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= psy2841
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U5E|L Chain L, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|L Chain L, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|L Chain L, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 199
Score = 136 bits (343), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 81/173 (46%), Positives = 111/173 (64%), Gaps = 13/173 (7%)
Query: 6 HFHKDWQKYIKCWFNQPARKFRRRQARIKKAKEIAPRPAAGPLRPIVRCPTVRYHKRVRA 65
HF K WQ+ +K F+Q +K RR AR +A +IAPRP LRP+VR PTV+Y+++VRA
Sbjct: 13 HFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPL-DLLRPVVRAPTVKYNRKVRA 71
Query: 66 GRGFTLEEIRGAGLNARFARSVGIAVDARRRSKSMESLQLNIQRLKEYKSKLIVFPRREK 125
GRGFTL E++ AGL A +AR++GIAVD RR++++ E N+QRLKEY+SK+IVFPR K
Sbjct: 72 GRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQSKIIVFPRNGK 131
Query: 126 KKLRKGEATPEERKVATQLKGPLMPIRQSKPKSKARIPSEAEKKFSAFQTLRM 178
PE +V + PI Q +AR + + SAF+TLR+
Sbjct: 132 --------APEAEQVLS--AAATFPIAQPATDVEARAVQDNGE--SAFRTLRL 172
>pdb|3ZF7|N Chain N, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 218
Score = 127 bits (318), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 78/148 (52%), Positives = 105/148 (70%), Gaps = 8/148 (5%)
Query: 2 IPNAHFHKDW------QKYIKCWFNQPARKFRRRQARIKKAKEIAPRPAAGPLRPIVRCP 55
IP+ H K W + +K +FNQPA+K RRR+ R+ KAK+I PRP LRP V CP
Sbjct: 8 IPHVHQRKHWNPCSSQKGNVKVFFNQPAQKQRRRRLRLLKAKKIFPRPLKA-LRPQVNCP 66
Query: 56 TVRYHKRVRAGRGFTLEEIRGAGLNARFARSVGIAVDARRRSKSMESLQLNIQRLKEYKS 115
TVRY+ + R GRGF+LEE++ AG+ R+AR++GI VD RR++KS E + +N+QRLK Y S
Sbjct: 67 TVRYNMKRRLGRGFSLEELKAAGVKPRYARTIGIRVDRRRKNKSEEGMNINVQRLKTYMS 126
Query: 116 KLIVFPRREKKKLRKGEATPEERKVATQ 143
KL++FP +KK +KG+AT EE K ATQ
Sbjct: 127 KLVLFP-LNRKKPQKGDATEEEVKAATQ 153
>pdb|4A18|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 206
Score = 112 bits (280), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 60/125 (48%), Positives = 84/125 (67%), Gaps = 1/125 (0%)
Query: 2 IPNAHFHKDWQKYIKCWFNQPARKFRRRQARIKKAKEIAPRPAAGPLRPIVRCPTVRYHK 61
+P A K Q IK +FNQ A+K R AR +A + PRP L+P+VR T RY+K
Sbjct: 7 LPVAQLRKHQQFRIKTFFNQAAQKKARLHARRAQAAAVFPRPTE-KLQPVVRKQTQRYNK 65
Query: 62 RVRAGRGFTLEEIRGAGLNARFARSVGIAVDARRRSKSMESLQLNIQRLKEYKSKLIVFP 121
+ GRGFTL+E++ AG++A FA+S+GI VD RR+++ ESL+LN +RL Y SKL++FP
Sbjct: 66 STKLGRGFTLQELKAAGISAAFAQSIGIKVDHRRKNRCQESLELNKKRLLAYVSKLVLFP 125
Query: 122 RREKK 126
R + K
Sbjct: 126 RHQGK 130
>pdb|3E4B|A Chain A, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|B Chain B, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|C Chain C, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
pdb|3E4B|D Chain D, Crystal Structure Of Algk From Pseudomonas Fluorescens
Wcs374r
Length = 452
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 127 KLRKGEATPEERKVATQLKGPLMPIRQSK 155
+L K + TPE +ATQL+ PL P ++++
Sbjct: 382 QLAKAQDTPEANDLATQLEAPLTPAQRAE 410
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 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,820,089
Number of Sequences: 62578
Number of extensions: 170925
Number of successful extensions: 362
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 350
Number of HSP's gapped (non-prelim): 11
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
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: 48 (23.1 bits)