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= psy16179
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|6 Chain 6, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 115
Score = 113 bits (282), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 49/56 (87%), Positives = 53/56 (94%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
RKSEIEYYAMLAKTGVHHY+GNNIELGTACGKY+RVCTL+I D GDSDIIRSMP +
Sbjct: 56 RKSEIEYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQ 111
>pdb|3VI6|A Chain A, Crystal Structure Of Human L30e
Length = 125
Score = 112 bits (281), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 49/56 (87%), Positives = 53/56 (94%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMPSE 144
RKSEIEYYAMLAKTGVHHY+GNNIELGTACGKY+RVCTL+I D GDSDIIRSMP +
Sbjct: 57 RKSEIEYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQ 112
>pdb|1YSH|C Chain C, Localization And Dynamic Behavior Of Ribosomal Protein
L30e
Length = 104
Score = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 40/50 (80%), Positives = 44/50 (88%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
RKSEIEYYAMLAK VHH+ GNN++LGTACGKY+RVC LSI D GDSDII
Sbjct: 51 RKSEIEYYAMLAKISVHHFHGNNVDLGTACGKYYRVCCLSILDPGDSDII 100
>pdb|3ZF7|GG Chain g, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 105
Score = 86.3 bits (212), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 35/49 (71%), Positives = 43/49 (87%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDI 137
RK+EIEYY L+KT +HHY+GNN++LGTACG++FR C LSITD GDSDI
Sbjct: 54 RKAEIEYYCTLSKTPIHHYSGNNLDLGTACGRHFRACVLSITDVGDSDI 102
>pdb|4A18|G Chain G, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|G Chain G, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|G Chain G, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|G Chain G, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2.
pdb|4ADX|6 Chain 6, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 104
Score = 82.4 bits (202), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 34/52 (65%), Positives = 44/52 (84%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRS 140
RKSEIEYYA LA+ +HH+ G+N+ELGTACGKY R T++I DAGDSDI+++
Sbjct: 52 RKSEIEYYASLAQISIHHFVGSNVELGTACGKYHRCSTMAILDAGDSDILKT 103
>pdb|3IZR|FF Chain f, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 112
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/45 (75%), Positives = 38/45 (84%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAG 133
RKSEIE YAMLAK VHH+ GNN++LGTACGKY+RVC LSI D G
Sbjct: 56 RKSEIETYAMLAKISVHHFHGNNVDLGTACGKYYRVCCLSILDPG 100
>pdb|1T0K|B Chain B, Joint X-ray And Nmr Refinement Of Yeast L30e-mrna Complex
pdb|3IZS|FF Chain f, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|Z Chain Z, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Z Chain Z, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|CC Chain c, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 105
Score = 76.6 bits (187), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 44/56 (78%)
Query: 87 VYRKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMP 142
V RKSE+EYYAML+KT V+++ G N ELGTA GK FRV +SI +AGDSDI+ ++
Sbjct: 50 VLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA 105
>pdb|1CK2|A Chain A, Yeast (Saccharomyces Cerevisiae) Ribosomal Protein L30
pdb|1CN7|A Chain A, Yeast Ribosomal Protein L30
pdb|1NMU|B Chain B, Mbp-L30
pdb|1NMU|D Chain D, Mbp-L30
Length = 104
Score = 76.3 bits (186), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 34/55 (61%), Positives = 44/55 (80%)
Query: 87 VYRKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSM 141
V RKSE+EYYAML+KT V+++ G N ELGTA GK FRV +SI +AGDSDI+ ++
Sbjct: 49 VLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTL 103
>pdb|3JYW|2 Chain 2, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 98
Score = 76.3 bits (186), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 44/56 (78%)
Query: 87 VYRKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDIIRSMP 142
V RKSE+EYYAML+KT V+++ G N ELGTA GK FRV +SI +AGDSDI+ ++
Sbjct: 43 VLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA 98
>pdb|2BO1|A Chain A, Crystal Structure Of A Hybrid Ribosomal Protein L30e With
Surface Residues From T. Celer, And Core Residues From
Yeast
Length = 101
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 35/50 (70%)
Query: 89 RKSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
RK ++EYYA L+ T V+ + G N+ELGTA GK V +SI DAG+S I+
Sbjct: 46 RKEDLEYYARLSGTPVYEFEGTNVELGTAVGKPHTVSVVSILDAGESRIL 95
>pdb|3J21|Z Chain Z, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 99
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +I YYA L+ V+ + G ++ELGT GK F V +L+I D G+S I+
Sbjct: 46 KDDIYYYAKLSDIPVYEFEGTSVELGTLLGKPFVVASLAIVDPGESKIL 94
>pdb|1W3E|X Chain X, Ribosomal L30e Of Thermococcus Celer, P59a Mutant
Length = 101
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 47 KEDIEYYARLSGIAVYEFEGTSVELGTLLGRPHTVSALAVVDPGESRIL 95
>pdb|3N4Z|A Chain A, Crystal Structure Of Quintuple Arg-To-Lys Variant Of T.
Celer L30e
pdb|3N4Z|B Chain B, Crystal Structure Of Quintuple Arg-To-Lys Variant Of T.
Celer L30e
Length = 101
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT GK V L++ D G+S I+
Sbjct: 47 KEDIEYYAKLSGIPVYEFEGTSVELGTLLGKPHTVSALAVVDPGESRIL 95
>pdb|3N4Y|A Chain A, Crystal Structure Of Wild-Type T. Celer L30e In Low Ionic
Strength Condition Without Precipitant
Length = 101
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGESRIL 95
>pdb|1W40|A Chain A, T. Celer L30e K9a Variant
Length = 101
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGESRIL 95
>pdb|1W42|A Chain A, T. Celer L30e R92a Variant
Length = 101
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGESAIL 95
>pdb|3RA5|A Chain A, Crystal Structure Of T. Celer L30e E6aR92A VARIANT
pdb|3RA5|B Chain B, Crystal Structure Of T. Celer L30e E6aR92A VARIANT
Length = 101
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGESAIL 95
>pdb|1H7M|A Chain A, Ribosomal Protein L30e From Thermococcus Celer
pdb|1GO0|A Chain A, Nmr Structure Of Ribosomal Protein L30e From Thermococcus
Celer
pdb|1GO1|A Chain A, Nmr Structure Of Ribosomal Protein L30e From Thermococcus
Celer
Length = 102
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 48 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGESRIL 96
>pdb|1W41|A Chain A, T.Celer L30e E90a Variant
Length = 101
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGASRIL 95
>pdb|3LFO|A Chain A, Crystal Structure Of T. Celer L30e E90aR92A VARIANT
Length = 101
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
K +IEYYA L+ V+ + G ++ELGT G+ V L++ D G S I+
Sbjct: 47 KEDIEYYARLSGIPVYEFEGTSVELGTLLGRPHTVSALAVVDPGASAIL 95
>pdb|3RA6|A Chain A, Crystal Structure Of T. Celer L30e E62aK46A VARIANT
Length = 101
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 92 EIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
+IEYYA L+ V+ + G ++ELGT G+ V L++ D G+S I+
Sbjct: 49 DIEYYARLSGIPVYAFEGTSVELGTLLGRPHTVSALAVVDPGESRIL 95
>pdb|3CPQ|A Chain A, Crystal Structure Of L30e A Ribosomal Protein From
Methanocaldococcus Jannaschii Dsm2661 (Mj1044)
pdb|3CPQ|B Chain B, Crystal Structure Of L30e A Ribosomal Protein From
Methanocaldococcus Jannaschii Dsm2661 (Mj1044)
Length = 110
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 90 KSEIEYYAMLAKTGVHHYTGNNIELGTACGKYFRVCTLSITDAGDSDII 138
+ +++YYA L+ V+ + ++ELG CGK F V L + D G S+I+
Sbjct: 52 EEDVKYYAKLSNIPVYQHKITSLELGAVCGKPFPVAALLVLDEGLSNIM 100
>pdb|1W9H|A Chain A, The Structure Of A Piwi Protein From Archaeoglobus
Fulgidus.
pdb|2BGG|A Chain A, The Structure Of A Piwi Protein From Archaeoglobus
Fulgidus Complexed With A 16nt Sirna Duplex.
pdb|2BGG|B Chain B, The Structure Of A Piwi Protein From Archaeoglobus
Fulgidus Complexed With A 16nt Sirna Duplex.
pdb|2W42|A Chain A, The Structure Of A Piwi Protein From Archaeoglobus
Fulgidus Complexed With A 16nt Dna Duplex.
pdb|2W42|B Chain B, The Structure Of A Piwi Protein From Archaeoglobus
Fulgidus Complexed With A 16nt Dna Duplex
Length = 427
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 19 ITTPATTLSLELPVDVWTSIARISNKVLVLKTIITLSKL----FRNQEMEI 65
+ TP LS+E+ D WTS N +L I LSK+ FR++ + +
Sbjct: 339 MVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPV 389
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
0.322 0.134 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,091,875
Number of Sequences: 62578
Number of extensions: 138314
Number of successful extensions: 217
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 194
Number of HSP's gapped (non-prelim): 23
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)