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= 034304
(98 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XY7|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis
Thaliana At5g48480
pdb|1XY7|B Chain B, X-Ray Structure Of Gene Product From Arabidopsis
Thaliana At5g48480
pdb|2Q48|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Arabidopsis Thaliana At5g48480
pdb|2Q48|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Gene Product From Arabidopsis Thaliana At5g48480
Length = 166
Score = 48.9 bits (115), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 33/56 (58%), Gaps = 6/56 (10%)
Query: 10 FMGMKLQLLVEASKAIDAIQFYKTAFGAVEISRIMETKRKAEKELNSRLSAPHFLS 65
F K LLVEA K DA+ FYK+AFGA+E + KRK ++EL PH LS
Sbjct: 23 FTEFKQXLLVEAQKVGDAVTFYKSAFGAIESGHSLYPKRKLDQEL------PHVLS 72
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
pdb|4DZS|B Chain B, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
Length = 357
Score = 30.4 bits (67), Expect = 0.29, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 13 MKLQLLVEASKAIDAI---------QFYKTAFGAVEISRIMETKRKAEKELNSRLSAPHF 63
++ QL + SKA DAI + +FG I +++E ++ + +++S+PHF
Sbjct: 50 LQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHF 109
Query: 64 LSLTF 68
+ ++
Sbjct: 110 VEISL 114
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
pdb|3BX3|B Chain B, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
Length = 335
Score = 30.4 bits (67), Expect = 0.29, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 13 MKLQLLVEASKAIDAI---------QFYKTAFGAVEISRIMETKRKAEKELNSRLSAPHF 63
++ QL + SKA DAI + +FG I +++E ++ + +++S+PHF
Sbjct: 28 LQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHF 87
Query: 64 LSLTF 68
+ ++
Sbjct: 88 VEISL 92
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 30.4 bits (67), Expect = 0.29, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 13 MKLQLLVEASKAIDAI---------QFYKTAFGAVEISRIMETKRKAEKELNSRLSAPHF 63
++ QL + SKA DAI + +FG I +++E ++ + +++S+PHF
Sbjct: 28 LQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHF 87
Query: 64 LSLTF 68
+ ++
Sbjct: 88 VEISL 92
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 30.4 bits (67), Expect = 0.29, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 13 MKLQLLVEASKAIDAI---------QFYKTAFGAVEISRIMETKRKAEKELNSRLSAPHF 63
++ QL + SKA DAI + +FG I +++E ++ + +++S+PHF
Sbjct: 28 LQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHF 87
Query: 64 LSLTF 68
+ ++
Sbjct: 88 VEISL 92
>pdb|2PFB|A Chain A, Structure Of Oxidized Ohrr From Xanthamonas Campestris
pdb|2PFB|B Chain B, Structure Of Oxidized Ohrr From Xanthamonas Campestris
Length = 153
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 64 LSLTFPMILLQLRIWESDASS----GRRL 88
L LT+P L+ L +WE+D S G RL
Sbjct: 43 LDLTYPQYLVMLVLWETDERSVSEIGERL 71
>pdb|2PEX|A Chain A, Structure Of Reduced C22s Ohrr From Xanthamonas
Campestris
pdb|2PEX|B Chain B, Structure Of Reduced C22s Ohrr From Xanthamonas
Campestris
Length = 153
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 64 LSLTFPMILLQLRIWESDASS----GRRL 88
L LT+P L+ L +WE+D S G RL
Sbjct: 43 LDLTYPQYLVMLVLWETDERSVSEIGERL 71
>pdb|2NSB|A Chain A, Structures Of And Interactions Between Domains Of
Trigger Factor From Themotoga Maritima
pdb|2NSC|A Chain A, Structures Of And Interactions Between Domains Of
Trigger Factor From Themotoga Maritima
Length = 109
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 34 AFGAVEISRIMETKRKAEKELNSRLSAPHFLSLTFPMILLQLRIWES 80
FGA EI+ + + KA + LN R+ P F P +L++++ E
Sbjct: 18 VFGAEEIA---QAEDKAVRYLNQRVEIPGFRKGRIPKNVLKMKLGEE 61
>pdb|3GTY|X Chain X, Promiscuous Substrate Recognition In Folding And
Assembly Activities Of The Trigger Factor Chaperone
Length = 433
Score = 25.4 bits (54), Expect = 9.2, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 35 FGAVEISRIMETKRKAEKELNSRLSAPHFLSLTFPMILLQLRIWE 79
FGA EI+ + + KA + LN R+ P F P +L++++ E
Sbjct: 19 FGAEEIA---QAEDKAVRYLNQRVEIPGFRKGRIPKNVLKMKLGE 60
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
0.322 0.130 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,056,897
Number of Sequences: 62578
Number of extensions: 51197
Number of successful extensions: 109
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 101
Number of HSP's gapped (non-prelim): 15
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)