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= psy1519
(210 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TWO|A Chain A, The Crystal Structure Of Cad From Helicobacter Pylori
Complexed With Nadp(H)
pdb|3TWO|B Chain B, The Crystal Structure Of Cad From Helicobacter Pylori
Complexed With Nadp(H)
Length = 348
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 64 PHENYRKVM----VYVASVFRGVLEPEVQEIFATSYKPDYRLIPKHEEQEWLRRTGKGEK 119
PH+ R + V + ++ G+ ++ ++ + Y +IP HE ++ GKG K
Sbjct: 19 PHDFSRHAVGPRDVLIDILYAGICHSDIHSAYSEWKEGIYPMIPGHEIAGIIKEVGKGVK 78
Query: 120 KIQYID 125
K + D
Sbjct: 79 KFKIGD 84
>pdb|4GIM|A Chain A, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Pseudouridine 5'-Phosphate
pdb|4GIM|B Chain B, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Pseudouridine 5'-Phosphate
pdb|4GIM|C Chain C, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Pseudouridine 5'-Phosphate
Length = 335
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 8/37 (21%)
Query: 173 ENHPADIKIESFFGTPLSPELYEIKPEVAEYFKQKKP 209
+ H +++KI SPEL +I PEV + K KKP
Sbjct: 21 QGHMSELKI--------SPELLQISPEVQDALKNKKP 49
>pdb|4GIJ|A Chain A, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Sulfate
pdb|4GIJ|B Chain B, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Sulfate
pdb|4GIJ|C Chain C, Crystal Structure Of Pseudouridine Monophosphate
Glycosidase Complexed With Sulfate
pdb|4GIK|A Chain A, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR R5p Adduct
pdb|4GIK|B Chain B, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR R5p Adduct
pdb|4GIK|C Chain C, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR R5p Adduct
pdb|4GIL|A Chain A, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR Pseudouridine 5'-Phosphate Adduct
pdb|4GIL|B Chain B, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR Pseudouridine 5'-Phosphate Adduct
pdb|4GIL|C Chain C, Crystal Structure Of Pseudouridine Monophosphate
GlycosidaseLINEAR Pseudouridine 5'-Phosphate Adduct
Length = 335
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 8/37 (21%)
Query: 173 ENHPADIKIESFFGTPLSPELYEIKPEVAEYFKQKKP 209
+ H +++KI SPEL +I PEV + K KKP
Sbjct: 21 QGHMSELKI--------SPELLQISPEVQDALKNKKP 49
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1119
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 74 YVASVFRGVLEPEVQEIFATSY 95
Y++ VF G EPE++E+ A ++
Sbjct: 901 YISPVFDGATEPEIKELLAEAF 922
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1119
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 74 YVASVFRGVLEPEVQEIFATSY 95
Y++ VF G EPE++E+ A ++
Sbjct: 901 YISPVFDGATEPEIKELLAEAF 922
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 74 YVASVFRGVLEPEVQEIFATSY 95
Y++ VF G EPE++E+ A ++
Sbjct: 900 YISPVFDGATEPEIKELLAEAF 921
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 74 YVASVFRGVLEPEVQEIFATSY 95
Y++ VF G EPE++E+ A ++
Sbjct: 900 YISPVFDGATEPEIKELLAEAF 921
>pdb|2OV1|A Chain A, Crystal Structure Of Apo Form Of Znua With Flexible Loop
Deletion
pdb|2OV3|A Chain A, Crystal Structure Of 138-173 Znua Deletion Mutant Plus
Zinc Bound
Length = 260
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 84 EPEVQEIFATSYKPDYRLIPKHEEQEWLRRTGKGEKKIQYIDPWVDMPPL 133
EP+ Q++ A S Y LI EQ WL + ++ ID + PL
Sbjct: 40 EPKPQQLAALSEAEAYVLIGLGFEQPWLEKLKAANANMKLIDSAQGITPL 89
>pdb|1PQ4|A Chain A, Crystal Structure Of Znua
pdb|1PQ4|B Chain B, Crystal Structure Of Znua
Length = 291
Score = 26.6 bits (57), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 84 EPEVQEIFATSYKPDYRLIPKHEEQEWLRRTGKGEKKIQYIDPWVDMPPL 133
EP+ Q++ A S Y LI EQ WL + ++ ID + PL
Sbjct: 40 EPKPQQLAALSEAEAYVLIGLGFEQPWLEKLKAANANMKLIDSAQGITPL 89
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 0.139 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,137,056
Number of Sequences: 62578
Number of extensions: 307020
Number of successful extensions: 825
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 816
Number of HSP's gapped (non-prelim): 16
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
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)