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= 041166
(133 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
Length = 217
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 13/97 (13%)
Query: 31 WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQR-TVLKQLQWRXXXXXXXXXXX 89
+ P P+L+ + Y+DD + +NKPSGL +PG L + + +V ++Q
Sbjct: 4 YNPPQEPWLV-ILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAES----- 57
Query: 90 XXHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
VHRL TSG+++ A TK A+ + F ++
Sbjct: 58 ------VHRLDXATSGVIVVALTKAAERELKRQFRER 88
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
Synthase Rlud From Escherichia Coli
pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
Length = 325
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 35 DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
D+P L++ YED+D+I +NKP L V PG TVL L
Sbjct: 80 DIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 133
Query: 95 PVHRLGRGTSGILLCAKTKLAKT 117
VHRL + T+G+++ AKT A+T
Sbjct: 134 -VHRLDKDTTGLMVVAKTVPAQT 155
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 35 DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
D+P L++ YED+D+I +NKP L V PG TVL L
Sbjct: 7 DIP--LDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 60
Query: 95 PVHRLGRGTSGILLCAKTKLAKT 117
VHRL + T+G+ + AKT A+T
Sbjct: 61 -VHRLDKDTTGLXVVAKTVPAQT 82
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 35 DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
D+P L++ YED+D+I +NKP L V PG TVL L
Sbjct: 104 DIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 157
Query: 95 PVHRLGRGTSGILLCAKTKLAKT 117
VHRL + T+G+ + AKT A+T
Sbjct: 158 -VHRLDKDTTGLXVVAKTVPAQT 179
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
Length = 231
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 42 VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPVPVHRLGR 101
+ YEDD ++ LNKPSG V GG V++ L+ VHRL R
Sbjct: 7 ILYEDDHILVLNKPSGTAV-HGGSGLSFGVIEGLRALRPEARFLEL--------VHRLDR 57
Query: 102 GTSGILLCAKTKLAKTCIAAYFADK 126
TSG+LL AK + A + +K
Sbjct: 58 DTSGVLLVAKKRSALRSLHEQLREK 82
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
Length = 228
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 42 VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPVPVHRLGR 101
+ YEDD ++ LNKPSG V GG V++ L+ VHRL R
Sbjct: 4 IXYEDDHILVLNKPSGTAV-HGGSGLSFGVIEGLRALRPEARFLEL--------VHRLDR 54
Query: 102 GTSGILLCAKTKLAKTCIAAYFADKTSVVD 131
TSG+LL AK + A + +K D
Sbjct: 55 DTSGVLLVAKKRSALRSLHEQLREKGXQKD 84
>pdb|1UG9|A Chain A, Crystal Structure Of Glucodextranase From Arthrobacter
Globiformis I42
pdb|1ULV|A Chain A, Crystal Structure Of Glucodextranase Complexed With
Acarbose
Length = 1020
Score = 25.4 bits (54), Expect = 8.5, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 11 HKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSG 57
H +A L G E V RL K P PY+ + E D I+ P G
Sbjct: 518 HPENAVLDGGFLEFV--RLGVKAPADPYVADSLAETDASISQETPGG 562
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 0.138 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,724,342
Number of Sequences: 62578
Number of extensions: 129722
Number of successful extensions: 271
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 259
Number of HSP's gapped (non-prelim): 7
length of query: 133
length of database: 14,973,337
effective HSP length: 88
effective length of query: 45
effective length of database: 9,466,473
effective search space: 425991285
effective search space used: 425991285
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: 46 (22.3 bits)