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= psy5395
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HAJ|A Chain A, Solution Structure Of The Helicase-Binding Domain Of
Escherichia Coli Primase
Length = 148
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 31/114 (27%), Positives = 53/114 (46%), Gaps = 18/114 (15%)
Query: 84 MAGFAVRNPN-GQIVHPYEWKKNAEYQDTPPHGGYYSV---CIDNQFSRNAGKLVNMY-- 137
+ G V+NP +V P E N + P G + + C+ +Q G+L+ Y
Sbjct: 21 LIGLLVQNPELATLVPPLE---NLDENKLPGLGLFRELVNTCL-SQPGLTTGQLLEHYRG 76
Query: 138 ----LTVVRYDQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSR 187
T+ + WD +I D N++ Q FTDS+ + ++ E+ Q++ AR R
Sbjct: 77 TNNAATLEKLSMWD----DIADKNIAEQTFTDSLNHMFDSLLELRQEELIARER 126
>pdb|1T3W|A Chain A, Crystal Structure Of The E.coli Dnag C-terminal Domain
(residues 434 To 581)
pdb|1T3W|B Chain B, Crystal Structure Of The E.coli Dnag C-terminal Domain
(residues 434 To 581)
Length = 148
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 31/114 (27%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 84 MAGFAVRNPN-GQIVHPYEWKKNAEYQDTPPHGGYYSV---CIDNQFSRNAGKLVNMY-- 137
+ G V+NP +V P E N + P G + + C+ +Q G+L+ Y
Sbjct: 21 LIGLLVQNPELATLVPPLE---NLDENKLPGLGLFRELVNTCL-SQPGLTTGQLLEHYRG 76
Query: 138 ----LTVVRYDQWDKYHKEIEDLNVSVQNFTDSVRTVERNINEILQQQYHARSR 187
T+ + WD +I D N++ Q FTDS+ ++ E+ Q++ AR R
Sbjct: 77 TNNAATLEKLSXWD----DIADKNIAEQTFTDSLNHXFDSLLELRQEELIARER 126
>pdb|2WPQ|A Chain A, Salmonella Enterica Sada 479-519 Fused To Gcn4 Adaptors (
Sadak3, In-Register Fusion)
pdb|2WPQ|B Chain B, Salmonella Enterica Sada 479-519 Fused To Gcn4 Adaptors (
Sadak3, In-Register Fusion)
pdb|2WPQ|C Chain C, Salmonella Enterica Sada 479-519 Fused To Gcn4 Adaptors (
Sadak3, In-Register Fusion)
Length = 99
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 159 SVQNFTDSVRTVERNINEILQQQYHARSREAR 190
++ N +DS++ +E I EIL + YH + AR
Sbjct: 63 NINNLSDSMKQIEDKIEEILSKIYHIENEIAR 94
>pdb|2OQ6|A Chain A, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Trimethylated At Lys9
pdb|2OQ6|B Chain B, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Trimethylated At Lys9
pdb|2OQ7|A Chain A, The Crystal Structure Of Jmjd2a Complexed With Ni And
N-Oxalylglycine
pdb|2OQ7|B Chain B, The Crystal Structure Of Jmjd2a Complexed With Ni And
N-Oxalylglycine
pdb|2OS2|A Chain A, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Trimethylated At Lys36
pdb|2OS2|B Chain B, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Trimethylated At Lys36
pdb|2OT7|A Chain A, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Monomethylated At Lys9
pdb|2OT7|B Chain B, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Monomethylated At Lys9
pdb|2OX0|A Chain A, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Dimethylated At Lys9
pdb|2OX0|B Chain B, Crystal Structure Of Jmjd2a Complexed With Histone H3
Peptide Dimethylated At Lys9
pdb|2VD7|A Chain A, Crystal Structure Of Jmjd2a Complexed With Inhibitor
Pyridine-2,4-Dicarboxylic Acid
pdb|2VD7|B Chain B, Crystal Structure Of Jmjd2a Complexed With Inhibitor
Pyridine-2,4-Dicarboxylic Acid
pdb|3NJY|A Chain A, Crystal Structure Of Jmjd2a Complexed With 5-Carboxy-8-
Hydroxyquinoline
pdb|3NJY|B Chain B, Crystal Structure Of Jmjd2a Complexed With 5-Carboxy-8-
Hydroxyquinoline
pdb|2YBP|A Chain A, Jmjd2a Complexed With R-2-Hydroxyglutarate And Histone
H3k36me3 Peptide (30-41)
pdb|2YBP|B Chain B, Jmjd2a Complexed With R-2-Hydroxyglutarate And Histone
H3k36me3 Peptide (30-41)
pdb|2YBS|A Chain A, Jmjd2a Complexed With S-2-Hydroxyglutarate And Histone
H3k36me3 Peptide (30-41)
pdb|2YBS|B Chain B, Jmjd2a Complexed With S-2-Hydroxyglutarate And Histone
H3k36me3 Peptide (30-41)
pdb|3PDQ|A Chain A, Crystal Structure Of Jmjd2a Complexed With Bipyridyl
Inhibitor
pdb|3PDQ|B Chain B, Crystal Structure Of Jmjd2a Complexed With Bipyridyl
Inhibitor
pdb|2YBK|A Chain A, Jmjd2a Complexed With R-2-Hydroxyglutarate
pdb|2YBK|B Chain B, Jmjd2a Complexed With R-2-Hydroxyglutarate
pdb|3U4S|A Chain A, Histone Lysine Demethylase Jmjd2a In Complex With T11c
Peptide Substrate Crosslinked To N-Oxalyl-D-Cysteine
pdb|3U4S|B Chain B, Histone Lysine Demethylase Jmjd2a In Complex With T11c
Peptide Substrate Crosslinked To N-Oxalyl-D-Cysteine
pdb|3RVH|A Chain A, Crystal Structure Of Jmjd2a Complexed With Inhibitor
pdb|3RVH|B Chain B, Crystal Structure Of Jmjd2a Complexed With Inhibitor
pdb|4GD4|A Chain A, Crystal Structure Of Jmjd2a Complexed With Inhibitor
pdb|4GD4|B Chain B, Crystal Structure Of Jmjd2a Complexed With Inhibitor
pdb|4AI9|A Chain A, Jmjd2a Complexed With Daminozide
pdb|4AI9|B Chain B, Jmjd2a Complexed With Daminozide
Length = 381
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 15/73 (20%)
Query: 53 IDPGKEDCFFQ-------YVNPGA---TFYVNFQVLRGGDGMAGF-----AVRNPNGQIV 97
+D G E+ +FQ +NP A TFY + R + A R ++V
Sbjct: 11 VDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVV 70
Query: 98 HPYEWKKNAEYQD 110
P EWK A Y D
Sbjct: 71 PPKEWKPRASYDD 83
>pdb|3NAF|A Chain A, Structure Of The Intracellular Gating Ring From The Human
High- Conductance Ca2+ Gated K+ Channel (Bk Channel)
Length = 798
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 167 VRTVERNINEILQQQYHARSREARDFNLLEDNNRYVMNWSVI 208
++ +E + EIL + YH + AR LL + +Y ++S +
Sbjct: 9 MKQIEDKLEEILSKLYHIENELARIKKLLGERKKYGGSYSAV 50
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
0.321 0.135 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,521,804
Number of Sequences: 62578
Number of extensions: 326375
Number of successful extensions: 754
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 748
Number of HSP's gapped (non-prelim): 10
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)