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= psy4559
(336 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
Length = 327
Score = 34.3 bits (77), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 190 AGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLI 249
+ ++ ++ Y+ ARQG P + VY L + + + +E+HC ++ +I
Sbjct: 140 SALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHC--SKGTYIRTII 197
Query: 250 YDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWR 285
DLG KL A ++ + +++ +E + +H R
Sbjct: 198 DDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLR 233
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
Trub Bound To A T Stem-Loop Rna
Length = 327
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 190 AGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLI 249
+ ++ ++ Y+ ARQG P + VY L + + + +E+HC ++ +I
Sbjct: 140 SALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHC--SKGTYIRTII 197
Query: 250 YDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWR 285
DLG KL A ++ + +++ +E + +H R
Sbjct: 198 DDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLR 233
>pdb|1Q14|A Chain A, Structure And Autoregulation Of The Yeast Hst2 Homolog Of
Sir2
Length = 361
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 7/94 (7%)
Query: 242 EEFLIRLIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENIAHNETLVD 301
+EF +L+ +LG + I T AQ G+ + + + H +EN++ +++ +
Sbjct: 275 DEFAEQLVEELGWQEDFEKILT-------AQGGMGDNSKEQLLEIVHDLENLSLDQSEHE 327
Query: 302 KMDPMRPQLQSVNMTDSDSTDGSNVSDGNRTVLE 335
D +LQ +N DSD SN S + E
Sbjct: 328 SADKKDKKLQRLNGHDSDEDGASNSSSSQKAAKE 361
>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
Its Rna Complex: Rna-Protein Recognition Through A
Combination Of Rigid Docking And Induced Fit
Length = 314
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 46/96 (47%), Gaps = 2/96 (2%)
Query: 190 AGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLI 249
+ ++ ++ Y+ ARQG P + VY L + + + +E+HC ++ +I
Sbjct: 127 SALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHC--SKGTYIRTII 184
Query: 250 YDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWR 285
DLG KL A ++ + +++ +E + +H R
Sbjct: 185 DDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLR 220
>pdb|4IH4|A Chain A, Crystal Structure Of Arabidopsis Dwarf14 Orthologue, Atd14
pdb|4IH4|B Chain B, Crystal Structure Of Arabidopsis Dwarf14 Orthologue, Atd14
pdb|4IH4|C Chain C, Crystal Structure Of Arabidopsis Dwarf14 Orthologue, Atd14
pdb|4IH4|D Chain D, Crystal Structure Of Arabidopsis Dwarf14 Orthologue, Atd14
Length = 267
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 141 VVYGLKCVHFKPPDFTIGNLYSALLPWQEAVLKITDN----NCLFVCLFVHRQAGV 192
V+Y L C PD+ N Y+ L P+ + +L I D+ NC +V V G+
Sbjct: 49 VLYDLVCAGSVNPDYFDFNRYTTLDPYVDDLLNIVDSLGIQNCAYVGHSVSAMIGI 104
>pdb|3UOG|A Chain A, Crystal Structure Of Putative Alcohol Dehydrogenase From
Sinorhizobium Meliloti 1021
pdb|3UOG|B Chain B, Crystal Structure Of Putative Alcohol Dehydrogenase From
Sinorhizobium Meliloti 1021
Length = 363
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 122 EAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNL 160
E ++V+ GP+ P LLK PVV G+ H + + +G +
Sbjct: 290 EGFEVS--GPVGPLLLKSPVVQGISVGHRRALEDLVGAV 326
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 198 EAYDIARQGPIRPALLKEPVVYGLKCVH 225
E ++++ GP+ P LLK PVV G+ H
Sbjct: 290 EGFEVS--GPVGPLLLKSPVVQGISVGH 315
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
0.323 0.138 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,173,527
Number of Sequences: 62578
Number of extensions: 415555
Number of successful extensions: 601
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 597
Number of HSP's gapped (non-prelim): 7
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)