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= 040226
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 227
Score = 217 bits (552), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 109/134 (81%), Positives = 118/134 (88%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MATQISKK+KFV+DGVF+AELNE+LTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1 MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
EKGRRIRELTSVVQKRF F EN VELYAEKV NRGLCAIAQAESLRYKLLGGLAVRR
Sbjct: 61 EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY 120
Query: 121 IISQILSNKALRSC 134
+ + + + C
Sbjct: 121 GVLRFVMESGAKGC 134
>pdb|2ZKQ|CC Chain c, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 243
Score = 213 bits (541), Expect = 3e-56, Method: Compositional matrix adjust.
Identities = 107/134 (79%), Positives = 113/134 (84%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MA QISKKRKFVADG+F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLG
Sbjct: 1 MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
EKGRRIRELT+VVQKRF FPE SVELYAEKV RGLCAIAQAESLRYKLLGGLAVRR
Sbjct: 61 EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY 120
Query: 121 IISQILSNKALRSC 134
+ + + + C
Sbjct: 121 GVLRFIMESGAKGC 134
>pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 240
Score = 176 bits (445), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 85/134 (63%), Positives = 105/134 (78%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
M ISKKRK VADGVF+AELNE TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLG
Sbjct: 1 MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
E GRRI ELT +VQKRFK+ ++ LYAE+V +RGL A+AQAES+++KLL GLA+RR
Sbjct: 61 ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY 120
Query: 121 IISQILSNKALRSC 134
+ + + + C
Sbjct: 121 GVVRYVMESGAKGC 134
>pdb|1S1H|C Chain C, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
In File 1s1i
Length = 192
Score = 174 bits (441), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 84/130 (64%), Positives = 104/130 (80%)
Query: 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGR 64
ISKKRK VADGVF+AELNE TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLGE GR
Sbjct: 4 ISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGR 63
Query: 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQ 124
RI ELT +VQKRFK+ ++ LYAE+V +RGL A+AQAES+++KLL GLA+RR + +
Sbjct: 64 RINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVR 123
Query: 125 ILSNKALRSC 134
+ + C
Sbjct: 124 YVMESGAKGC 133
>pdb|3JYV|C Chain C, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 188
Score = 172 bits (437), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 83/129 (64%), Positives = 103/129 (79%)
Query: 6 SKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRR 65
SKKRK VADGVF+AELNE TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLGE GRR
Sbjct: 1 SKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRR 60
Query: 66 IRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQI 125
I ELT +VQKRFK+ ++ LYAE+V +RGL A+AQAES+++KLL GLA+RR + +
Sbjct: 61 INELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRY 120
Query: 126 LSNKALRSC 134
+ + C
Sbjct: 121 VMESGAKGC 129
>pdb|3ZEY|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 214
Score = 154 bits (388), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 76/130 (58%), Positives = 99/130 (76%)
Query: 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGR 64
+SKKR V DGVF+AEL E L RELA+DG++GVE RVTP RTEI+IR+T+T+ VLGEKGR
Sbjct: 4 LSKKRMMVRDGVFYAELFEFLKRELADDGFAGVEHRVTPTRTEIVIRSTKTREVLGEKGR 63
Query: 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQ 124
RIRELT+ +Q+RF + E ++L+AE+V RGL A+AQAESLR+KLL L VRR + I +
Sbjct: 64 RIRELTACLQQRFNYKEGKLQLFAERVEVRGLSAMAQAESLRFKLLSNLQVRRAAMGIIR 123
Query: 125 ILSNKALRSC 134
+ + C
Sbjct: 124 YVMESGAKGC 133
>pdb|1WH9|A Chain A, Solution Structure Of The Kh Domain Of Human Ribosomal
Protein S3
Length = 92
Score = 139 bits (349), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 70/79 (88%), Positives = 71/79 (89%)
Query: 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKR 76
F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLGEKGRRIRELT+VVQKR
Sbjct: 8 FKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKR 67
Query: 77 FKFPENSVELYAEKVNNRG 95
F FPE SVELYAEKV RG
Sbjct: 68 FGFPEGSVELYAEKVATRG 86
>pdb|2XZM|C Chain C, 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|C Chain C, 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 = 243
Score = 124 bits (312), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 55/112 (49%), Positives = 84/112 (75%)
Query: 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGR 64
I+KK+KFVADGVF AEL+ ++ L + GY+G+EVR TP +TEI I+AT+ Q V+G +G+
Sbjct: 8 INKKKKFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIGVEGK 67
Query: 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVR 116
+ +ELT +QKRF + ++ ++++AE + +GLCA AQ E++ YKLL + VR
Sbjct: 68 KHKELTQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVR 119
>pdb|3J20|C Chain C, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 210
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/95 (36%), Positives = 57/95 (60%), Gaps = 2/95 (2%)
Query: 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIR 67
+R F+ + V ++E L +EL GY G++++ TP+ T++II A V+G GRRIR
Sbjct: 4 ERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIR 63
Query: 68 ELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQA 102
ELT +++K+F +E+ E++ N L A QA
Sbjct: 64 ELTRILEKQFGLENPQIEV--EEIKNPYLNAKVQA 96
>pdb|3UJZ|A Chain A, Crystal Structure Of Enterohemorrhagic E. Coli Stce
Length = 869
Score = 26.6 bits (57), Expect = 5.1, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEV 39
K+ FV+DG F+ E + V TRE + GV V
Sbjct: 628 KKSFVSDGQFWKERDVVDTREARKPEQFGVPV 659
>pdb|2ISM|A Chain A, Crystal Structure Of The Putative Oxidoreductase (Glucose
Dehydrogenase) (Ttha0570) From Thermus Theromophilus Hb8
pdb|2ISM|B Chain B, Crystal Structure Of The Putative Oxidoreductase (Glucose
Dehydrogenase) (Ttha0570) From Thermus Theromophilus Hb8
Length = 352
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 11 FVADGVFFAELNEVLTRELAED--GYSGVEVRVTP 43
F DG+ + EV RELA+D G +R+TP
Sbjct: 142 FGPDGMLYVTTGEVYERELAQDLASLGGKILRLTP 176
>pdb|3J0J|J Chain J, Fitted Atomic Models Of Thermus Thermophilus V-Atpase
Subunits Into Cryo-Em Map
pdb|3J0J|L Chain L, Fitted Atomic Models Of Thermus Thermophilus V-Atpase
Subunits Into Cryo-Em Map
Length = 188
Score = 25.8 bits (55), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 47 EIIIRATRTQ---NVLGEKGRRIRELTSVVQKRFKFPE 81
E+++ RTQ VL E RR+RE + ++ ++PE
Sbjct: 65 ELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPE 102
>pdb|3V6I|A Chain A, Crystal Structure Of The Peripheral Stalk Of Thermus
Thermophilus H+- AtpaseSYNTHASE AT 2.25 A RESOLUTION
pdb|3V6I|Y Chain Y, Crystal Structure Of The Peripheral Stalk Of Thermus
Thermophilus H+- AtpaseSYNTHASE AT 2.25 A RESOLUTION
Length = 187
Score = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 47 EIIIRATRTQ---NVLGEKGRRIRELTSVVQKRFKFPE 81
E+++ RTQ VL E RR+RE + ++ ++PE
Sbjct: 64 ELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPE 101
>pdb|3K5B|E Chain E, Crystal Structure Of The Peripheral Stalk Of Thermus
Thermophilus H+- AtpaseSYNTHASE
pdb|3K5B|A Chain A, Crystal Structure Of The Peripheral Stalk Of Thermus
Thermophilus H+- AtpaseSYNTHASE
Length = 188
Score = 25.4 bits (54), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 47 EIIIRATRTQ---NVLGEKGRRIRELTSVVQKRFKFPE 81
E+++ RTQ VL E RR+RE + ++ ++PE
Sbjct: 65 ELLVATARTQARGEVLEEVRRRVREALEALPQKPEWPE 102
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
0.322 0.137 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,127,098
Number of Sequences: 62578
Number of extensions: 105019
Number of successful extensions: 285
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 269
Number of HSP's gapped (non-prelim): 25
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)