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= psy7990
(76 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 195
Score = 72.8 bits (177), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 32/44 (72%), Positives = 40/44 (90%)
Query: 21 KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAA 64
+Q+VNIPSF+VR++S+KHIDFSL SPFGGG GRVKRKN +KA+
Sbjct: 140 RQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKKAS 183
>pdb|3IZB|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|J Chain J, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|J Chain J, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 197
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 33/50 (66%), Positives = 39/50 (78%), Gaps = 1/50 (2%)
Query: 18 GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKN-LRKAASS 66
V KQ+VNIPSF+VRLDS+KHIDF+ SPFGG GRV R+N RKA +S
Sbjct: 135 AVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEAS 184
>pdb|1S1H|D Chain D, 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 = 179
Score = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 33/50 (66%), Positives = 39/50 (78%), Gaps = 1/50 (2%)
Query: 18 GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKN-LRKAASS 66
V KQ+VNIPSF+VRLDS+KHIDF+ SPFGG GRV R+N RKA +S
Sbjct: 117 AVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEAS 166
>pdb|2XZM|D Chain D, 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|D Chain D, 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 = 181
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 27/44 (61%), Positives = 34/44 (77%)
Query: 21 KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAA 64
K +VN+PSF+VR DS+K IDF+ SP GGG GR KRKN +K+A
Sbjct: 138 KNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKKSA 181
>pdb|3ZEY|6 Chain 6, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 190
Score = 55.5 bits (132), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 18 GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDE 75
V KQ+V IPSF+VR+ S+ HI F+ SPFG G GRVKR R AA + ++DE
Sbjct: 134 AVAKQIVTIPSFIVRVSSEHHIAFADASPFGNGRPGRVKRVK-RNAAKKGSGGGDDDE 190
>pdb|3JYV|D Chain D, 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 = 158
Score = 48.5 bits (114), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 21/29 (72%), Positives = 25/29 (86%)
Query: 18 GVRKQVVNIPSFVVRLDSQKHIDFSLNSP 46
V KQ+VNIPSF+VRLDS+KHIDF+ SP
Sbjct: 130 AVGKQIVNIPSFMVRLDSEKHIDFAPTSP 158
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 25.8 bits (55), Expect = 7.4, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 9 TQYWEHQGPGVRKQVVNIPSFVVRLDS-------QKHIDF 41
T + H PG+ +QV N+ V R+D+ +H++F
Sbjct: 210 TDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEF 249
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 25.4 bits (54), Expect = 8.7, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 9 TQYWEHQGPGVRKQVVNIPSFVVRLDS-------QKHIDF 41
T + H PG+ +QV N+ V R+D+ +H++F
Sbjct: 190 TDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEF 229
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
0.315 0.131 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,384,873
Number of Sequences: 62578
Number of extensions: 83892
Number of successful extensions: 134
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 126
Number of HSP's gapped (non-prelim): 8
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)