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= psy4476
(266 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 142 bits (358), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 67/104 (64%), Positives = 79/104 (75%), Gaps = 1/104 (0%)
Query: 52 EVGLELKSSAGAPTESYHGLFCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGH 111
E+ +EL+SS GAP E H F WKSTSFDRMQ AL+ FAVD+ SVS YIYH+LLGH
Sbjct: 100 EIAIELRSSVGAPVEVTHN-FQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGH 158
Query: 112 NVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQG 155
V++V+ +C LPK F+A LPDLN SQVYAVK +QRPLSLIQG
Sbjct: 159 EVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQG 202
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 142 bits (357), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 67/104 (64%), Positives = 79/104 (75%), Gaps = 1/104 (0%)
Query: 52 EVGLELKSSAGAPTESYHGLFCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGH 111
E+ +EL+SS GAP E H F WKSTSFDRMQ AL+ FAVD+ SVS YIYH+LLGH
Sbjct: 99 EIAIELRSSVGAPVEVTHN-FQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGH 157
Query: 112 NVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQG 155
V++V+ +C LPK F+A LPDLN SQVYAVK +QRPLSLIQG
Sbjct: 158 EVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQG 201
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 141 bits (356), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 67/104 (64%), Positives = 79/104 (75%), Gaps = 1/104 (0%)
Query: 52 EVGLELKSSAGAPTESYHGLFCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGH 111
E+ +EL+SS GAP E H F WKSTSFDRMQ AL+ FAVD+ SVS YIYH+LLGH
Sbjct: 276 EIAIELRSSVGAPVEVTHN-FQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGH 334
Query: 112 NVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQG 155
V++V+ +C LPK F+A LPDLN SQVYAVK +QRPLSLIQG
Sbjct: 335 EVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQG 378
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 108 bits (270), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 53/101 (52%), Positives = 65/101 (64%)
Query: 55 LELKSSAGAPTESYHGLFCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVD 114
LELK S P F WK TS+DRMQ AL+KFA+D +S+S Y+Y+++LGH V
Sbjct: 282 LELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVV 341
Query: 115 EVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQG 155
++ F LPK FS PN LN SQ AV H +QRPLSLIQG
Sbjct: 342 DISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQG 382
>pdb|4DYE|A Chain A, Crystal Structure Of An Enolase (Putative Sugar Isomerase,
Target Efi- 502095) From Streptomyces Coelicolor, No Mg,
Ordered Loop
Length = 398
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 121 HLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGMNQRSNGLHHQPGGAGIGNSANTNR 180
HL S P L S Y I PL L NG P G G+G S + ++
Sbjct: 330 HLAVVSSTPVLSRAIDSMYYLHADDIIEPLHL-------ENGRLRVPSGPGLGVSVDEDK 382
Query: 181 LRNKSNLNHR 190
LR+ + +N R
Sbjct: 383 LRHYAGVNER 392
>pdb|2OQH|A Chain A, Crystal Structure Of An Isomerase From Streptomyces
Coelicolor A3(2)
pdb|2OQH|B Chain B, Crystal Structure Of An Isomerase From Streptomyces
Coelicolor A3(2)
pdb|2OQH|C Chain C, Crystal Structure Of An Isomerase From Streptomyces
Coelicolor A3(2)
pdb|2OQH|D Chain D, Crystal Structure Of An Isomerase From Streptomyces
Coelicolor A3(2)
Length = 385
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 121 HLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGMNQRSNGLHHQPGGAGIGNSANTNR 180
HL S P L S Y I PL L NG P G G+G S + ++
Sbjct: 309 HLAVVSSTPVLSRAIDSXYYLHADDIIEPLHL-------ENGRLRVPSGPGLGVSVDEDK 361
Query: 181 LRNKSNLNHR 190
LR+ + +N R
Sbjct: 362 LRHYAGVNER 371
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
0.316 0.132 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,871,879
Number of Sequences: 62578
Number of extensions: 299152
Number of successful extensions: 642
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 635
Number of HSP's gapped (non-prelim): 6
length of query: 266
length of database: 14,973,337
effective HSP length: 97
effective length of query: 169
effective length of database: 8,903,271
effective search space: 1504652799
effective search space used: 1504652799
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)