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= 025698
(249 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5C|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|C Chain C, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 236
Score = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 122/241 (50%), Positives = 147/241 (60%), Gaps = 5/241 (2%)
Query: 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDALGEEFKGYVFKIMGGCDKQG 60
MK NI+ P G QK EIDD+ ++R FFDKRI QEV+G+A+G+EFKGYVFKI GG DKQG
Sbjct: 1 MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG 60
Query: 61 FPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNLVIVKKGE 120
FPMKQGVL P R++LLL + C+ IV PDL+VL LVIVKKGE
Sbjct: 61 FPMKQGVLLPTRIKLLLTKNVSCY--RPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGE 118
Query: 121 HDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFTTKSGKKVSKAPKI 180
+L GLTDT P+ GPKRA+ IRK F LSKEDDVR +V R TK K +KAPKI
Sbjct: 119 QELEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVI---RREVTKGEKTYTKAPKI 175
Query: 181 QRLVTPLTLXXXXXXXXXXXXXXXXXXXXXXEYQKLLATRLKEQRERRSESLAKKRSRLS 240
QRLVTP L EY +LLA RL E++ ++E ++ S L
Sbjct: 176 QRLVTPQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLK 235
Query: 241 A 241
A
Sbjct: 236 A 236
>pdb|2XZM|Y Chain Y, 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|Y Chain Y, 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 = 293
Score = 199 bits (505), Expect = 1e-51, Method: Compositional matrix adjust.
Identities = 114/228 (50%), Positives = 134/228 (58%), Gaps = 8/228 (3%)
Query: 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDALGEEFKGYVFKIMGGCDKQG 60
MKFNI+ P TG QK +EIDDD+K F DK++ QEV GD LG+EFKGYVFKI GG DK G
Sbjct: 1 MKFNISYPLTGAQKCIEIDDDKKCNIFMDKKMGQEVEGDTLGDEFKGYVFKIAGGNDKDG 60
Query: 61 FPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNLVIVKKGE 120
FPMKQGV+ GRVRLLL G CF CIV PD+ VL L IVKKG
Sbjct: 61 FPMKQGVMVRGRVRLLLSEGHSCF--TSRRSGFRKRKSVRGCIVGPDMRVLALQIVKKGV 118
Query: 121 HDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDD---VRKYVNTYRRTFTTKSGKKVSKA 177
++ GLT PR GPKRA+ I+KLF L KEDD ++K V RRTF T GK +K
Sbjct: 119 AEIDGLTTVTLPRKLGPKRANNIKKLFGLKKEDDPILIKKSV--IRRTFKTAKGKDRTKC 176
Query: 178 PKIQRLVTPLTLXXXXXXXXXXXXXXXXXXXXXXEYQKLLATRLKEQR 225
PKIQRL+TP + EY+K L + K+QR
Sbjct: 177 PKIQRLITPERILRKKVYKAEKTQRYVKTNAAKEEYEKFL-SEWKKQR 223
>pdb|3ZEY|3 Chain 3, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 250
Score = 165 bits (418), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 88/186 (47%), Positives = 111/186 (59%), Gaps = 3/186 (1%)
Query: 1 MKFNIANPTTGCQKKLEIDDDQKLRAFF-DKRISQEVNGDALGEEFKGYVFKIMGGCDKQ 59
MK N+A P G K++E+ D+ R D R+ EV+G GE F+GY FK+ GG DK+
Sbjct: 1 MKLNVAYPRNGTVKQVEVTDEVLRRVNLGDYRLGNEVDGAIFGEAFRGYTFKLRGGSDKE 60
Query: 60 GFPMKQGVLTPGRVRLLLHRGTPCFXXXXXXXXXXXXXXXXXCIVSPDLSVLNLVIVKKG 119
GFPM QGV+ P RV LL+ RG F CI+ D++VLN+ + K G
Sbjct: 61 GFPMVQGVMAPSRVSLLVKRGAVGFNTFRGYQGERRRKSLRGCILGSDIAVLNVTVEKVG 120
Query: 120 EHDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFTTKSGKKVSKAPK 179
E + G+TD PR GPKRA+KIRKLFNL + DDVRKYV RR T + K KAPK
Sbjct: 121 EQPIEGVTDVSVPRRLGPKRANKIRKLFNLGRTDDVRKYV--IRRKVTKEGKKDRFKAPK 178
Query: 180 IQRLVT 185
IQRL+T
Sbjct: 179 IQRLIT 184
>pdb|3J20|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 125
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/93 (35%), Positives = 47/93 (50%), Gaps = 11/93 (11%)
Query: 1 MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVNGDAL--------GEEFKGYV-FK 51
K I++P +G K++EI + KRI ++ L G+EF V +
Sbjct: 4 FKLVISDPKSGIAKQVEITGAE-TEKLIGKRIGDQIPAKELNINLNELFGKEFPEDVKLE 62
Query: 52 IMGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCF 84
I GG DK GFPM+ + P RVR+LL +G P F
Sbjct: 63 IRGGTDKDGFPMRPDIHGPRRVRVLLSKG-PGF 94
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
0.319 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,791,462
Number of Sequences: 62578
Number of extensions: 194717
Number of successful extensions: 350
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 339
Number of HSP's gapped (non-prelim): 4
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)