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= 034307
(98 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|U Chain U, Localization Of The Small Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 138
Score = 168 bits (425), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 78/99 (78%), Positives = 93/99 (93%), Gaps = 4/99 (4%)
Query: 1 MAD----KAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANA 56
MAD A+T+RTRKFMTNRLLSRKQFV++VLHPGRANVSKA+LKEKLA++Y+V+D+N
Sbjct: 1 MADTKTAPAVTLRTRKFMTNRLLSRKQFVLEVLHPGRANVSKADLKEKLAKLYEVKDSNC 60
Query: 57 IFVFKFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRLIR 95
IFVFKFRTHFGGGKSTGFGLIYD++++AKK+EPKYRLIR
Sbjct: 61 IFVFKFRTHFGGGKSTGFGLIYDNLDAAKKYEPKYRLIR 99
>pdb|3IZB|U Chain U, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|D Chain D, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 135
Score = 131 bits (330), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 64/95 (67%), Positives = 78/95 (82%), Gaps = 2/95 (2%)
Query: 1 MADKAITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVF 60
M+D A+TIRTRK ++N LL+RKQFV+DVLHP RANVSK EL+EKLA +Y + +A+ VF
Sbjct: 1 MSD-AVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKA-EKDAVSVF 58
Query: 61 KFRTHFGGGKSTGFGLIYDSVESAKKFEPKYRLIR 95
FRT FGGGKS GFGL+Y+SV AKKFEP YRL+R
Sbjct: 59 GFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVR 93
>pdb|2XZM|P Chain P, 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|P Chain P, 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 = 149
Score = 95.5 bits (236), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 45/92 (48%), Positives = 62/92 (67%), Gaps = 1/92 (1%)
Query: 5 AITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRT 64
I IRT+K + N LLSR+Q +DVLHP SK +++E+LA+ V DA + V+ F T
Sbjct: 2 TIVIRTKKILVNPLLSRRQLSLDVLHPDSPTASKEKIREELAKQLKV-DARNVVVYGFST 60
Query: 65 HFGGGKSTGFGLIYDSVESAKKFEPKYRLIRV 96
+GGGKSTGF L+YD+ + K+EP YRL +V
Sbjct: 61 QYGGGKSTGFALVYDNQQYLLKYEPNYRLRKV 92
>pdb|3ZEY|T Chain T, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 137
Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 48/92 (52%), Positives = 65/92 (70%), Gaps = 1/92 (1%)
Query: 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAEL-KEKLARMYDVRDANAIFVFKFRT 64
+T+RT +F N+LL+RKQFV++V HPG A+L + +LA +Y V D N I VF F+T
Sbjct: 10 VTVRTSQFKVNKLLNRKQFVVEVNHPGWCGTVPAKLIRNRLASLYKVADENQISVFGFKT 69
Query: 65 HFGGGKSTGFGLIYDSVESAKKFEPKYRLIRV 96
FGGGK+TGFGLIYD + + K+ EP YR R+
Sbjct: 70 KFGGGKTTGFGLIYDDLAAMKRIEPNYRKARL 101
>pdb|3J20|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|6 Chain 6, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 99
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 1/90 (1%)
Query: 6 ITIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTH 65
+ IR ++ N+L+ RK+ ++ HPG S+ ++K KL M D+ + + R++
Sbjct: 1 MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQY-IRSY 59
Query: 66 FGGGKSTGFGLIYDSVESAKKFEPKYRLIR 95
FG S G+ YDS E EP+Y LIR
Sbjct: 60 FGSYISKGYAKAYDSKERMLYIEPEYILIR 89
>pdb|2V94|A Chain A, Crystal Structure Of P. Abyssi Rps24
pdb|2V94|B Chain B, Crystal Structure Of P. Abyssi Rps24
Length = 107
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 8 IRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFG 67
I+ + N+L+ RK+ ++ HPG S+ ++K KL D+ + + R++FG
Sbjct: 11 IKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAXLDLNPETTVIQY-IRSYFG 69
Query: 68 GGKSTGFGLIYDSVESAKKFEPKYRLIR 95
KS G+ Y + EP+Y LIR
Sbjct: 70 SYKSKGYAKYYYDKDRXLYIEPEYILIR 97
>pdb|2G1D|A Chain A, Solution Structure Of Ribosomal Protein S24e From
Thermoplasma Acidophilum
Length = 98
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 16 NRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYDVRDANAIFVFKFRTHFGGGKSTGFG 75
N +L RK+ + S+ E+KE +A+ V D + V + G + G+
Sbjct: 11 NPILKRKEIKYVLKFDSSRTPSREEIKELIAKHEGV-DKELVIVDNNKQLTGKHEIEGYT 69
Query: 76 LIYDSVESAKKFEPKYRLIR 95
IY SA +EP Y LIR
Sbjct: 70 KIYADKPSAMLYEPDYELIR 89
>pdb|1QDL|A Chain A, The Crystal Structure Of Anthranilate Synthase From
Sulfolobus Solfataricus
Length = 422
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 53 DANAIFVFKFRTHFGGGK----STGFGLIYDSVESAKKFEPKYRL 93
D NA F RT F + G G++YDS ++ FE +++L
Sbjct: 368 DGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEHKL 412
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
0.326 0.140 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,554,469
Number of Sequences: 62578
Number of extensions: 87308
Number of successful extensions: 404
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 393
Number of HSP's gapped (non-prelim): 12
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
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)