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= psy8135
(295 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1HU3|A Chain A, Middle Domain Of Human Eif4gii
Length = 260
Score = 145 bits (365), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 103/268 (38%), Positives = 145/268 (54%), Gaps = 27/268 (10%)
Query: 17 PENVQ-DATFRKVRELLNKLTPEXXXXXXXXXXXXXXXXXXILKGVILLIFEKALHETKY 75
PEN++ FRKVR +LNKLTP+ LKGVI L+FEKA+ E +
Sbjct: 3 PENIKTQELFRKVRSILNKLTPQXFNQLXKQVSGLTVDTEERLKGVIDLVFEKAIDEPSF 62
Query: 76 TSMYARLCKRL-TEQAPNFEPPDESCTFKKHLLWVCKNEFENRSRATEAF----GNLPLS 130
+ YA C+ L T + P + P + F+K LL C+ EFE + F L +
Sbjct: 63 SVAYANXCRCLVTLKVPXADKPGNTVNFRKLLLNRCQKEFEKDKADDDVFEKKQKELEAA 122
Query: 131 PDDEDRRQL----------AKQKMLGNIKFIGELGKHEIVTESILHTCIQELLPKNRKVQ 180
E+R +L A+++ +GNIKFIGEL K + +TE+I H C+ +LL
Sbjct: 123 SAPEERTRLHDELEEAKDKARRRSIGNIKFIGELFKLKXLTEAIXHDCVVKLLK------ 176
Query: 181 TNKDVSENLECLCQIMKTCGRILDSEKGQGLMNQYFSRMKTVQTSTPHLPLRIRFMLQDV 240
N D E+LECLC+++ T G+ LD EK + +QYF++ + + RIRF LQDV
Sbjct: 177 -NHD-EESLECLCRLLTTIGKDLDFEKAKPRXDQYFNQXEKI-VKERKTSSRIRFXLQDV 233
Query: 241 EDLRRNNWVPRQANNPEKPVPINQIIEE 268
DLR NWV R+A+ + P I QI +E
Sbjct: 234 IDLRLCNWVSRRAD--QGPKTIEQIHKE 259
>pdb|2VSO|E Chain E, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|F Chain F, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|E Chain E, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|F Chain F, Crystal Structure Of A Translation Initiation Complex
Length = 284
Score = 67.4 bits (163), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 73/281 (25%), Positives = 121/281 (43%), Gaps = 41/281 (14%)
Query: 3 RWIPPSA-------LRRDALTPENVQDATFRKVRELLNKLTPEXXXXXXXXXXXXXXXXX 55
RW+P L D T +D RK++ LLNKLT E
Sbjct: 8 RWVPKFKSKKTEKKLAPDGKTELLDKDEVERKMKSLLNKLTLEMFDAISSEILAIANISV 67
Query: 56 -----XILKGVILLIFEKALHETKYTSMYARLCKRLTEQAPNFEPPDESCTFKK------ 104
LK VI IF KA E ++SMYA+LC ++ ++ N + DE+ K
Sbjct: 68 WETNGETLKAVIEQIFLKACDEPHWSSMYAQLCGKVVKEL-NPDITDETNEGKTGPKLVL 126
Query: 105 -HLLWVCKNEFEN--RSRATEAFGNLPLSPDDEDRRQL----AKQKMLGNIKFIGELGKH 157
+L+ C EF+ + PL P+ AK++ LG ++FIG L +
Sbjct: 127 HYLVARCHAEFDKGWTDKLPTNEDGTPLEPEMMSEEYYAAASAKRRGLGLVRFIGFLYRL 186
Query: 158 EIVTESILHTCIQELLPKNRKVQTNKDVSENLECLCQIMKTCGRILDSE---------KG 208
++T ++ C + L+ K T+ E LE + +++ T G +++ +G
Sbjct: 187 NLLTGKMMFECFRRLM----KDLTDSPSEETLESVVELLNTVGEQFETDSFRTGQATLEG 242
Query: 209 QGLMNQYFSRMKTVQTSTPHLPLRIRFMLQDVEDLRRN-NW 248
L++ F + + T + RI+F L D+++LR + NW
Sbjct: 243 SQLLDSLFGILDNI-IQTAKISSRIKFKLIDIKELRHDKNW 282
>pdb|3RK6|A Chain A, Crystal Structure Of The Middle Domain Of Human Paip1
pdb|3RK6|B Chain B, Crystal Structure Of The Middle Domain Of Human Paip1
Length = 234
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 44/176 (25%), Positives = 84/176 (47%), Gaps = 31/176 (17%)
Query: 58 LKGVILLIFEKALHETKYTSMYARLCKRLTEQAPNFEPPDESCTFKKHLLWVCKNEFENR 117
L+ ++ LI+++A ++ M ARLC L+ + +S F++ LL C+ E+E +
Sbjct: 58 LQELVELIYQQATSIPNFSYMGARLCNYLSH---HLTISPQSGNFRQLLLQRCRTEYEVK 114
Query: 118 SRATEAFGNLPLSPDDEDRRQLAKQKMLGNIKFIGEL-------GKHEIVTES-ILHTCI 169
+A + DE + +++ + F+GEL G + VT + IL +
Sbjct: 115 DQAAKG---------DE----VTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGL 161
Query: 170 QELLPKNRKVQTNKDVSENLECLCQIMKTCGRILDS---EKGQGLMNQYFSRMKTV 222
+ELL + + +NL C +++K G +L+ EKG+ M + R++ V
Sbjct: 162 RELL----NALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKMDMEEIIQRIENV 213
>pdb|1UW4|B Chain B, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
pdb|1UW4|D Chain D, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
Length = 248
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 28/123 (22%), Positives = 52/123 (42%), Gaps = 23/123 (18%)
Query: 142 QKMLGNIKFIGELGKHEIVTESILHTCIQELLPKNRKVQTNKDVSEN----------LEC 191
Q+ + + KF+GEL + +V +++ + N D S + +
Sbjct: 99 QRRISSAKFLGELYNYRMVESAVIFRTLYSF----TSFGVNPDGSPSSLDPPEHLFRIRL 154
Query: 192 LCQIMKTCGRILD---SEKGQGLMNQYFSRM----KTVQTSTPH--LPLRIRFMLQDVED 242
+C I+ TCG+ D S++ YF R K+++ T P+ I +M+ D +
Sbjct: 155 VCTILDTCGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPIDIDYMISDTLE 214
Query: 243 LRR 245
L R
Sbjct: 215 LLR 217
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
0.319 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,369,771
Number of Sequences: 62578
Number of extensions: 318889
Number of successful extensions: 644
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 632
Number of HSP's gapped (non-prelim): 5
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
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: 51 (24.3 bits)