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= 030771
(171 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|R Chain R, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 188
Score = 227 bits (578), Expect = 3e-60, Method: Compositional matrix adjust.
Identities = 111/137 (81%), Positives = 124/137 (90%), Gaps = 1/137 (0%)
Query: 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKP 60
MGIDLVAGG++K++KR APKSDD+YLKLLVKLYRFLVRRT S FN VILKRLFMSK N+P
Sbjct: 1 MGIDLVAGGRNKRTKRVAPKSDDVYLKLLVKLYRFLVRRTKSKFNAVILKRLFMSKTNRP 60
Query: 61 PLSLSRLINFMKGKEDK-IAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGEC 119
PLS+ RL NFMKGKE+K IAVVVGT+TDD+R EVPA+KVTALRFTETARARI AGGEC
Sbjct: 61 PLSMRRLSNFMKGKEEKNIAVVVGTITDDMRIQEVPAMKVTALRFTETARARIINAGGEC 120
Query: 120 LTFDQLALRAPLGQNTV 136
LTFDQLALRAP G+NT+
Sbjct: 121 LTFDQLALRAPTGENTI 137
>pdb|3IZS|R Chain R, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|Q Chain Q, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 186
Score = 157 bits (396), Expect = 4e-39, Method: Compositional matrix adjust.
Identities = 85/138 (61%), Positives = 104/138 (75%), Gaps = 2/138 (1%)
Query: 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKP 60
MGID + + RTAPKSD++YLKLLVKLY FL RRTD+ FNKV+LK LF+SK+N+P
Sbjct: 1 MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP 60
Query: 61 PLSLSRLINFMK--GKEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGE 118
P+S+SR+ +K G +K VVVGTVTDD R +E P V ALRFT ARA+I KAGGE
Sbjct: 61 PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE 120
Query: 119 CLTFDQLALRAPLGQNTV 136
C+T DQLA+RAP GQNT+
Sbjct: 121 CITLDQLAVRAPKGQNTL 138
>pdb|2ZKR|OO Chain o, 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 = 188
Score = 153 bits (387), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 90/140 (64%), Positives = 110/140 (78%), Gaps = 3/140 (2%)
Query: 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKP 60
MG+D + K +K +R PKS DIYL+LLVKLYRFL RRT+S FN+V+LKRLFMS+ N+P
Sbjct: 1 MGVD-IRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRP 59
Query: 61 PLSLSRLINFMK--GKEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGE 118
PLSLSR+I MK G+E+K AVVVGTVTDD+R EVP LKV ALR + AR+RI KAGG+
Sbjct: 60 PLSLSRMIRKMKLPGRENKTAVVVGTVTDDVRILEVPKLKVCALRVSSRARSRILKAGGK 119
Query: 119 CLTFDQLALRAPLGQNTVCV 138
LTFDQLAL +P G+ TV +
Sbjct: 120 ILTFDQLALESPKGRGTVLL 139
>pdb|3ZF7|I Chain I, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 193
Score = 144 bits (362), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 75/144 (52%), Positives = 100/144 (69%), Gaps = 8/144 (5%)
Query: 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKP 60
MG+DL K K+ R S + Y+KLL+KLY+FL +RT+S FNK+I KRL S+ N+
Sbjct: 1 MGVDLTGVQKKKRVVRHHTYSTNPYIKLLIKLYKFLGKRTNSPFNKLIHKRLLKSRNNRA 60
Query: 61 PLSLSRLINFM--------KGKEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARI 112
P+SLSR+ M KGK+ IAV+VG V DD+R +PAL++ ALRF+++AR RI
Sbjct: 61 PISLSRIAVCMRRRTVWLKKGKKSPIAVIVGDVLDDVRMTRIPALRICALRFSKSARERI 120
Query: 113 EKAGGECLTFDQLALRAPLGQNTV 136
AGGECLTFDQLA+ AP G+NT+
Sbjct: 121 TGAGGECLTFDQLAMMAPTGKNTM 144
>pdb|3JYW|O Chain O, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 121
Score = 139 bits (351), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 76/118 (64%), Positives = 93/118 (78%), Gaps = 2/118 (1%)
Query: 21 SDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMK--GKEDKI 78
SD++YLKLLVKLY FL RRTD+ FNKV+LK LF+SK+N+PP+S+SR+ +K G +K
Sbjct: 1 SDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSVSRIARALKQEGAANKT 60
Query: 79 AVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTV 136
VVVGTVTDD R +E P V ALRFT ARA+I KAGGEC+T DQLA+RAP GQNT+
Sbjct: 61 VVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTL 118
>pdb|4A17|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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 = 181
Score = 139 bits (350), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 77/136 (56%), Positives = 97/136 (71%), Gaps = 2/136 (1%)
Query: 1 MGIDLVAGGKS-KKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNK 59
M IDL G+ K+S KS ++Y KLL+KLY+FLVRRTDS FN+ ILKRL S++NK
Sbjct: 1 MAIDLHKQGRVVKRSVVRQTKSTNVYHKLLIKLYKFLVRRTDSKFNQNILKRLSSSRLNK 60
Query: 60 PPLSLSRLI-NFMKGKEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGE 118
PLSLSR++ N + ++++ V TVT+D R VP L V AL+FTETAR RI AGG+
Sbjct: 61 FPLSLSRIVKNLNETNKEQVIVSTSTVTNDERLLTVPKLTVCALKFTETARKRILAAGGK 120
Query: 119 CLTFDQLALRAPLGQN 134
CLTFDQLAL+AP G N
Sbjct: 121 CLTFDQLALKAPTGTN 136
>pdb|1S1I|O Chain O, 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 = 120
Score = 137 bits (346), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 75/117 (64%), Positives = 92/117 (78%), Gaps = 2/117 (1%)
Query: 22 DDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMK--GKEDKIA 79
D++YLKLLVKLY FL RRTD+ FNKV+LK LF+SK+N+PP+S+SR+ +K G +K
Sbjct: 1 DNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSVSRIARALKQEGAANKTV 60
Query: 80 VVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTV 136
VVVGTVTDD R +E P V ALRFT ARA+I KAGGEC+T DQLA+RAP GQNT+
Sbjct: 61 VVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTL 117
>pdb|3J21|P Chain P, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 120
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 63/121 (52%), Gaps = 12/121 (9%)
Query: 15 KRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKV---ILKRLFMSKVNKPPLSLSRLINFM 71
KRT P + L +L R+L ++++ K+ + RL + + +++S++ +
Sbjct: 2 KRTGPTDPN-----LRRLIRYLRKKSNEYGVKIWKDVAWRLERPRRQRAEVNVSKINRYA 56
Query: 72 KGKEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPL 131
E + VV G+V + + + V A +F+ETAR +I +AGGE +T ++L R P
Sbjct: 57 NDGE--MIVVPGSVLGAGKLEK--KVIVAAWKFSETARRKIIEAGGEAITIEELIERNPT 112
Query: 132 G 132
G
Sbjct: 113 G 113
>pdb|3BTA|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype A
pdb|2NYY|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Cr1
pdb|2NZ9|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Ar2
pdb|2NZ9|B Chain B, Crystal Structure Of Botulinum Neurotoxin Type A Complexed
With Monoclonal Antibody Ar2
Length = 1295
Score = 26.6 bits (57), Expect = 6.8, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 29 LVKLYRFLVRRTDSNFNKVILKRLFMSKVN 58
VK ++ L R+T NF+K + K + KVN
Sbjct: 353 FVKFFKVLNRKTYLNFDKAVFKINIVPKVN 382
>pdb|3ZUR|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc0-A-Snap25-Hn-A
pdb|3ZUR|B Chain B, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc0-A-Snap25-Hn-A
Length = 960
Score = 26.6 bits (57), Expect = 7.0, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 29 LVKLYRFLVRRTDSNFNKVILKRLFMSKVN 58
VK ++ L R+T NF+K + K + KVN
Sbjct: 357 FVKFFKVLNRKTYLNFDKAVFKINIVPKVN 386
>pdb|3ZUS|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc-A-Snap23-Hn-A
pdb|3ZUS|B Chain B, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc-A-Snap23-Hn-A
pdb|3ZUS|C Chain C, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc-A-Snap23-Hn-A
pdb|3ZUS|D Chain D, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type A-Snare23 Derivative, Lc-A-Snap23-Hn-A
Length = 927
Score = 26.6 bits (57), Expect = 7.3, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 29 LVKLYRFLVRRTDSNFNKVILKRLFMSKVN 58
VK ++ L R+T NF+K + K + KVN
Sbjct: 355 FVKFFKVLNRKTYLNFDKAVFKINIVPKVN 384
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
0.327 0.140 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,369,128
Number of Sequences: 62578
Number of extensions: 150946
Number of successful extensions: 428
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 394
Number of HSP's gapped (non-prelim): 33
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)