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= psy17590
(98 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|PP Chain p, 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 = 196
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 10/65 (15%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELI-----KLSSSAHQSIN-----KSRYKG 92
G++K++L TNE+A + ++ +I +LIK+ LI + S A N K R+ G
Sbjct: 18 GKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKGRHMG 77
Query: 93 VGRGK 97
+G+ K
Sbjct: 78 IGKRK 82
>pdb|3J21|Q Chain Q, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 150
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELIK----------LSSSAHQSINKSRYKG 92
GE ++++ E +++A + + +I RLIKE +IK + H+ K R++G
Sbjct: 18 GENRIWIDPERIDDVASAITREDIKRLIKEGVIKKKPIKGQSRYRAKIRHEQKKKGRHRG 77
Query: 93 VG 94
G
Sbjct: 78 PG 79
>pdb|3M7O|A Chain A, Crystal Structure Of Mouse Md-1 In Complex With
Phosphatidyl
pdb|3M7O|B Chain B, Crystal Structure Of Mouse Md-1 In Complex With
Phosphatidyl
pdb|3M7O|C Chain C, Crystal Structure Of Mouse Md-1 In Complex With
Phosphatidyl
pdb|3M7O|D Chain D, Crystal Structure Of Mouse Md-1 In Complex With
Phosphatidyl
Length = 162
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 36 PGKNPPEGERKLFLAIESTNELAVSKAKVEIT 67
PG + P+GE +L L + + N V+ A +T
Sbjct: 129 PGLDVPQGEYQLLLELYNENRATVACANATVT 160
>pdb|3P7I|A Chain A, Crystal Structure Of Escherichia Coli Phnd In Complex With
2- Aminoethyl Phosphonate
Length = 321
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 23 SEAGITVRGIYIPPGKNPPEGE-RKLFLAIESTNELAVSKAKVEITRLIKEELIKLSSSA 81
S +G V G Y+ N + ++ A TN LAV+ +V++ E L KL +SA
Sbjct: 136 STSGFLVPGYYVFAKNNISASDFKRTVNAGHETNALAVANKQVDVATNNTENLDKLKTSA 195
Query: 82 HQSINK 87
+ + +
Sbjct: 196 PEKLKE 201
>pdb|3T6Q|C Chain C, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|D Chain D, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 145
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 36 PGKNPPEGERKLFLAIESTNELAVSKAKVEIT 67
PG + P+GE +L L + + N V+ A +T
Sbjct: 110 PGLDVPQGEYQLLLELYNENRATVACANATVT 141
>pdb|3JYW|P Chain P, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 176
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 10/65 (15%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELI---------KLSSSAH-QSINKSRYKG 92
G+RK++L T+E+A + ++ I +L+K I K + AH QS + R+ G
Sbjct: 17 GKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSG 76
Query: 93 VGRGK 97
G+ K
Sbjct: 77 YGKRK 81
>pdb|2PX7|A Chain A, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidylyltransferase From Thermus Thermophilus Hb8
pdb|2PX7|B Chain B, Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate
Cytidylyltransferase From Thermus Thermophilus Hb8
Length = 236
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 32 IYIPPGKNPPEGERKLFLAIESTNELAVSK 61
+ +PPG PP+G +FL +T + +V++
Sbjct: 70 VALPPGAEPPKGLGAVFLEGGATRQASVAR 99
>pdb|3QK6|A Chain A, Crystal Structure Of Escherichia Coli Phnd
pdb|3QK6|B Chain B, Crystal Structure Of Escherichia Coli Phnd
pdb|3QUJ|A Chain A, Crystal Structure Of The Phosphonate Binding Protein,
Phnd, From Escherichia Coli
pdb|3QUJ|B Chain B, Crystal Structure Of The Phosphonate Binding Protein,
Phnd, From Escherichia Coli
pdb|3QUJ|C Chain C, Crystal Structure Of The Phosphonate Binding Protein,
Phnd, From Escherichia Coli
pdb|3QUJ|D Chain D, Crystal Structure Of The Phosphonate Binding Protein,
Phnd, From Escherichia Coli
Length = 321
Score = 26.2 bits (56), Expect = 5.3, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 23 SEAGITVRGIYIPPGKNPPEGE-RKLFLAIESTNELAVSKAKVEITRLIKEELIKLSSSA 81
S +G V G Y+ N + ++ A TN LAV+ +V++ E L KL +SA
Sbjct: 136 STSGFLVPGYYVFAKNNISASDFKRTVNAGHETNALAVANKQVDVATNNTENLDKLKTSA 195
Query: 82 HQSINK 87
+ + +
Sbjct: 196 PEKLKE 201
>pdb|1S1I|P Chain P, 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, 1s1i, Contains 60s Subunit. The 40s Ribosomal
Subunit Is In File 1s1h
Length = 142
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 10/65 (15%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELI---------KLSSSAH-QSINKSRYKG 92
G+RK++L T+E+A + ++ I +L+K I K + AH QS + R+ G
Sbjct: 17 GKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSG 76
Query: 93 VGRGK 97
G+ K
Sbjct: 77 YGKRK 81
>pdb|2WW9|J Chain J, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|J Chain J, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
The Yeast 80s Ribosome
pdb|2WWB|J Chain J, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
To The Actively Translating Wheat Germ 80s Ribosome
pdb|3IZS|T Chain T, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|S Chain S, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|S Chain S, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|R Chain R, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 189
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 10/65 (15%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELI---------KLSSSAH-QSINKSRYKG 92
G+RK++L T+E+A + ++ I +L+K I K + AH QS + R+ G
Sbjct: 18 GKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSG 77
Query: 93 VGRGK 97
G+ K
Sbjct: 78 YGKRK 82
>pdb|3S4U|A Chain A, Crystal Structure Of Open, Unliganded E. Coli Phnd H157a
Length = 321
Score = 25.8 bits (55), Expect = 6.2, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 23 SEAGITVRGIYIPPGKNPPEGE-RKLFLAIESTNELAVSKAKVEITRLIKEELIKLSSSA 81
S +G V G Y+ N + ++ A TN LAV+ +V++ E L KL +SA
Sbjct: 136 STSGFLVPGYYVFAKNNISASDFKRTVNAGAETNALAVANKQVDVATNNTENLDKLKTSA 195
Query: 82 HQSINK 87
+ + +
Sbjct: 196 PEKLKE 201
>pdb|3IZR|T Chain T, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 209
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 10/63 (15%)
Query: 43 GERKLFLAIESTNELAVSKAKVEITRLIKEELI-----KLSS-----SAHQSINKSRYKG 92
G+ K++L NE++++ ++ I +L+K+ I K+ S AH++ K R+ G
Sbjct: 18 GKGKVWLDPNEVNEISMANSRQNIRKLVKDGFIIRKPQKIHSRSRARRAHEAKQKGRHSG 77
Query: 93 VGR 95
G+
Sbjct: 78 YGK 80
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
0.312 0.132 0.350
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,598,943
Number of Sequences: 62578
Number of extensions: 83847
Number of successful extensions: 170
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 161
Number of HSP's gapped (non-prelim): 20
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)