb|3J20|I Chain I, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 130
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/77 (41%), Positives = 45/77 (58%), Gaps = 6/77 (7%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTV 60
M ++ L++AL I N+E+ GKR+V I+P SK+I + L VM K+G + E I R V
Sbjct: 1 MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGV 60
Query: 61 Y-----CMINWSG-IKP 71
Y IN +G IKP
Sbjct: 61 YRVQLLGRINKAGAIKP 77
>pdb|1I6U|A Chain A, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
pdb|1I6U|B Chain B, Rna-Protein Interactions: The Crystal Structure Of
Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS
Jannaschii
Length = 130
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVILGIRTTV 60
M ++ L++AL I+N E+ GK+ V I+P SK+I + L V +G + E I R +
Sbjct: 1 MSLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVXQDNGYIGEFEFIEDGRAGI 60
Query: 61 Y 61
+
Sbjct: 61 F 61
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
0.327 0.140 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,104,850
Number of Sequences: 62578
Number of extensions: 62840
Number of successful extensions: 86
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 77
Number of HSP's gapped (non-prelim): 9
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)