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= 045084
(365 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MP4|A Chain A, W224h Variant Of S. Enterica Rmla
pdb|1MP4|B Chain B, W224h Variant Of S. Enterica Rmla
Length = 292
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 112 WRKSGKRSQLKYGMNFAHGGTGVFNTLVDEPNMTTQVKFFQQLL----EEKVFTKHDLNS 167
+ + G+ S G +AH TG +L++ N ++ Q L EE F K+ +N+
Sbjct: 207 YMEQGRLSVAMMGRGYAHLDTGTHQSLIEASNFIATIEERQGLKVSCPEEIAFRKNFINA 266
Query: 168 SVALVSLAG----NDYATYLVK 185
++ LAG NDY YL+K
Sbjct: 267 Q-QVIELAGPLSKNDYGKYLLK 287
>pdb|2AB4|A Chain A, Dissecting The Roles Of A Strictly Conserved Tyrosine In
Substrate Recognition And Catalysis By Pseudouridine 55
Synthase
Length = 309
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 229 CLPQLSAVYSYKNCSESLNSASKFHNQLLQQ-------EILQTFNNESKRPVIFTLDLYS 281
CL L V ++ ++ + + S+ H ++L++ E+++ FN E + + + S
Sbjct: 225 CLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNS 284
Query: 282 AFMSALMKKENHSGNVELKTSLQ 304
+F+ L K E + L+ Q
Sbjct: 285 SFLETLRKHERQERVLTLRKVFQ 307
>pdb|1ZE2|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE2|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 229 CLPQLSAVYSYKNCSESLNSASKFHNQLLQQ-------EILQTFNNESKRPVIFTLDLYS 281
CL L V ++ ++ + + S+ H ++L++ E+++ FN E + + + S
Sbjct: 225 CLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNS 284
Query: 282 AFMSALMKKENHSGNVELKTSLQ 304
+F+ L K E + L+ Q
Sbjct: 285 SFLETLRKHERQERVLTLRKVFQ 307
>pdb|1ZE1|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|C Chain C, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|D Chain D, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 229 CLPQLSAVYSYKNCSESLNSASKFHNQLLQQ-------EILQTFNNESKRPVIFTLDLYS 281
CL L V ++ ++ + + S+ H ++L++ E+++ FN E + + + S
Sbjct: 225 CLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNS 284
Query: 282 AFMSALMKKENHSGNVELKTSLQ 304
+F+ L K E + L+ Q
Sbjct: 285 SFLETLRKHERQRRVLTLRKVFQ 307
>pdb|1R3E|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 = 309
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 229 CLPQLSAVYSYKNCSESLNSASKFHNQLLQQ-------EILQTFNNESKRPVIFTLDLYS 281
CL L V ++ ++ + + S+ H ++L++ E+++ FN E + + + S
Sbjct: 225 CLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNS 284
Query: 282 AFMSALMKKENHSGNVELK 300
+F+ L K E + + L+
Sbjct: 285 SFLETLRKHERNERVLTLR 303
>pdb|3JYW|C Chain C, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 362
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 91 RVLTDYIAPYLGTKSPVS-YKNWRKSGKRSQLKYGMNFAHGGTGVFNTLV 139
R LT A +L + YKNW KS K++ KY +A G G+ L
Sbjct: 96 RSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELA 145
>pdb|1S1I|C Chain C, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 386
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 91 RVLTDYIAPYLGTKSPVS-YKNWRKSGKRSQLKYGMNFAHGGTGVFNTLV 139
R LT A +L + YKNW KS K++ KY +A G G+ L
Sbjct: 99 RSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELA 148
>pdb|3O58|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|B Chain B, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|B Chain B, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 387
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 91 RVLTDYIAPYLGTKSPVS-YKNWRKSGKRSQLKYGMNFAHGGTGVFNTLV 139
R LT A +L + YKNW KS K++ KY +A G G+ L
Sbjct: 100 RSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELA 149
>pdb|3IZS|C Chain C, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 388
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 91 RVLTDYIAPYLGTKSPVS-YKNWRKSGKRSQLKYGMNFAHGGTGVFNTLV 139
R LT A +L + YKNW KS K++ KY +A G G+ L
Sbjct: 100 RSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELA 149
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
0.320 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,254,259
Number of Sequences: 62578
Number of extensions: 421820
Number of successful extensions: 940
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 936
Number of HSP's gapped (non-prelim): 12
length of query: 365
length of database: 14,973,337
effective HSP length: 100
effective length of query: 265
effective length of database: 8,715,537
effective search space: 2309617305
effective search space used: 2309617305
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: 52 (24.6 bits)