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= 033859
(110 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 112
Score = 191 bits (486), Expect = 6e-50, Method: Compositional matrix adjust.
Identities = 94/106 (88%), Positives = 101/106 (95%)
Query: 1 MAPKQPNTGLFVGLNKGHVVTKKELPPRPSDRKGKTSKRVHFVKNLIREVAGFAPYERRI 60
MAP QP +GLFVG+NKGHVVTK+ELPPRPSDRKGK +KRVHFV+NLIREVAGFAPYE+RI
Sbjct: 1 MAPSQPKSGLFVGINKGHVVTKRELPPRPSDRKGKGTKRVHFVRNLIREVAGFAPYEKRI 60
Query: 61 TELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSNALRKMRSAGGA 106
TELLKVGKDKRALKVAKRKLGTHKRAKKKREEMS+ LRKMRSAGG
Sbjct: 61 TELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSSVLRKMRSAGGG 106
>pdb|3IZS|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|II 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|II 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|II Chain i, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 100
Score = 91.3 bits (225), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/90 (50%), Positives = 64/90 (71%)
Query: 8 TGLFVGLNKGHVVTKKELPPRPSDRKGKTSKRVHFVKNLIREVAGFAPYERRITELLKVG 67
TG+ +GLNKG VT P+ S +KG S R FV++L+RE+AG +PYERR+ +L++
Sbjct: 5 TGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNS 64
Query: 68 KDKRALKVAKRKLGTHKRAKKKREEMSNAL 97
+KRA KVAK++LG+ RAK K EEM+N +
Sbjct: 65 GEKRARKVAKKRLGSFTRAKAKVEEMNNII 94
>pdb|3ZF7|MM Chain m, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 109
Score = 87.8 bits (216), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 44/94 (46%), Positives = 64/94 (68%)
Query: 6 PNTGLFVGLNKGHVVTKKELPPRPSDRKGKTSKRVHFVKNLIREVAGFAPYERRITELLK 65
P TG+ G NKG+ T++ P +DR K++ VK +I ++ GF+P ERR+ ELL+
Sbjct: 11 PRTGIIAGFNKGYKTTRRARRPSSNDRYALPHKKLRAVKAIISDLVGFSPMERRVQELLR 70
Query: 66 VGKDKRALKVAKRKLGTHKRAKKKREEMSNALRK 99
VGKDKRALK K++LG+ K AKK+R ++ ALR+
Sbjct: 71 VGKDKRALKFCKKRLGSIKAAKKRRAKVEEALRQ 104
>pdb|4A18|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 104
Score = 84.0 bits (206), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 50/99 (50%), Positives = 68/99 (68%), Gaps = 6/99 (6%)
Query: 9 GLFVGLNKGHVVTK--KELPPRPS-DRKGKTSKRVHFVKNLIREVAGFAPYERRITELLK 65
G VG+NKG + T+ K+L + RKGK KRV V+ +IREV GFAPYE+RI EL+K
Sbjct: 4 GQAVGINKGFITTQLEKKLQKHSAVQRKGKLGKRVALVRQVIREVTGFAPYEKRIIELIK 63
Query: 66 VG--KD-KRALKVAKRKLGTHKRAKKKREEMSNALRKMR 101
G KD K+A K+A+++LGTH+RAK K+ + A+R R
Sbjct: 64 AGSAKDSKKATKIARKRLGTHRRAKVKKALLEEAVRAQR 102
>pdb|2ETD|A Chain A, Crystal Structure Of A Lema Protein (Tm0961) From
Thermotoga Maritima Msb8 At 2.28 A Resolution
Length = 171
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 19 VVTKKELPPRPSDRKGKTSKRVHFVKNLIREVAGFAPYERRITELLKVGKDKRALKVAKR 78
V ++E+ S + + +R + NL+ V G+A +E I E + + RA +
Sbjct: 14 VSLEQEVQEXYSQIQNQLQRRADLIPNLVETVXGYAAHEXEILEEI---ANARAXLIGAX 70
Query: 79 KLGTHKRAKKKREEMSNALRKM 100
T + + + E+S+AL ++
Sbjct: 71 ---TPQESAQADAELSSALSRL 89
>pdb|3AV0|A Chain A, Crystal Structure Of Mre11-Rad50 Bound To Atp S
Length = 386
Score = 25.8 bits (55), Expect = 5.8, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 81 GTHKRAKKKREEMSNALRKMRSAGGAEKKK 110
GT+ K KREEM + L+ S KKK
Sbjct: 144 GTYYHKKSKREEMLDKLKNFESEAKNYKKK 173
>pdb|3AUZ|A Chain A, Crystal Structure Of Mre11 With Manganese
Length = 333
Score = 25.8 bits (55), Expect = 7.3, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 81 GTHKRAKKKREEMSNALRKMRSAGGAEKKK 110
GT+ K KREEM + L+ S KKK
Sbjct: 144 GTYYHKKSKREEMLDKLKNFESEAKNYKKK 173
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
0.314 0.131 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,058,225
Number of Sequences: 62578
Number of extensions: 101656
Number of successful extensions: 152
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 141
Number of HSP's gapped (non-prelim): 11
length of query: 110
length of database: 14,973,337
effective HSP length: 74
effective length of query: 36
effective length of database: 10,342,565
effective search space: 372332340
effective search space used: 372332340
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)