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= psy11013
(176 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5C|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 255
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/65 (46%), Positives = 47/65 (72%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+H+R IRK + EI+ EV S L ++ +KL+P+ I KEIE + I+PL ++ +RKVK+L
Sbjct: 159 SHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLL 218
Query: 133 KKPRF 137
K+P+F
Sbjct: 219 KQPKF 223
>pdb|2XZM|4 Chain 4, 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|4 Chain 4, 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 = 265
Score = 57.4 bits (137), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 41/65 (63%)
Query: 73 THVRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVL 132
+ VR IR+K+ I NE K + E L+ + K+IEK+ + I+PL ++ IRKVKVL
Sbjct: 165 SQVRAIRRKINTFITNEAAKLGIAEFSKNLIGEDYTKKIEKETKNIFPLQNITIRKVKVL 224
Query: 133 KKPRF 137
K+P+
Sbjct: 225 KRPKL 229
>pdb|3ZEY|0 Chain 0, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 256
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 12/101 (11%)
Query: 75 VRQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKK 134
V+ +R + II + K D+ + V+ L + + + K+C I PL D+ IRKVKV++
Sbjct: 163 VKWVRMRATNIIRRRLAKLDINDAVSLLTRNILRDRLAKRCNPIIPLRDLRIRKVKVIRT 222
Query: 135 PRFXXXXXXXXXXXXXXXATIDESGETVDRPEGYEPPVQEA 175
P+F A I GE EG V+EA
Sbjct: 223 PKF------------DAQALIAAHGEVPTSAEGEARVVEEA 251
>pdb|3J20|A Chain A, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 198
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%)
Query: 76 RQIRKKMVEIIINEVVKSDLKEVVNKLLPDSIAKEIEKKCQGIYPLHDVFIRKVKVLKKP 135
R IRK M EII + + + K+ V + + IA EI K+ + IYPL IRK+KVL++P
Sbjct: 135 RAIRKIMQEIIYKKAEELNFKDFVLESVNGKIAAEIAKEAKKIYPLRKAEIRKIKVLEEP 194
Query: 136 R 136
+
Sbjct: 195 Q 195
>pdb|3JVB|A Chain A, Crystal Structure Of Infectious Baculovirus Polyhedra
Length = 243
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 7/64 (10%)
Query: 47 QSLNTFLLGD---CGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDLKEVVNKLL 103
SL+ +L+ + CGP G + KL LFK +R I+ +++I+N K L+E + +
Sbjct: 47 DSLDKYLVAEDPFCGP-GKNQKLT--LFK-EIRNIKPDTMKLIVNWSGKEFLRETWTRFM 102
Query: 104 PDSI 107
DS
Sbjct: 103 EDSF 106
>pdb|1K20|A Chain A, Inorganic Pyrophosphatase (Family Ii) From Streptococcus
Gordonii At 1.5 A Resolution
pdb|1K20|B Chain B, Inorganic Pyrophosphatase (Family Ii) From Streptococcus
Gordonii At 1.5 A Resolution
Length = 310
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/37 (27%), Positives = 23/37 (62%)
Query: 59 PRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDL 95
P GS+ +VY++FK H + K++ ++++ ++ L
Sbjct: 116 PVGSASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTL 152
>pdb|3GAJ|A Chain A, Structure Of A C-Terminal Deletion Variant Of A Pduo-Type
Atp:corrinoid Adenosyltransferase From Lactobacillus
Reuteri Complexed With Cobalamin And Atp
Length = 187
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 34 WMKLMTTGYLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKS 93
W++ Y + ++ F+L P G+ L + +T R+ +++V+++ E +
Sbjct: 100 WLEEKIDNYTQVVPAVKKFIL----PGGTQLASALHVARTITRRAERQIVQLMREEQINQ 155
Query: 94 DLKEVVNKL 102
D+ +N+L
Sbjct: 156 DVLIFINRL 164
>pdb|3CI1|A Chain A, Structure Of The Pduo-Type Atp:co(I)rrinoid
Adenosyltransferase From Lactobacillus Reuteri Complexed
With Four-Coordinate Cob(Ii)alamin And Atp
pdb|3CI3|A Chain A, Structure Of The Pduo-Type Atp:co(I)rrinoid
Adenosyltransferase From Lactobacillus Reuteri Complexed
With Partial Adenosylcobalamin And Pppi
pdb|3CI4|A Chain A, Structure Of The Pduo-Type Atp:co(I)rrinoid
Adenosyltransferase From Lactobacillus Reuteri Complexed
With Four-Coordinate Cob(Ii)inamide And Atp
Length = 194
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 34 WMKLMTTGYLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKS 93
W++ Y + ++ F+L P G+ L + +T R+ +++V+++ E +
Sbjct: 100 WLEEKIDNYTQVVPAVKKFIL----PGGTQLASALHVARTITRRAERQIVQLMREEQINQ 155
Query: 94 DLKEVVNKL 102
D+ +N+L
Sbjct: 156 DVLIFINRL 164
>pdb|2R6X|A Chain A, Structure Of A D35n Variant Pduo-type Atp:co(i)rrinoid
Adenosyltransferase From Lactobacillus Reuteri Complexed
With Atp
pdb|2R6X|B Chain B, Structure Of A D35n Variant Pduo-type Atp:co(i)rrinoid
Adenosyltransferase From Lactobacillus Reuteri Complexed
With Atp
Length = 194
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 34 WMKLMTTGYLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKS 93
W++ Y + ++ F+L P G+ L + +T R+ +++V+++ E +
Sbjct: 100 WLEEKIDNYTQVVPAVKKFIL----PGGTQLASALHVARTITRRAERQIVQLMREEQINQ 155
Query: 94 DLKEVVNKL 102
D+ +N+L
Sbjct: 156 DVLIFINRL 164
>pdb|2NT8|A Chain A, Atp Bound At The Active Site Of A Pduo Type
Atp:co(i)rrinoid Adenosyltransferase From Lactobacillus
Reuteri
Length = 223
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 34 WMKLMTTGYLHLSQSLNTFLLGDCGPRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKS 93
W++ Y + ++ F+L P G+ L + +T R+ +++V+++ E +
Sbjct: 129 WLEEKIDNYTQVVPAVKKFIL----PGGTQLASALHVARTITRRAERQIVQLMREEQINQ 184
Query: 94 DLKEVVNKL 102
D+ +N+L
Sbjct: 185 DVLIFINRL 193
>pdb|1WPP|A Chain A, Structure Of Streptococcus Gordonii Inorganic
Pyrophosphatase
pdb|1WPP|B Chain B, Structure Of Streptococcus Gordonii Inorganic
Pyrophosphatase
Length = 311
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 10/37 (27%), Positives = 23/37 (62%)
Query: 59 PRGSSLKLVYQLFKTHVRQIRKKMVEIIINEVVKSDL 95
P GS+ +VY++FK H + K++ ++++ ++ L
Sbjct: 117 PVGSASSIVYRMFKEHGVAVPKEIAGLMLSGLISDTL 153
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
0.320 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,413,218
Number of Sequences: 62578
Number of extensions: 141198
Number of successful extensions: 377
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 369
Number of HSP's gapped (non-prelim): 21
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)