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= 013803
(436 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 (366), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 87/248 (35%), Positives = 127/248 (51%), Gaps = 11/248 (4%)
Query: 139 RGDIGRLNAPNFKKLFEQVKAVNIDNAVTLAGVVSQIFDKALMEPTFCEMYANFFYFLAG 198
R + +L F +L +QV + +D L GV+ +F+KA+ EP+F YAN L
Sbjct: 16 RSILNKLTPQXFNQLXKQVSGLTVDTEERLKGVIDLVFEKAIDEPSFSVAYANXCRCLVT 75
Query: 199 -ELPDFSEDNEKITFKRLLLNKCXXXXXXXXXXXXXANK-------ADXXXXXXXXXXXX 250
++P + + F++LLLN+C K A
Sbjct: 76 LKVPXADKPGNTVNFRKLLLNRCQKEFEKDKADDDVFEKKQKELEAASAPEERTRLHDEL 135
Query: 251 XXXXXXXXXXWLGNIRLIGELYKKKMLTERIMHECIKKLLGQYENPDEEDVEALCILMST 310
+GNI+ IGEL+K K LTE I H+C+ KLL +N DEE +E LC L++T
Sbjct: 136 EEAKDKARRRSIGNIKFIGELFKLKXLTEAIXHDCVVKLL---KNHDEESLECLCRLLTT 192
Query: 311 IGEMIDHPKAKEHMDAYFDRMEKLSNNMKLSSRVRLMLKDSIELRKNKWQQRRKVEGPKK 370
IG+ +D KAK D YF++ EK+ K SSR+R L+D I+LR W RR +GPK
Sbjct: 193 IGKDLDFEKAKPRXDQYFNQXEKIVKERKTSSRIRFXLQDVIDLRLCNWVSRRADQGPKT 252
Query: 371 IEEVHRDA 378
IE++H++A
Sbjct: 253 IEQIHKEA 260
>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 = 72.4 bits (176), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 65/238 (27%), Positives = 108/238 (45%), Gaps = 22/238 (9%)
Query: 142 IGRLNAPNFKKLFEQVKAV-NID----NAVTLAGVVSQIFDKALMEPTFCEMYANFFYFL 196
+ +L F + ++ A+ NI N TL V+ QIF KA EP + MYA +
Sbjct: 44 LNKLTLEMFDAISSEILAIANISVWETNGETLKAVIEQIFLKACDEPHWSSMYAQLCGKV 103
Query: 197 AGEL-PDFS-EDNEKITFKRLLLN----KCXXXXXXXXXXXXXANKADXXXXXXXXXXXX 250
EL PD + E NE T +L+L+ +C N+ D
Sbjct: 104 VKELNPDITDETNEGKTGPKLVLHYLVARCHAEFDKGWTDKLPTNE-DGTPLEPEMMSEE 162
Query: 251 XXXXXXXXXXWLGNIRLIGELYKKKMLTERIMHECIKKLLGQY-ENPDEEDVEALCILMS 309
LG +R IG LY+ +LT ++M EC ++L+ ++P EE +E++ L++
Sbjct: 163 YYAAASAKRRGLGLVRFIGFLYRLNLLTGKMMFECFRRLMKDLTDSPSEETLESVVELLN 222
Query: 310 TIGEMIDHP---------KAKEHMDAYFDRMEKLSNNMKLSSRVRLMLKDSIELRKNK 358
T+GE + + + +D+ F ++ + K+SSR++ L D ELR +K
Sbjct: 223 TVGEQFETDSFRTGQATLEGSQLLDSLFGILDNIIQTAKISSRIKFKLIDIKELRHDK 280
>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 = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 23/118 (19%), Positives = 47/118 (39%), Gaps = 21/118 (17%)
Query: 262 LGNIRLIGELYKKKMLTERIMHECIKKLLGQYENPDEED-----------VEALCILMST 310
+ + + +GELY +M+ ++ + NPD + +C ++ T
Sbjct: 102 ISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHLFRIRLVCTILDT 161
Query: 311 IGEMIDHPKAKEHMDA---YFDR-------MEKLSNNMKLSSRVRLMLKDSIELRKNK 358
G+ D +K +D YF R +E + + + M+ D++EL + K
Sbjct: 162 CGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPIDIDYMISDTLELLRPK 219
>pdb|2Y7C|A Chain A, Atomic Model Of The Ocr-Bound Methylase Complex From The
Type I Restriction-Modification Enzyme Ecoki (M2s1).
Based On Fitting Into Em Map 1534.
pdb|2Y7H|A Chain A, Atomic Model Of The Dna-Bound Methylase Complex From The
Type I Restriction-Modification Enzyme Ecoki (M2s1).
Based On Fitting Into Em Map 1534
Length = 464
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 53/113 (46%), Gaps = 6/113 (5%)
Query: 282 MHECIKKLLGQYENPDEEDVEALCILMSTIGEMIDHPKAKEHMDAYFDRMEKLSNN--MK 339
M C+K GQ + +D+++ +L+ + E + + E + AY D +EK NN +
Sbjct: 347 MMNCVKTTSGQ-KGISGKDIKSQVVLLPPVKEQAEIVRRVEQLFAYADTIEKQVNNALAR 405
Query: 340 LSSRVRLMLKDSIELRKNKWQQRRKVEGPKKIEEVHRDAAQERQAQASRLARG 392
+++ + +L + + + + + E P I + AA + +A R A G
Sbjct: 406 VNNLTQSILAKAF---RGELTAQWRAENPDLISGENSAAALLEKIKAERAASG 455
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 0.135 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,857,849
Number of Sequences: 62578
Number of extensions: 375147
Number of successful extensions: 928
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 919
Number of HSP's gapped (non-prelim): 7
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
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: 53 (25.0 bits)