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= psy1718
(142 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 112
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 39/56 (69%)
Query: 2 RPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLY 57
RPS KG TK F R+L+REV G APYEKR ELLKV KDKRALK KR++ +
Sbjct: 28 RPSDRKGKGTKRVHFVRNLIREVAGFAPYEKRITELLKVGKDKRALKVAKRKLGTH 83
>pdb|3IZS|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|II Chain i, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 100
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 35/51 (68%)
Query: 7 KGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLY 57
KG + TKF R LVRE+ G +PYE+R ++L++ S +KRA K K+R+ +
Sbjct: 30 KGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNSGEKRARKVAKKRLGSF 80
>pdb|3ZF7|MM Chain m, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 109
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 30/44 (68%)
Query: 12 KNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVS 55
K + + ++ ++ G +P E+R ELL+V KDKRALKF K+R+
Sbjct: 43 KKLRAVKAIISDLVGFSPMERRVQELLRVGKDKRALKFCKKRLG 86
>pdb|4A18|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 104
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 7 KGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKV--SKD-KRALKFLKRRVSLY 57
KG K R ++REV G APYEKR +EL+K +KD K+A K ++R+ +
Sbjct: 31 KGKLGKRVALVRQVIREVTGFAPYEKRIIELIKAGSAKDSKKATKIARKRLGTH 84
>pdb|3M7R|A Chain A, Crystal Structure Of Vdr H305q Mutant
Length = 253
Score = 29.3 bits (64), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 46/101 (45%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALK-FLKRRVSL---------YVLRSA 62
N FT D + CG+ Y+ R ++ K + ++ +K +V L +VL A
Sbjct: 106 NESFTMDDMSWTCGNQDYKYRVSDVTKAGQSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 165
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 166 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 199
>pdb|3P8X|A Chain A, Synthesis, Structure, And Biological Activity Of Des-Side
Chain Analogues Of 1alpha,25-Dihydroxyvitamin D3 With
Substituents At C-18
Length = 280
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 129 NESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 188
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 189 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 222
>pdb|3A2J|A Chain A, Crystal Structure Of The Human Vitamin D Receptor
(H305fH397F) LIGAND Binding Domain Complexed With
Tei-9647
Length = 263
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 112 NESFTMDDMSWTCGNQDYKYRVSDVTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 171
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 172 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 205
>pdb|1S0Z|A Chain A, Crystal Structure Of The Vdr Lbd Complexed To Seocalcitol.
pdb|1S19|A Chain A, Crystal Structure Of Vdr Ligand Binding Domain Complexed
To Calcipotriol.
pdb|1TXI|A Chain A, Crystal Structure Of The Vdr Ligand Binding Domain
Complexed To Tx522
pdb|2HAM|A Chain A, Crystal Structure Of Vdr Lbd Complexed To 2alpha-Propyl-
Calcitriol
pdb|2HAR|A Chain A, Crystal Structure Of Vdr Lbd In Complex With 2 Alpha-(3-
Hydroxy-1-Propoxy) Calcitriol
pdb|2HAS|A Chain A, Crystal Structure Of Vdr Lbd In Complex With 2alpha-(1-
Propoxy) Calcitriol
pdb|2HB7|A Chain A, Crystal Structure Of Vdr Lbd In Complex With 2alpha(3-
Hydroxy-1-Propyl) Calcitriol
pdb|2HB8|A Chain A, Crystal Structure Of Vdr Lbd In Complex With 2alpha-Methyl
Calcitriol
pdb|3CS4|A Chain A, Structure-Based Design Of A Superagonist Ligand For The
Vitamin D Nuclear Receptor
pdb|3CS6|A Chain A, Structure-Based Design Of A Superagonist Ligand For The
Vitamin D Nuclear Receptor
pdb|3A3Z|X Chain X, Crystal Structure Of The Human Vdr Ligand Binding Domain
Bound To The Synthetic Agonist Compound 2alpha-Methyl-
Amcr277a(C23s)
pdb|3A40|X Chain X, Crystal Structure Of The Human Vdr Ligand Binding Domain
Bound To The Synthetic Agonist Compound 2alpha-Methyl-
Amcr277b(C23r)
pdb|3A78|A Chain A, Crystal Structure Of The Human Vdr Ligand Binding Domain
Bound To The Natural Metabolite
1alpha,25-Dihydroxy-3-Epi-Vitamin D3
pdb|3AUQ|A Chain A, Crystal Structure Of The Human Vitamin D Receptor Ligand
Binding Domain Complexed With Yne-Diene Type Analog Of
Active 14-Epi-2alpha- Methyl-19-Norvitamin D3
pdb|3AUR|A Chain A, Crystal Structure Of The Human Vitamin D Receptor Ligand
Binding Domain Complexed With Yne-Diene Type Analog Of
Active 14-Epi-2beta- Methyl-19-Norvitamin D3
pdb|3AX8|A Chain A, Crystal Structure Of The Human Vitamin D Receptor Ligand
Binding Domain Complexed With
15alpha-Methoxy-1alpha,25-Dihydroxyvitamin D3
Length = 263
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 112 NESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 171
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 172 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 205
>pdb|3A2I|A Chain A, Crystal Structure Of The Human Vitamin D Receptor (H305f)
Ligand Binding Domain Complexed With Tei-9647
Length = 263
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 112 NESFTMDDMSWTCGNQDYKYRVSDVTKAGFSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 171
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 172 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 205
>pdb|1DB1|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D
Complexed To Vitamin D
pdb|1IE8|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D
Ligand Binding Domain Bound To Kh1060
pdb|1IE9|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D
Ligand Binding Domain Bound To Mc1288
pdb|3OGT|A Chain A, Design, Chemical Synthesis, Functional Characterization
And Crystal Structure Of The Sidechain Analogue Of
1,25-Dihydroxyvitamin D3.
pdb|3KPZ|A Chain A, Crystal Structure Of A Novel Vitamin D3 Analogue, Zk203278
Showing Dissociated Profile
pdb|3TKC|A Chain A, Design, Synthesis, Evaluation And Structure Of Vitamin D
Analogues With Furan Side Chains
pdb|4G2I|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
Length = 259
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 108 NESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 167
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 168 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 201
>pdb|3AZ1|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor
pdb|3AZ2|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor
pdb|3AZ3|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor
Length = 253
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 106 NESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 165
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 166 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 199
>pdb|3B0T|A Chain A, Human Vdr Ligand Binding Domain In Complex With
Maxacalcitol
Length = 254
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 18/101 (17%)
Query: 13 NTKFTRDLVREVCGHAPYEKRAMELLKVS----------KDKRALKFLKRRVSLYVLRSA 62
N FT D + CG+ Y+ R ++ K K + LK L +VL A
Sbjct: 107 NESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMA 166
Query: 63 V-VLCPTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKC 102
+ ++ P + D A + I+DR S+ Q T+++C
Sbjct: 167 ICIVSPDRPGVQDAALIEAIQDRLSNTLQ-------TYIRC 200
>pdb|1VSY|5 Chain 5, Proteasome Activator Complex
pdb|1VSY|8 Chain 8, Proteasome Activator Complex
pdb|3L5Q|6 Chain 6, Proteasome Activator Complex
pdb|3L5Q|8 Chain 8, Proteasome Activator Complex
Length = 997
Score = 28.1 bits (61), Expect = 1.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 67 PTKSRKFDRATRDIIRDRESSHFQLSQKIPTTFVKCESFYHNSIMLTWYK 116
P K + + +II++ E S L+ P F+K + FY S + W K
Sbjct: 696 PEKVDAYIKKQFEIIKNLEDSVVGLN---PQQFIKTDYFYRTSTIFYWIK 742
>pdb|1IRU|K Chain K, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
pdb|1IRU|Y Chain Y, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
Length = 201
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 48 KFLKRRVSLYVLRSAVVLCPTKSRKFD-RATRDIIRDRESSHFQL 91
+++++ V LY +R+ L PT + F R D +R R H L
Sbjct: 58 EYIQKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNL 102
>pdb|3UNB|J Chain J, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|X Chain X, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|LL Chain l, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|ZZ Chain z, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNE|J Chain J, Mouse Constitutive 20s Proteasome
pdb|3UNE|X Chain X, Mouse Constitutive 20s Proteasome
pdb|3UNE|LL Chain l, Mouse Constitutive 20s Proteasome
pdb|3UNE|ZZ Chain z, Mouse Constitutive 20s Proteasome
pdb|3UNF|J Chain J, Mouse 20s Immunoproteasome In Complex With Pr-957
pdb|3UNF|X Chain X, Mouse 20s Immunoproteasome In Complex With Pr-957
pdb|3UNH|J Chain J, Mouse 20s Immunoproteasome
pdb|3UNH|X Chain X, Mouse 20s Immunoproteasome
Length = 201
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 48 KFLKRRVSLYVLRSAVVLCPTKSRKFD-RATRDIIRDRESSHFQL 91
+++++ V LY +R+ L PT + F R D +R R H L
Sbjct: 58 EYIQKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNL 102
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 0.134 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,802,752
Number of Sequences: 62578
Number of extensions: 122240
Number of successful extensions: 381
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 377
Number of HSP's gapped (non-prelim): 15
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
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: 46 (22.3 bits)