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= psy14851
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A0C|A Chain A, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|B Chain B, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 1253
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 38 ALQPRALIVYGCICLCIPANNTIFIKSISE---TLAKNEPHLTLEFLEECISGFKQSTIV 94
A++ R +I G L + N +F+ I L+KN+ T +CI+ +
Sbjct: 213 AVRKRTIIALGH--LVMSCGNIVFVDLIEHLLSELSKNDSMSTTRTYIQCIAAISRQA-- 268
Query: 95 LKHLCLEYMTPWLPNLVKFCKQSDEGKRQ 123
H EY+ +P +VKFC D+ R+
Sbjct: 269 -GHRIGEYLEKIIPLVVKFCNVDDDELRE 296
>pdb|1U6G|C Chain C, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
Length = 1230
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 38 ALQPRALIVYGCICLCIPANNTIFIKSISE---TLAKNEPHLTLEFLEECISGFKQSTIV 94
A++ R +I G L + N +F+ I L+KN+ T +CI+ +
Sbjct: 190 AVRKRTIIALGH--LVMSCGNIVFVDLIEHLLSELSKNDSMSTTRTYIQCIAAISRQA-- 245
Query: 95 LKHLCLEYMTPWLPNLVKFCKQSDEGKRQ 123
H EY+ +P +VKFC D+ R+
Sbjct: 246 -GHRIGEYLEKIIPLVVKFCNVDDDELRE 273
>pdb|3RIT|A Chain A, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg And Dipeptide
L-Arg-D-Lys
pdb|3RIT|B Chain B, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg And Dipeptide
L-Arg-D-Lys
pdb|3RIT|C Chain C, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg And Dipeptide
L-Arg-D-Lys
pdb|3RIT|D Chain D, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg And Dipeptide
L-Arg-D-Lys
pdb|3RIT|E Chain E, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg And Dipeptide
L-Arg-D-Lys
pdb|3RO6|B Chain B, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
pdb|3RO6|A Chain A, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
pdb|3RO6|C Chain C, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
pdb|3RO6|D Chain D, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
pdb|3RO6|E Chain E, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
pdb|3RO6|F Chain F, Crystal Structure Of Dipeptide Epimerase From
Methylococcus Capsulatus Complexed With Mg Ion
Length = 356
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 54 IPANNTIFIKSISETLAKNEPHLTLEF 80
+P + TI IK + ETLA+ HL L F
Sbjct: 130 LPTSVTIGIKPVEETLAEAREHLALGF 156
>pdb|4GWP|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|B Chain B, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 687
Score = 28.5 bits (62), Expect = 2.6, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 69 LAKNEPHLTLEFLEECISGFKQSTIVLKHLCLEYMTPWLPNLVK 112
LA NE L LEF+ +S K+ST + M+P+L +VK
Sbjct: 213 LAMNESSLALEFVSLLLSSVKEST------GMSSMSPFLRKVVK 250
>pdb|3MK4|A Chain A, X-Ray Structure Of Human Pex3 In Complex With A Pex19
Derived Peptide
Length = 334
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 145 PSIQAKIWGSIGQVHLIRSACQVYL--IVCVLIRYQVDLIGRPDQVYLSGLRDGLPG 199
PS + +IW + + RS VY ++ VL+R Q+++IG +YL G G
Sbjct: 58 PSNKLEIWEDLKIISFTRSTVAVYSTCMLVVLLRVQLNIIG--GYIYLDNAAVGKNG 112
>pdb|3AJB|A Chain A, Crystal Structure Of Human Pex3p In Complex With
N-Terminal Pex19p Peptide
Length = 330
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 145 PSIQAKIWGSIGQVHLIRSACQVYL--IVCVLIRYQVDLIGRPDQVYLSGLRDGLPG 199
PS + +IW + + RS VY ++ VL+R Q+++IG +YL G G
Sbjct: 54 PSNKLEIWEDLKIISFTRSTVAVYSTCMLVVLLRVQLNIIG--GYIYLDNAAVGKNG 108
>pdb|1XAP|A Chain A, Structure Of The Ligand Binding Domain Of The Retinoic
Acid Receptor Beta
pdb|4DM6|A Chain A, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM6|B Chain B, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM8|A Chain A, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
pdb|4DM8|B Chain B, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
Length = 267
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 12/98 (12%)
Query: 105 PWLPNLVKFCKQSDEGKRQQRVLGIMTKLIELTIKEVEMYPSIQAKIWGSIG-----QVH 159
P L L K+ S R + LG+ K EL K + ++ G G Q+
Sbjct: 46 PSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQIT 105
Query: 160 LIRSACQVYLIVCVLIRYQVDLIGRPDQVYLSGLRDGL 197
L+++AC LI+ + RY P+Q ++ DGL
Sbjct: 106 LLKAACLDILILRICTRYT------PEQDTMT-FSDGL 136
>pdb|1XDK|B Chain B, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
pdb|1XDK|F Chain F, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
Length = 303
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 12/98 (12%)
Query: 105 PWLPNLVKFCKQSDEGKRQQRVLGIMTKLIELTIKEVEMYPSIQAKIWGSIG-----QVH 159
P L L K+ S R + LG+ K EL K + ++ G G Q+
Sbjct: 48 PSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQIT 107
Query: 160 LIRSACQVYLIVCVLIRYQVDLIGRPDQVYLSGLRDGL 197
L+++AC LI+ + RY P+Q ++ DGL
Sbjct: 108 LLKAACLDILILRICTRYT------PEQDTMT-FSDGL 138
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
0.325 0.141 0.450
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,481,736
Number of Sequences: 62578
Number of extensions: 248646
Number of successful extensions: 667
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 666
Number of HSP's gapped (non-prelim): 9
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)