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= 033932
(108 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 108
Score = 117 bits (293), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 55/71 (77%), Positives = 64/71 (90%)
Query: 37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
VNN VLFD+ATYDKLLSE PKYK ITPS+LS+RLRINGSLAR+AI++L +RG IR+VS H
Sbjct: 37 VNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVH 96
Query: 97 ASQQIYTRATN 107
+SQ IYTRATN
Sbjct: 97 SSQLIYTRATN 107
>pdb|3ZEY|U Chain U, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 113
Score = 82.0 bits (201), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 37/69 (53%), Positives = 53/69 (76%)
Query: 37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
+ N V+FD+ T DKL+ E PKYK+ITPSI+SDRL+I+ +LA K ++ L +GLIR+VS
Sbjct: 42 LQNAVMFDKETMDKLMKEVPKYKVITPSIISDRLKISVALAGKGLQHLCRQGLIRLVSCS 101
Query: 97 ASQQIYTRA 105
+ ++YTRA
Sbjct: 102 SKFRVYTRA 110
>pdb|3IZB|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 108
Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 49/71 (69%)
Query: 38 NNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97
+ V+ DQ YD++L E P Y+ ++ S+L DRL+I GSLAR A+R L G+I+ +S H+
Sbjct: 37 QHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHS 96
Query: 98 SQQIYTRATNT 108
Q IYTRAT +
Sbjct: 97 KQAIYTRATAS 107
>pdb|2XZM|8 Chain 8, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|8 Chain 8, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 143
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 37 VNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95
VN+ V ++ + +++ K K++T S + ++L++NGSLAR+ +R + R L+ V+
Sbjct: 39 VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK 98
Query: 96 HASQQIYT 103
+ +Q +Y+
Sbjct: 99 NGNQWVYS 106
>pdb|2VN2|A Chain A, Crystal Structure Of The N-Terminal Domain Of Dnad Protein
From Geobacillus Kaustophilus Hta426
pdb|2VN2|B Chain B, Crystal Structure Of The N-Terminal Domain Of Dnad Protein
From Geobacillus Kaustophilus Hta426
pdb|2VN2|C Chain C, Crystal Structure Of The N-Terminal Domain Of Dnad Protein
From Geobacillus Kaustophilus Hta426
pdb|2VN2|D Chain D, Crystal Structure Of The N-Terminal Domain Of Dnad Protein
From Geobacillus Kaustophilus Hta426
Length = 128
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQ 100
TP+ L++R+ ++ + + +R L+ +G+I + H +Q
Sbjct: 53 TPAELAERMTVSAAECMEMVRRLLQKGMI-AIEEHTDEQ 90
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
0.321 0.131 0.351
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,687,949
Number of Sequences: 62578
Number of extensions: 43719
Number of successful extensions: 124
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 120
Number of HSP's gapped (non-prelim): 5
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)