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= psy2461
(462 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|G Chain G, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 219
Score = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 79/178 (44%), Positives = 112/178 (62%), Gaps = 9/178 (5%)
Query: 139 GGEKNGKERKVLIRKPKAYYPTKD-KIKKVRGRRPFRKHARRLRSSLKPGTIVILVAGVH 197
GG E+ I +PK +YP D K + V R+P H +LRS++ PGT++IL+AG +
Sbjct: 33 GGALPKAEKPAAIAEPK-FYPADDVKPRTVSTRKP---HPTKLRSTITPGTVLILLAGRY 88
Query: 198 KGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFF 257
GKR VFLKQL+SGLLL+TGPF +N +P+RRV+Q YVIATST++DIS V V + +D +F
Sbjct: 89 MGKRVVFLKQLQSGLLLITGPFKINGVPIRRVNQAYVIATSTKVDISKVNV-QKFDDKYF 147
Query: 258 RRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMDEQLLKVIKVHPEKKILL 315
R KK + +G+ LF K+ + +K QK +D +L+K I P+ K L
Sbjct: 148 AREKKTRAKKTEGE---LFESDKEATKNLPDFKKDDQKVIDAELIKAIDAVPDLKNYL 202
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/50 (56%), Positives = 38/50 (76%), Gaps = 3/50 (6%)
Query: 49 KKVRGRRPFRKHARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL 98
+ V R+P H +LRS++ PGT++IL+AG + GKR VFLKQL+SGLLL
Sbjct: 59 RTVSTRKP---HPTKLRSTITPGTVLILLAGRYMGKRVVFLKQLQSGLLL 105
>pdb|4A18|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|E Chain E, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 191
Score = 109 bits (272), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 66/163 (40%), Positives = 101/163 (61%), Gaps = 4/163 (2%)
Query: 144 GKERKVLIRKPKAYYPTKDKIKKVRGRRPFRKHARRLRSSLKPGTIVILVAGVHKGKRGV 203
GK R V K +Y D+ R+ + A +LR+ + PGT++IL+AG +GKR V
Sbjct: 7 GKNRGV--SKISKWYKADDEATPFHRRQLKKATATKLRNDIAPGTVLILLAGRFRGKRVV 64
Query: 204 FLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFRRIKKH 263
FLKQL+SGLLLVTGP+ +N +PL+RV+Q Y ++TST++D++GV + +D+F R +K
Sbjct: 65 FLKQLKSGLLLVTGPYKVNGVPLKRVNQAYTLSTSTKVDLTGVNTAKFEDDYFGR--EKA 122
Query: 264 NKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMDEQLLKVIK 306
K + K L ++KK+ + ARK Q+ +D LL +K
Sbjct: 123 RKNHKNLFKAELTEEQKKKETERKNARKQDQQAVDTPLLAAVK 165
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/46 (58%), Positives = 36/46 (78%), Gaps = 1/46 (2%)
Query: 54 RRPFRK-HARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL 98
RR +K A +LR+ + PGT++IL+AG +GKR VFLKQL+SGLLL
Sbjct: 30 RRQLKKATATKLRNDIAPGTVLILLAGRFRGKRVVFLKQLKSGLLL 75
>pdb|3IZS|G Chain G, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|F Chain F, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|F Chain F, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|E Chain E, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 176
Score = 97.1 bits (240), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 66/162 (40%), Positives = 99/162 (61%), Gaps = 12/162 (7%)
Query: 157 YYPTKDKIKKVRGRRPFRKHAR--RLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL 214
+YP++D V + RK AR +LR+SL PGT++IL+AG +GKR V+LK LE LL
Sbjct: 9 WYPSED----VAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLL 64
Query: 215 VTGPFALNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRS 274
++GPF +N +PLRRV+ YVIATST++ + GV V E N +F + K K+ ++ +
Sbjct: 65 ISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNV-EKFNVEYFAKEKLTKKEKKEAN--- 120
Query: 275 LFAKRKKRAYKVSKARKVMQKDMDEQLLKVIKVHPEKKILLS 316
LF +++ + K + QK +D+ L+ IK P K LS
Sbjct: 121 LFPEQQNKEIKAERVED--QKVVDKALIAEIKKTPLLKQYLS 160
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/43 (58%), Positives = 32/43 (74%), Gaps = 2/43 (4%)
Query: 58 RKHAR--RLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL 98
RK AR +LR+SL PGT++IL+AG +GKR V+LK LE LL
Sbjct: 22 RKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLL 64
>pdb|3ZF7|VV Chain v, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 192
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 55/150 (36%), Positives = 83/150 (55%), Gaps = 13/150 (8%)
Query: 180 LRSSLKPGTIVILVAGVHKGKRGVFLKQL-ESGLLLVTGPFALNAMPLRRVHQNYVIATS 238
+R S KPGTI I++AG +G+R V LKQL ++G L+++GP + +P+RR+ Y+IATS
Sbjct: 26 VRKSCKPGTIAIILAGRFRGRRAVILKQLPKNGPLVISGPMKYSGVPIRRIDSRYIIATS 85
Query: 239 TQLDISGVKVPEAANDHFFRRIKKHNKQPRKGD---------KRSLFAKRKKRAYK--VS 287
T++D++GV A F+R KK + +G+ S K K A K VS
Sbjct: 86 TRVDLTGVDT-SAITPEIFKREKKEKRVKSEGEFMGDKDKKKAESKAKKTSKAAPKGTVS 144
Query: 288 KARKVMQKDMDEQLLKVIKVHPEKKILLSY 317
R +Q +D L++ IK P K + Y
Sbjct: 145 DERAQLQNAIDTALIQAIKKDPLGKEMAGY 174
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 13/61 (21%)
Query: 64 LRSSLKPGTIVILVAGVHKGKRGVFLKQLE-------------SGLLLKKNRVNFFLATR 110
+R S KPGTI I++AG +G+R V LKQL SG+ +++ + +AT
Sbjct: 26 VRKSCKPGTIAIILAGRFRGRRAVILKQLPKNGPLVISGPMKYSGVPIRRIDSRYIIATS 85
Query: 111 T 111
T
Sbjct: 86 T 86
>pdb|2JOY|A Chain A, Nmr Structure Of 50s Ribosomal Protein L14e From
Sulfolobus Solfataricus: Northeast Structural Genomics
Consortium Target Ssr105
Length = 96
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 183 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLD 242
+++ G I + V G G + V + ++ +LVTGP + + RRV+ ++ T ++D
Sbjct: 3 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 62
Query: 243 I 243
I
Sbjct: 63 I 63
>pdb|2KDS|A Chain A, Structure Of Ribosomal Protein L14e From Sulfolobus
Solfataricus
Length = 95
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 33/61 (54%)
Query: 183 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLD 242
+++ G I + V G G + V + ++ +LVTGP + + RRV+ ++ T ++D
Sbjct: 2 AIEVGRICVKVKGREAGSKCVIVDIIDDNFVLVTGPKDITGVKRRRVNILHLEPTDKKID 61
Query: 243 I 243
I
Sbjct: 62 I 62
>pdb|3J21|5 Chain 5, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|K Chain K, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 83
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 183 SLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLD 242
++ G I +++AG G++ V + ++ +LVTG LN + RR++ ++ ++D
Sbjct: 3 AIDVGRIAVVIAGRRAGQKVVVVDIIDKNFVLVTGA-GLNKVKRRRMNIKHIEPLPQKID 61
Query: 243 ISGVKVPEAANDHFFR 258
I P A+D R
Sbjct: 62 I-----PRGASDEEVR 72
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 0.136 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,908,018
Number of Sequences: 62578
Number of extensions: 476021
Number of successful extensions: 1305
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1293
Number of HSP's gapped (non-prelim): 12
length of query: 462
length of database: 14,973,337
effective HSP length: 102
effective length of query: 360
effective length of database: 8,590,381
effective search space: 3092537160
effective search space used: 3092537160
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: 53 (25.0 bits)