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= 045444
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZM|2 Chain 2, 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|2 Chain 2, 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 = 208
Score = 211 bits (538), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 111/222 (50%), Positives = 145/222 (65%), Gaps = 22/222 (9%)
Query: 1 MGISRDSMHXXXXXXXXXXXXXXXXXYELGRQPANTKLSSNKT-------VRRIRVRGGN 53
MGISRDS H +E GR + TKL++ T +R +RVRGG+
Sbjct: 1 MGISRDSKHKRRATGGRMPVHRKKRAFEKGRPISMTKLTTQSTTITEKRRIRPVRVRGGH 60
Query: 54 VKWRALRLDTGNYSWGSEAVTRKTRILDVVYNASNNELVRTQTLVKSAIVQVDAAPFKQW 113
+K+RALRL GN+SWGSE +TRKT+ILDV YNA+NNELVRT+TLVK++IV++D+ PF++W
Sbjct: 61 LKFRALRLCEGNFSWGSENITRKTKILDVKYNATNNELVRTKTLVKNSIVEIDSTPFREW 120
Query: 114 YLQHYGVDIGRXXXXXXXXXXXXXXXXXXXXXXXXXXSNHVVRKLEKRQKDRTLDPHIEE 173
Y HYG+D+G S HV +++ KR K + L+ +IEE
Sbjct: 121 YKLHYGIDLG--------------LKKDRTVLGNKEKSRHVQKRV-KRTKAQALEKNIEE 165
Query: 174 QFGAGRLLACISSRPGQCGRADGYILEGKELEFYMKKLQRKK 215
QF + R+LACI+SRPGQ GRADGYILEGKELEFY++KLQ KK
Sbjct: 166 QFVSQRILACITSRPGQSGRADGYILEGKELEFYIRKLQSKK 207
>pdb|3U5C|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 200
Score = 208 bits (530), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 104/215 (48%), Positives = 131/215 (60%), Gaps = 15/215 (6%)
Query: 1 MGISRDSMHXXXXXXXXXXXXXXXXXYELGRQPANTKLSSNKTVRRIRVRGGNVKWRALR 60
MGISRDS H +ELGRQPANTK+ + K + +R RGGN K+RALR
Sbjct: 1 MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGA-KRIHSVRTRGGNKKYRALR 59
Query: 61 LDTGNYSWGSEAVTRKTRILDVVYNASNNELVRTQTLVKSAIVQVDAAPFKQWYLQHYGV 120
++TGN+SW SE +++KTRI VVY+ SNNELVRT TL K+AIVQ+DA PF+QW+ HYG
Sbjct: 60 IETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQ 119
Query: 121 DIGRXXXXXXXXXXXXXXXXXXXXXXXXXXSNHVVRKLEKRQKDRTLDPHIEEQFGAGRL 180
+G+ S + RK R ++ +E QF AGRL
Sbjct: 120 TLGK--------------KKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRL 165
Query: 181 LACISSRPGQCGRADGYILEGKELEFYMKKLQRKK 215
ACISSRPGQ GR DGYILEG+EL FY+++L KK
Sbjct: 166 YACISSRPGQSGRCDGYILEGEELAFYLRRLTAKK 200
>pdb|3ZEY|5 Chain 5, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 220
Score = 192 bits (489), Expect = 1e-49, Method: Compositional matrix adjust.
Identities = 103/220 (46%), Positives = 132/220 (60%), Gaps = 6/220 (2%)
Query: 1 MGISRDSMHXXXXXXXXXXXXXXXXXYELGRQPANTKLSSNKTVRRIRVRGGNVKWRALR 60
MGI R +H ELGR PANTKL + V +R RGGN K R LR
Sbjct: 1 MGIVRSRLHKRKITGGKTKIHRKRMKAELGRLPANTKLGPRR-VSPVRARGGNFKLRGLR 59
Query: 61 LDTGNYSWGSEAVTRKTRILDVVYNASNNELVRTQTLVKSAIVQVDAAPFKQWYLQHYGV 120
LDTGN++WG+EA ++ RILDVVYNA++NELVRT+TLVK+ IV VDAAPF+ WY +HYG+
Sbjct: 60 LDTGNFAWGTEASAQRARILDVVYNATSNELVRTKTLVKNCIVVVDAAPFRLWYAKHYGI 119
Query: 121 DIG-----RXXXXXXXXXXXXXXXXXXXXXXXXXXSNHVVRKLEKRQKDRTLDPHIEEQF 175
D+G + S+ + RK E R+K ++ + +Q
Sbjct: 120 DLGASKSKKATQKSTEKKSKKSAHAAVEKYDVKKASSKLKRKWEYRRKHHKIEKALADQL 179
Query: 176 GAGRLLACISSRPGQCGRADGYILEGKELEFYMKKLQRKK 215
GRLLA I+SRPGQ GRADG +LEG EL+FY+KKL +KK
Sbjct: 180 REGRLLARITSRPGQTGRADGALLEGAELQFYLKKLDKKK 219
>pdb|3J20|J Chain J, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 127
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 5/81 (6%)
Query: 28 ELGRQPANTKLSSNKTVRRIRVRGGNVKWRALRLDTGNYS--WGSEAVTRKTRILDVVYN 85
ELGR+P+NT+++ + IR GGN R +RL Y+ + RK RI+ V+ N
Sbjct: 27 ELGREPSNTRVAEQDKRKIIRTYGGN---RKVRLTAAAYANVFDKSGKGRKVRIIRVIEN 83
Query: 86 ASNNELVRTQTLVKSAIVQVD 106
+N + R + K AI++ +
Sbjct: 84 PANRQFARRNIITKGAIIETE 104
>pdb|2KCO|A Chain A, Solution Nmr Structure Of Ribosomal Protein Sso0164 From
Sulfolobus Solfataricus. Northeast Structural Genomics
Consortium (Nesg) Target Sst4
Length = 133
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%)
Query: 27 YELGRQPANTKLSSNKTVRRIRVRGGNVKWRALRLDTGNYSWGSEAVTRKTRILDVVYNA 86
YE+G P T LS+ + R GGN K R T N + +K +IL+++
Sbjct: 26 YEIGNPPTFTTLSAEDIRIKDRTLGGNFKVRLKYTTTANVLDPATNTAKKVKILEILETP 85
Query: 87 SNNELVRTQTLVKSAIVQVDAA 108
+N EL R +++ A ++ +A
Sbjct: 86 ANKELARRGIIIRGAKIRTEAG 107
>pdb|2WAF|A Chain A, Penicillin-Binding Protein 2b (Pbp-2b) From Streptococcus
Pneumoniae (Strain R6)
Length = 682
Score = 30.0 bits (66), Expect = 0.98, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 88 NNELVRTQTLVKSAIVQVDAAPFKQWYLQHYG 119
N L QTL +IV +AP WY Q YG
Sbjct: 399 NGVLSGNQTLTDQSIVFQGSAPINSWYTQAYG 430
>pdb|2KCY|A Chain A, Solution Structure Of Ribosomal Protein S8e From
Methanothermobacter Thermautotrophicus,
Northeaststructural Genomics Consortium (Nesg) Target
Tr71d
pdb|2KCP|A Chain A, Solution Structure Of 30s Ribosomal Protein S8e; From
Methanothermobacter Thermautotrophicus,
Northeaststructural Genomics Consortium (Nesg) Target
Tr71d
Length = 98
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 41 NKTVRRIRVRGGNVKWRA---LRLDTGNYSWGSEAVTRKTRILDVVYNASNNELVRTQTL 97
++ VR IR RGGN K R R++ + G + I +VV N +N VR +
Sbjct: 2 DRRVRLIRTRGGNTKVRLASDTRINVVDPETGKVEI---AEIRNVVENTANPHFVRRNII 58
Query: 98 VKSAIVQVD 106
+ A+V+ +
Sbjct: 59 TRGAVVETN 67
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
0.318 0.134 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,014,394
Number of Sequences: 62578
Number of extensions: 162141
Number of successful extensions: 302
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: 286
Number of HSP's gapped (non-prelim): 9
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)