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= 043998
(101 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 224
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/68 (54%), Positives = 49/68 (72%), Gaps = 1/68 (1%)
Query: 29 GICQSRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADYL 88
G C +R Q + + +SN+ HA+EAL RAKFKFP RQKII SRKWGFTKF+R +Y+
Sbjct: 124 GTC-ARVDIGQVLLSVRCKESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFTKFTREEYV 182
Query: 89 RWKSENRM 96
+ K+E R+
Sbjct: 183 KLKAEGRI 190
>pdb|3J0L|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0Q|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
Length = 219
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADYLR 89
+R Q IF + DSN E L RA++KFP +QKII+S+KWGFT R +YL+
Sbjct: 125 ARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLK 181
>pdb|3IZS|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|I Chain I, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 221
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADYLR 89
+R Q IF + DSN E L RA++KFP +QKII+S+KWGFT R +YL+
Sbjct: 127 ARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLK 183
>pdb|2ZKR|HH Chain h, 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 = 214
Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 36/58 (62%)
Query: 39 QTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWKSENRM 96
Q I + N H EAL RAKFKFP RQKI +S+KWGFTKF+ ++ +E R+
Sbjct: 133 QVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRL 190
>pdb|4A17|H Chain H, 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|H Chain H, 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|H Chain H, 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|H Chain H, 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 = 215
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 41/64 (64%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWKS 92
+R +F + + + +A +AL RAK KFP RQK++ S+KWGFTK +RA Y R ++
Sbjct: 127 ARVDIGSILFSVRVKEPHVKYAIDALTRAKAKFPGRQKVVTSQKWGFTKLTRAQYSRLRN 186
Query: 93 ENRM 96
+ ++
Sbjct: 187 QKKL 190
>pdb|2PA2|A Chain A, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
pdb|2PA2|B Chain B, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
Length = 151
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRADY 87
+R Q I + N H EAL RAKFKFP RQKI +S+KWGFTKF+ ++
Sbjct: 96 ARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEF 150
>pdb|3ZF7|K Chain K, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 213
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 21 QQSNQSSMGICQSRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFT 80
+QS G C +R + Q + + D+ A E+L RAK KFP RQ I++S+ WGFT
Sbjct: 116 RQSYGKPNGTC-ARVRIGQILLSMRTKDTYVPQALESLRRAKMKFPGRQIIVISKYWGFT 174
Query: 81 KFSRADYLRWKSENRM 96
R +Y + ++
Sbjct: 175 NILRNEYEELRDAGKL 190
>pdb|1S1I|I Chain I, 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 = 168
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVS 74
+R Q IF + DSN E L RA++KFP +QKII+S
Sbjct: 127 ARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 168
>pdb|3JYW|I Chain I, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 165
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVS 74
+R Q IF + DSN E L RA++KFP +QKII+S
Sbjct: 124 ARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 165
>pdb|3MEN|A Chain A, Crystal Structure Of Acetylpolyamine Aminohydrolase From
Burkholderia Pseudomallei, Iodide Soak
pdb|3MEN|B Chain B, Crystal Structure Of Acetylpolyamine Aminohydrolase From
Burkholderia Pseudomallei, Iodide Soak
pdb|3MEN|C Chain C, Crystal Structure Of Acetylpolyamine Aminohydrolase From
Burkholderia Pseudomallei, Iodide Soak
pdb|3MEN|D Chain D, Crystal Structure Of Acetylpolyamine Aminohydrolase From
Burkholderia Pseudomallei, Iodide Soak
Length = 362
Score = 30.4 bits (67), Expect = 0.25, Method: Composition-based stats.
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 28 MGICQSRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFP 66
MG +++ + ++ FHPD + HH + R + + P
Sbjct: 9 MGTLEAQTQGPGSMLTYFHPDQSLHHPRTYFSRGRMRMP 47
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 0.129 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,841,946
Number of Sequences: 62578
Number of extensions: 81260
Number of successful extensions: 266
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 256
Number of HSP's gapped (non-prelim): 12
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)