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= psy3939
(123 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A18|L Chain L, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|L Chain L, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|L Chain L, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|L Chain L, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2.
pdb|4ADX|4 Chain 4, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 123
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGH--CKIKLPGIEKAXXXXXXXXXXXXXXXXXXYGGVL 65
VKTPGGRLV Y+KK +C C + L GI + YGG L
Sbjct: 23 VKTPGGRLVAQYVKKVVNYTKCSEAGCNVALNGIAQVRPAEYATIARSAKTVSRVYGGEL 82
Query: 66 CHKCVKEKFIYCFFYSHCKI 85
CH CV+ + I F KI
Sbjct: 83 CHTCVRSRIIRAFLTEEVKI 102
>pdb|3U5E|GG Chain g, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|GG Chain g, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|GG Chain g, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 121
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 32/78 (41%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKAXXXXXXXXXXXXXXXXXXYGGVLCH 67
VKTPGG L ++KK P+CG C L GI YGG C
Sbjct: 23 VKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCA 82
Query: 68 KCVKEKFIYCFFYSHCKI 85
CVKE+ I F KI
Sbjct: 83 NCVKERIIRAFLIEEQKI 100
>pdb|3IZS|II Chain i, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 118
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 32/78 (41%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEKAXXXXXXXXXXXXXXXXXXYGGVLCH 67
VKTPGG L ++KK P+CG C L GI YGG C
Sbjct: 23 VKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCA 82
Query: 68 KCVKEKFIYCFFYSHCKI 85
CVKE+ I F KI
Sbjct: 83 NCVKERIIRAFLIEEQKI 100
>pdb|3IZR|II Chain i, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 119
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIE--KAXXXXXXXXXXXXXXXXXXYGGVL 65
VKTPGG+LVY Y KK P+C K+ GI + YGGVL
Sbjct: 23 VKTPGGKLVYQYTKKRASGPKCPVTGKKIQGIPHLRPTEYKRPRLSRNRRTVNRPYGGVL 82
Query: 66 CHKCVKEKFIYCFFYSHCKI 85
V+E+ I F KI
Sbjct: 83 SGPAVRERIIRAFLVEEQKI 102
>pdb|3ZF7|JJ Chain j, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 170
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 6/82 (7%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRC----GHCKIKLPGIEKAXXXXXXXXXXXXXXXXXXYGG 63
V+TPG RLV K + P GH + L G + YGG
Sbjct: 24 VRTPGNRLVMQKRGKRSQGPHTPWVLGHKR--LAGTKALRHTKARLAPRHQKTTSRPYGG 81
Query: 64 VLCHKCVKEKFIYCFFYSHCKI 85
VL H+ V+++ + F +I
Sbjct: 82 VLSHEQVRDRIVRAFLIEEQRI 103
>pdb|3J21|DD Chain d, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 89
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 8 VKTPGGRLVYHYLKKAGKVPRCGHCKIKLPGIEK 41
V+TPGGR+V H+ +K K+ C C L GI +
Sbjct: 15 VRTPGGRVVIHFERKKPKIAHCAMCGRPLNGIPR 48
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 0.147 0.503
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,984,417
Number of Sequences: 62578
Number of extensions: 76546
Number of successful extensions: 249
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 235
Number of HSP's gapped (non-prelim): 11
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
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: 45 (21.9 bits)