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= 028248
(211 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 327
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 94 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 149
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 94 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 149
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 333
Score = 27.3 bits (59), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 101 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 156
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 97 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 152
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 340
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 101 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 156
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|A Chain A, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|A Chain A, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 346
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK+ Q +K EI+ P + LR+RKVY
Sbjct: 101 QALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 156
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
pdb|2AUS|A Chain A, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
Length = 334
Score = 26.9 bits (58), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 28 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP-----RCSLRSRKVY 78
Q L A YVA + D DK++ +K EI+ P + LR+RKVY
Sbjct: 101 QALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRLRTRKVY 156
>pdb|1XQA|A Chain A, Structure Of A Possible Glyoxalase From Bacillus Cereus
pdb|1XQA|B Chain B, Structure Of A Possible Glyoxalase From Bacillus Cereus
Length = 113
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 22 MLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCS 71
+L+ + K ++ + G P S+E+ DK+ Q+LK +G +VE P+ +
Sbjct: 47 ILTLXKGKEVQYPKTFHVGFPQESEEQVDKINQRLKEDG--FLVEPPKHA 94
>pdb|3FKQ|A Chain A, Crystal Structure Of Ntrc-Like Two-Domain Protein
(Rer070207001320) From Eubacterium Rectale At 2.10 A
Resolution
Length = 373
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 19/44 (43%)
Query: 153 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY 196
+I PC GT V+ I + G +N CGTT V+
Sbjct: 146 VIFTSPCGGVGTSTVAAACAIAHANXGKKVFYLNIEQCGTTDVF 189
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
0.318 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,775,207
Number of Sequences: 62578
Number of extensions: 216151
Number of successful extensions: 649
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 646
Number of HSP's gapped (non-prelim): 16
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)