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= psy1342
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|LL Chain l, 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 = 148
Score = 120 bits (300), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 56/101 (55%), Positives = 67/101 (66%)
Query: 39 KKTRKLXXXXXXXXXXXXXXXXXXXXXXNAGGMHHHRINFDKYHPGYFGKVGMRNYHIKK 98
+KTRKL NAGGMHHHRINFDKYHPGYFGKVGM++YH+K+
Sbjct: 6 RKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMKHYHLKR 65
Query: 99 NAKWCPIINLDRLWTLVSDQTREKYKDNKEGKAPIIDCVKA 139
N +CP +NLD+ WTLVS+QTR NK G APIID V++
Sbjct: 66 NQSFCPTVNLDKPWTLVSEQTRVNAAKNKTGVAPIIDVVRS 106
>pdb|4A17|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 149
Score = 99.0 bits (245), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 41/69 (59%), Positives = 57/69 (82%), Gaps = 1/69 (1%)
Query: 71 MHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKYKDNKEGK 130
MHHHRI +K+HPGY+GK+GMR +H+KKN CP++N+D+LW+LVSD TR+KY ++K+ K
Sbjct: 40 MHHHRILMEKWHPGYYGKLGMRTFHLKKNPLHCPVVNIDKLWSLVSDATRQKYAEDKK-K 98
Query: 131 APIIDCVKA 139
P+ID KA
Sbjct: 99 VPVIDVTKA 107
>pdb|3IZS|O Chain O, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|AA Chain a, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 149
Score = 94.7 bits (234), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 68 AGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKY-KDN 126
AGG HHHRIN DKYHPGYFGKVGMR +H ++ W P++NLD+LWTL+ + R++Y K
Sbjct: 35 AGGQHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSA 94
Query: 127 KEGKAPIIDCVKA 139
+ AP+ID + A
Sbjct: 95 SKETAPVIDTLAA 107
>pdb|3O58|Y Chain Y, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Y Chain Y, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 149
Score = 94.0 bits (232), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 68 AGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKY-KDN 126
AGG HHHRIN DKYHPGYFGKVGMR +H ++ W P++NLD+LWTL+ + R++Y K
Sbjct: 35 AGGEHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSA 94
Query: 127 KEGKAPIIDCVKA 139
+ AP+ID + A
Sbjct: 95 SKETAPVIDTLAA 107
>pdb|1S1I|V Chain V, 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 = 148
Score = 94.0 bits (232), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 68 AGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKY-KDN 126
AGG HHHRIN DKYHPGYFGKVGMR +H ++ W P++NLD+LWTL+ + R++Y K
Sbjct: 34 AGGEHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSA 93
Query: 127 KEGKAPIIDCVKA 139
+ AP+ID + A
Sbjct: 94 SKETAPVIDTLAA 106
>pdb|3JYW|V Chain V, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 142
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 41/73 (56%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 68 AGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKY-KDN 126
AGG HHHRIN DKYHPGYFGKVGMR +H ++ W P++NLD+LWTL+ + R++Y K
Sbjct: 29 AGGEHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSA 88
Query: 127 KEGKAPIIDCVKA 139
+ AP+ID + A
Sbjct: 89 SKETAPVIDTLAA 101
>pdb|3ZF7|BB Chain b, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 145
Score = 82.8 bits (203), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 41/71 (57%), Positives = 46/71 (64%), Gaps = 2/71 (2%)
Query: 67 NAGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLVSDQTREKYKDN 126
NAGG HHHRINF KYHPGYFGK GM +YH KKN W P INLD L L++ E K
Sbjct: 34 NAGGEHHHRINFRKYHPGYFGKCGMNHYHKKKNTTWKPTINLDNLTKLMAKD--EAMKAK 91
Query: 127 KEGKAPIIDCV 137
K P+ID +
Sbjct: 92 KGEALPVIDLL 102
>pdb|3IZR|O Chain O, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 144
Score = 81.6 bits (200), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 34/49 (69%), Positives = 40/49 (81%)
Query: 67 NAGGMHHHRINFDKYHPGYFGKVGMRNYHIKKNAKWCPIINLDRLWTLV 115
NAGGMHHHRI FDKYHPGYFGKVGMR +H N CP +N++RLW++V
Sbjct: 34 NAGGMHHHRILFDKYHPGYFGKVGMRYFHRLSNRFHCPAVNVERLWSMV 82
>pdb|3Q9L|A Chain A, The Structure Of The Dimeric E.Coli Mind-Atp Complex
pdb|3Q9L|B Chain B, The Structure Of The Dimeric E.Coli Mind-Atp Complex
pdb|3R9I|A Chain A, 2.6a Resolution Structure Of Mind Complexed With Mine
(12-31) Peptide
pdb|3R9I|B Chain B, 2.6a Resolution Structure Of Mind Complexed With Mine
(12-31) Peptide
pdb|3R9I|C Chain C, 2.6a Resolution Structure Of Mind Complexed With Mine
(12-31) Peptide
pdb|3R9I|D Chain D, 2.6a Resolution Structure Of Mind Complexed With Mine
(12-31) Peptide
pdb|3R9J|A Chain A, 4.3a Resolution Structure Of A Mind-Mine(I24n) Protein
Complex
pdb|3R9J|B Chain B, 4.3a Resolution Structure Of A Mind-Mine(I24n) Protein
Complex
Length = 260
Score = 26.6 bits (57), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 111 LWTLVSDQTREKYKDNKEGKAPIIDCVKAV 140
L+ L + QTR+K +EG A ++D +KA+
Sbjct: 83 LYILPASQTRDKDALTREGVAKVLDDLKAM 112
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
0.320 0.134 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,058,450
Number of Sequences: 62578
Number of extensions: 129411
Number of successful extensions: 243
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 227
Number of HSP's gapped (non-prelim): 19
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)