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= 033924
(108 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 162
Score = 118 bits (295), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 59/64 (92%), Positives = 63/64 (98%)
Query: 1 MYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALREI 60
MYRKQHKKDI AEAVKK+RR+TKKPYSRSIVGATLEVIQK+R+EKPEVRDAAREAALREI
Sbjct: 56 MYRKQHKKDIHAEAVKKRRRTTKKPYSRSIVGATLEVIQKKRSEKPEVRDAAREAALREI 115
Query: 61 KERI 64
KERI
Sbjct: 116 KERI 119
>pdb|3IZS|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|W Chain W, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 155
Score = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 36/53 (67%), Gaps = 1/53 (1%)
Query: 1 MYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAR 53
++RK HKK I E KK+ R T K R I GA+L++I++RR+ KPEVR A R
Sbjct: 54 LFRKHHKKGITEEVAKKRSRKTVKA-QRPITGASLDLIKERRSLKPEVRKANR 105
>pdb|2ZKR|UU Chain u, 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 = 157
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 3/59 (5%)
Query: 1 MYRKQHKKDIAAEAVKKK-RRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALR 58
+YR++HKK + E KK+ RR+ K + R+I GA+L I +R +KPEVR A RE A+R
Sbjct: 54 LYRRKHKKGQSEEIQKKRTRRAVK--FQRAITGASLADIMAKRNQKPEVRKAQREQAIR 110
>pdb|4A17|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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 = 158
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 1 MYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALREI 60
+++K DIA + KKKR T +R+IVG +LE I +R+ + A E A+RE+
Sbjct: 60 LWKKVKATDIAQK--KKKRNVT---VARAIVGISLEEINRRKNLDASHKKAEAEKAVREL 114
Query: 61 KER 63
K++
Sbjct: 115 KQK 117
>pdb|2KKM|A Chain A, Solution Nmr Structure Of Yeast Protein Yor252w [residues
38-178]: Northeast Structural Genomics Consortium Target
Yt654
Length = 144
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 16/62 (25%)
Query: 7 KKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEK----------PEVRDAAREAA 56
+ D + +KKKRRS + P +R + ++Q+RR ++ P++ DA
Sbjct: 60 RDDTELDELKKKRRSNRPPSNRQV------LLQQRRDQELKEFKAGFLCPDLSDAKNMEF 113
Query: 57 LR 58
LR
Sbjct: 114 LR 115
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
0.310 0.122 0.305
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,482,613
Number of Sequences: 62578
Number of extensions: 38060
Number of successful extensions: 86
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 77
Number of HSP's gapped (non-prelim): 8
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
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)