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= psy15160
(366 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FU3|A Chain A, Cid Of Human Rprd1b
pdb|4FU3|B Chain B, Cid Of Human Rprd1b
Length = 135
Score = 136 bits (343), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 70/135 (51%), Positives = 88/135 (65%), Gaps = 1/135 (0%)
Query: 2 AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
+ F++SAL KL EL+ SQQS+QTLSLWLIHHRKH IV W E+ KA +RKLT +Y
Sbjct: 2 SSFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61
Query: 62 LANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQ 121
LANDVIQNSK+KGPE+ +EF VL AF V E + L R+LNIW+ER VY +
Sbjct: 62 LANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGGE 120
Query: 122 QIASFRTAFNAALEP 136
I + + + P
Sbjct: 121 FIQQLKLSXEDSKSP 135
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 193 EKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEP 230
E + L R+LNIW+ER VY + I + + + P
Sbjct: 98 EGCKKPLERLLNIWQERSVYGGEFIQQLKLSXEDSKSP 135
>pdb|4HFG|A Chain A, Cid Of Human Rprd1b
pdb|4HFG|B Chain B, Cid Of Human Rprd1b
Length = 135
Score = 135 bits (341), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 69/135 (51%), Positives = 87/135 (64%), Gaps = 1/135 (0%)
Query: 2 AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
+ F++SAL KL EL+ SQ S+QTLSLWLIHHRKH IV W E+ KA +RKLT +Y
Sbjct: 2 SSFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLY 61
Query: 62 LANDVIQNSKKKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDKQ 121
LANDVIQNSK+KGPE+ +EF VL AF V E + L R+LNIW+ER VY +
Sbjct: 62 LANDVIQNSKRKGPEFTREFESVLVDAFSHVAR-EADEGCKKPLERLLNIWQERSVYGGE 120
Query: 122 QIASFRTAFNAALEP 136
I + + + P
Sbjct: 121 FIQQLKLSMEDSKSP 135
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 193 EKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALEP 230
E + L R+LNIW+ER VY + I + + + P
Sbjct: 98 EGCKKPLERLLNIWQERSVYGGEFIQQLKLSMEDSKSP 135
>pdb|4FLB|A Chain A, Cid Of Human Rprd2
Length = 132
Score = 93.2 bits (230), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 53/134 (39%), Positives = 76/134 (56%), Gaps = 5/134 (3%)
Query: 2 AGFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEKADDHRKLTLMY 61
AG +S+L K + + + +SIQ LS W I ++KHHSTIV W+ + ++ +L L Y
Sbjct: 3 AGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFY 62
Query: 62 LANDVIQNSKKKGPEYGKE-FGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYDK 120
LANDVIQN K+K +E F VL +A V D S+ S+ RI IWE+R VY +
Sbjct: 63 LANDVIQNCKRKNAIIFRESFADVLPEAAALVKDPSVSK----SVERIFKIWEDRNVYPE 118
Query: 121 QQIASFRTAFNAAL 134
+ I + R A +
Sbjct: 119 EMIVALREALSTTF 132
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 198 SLSRILNIWEERGVYDKQQIASFRTAFNAAL 228
S+ RI IWE+R VY ++ I + R A +
Sbjct: 102 SVERIFKIWEDRNVYPEEMIVALREALSTTF 132
>pdb|4FLA|A Chain A, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
pdb|4FLA|B Chain B, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
pdb|4FLA|C Chain C, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
pdb|4FLA|D Chain D, Crystal Structure Of Human Rprd1b, Carboxy-Terminal Domain
Length = 152
Score = 72.4 bits (176), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 40/91 (43%), Positives = 57/91 (62%), Gaps = 8/91 (8%)
Query: 243 EVLYDVDELETSASSDANIREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLSIQV 302
E++ + +LE +AS DA +R+KIA LP EV ++ LL K+ D+ AAE LS V
Sbjct: 26 ELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKI--------TDKEAAERLSKTV 77
Query: 303 NEAVDLLTNYNTRLVTEMEDRKRASAMLKDY 333
+EA LL YN RL E+EDR++ + ML +Y
Sbjct: 78 DEACLLLAEYNGRLAAELEDRRQLARMLVEY 108
>pdb|2KM4|A Chain A, Solution Structure Of Rtt103 Ctd Interacting Domain
pdb|2L0I|A Chain A, Solution Structure Of Rtt103 Ctd-Interacting Domain Bound
To A Ser2 Phosphorylated Ctd Peptide
Length = 142
Score = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 38/136 (27%), Positives = 66/136 (48%), Gaps = 4/136 (2%)
Query: 3 GFTQSALISKLEELNASQQSIQTLSLWLIHHRKHHSTIVKTWIDEVEK--ADDHRKLTLM 60
F+ +KL L SQ+SI + S WL+ + + + W + + + + RKL +
Sbjct: 2 AFSSEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61
Query: 61 YLANDVIQNSK-KKGPEYGKEFGHVLKQAFVSVGDVHCSEKTRSSLSRILNIWEERGVYD 119
YL N V+Q +K +K ++ FG V + + + LSR++NI +ER ++
Sbjct: 62 YLMNHVVQQAKGQKIIQFQDSFGKVAAEVLGRINQ-EFPRDLKKKLSRVVNILKERNIFS 120
Query: 120 KQQIASFRTAFNAALE 135
KQ + + AALE
Sbjct: 121 KQVVNDIERSLAAALE 136
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 196 RSSLSRILNIWEERGVYDKQQIASFRTAFNAALE 229
+ LSR++NI +ER ++ KQ + + AALE
Sbjct: 103 KKKLSRVVNILKERNIFSKQVVNDIERSLAAALE 136
>pdb|2J0R|A Chain A, Structure Of The Haem-Chaperone Proteobacteria-Protein
Hems
Length = 345
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 54/125 (43%), Gaps = 19/125 (15%)
Query: 97 CSEKTRSSLSRILNIWEERG-----VYDKQQ---------IASFRTAFNA--ALEPQTKR 140
+E+TR + + ++ +G VY +Q +A F T N LEP +
Sbjct: 114 LTEETRHGVRHSIQFFDHQGDALHKVYVTEQTDMPAWEALLAQFITTENPELQLEPLSAP 173
Query: 141 RKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLS 200
+ T+ D + FF + +RN ++QAF +VG+ + SSL+
Sbjct: 174 EVTEPTATDEAVDAEWRAMTDVHQFFQL---LKRNNLTRQQAFRAVGNDLAYQVDNSSLT 230
Query: 201 RILNI 205
++LNI
Sbjct: 231 QLLNI 235
>pdb|2J0P|A Chain A, Structure Of The Haem-Chaperone Proteobacteria-Protein
Hems
Length = 345
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 54/125 (43%), Gaps = 19/125 (15%)
Query: 97 CSEKTRSSLSRILNIWEERG-----VYDKQQ---------IASFRTAFNA--ALEPQTKR 140
+E+TR + + ++ +G VY +Q +A F T N LEP +
Sbjct: 114 LTEETRHGVRHSIQFFDHQGDALHKVYVTEQTDMPAWEALLAQFITTENPELQLEPLSAP 173
Query: 141 RKLSESNTEVLYDVDGNVPIGYFTFFHIDGKGRRNKYDKKQAFVSVGDVHCSEKTRSSLS 200
+ T+ D + FF + +RN ++QAF +VG+ + SSL+
Sbjct: 174 EVTEPTATDEAVDAEWRAMTDVHEFFQL---LKRNNLTRQQAFRAVGNDLAYQVDNSSLT 230
Query: 201 RILNI 205
++LNI
Sbjct: 231 QLLNI 235
>pdb|2P5X|A Chain A, Crystal Structure Of Maf Domain Of Human N-Acetylserotonin
O- Methyltransferase-Like Protein
pdb|2P5X|B Chain B, Crystal Structure Of Maf Domain Of Human N-Acetylserotonin
O- Methyltransferase-Like Protein
Length = 230
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 41/105 (39%), Gaps = 20/105 (19%)
Query: 124 ASFRTAFNAALEPQTKRRKLSESNTEVLYDVDGNVP---IGYFTFFHIDGKGRRNKYDKK 180
ASF T + A+E K++ L +N LY D P IG T + G DK+
Sbjct: 40 ASFATPYGYAME-TAKQKALEVANR--LYQKDLRAPDVVIGADTIVTVGGLILEKPVDKQ 96
Query: 181 QA--------------FVSVGDVHCSEKTRSSLSRILNIWEERGV 211
A F V VHCS K +R+ +EE V
Sbjct: 97 DAYRMLSRLSGREHSVFTGVAIVHCSSKDHQLDTRVSEFYEETKV 141
>pdb|3QYQ|A Chain A, 1.8 Angstrom Resolution Crystal Structure Of A Putative
Deoxyribose- Phosphate Aldolase From Toxoplasma Gondii
Me49
pdb|3QYQ|B Chain B, 1.8 Angstrom Resolution Crystal Structure Of A Putative
Deoxyribose- Phosphate Aldolase From Toxoplasma Gondii
Me49
pdb|3QYQ|C Chain C, 1.8 Angstrom Resolution Crystal Structure Of A Putative
Deoxyribose- Phosphate Aldolase From Toxoplasma Gondii
Me49
pdb|3QYQ|D Chain D, 1.8 Angstrom Resolution Crystal Structure Of A Putative
Deoxyribose- Phosphate Aldolase From Toxoplasma Gondii
Me49
Length = 293
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 261 IREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLS 299
IR+++ K PEV+ I++ + V TG PD V+ E +
Sbjct: 71 IRQELVKSAPEVAGIKVCAAVNFPEGTGTPDTVSLEAVG 109
>pdb|4EIV|A Chain A, 1.37 Angstrom Resolution Crystal Structure Of Apo-Form Of
A Putative Deoxyribose-Phosphate Aldolase From
Toxoplasma Gondii Me49
pdb|4EIV|B Chain B, 1.37 Angstrom Resolution Crystal Structure Of Apo-Form Of
A Putative Deoxyribose-Phosphate Aldolase From
Toxoplasma Gondii Me49
Length = 297
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 261 IREKIAKLPPEVSEIQLLSKVQGKNITGQPDRVAAENLS 299
IR+++ K PEV+ I++ + V TG PD V+ E +
Sbjct: 70 IRQELVKSAPEVAGIKVCAAVNFPEGTGTPDTVSLEAVG 108
>pdb|3D9I|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9I|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
Length = 145
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 49/106 (46%), Gaps = 9/106 (8%)
Query: 35 KHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKE---FGHVLKQAFVS 91
K + +V++ ++K K+ +Y+ + +++ S+ ++G+E F +S
Sbjct: 38 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRH---QFGQEKDVFAPRFSNNIIS 94
Query: 92 VGD--VHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALE 135
C +S + R+LN+W++ V+ K +I AALE
Sbjct: 95 TFQNLYRCPGDDKSKIVRVLNLWQKNNVF-KSEIIQPLLDMAAALE 139
>pdb|3D9J|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9J|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9K|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9K|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9L|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9L|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9M|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9M|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9N|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9N|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
Length = 145
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 49/106 (46%), Gaps = 9/106 (8%)
Query: 35 KHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKE---FGHVLKQAFVS 91
K + +V++ ++K K+ +Y+ + +++ S+ ++G+E F +S
Sbjct: 38 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRH---QFGQEKDVFAPRFSNNIIS 94
Query: 92 VGD--VHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALE 135
C +S + R+LN+W++ V+ K +I AALE
Sbjct: 95 TFQNLYRCPGDDKSKIVRVLNLWQKNNVF-KSEIIQPLLDMAAALE 139
>pdb|3D9O|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9O|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
Length = 145
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 49/106 (46%), Gaps = 9/106 (8%)
Query: 35 KHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKKGPEYGKE---FGHVLKQAFVS 91
K + +V++ ++K K+ +Y+ + +++ S+ ++G+E F +S
Sbjct: 38 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRH---QFGQEKDVFAPRFSNNIIS 94
Query: 92 VGD--VHCSEKTRSSLSRILNIWEERGVYDKQQIASFRTAFNAALE 135
C +S + R+LN+W++ V+ K +I AALE
Sbjct: 95 TFQNLYRCPGDDKSKIVRVLNLWQKNNVF-KSEIIQPLLDXAAALE 139
>pdb|2DIW|A Chain A, Solution Structure Of The Rpr Domain Of Putative Rna-
Binding Protein 16
Length = 152
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/93 (19%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 35 KHHSTIVKTWIDEVEKADDHRKLTLMYLANDVIQNSKKK-GPE---YGKEFGHVLKQAFV 90
K + +V++ ++K K+ +Y+ + +++ S+ + G E + F + + F
Sbjct: 47 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQ 106
Query: 91 SVGDVHCSEKTRSSLSRILNIWEERGVYDKQQI 123
++ C +S + R+LN+W++ V+ + I
Sbjct: 107 NL--YRCPGDDKSKIVRVLNLWQKNNVFKSEII 137
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
0.315 0.130 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,491,192
Number of Sequences: 62578
Number of extensions: 356795
Number of successful extensions: 1425
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 1383
Number of HSP's gapped (non-prelim): 53
length of query: 366
length of database: 14,973,337
effective HSP length: 100
effective length of query: 266
effective length of database: 8,715,537
effective search space: 2318332842
effective search space used: 2318332842
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)