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= 017537
(369 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 = 144 bits (364), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 87/248 (35%), Positives = 127/248 (51%), Gaps = 11/248 (4%)
Query: 72 RGDIGRLNAPNFKKLFEQVKAVNIDNAVTLAGVVSQIFDKALMEPTFCEMYANFFYFLAG 131
R + +L F +L +QV + +D L GV+ +F+KA+ EP+F YAN L
Sbjct: 16 RSILNKLTPQXFNQLXKQVSGLTVDTEERLKGVIDLVFEKAIDEPSFSVAYANXCRCLVT 75
Query: 132 -ELPDFSEDNEKITFKRLLLNKCXXXXXXXXXXXXXANK-------ADXXXXXXXXXXXX 183
++P + + F++LLLN+C K A
Sbjct: 76 LKVPXADKPGNTVNFRKLLLNRCQKEFEKDKADDDVFEKKQKELEAASAPEERTRLHDEL 135
Query: 184 XXXXXXXXXXWLGNIRLIGELYKKKMLTERIMHECIKKLLGQYENPDEEDVEALCILMST 243
+GNI+ IGEL+K K LTE I H+C+ KLL +N DEE +E LC L++T
Sbjct: 136 EEAKDKARRRSIGNIKFIGELFKLKXLTEAIXHDCVVKLL---KNHDEESLECLCRLLTT 192
Query: 244 IGEMIDHPKAKEHMDAYFDRMEKLSNNMKLSSRVRLMLKDSIELRKNKWQQRRKVEGPKK 303
IG+ +D KAK D YF++ EK+ K SSR+R L+D I+LR W RR +GPK
Sbjct: 193 IGKDLDFEKAKPRXDQYFNQXEKIVKERKTSSRIRFXLQDVIDLRLCNWVSRRADQGPKT 252
Query: 304 IEEVHRDA 311
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 = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 60/211 (28%), Positives = 97/211 (45%), Gaps = 17/211 (8%)
Query: 97 NAVTLAGVVSQIFDKALMEPTFCEMYANFFYFLAGEL-PDFS-EDNEKITFKRLLLN--- 151
N TL V+ QIF KA EP + MYA + EL PD + E NE T +L+L+
Sbjct: 71 NGETLKAVIEQIFLKACDEPHWSSMYAQLCGKVVKELNPDITDETNEGKTGPKLVLHYLV 130
Query: 152 -KCXXXXXXXXXXXXXANKADXXXXXXXXXXXXXXXXXXXXXXWLGNIRLIGELYKKKML 210
+C N+ D LG +R IG LY+ +L
Sbjct: 131 ARCHAEFDKGWTDKLPTNE-DGTPLEPEMMSEEYYAAASAKRRGLGLVRFIGFLYRLNLL 189
Query: 211 TERIMHECIKKLLGQY-ENPDEEDVEALCILMSTIGEMIDHP---------KAKEHMDAY 260
T ++M EC ++L+ ++P EE +E++ L++T+GE + + + +D+
Sbjct: 190 TGKMMFECFRRLMKDLTDSPSEETLESVVELLNTVGEQFETDSFRTGQATLEGSQLLDSL 249
Query: 261 FDRMEKLSNNMKLSSRVRLMLKDSIELRKNK 291
F ++ + K+SSR++ L D ELR +K
Sbjct: 250 FGILDNIIQTAKISSRIKFKLIDIKELRHDK 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 = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/118 (19%), Positives = 47/118 (39%), Gaps = 21/118 (17%)
Query: 195 LGNIRLIGELYKKKMLTERIMHECIKKLLGQYENPDEED-----------VEALCILMST 243
+ + + +GELY +M+ ++ + NPD + +C ++ T
Sbjct: 102 ISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHLFRIRLVCTILDT 161
Query: 244 IGEMIDHPKAKEHMDA---YFDR-------MEKLSNNMKLSSRVRLMLKDSIELRKNK 291
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 = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 215 MHECIKKLLGQYENPDEEDVEALCILMSTIGEMIDHPKAKEHMDAYFDRMEKLSNN 270
M C+K GQ + +D+++ +L+ + E + + E + AY D +EK NN
Sbjct: 347 MMNCVKTTSGQ-KGISGKDIKSQVVLLPPVKEQAEIVRRVEQLFAYADTIEKQVNN 401
>pdb|2WDA|A Chain A, The X-Ray Structure Of The Streptomyces Coelicolor A3
Chondroitin Ac Lyase In Complex With Chondroitin
Sulphate
pdb|2WCO|A Chain A, Structures Of The Streptomyces Coelicolor A3(2) Hyaluronan
Lyase In Complex With Oligosaccharide Substrates And An
Inhibitor
Length = 765
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 16/76 (21%)
Query: 25 LTMNLNSRMIIMRGMTRNIEIHVIRSDNRGKRRLSKRMRNL----------KWHIECRGD 74
L M+ + I RG ++ ++HV+RSD+ ++L M L +WH +G
Sbjct: 299 LVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGW 358
Query: 75 IGR------LNAPNFK 84
I R L AP F
Sbjct: 359 IERDTVTPVLTAPQFP 374
>pdb|2X03|A Chain A, The X-Ray Structure Of The Streptomyces Coelicolor A3
Chondroitin Ac Lyase Y253 Mutant
pdb|2X03|B Chain B, The X-Ray Structure Of The Streptomyces Coelicolor A3
Chondroitin Ac Lyase Y253 Mutant
Length = 765
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 16/76 (21%)
Query: 25 LTMNLNSRMIIMRGMTRNIEIHVIRSDNRGKRRLSKRMRNL----------KWHIECRGD 74
L M+ + I RG ++ ++HV+RSD+ ++L M L +WH +G
Sbjct: 299 LVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGW 358
Query: 75 IGR------LNAPNFK 84
I R L AP F
Sbjct: 359 IERDTVTPVLTAPQFP 374
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
0.324 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,055,852
Number of Sequences: 62578
Number of extensions: 314886
Number of successful extensions: 1074
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1065
Number of HSP's gapped (non-prelim): 9
length of query: 369
length of database: 14,973,337
effective HSP length: 100
effective length of query: 269
effective length of database: 8,715,537
effective search space: 2344479453
effective search space used: 2344479453
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)