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= psy1176
(232 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U28|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From
Saccharomyces Cerevisiae
pdb|3UAI|A Chain A, Structure Of The Shq1-Cbf5-Nop10-Gar1 Complex From
Saccharomyces Cerevisiae
Length = 400
Score = 244 bits (622), Expect = 4e-65, Method: Compositional matrix adjust.
Identities = 122/216 (56%), Positives = 150/216 (69%), Gaps = 10/216 (4%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
NFDKL VR+ HYTP+P G SPL+R ++ YI +G +NLDKPSNPSSHEVVAWIKRILRCEK
Sbjct: 28 NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEK 87
Query: 61 TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
TGHSGTLDPK +GCLIVCIDRATRLVKSQQ AGKEY+ I +LH A+ K + +
Sbjct: 88 TGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDAL-------KDEKDLG 140
Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVR 180
+ L + G + P + + + T +SNLI D + G+ W C+AGTY+R
Sbjct: 141 RSLENLTGALFQRPPLISAVKRQL---RVRTIYESNLIEFDNKRNLGVFWASCEAGTYMR 197
Query: 181 TYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTF 216
T CVH+G++LGVG M ELRR RSG SE D +VT
Sbjct: 198 TLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTL 233
Score = 34.3 bits (77), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 16/30 (53%), Positives = 19/30 (63%)
Query: 112 ASKKKMMIKQGLLDKHGKPNENTPASYLAE 141
A KKK M G LDK+G+ NENTP + E
Sbjct: 356 AQKKKQMKADGKLDKYGRVNENTPEQWKKE 385
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
pdb|2AUS|A Chain A, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5
Complex
Length = 334
Score = 150 bits (379), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 88/204 (43%), Positives = 118/204 (57%), Gaps = 21/204 (10%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIKRIL EK GH GTLDPK SG L
Sbjct: 31 WGFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLP 90
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAV-ENVAKASKKKM---MIKQGLLDKHGKPNE 132
V ++RATR+V++ AGKEY+++ LH V E+ +A K+ +I++ L K
Sbjct: 91 VALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRAVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 133 NTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGV 192
T Y E+ + DV G+ +AGTY+R+ H+GL LGV
Sbjct: 151 RTRKVYYIEI------------LEIDGRDVLFRVGV-----EAGTYIRSLIHHIGLALGV 193
Query: 193 GAQMIELRRNRSGIQSEEDGLVTF 216
GA M ELRR RSG E++ LVT
Sbjct: 194 GAHMAELRRTRSGPFKEDETLVTL 217
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
pdb|3HJY|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 327
Score = 144 bits (362), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 82/205 (40%), Positives = 115/205 (56%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTLDPK SG L
Sbjct: 24 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLP 83
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 84 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 143
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 144 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 185
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 186 VGAHMSELRRTRSGPFKEDETLITL 210
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 144 bits (362), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 82/205 (40%), Positives = 115/205 (56%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTLDPK SG L
Sbjct: 24 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLP 83
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 84 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 143
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 144 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 185
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 186 VGAHMSELRRTRSGPFKEDETLITL 210
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
pdb|2EY4|B Chain B, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
Length = 333
Score = 143 bits (361), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 82/205 (40%), Positives = 115/205 (56%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTLDPK SG L
Sbjct: 31 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLP 90
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 91 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 151 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 192
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 193 VGAHMSELRRTRSGPFKEDETLITL 217
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
Length = 340
Score = 143 bits (361), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 82/205 (40%), Positives = 115/205 (56%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTLDPK SG L
Sbjct: 31 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLP 90
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 91 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 151 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 192
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 193 VGAHMSELRRTRSGPFKEDETLITL 217
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|A Chain A, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|A Chain A, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 346
Score = 143 bits (361), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 82/205 (40%), Positives = 115/205 (56%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTLDPK SG L
Sbjct: 31 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLP 90
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 91 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 151 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 192
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 193 VGAHMSELRRTRSGPFKEDETLITL 217
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 140 bits (352), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 81/205 (39%), Positives = 114/205 (55%), Gaps = 23/205 (11%)
Query: 17 FGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLI 76
+G P +R I+ +I+ G +NLDKP P+SHEVVAWIK+IL EK GH GTL PK SG L
Sbjct: 27 WGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLP 86
Query: 77 VCIDRATRLVKSQQSAGKEYISIFKLHSAVE-----NVAKASKKKMMIKQGLLDKHGKPN 131
V +++ATR+V++ AGKEY+++ LH V V K + +++ + L +
Sbjct: 87 VALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRL 146
Query: 132 ENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLG 191
Y+ LE + DV G+ +AGTY+R+ H+GL LG
Sbjct: 147 RTRKVYYIEVLE-------------IEGRDVLFRVGV-----EAGTYIRSLIHHIGLALG 188
Query: 192 VGAQMIELRRNRSGIQSEEDGLVTF 216
VGA M ELRR RSG E++ L+T
Sbjct: 189 VGAHMSELRRTRSGPFKEDETLITL 213
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5
Nop10 Complex
Length = 357
Score = 118 bits (296), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 73/214 (34%), Positives = 113/214 (52%), Gaps = 19/214 (8%)
Query: 3 DKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTG 62
++L V+ T +G +P +R I++ I+ G V +DKP P+SHEV W+K+IL +K G
Sbjct: 37 EELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAG 96
Query: 63 HSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLH--SAVENVAKASKKKMMIK 120
H GTLDPK +G L V ++RAT+ + KEY+ + LH ++ E++ + K+
Sbjct: 97 HGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKEFT--- 153
Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMK-SNLISSDVTLSTGIIWLKCQAGTYV 179
G+ + P L+AA ++ K L D + +KCQ+GTY+
Sbjct: 154 -------GRIYQRPP------LKAAVKRRLRIRKIHELELLDKDGKDVLFRVKCQSGTYI 200
Query: 180 RTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGL 213
R C +G LG A M ELRR +SG E+D +
Sbjct: 201 RKLCEDIGEALGTSAHMQELRRTKSGCFEEKDAV 234
>pdb|1SGV|A Chain A, Structure Of Trna Psi55 Pseudouridine Synthase (Trub)
pdb|1SGV|B Chain B, Structure Of Trna Psi55 Pseudouridine Synthase (Trub)
Length = 316
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 57/206 (27%), Positives = 92/206 (44%), Gaps = 40/206 (19%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G V +DKP+ +SH+VV +RI + GH+GTLDP +G L++ I+RAT+++ +A
Sbjct: 7 GIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAA 66
Query: 93 GKEYISIFKL------HSAVENVAKASKKKMMIKQGL---LDKHGKPNENTPASYLA--- 140
K Y + +L A V ++ K + + + +++ P+S A
Sbjct: 67 PKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKV 126
Query: 141 ---------------ELEAAPNKKPTY------MKSNLISSDVTLSTGIIWLKCQAGTYV 179
+LEA P + + + LI DV + C +GTY+
Sbjct: 127 GGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDV-------EIDCSSGTYI 179
Query: 180 RTYCVHMGLVLGVGAQMIELRRNRSG 205
R +G LGVG + LRR R G
Sbjct: 180 RALARDLGDALGVGGHVTALRRTRVG 205
>pdb|1R3E|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
Its Rna Complex: Rna-Protein Recognition Through A
Combination Of Rigid Docking And Induced Fit
Length = 309
Score = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 54/204 (26%), Positives = 90/204 (44%), Gaps = 31/204 (15%)
Query: 39 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY-- 96
KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++ + K Y
Sbjct: 10 KPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWV 69
Query: 97 -------ISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASY----------- 138
F + V + + + I++ + G+ ++ PA
Sbjct: 70 KMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYK 129
Query: 139 LAELEAAPNKKPTYMK------SNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGV 192
LA N P +K N+ DV+ ++ GTY+R+ C+ +G LG
Sbjct: 130 LAREGKIINLPPKRVKIFKIWDVNIEGRDVSFR-----VEVSPGTYIRSLCMDIGYKLGC 184
Query: 193 GAQMIELRRNRSGIQSEEDGLVTF 216
GA +EL R G + E+ L F
Sbjct: 185 GATAVELVRESVGPHTIEESLNVF 208
>pdb|1ZE1|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|C Chain C, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|D Chain D, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 54/204 (26%), Positives = 90/204 (44%), Gaps = 31/204 (15%)
Query: 39 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY-- 96
KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++ + K Y
Sbjct: 10 KPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWV 69
Query: 97 -------ISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASY----------- 138
F + V + + + I++ + G+ ++ PA
Sbjct: 70 KMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYK 129
Query: 139 LAELEAAPNKKPTYMK------SNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGV 192
LA N P +K N+ DV+ ++ GTY+R+ C+ +G LG
Sbjct: 130 LAREGKIINLPPKRVKIFKIWDVNIEGRDVSFR-----VEVSPGTYIRSLCMDIGYKLGC 184
Query: 193 GAQMIELRRNRSGIQSEEDGLVTF 216
GA +EL R G + E+ L F
Sbjct: 185 GATAVELVRESVGPHTIEESLNVF 208
>pdb|1ZE2|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE2|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 71.6 bits (174), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 54/204 (26%), Positives = 90/204 (44%), Gaps = 31/204 (15%)
Query: 39 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY-- 96
KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++ + K Y
Sbjct: 10 KPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWV 69
Query: 97 -------ISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASY----------- 138
F + V + + + I++ + G+ ++ PA
Sbjct: 70 KMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYK 129
Query: 139 LAELEAAPNKKPTYMK------SNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGV 192
LA N P +K N+ DV+ ++ GTY+R+ C+ +G LG
Sbjct: 130 LAREGKIINLPPKRVKIFKIWDVNIEGRDVSFR-----VEVSPGTYIRSLCMDIGYKLGC 184
Query: 193 GAQMIELRRNRSGIQSEEDGLVTF 216
GA +EL R G + E+ L F
Sbjct: 185 GATAVELVRESVGPHTIEESLNVF 208
>pdb|2AB4|A Chain A, Dissecting The Roles Of A Strictly Conserved Tyrosine In
Substrate Recognition And Catalysis By Pseudouridine 55
Synthase
Length = 309
Score = 70.5 bits (171), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 53/204 (25%), Positives = 90/204 (44%), Gaps = 31/204 (15%)
Query: 39 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEY-- 96
KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++ + K +
Sbjct: 10 KPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVFWV 69
Query: 97 -------ISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASY----------- 138
F + V + + + I++ + G+ ++ PA
Sbjct: 70 KMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYK 129
Query: 139 LAELEAAPNKKPTYMK------SNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGV 192
LA N P +K N+ DV+ ++ GTY+R+ C+ +G LG
Sbjct: 130 LAREGKIINLPPKRVKIFKIWDVNIEGRDVSFR-----VEVSPGTYIRSLCMDIGYKLGC 184
Query: 193 GAQMIELRRNRSGIQSEEDGLVTF 216
GA +EL R G + E+ L F
Sbjct: 185 GATAVELVRESVGPHTIEESLNVF 208
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
Trub Bound To A T Stem-Loop Rna
Length = 327
Score = 60.8 bits (146), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 52/191 (27%), Positives = 82/191 (42%), Gaps = 23/191 (12%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP SS++ + +KRI + GH+G LDP +G L +C+ AT+ + +
Sbjct: 26 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDS 85
Query: 93 GKEYISIFKL------HSAVENVAKASKKKMMIKQ--GLLDKHGKPNENTPASYLAELEA 144
K Y I +L A + + +Q LD E P+ Y A L+
Sbjct: 86 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSA-LKY 144
Query: 145 APNKKPTYMKSNL----ISSDVTLSTGI----------IWLKCQAGTYVRTYCVHMGLVL 190
K Y + + + +T+ + + + C GTY+RT +G L
Sbjct: 145 QGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKL 204
Query: 191 GVGAQMIELRR 201
G GA +I LRR
Sbjct: 205 GCGAHVIYLRR 215
>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
Its Rna Complex: Rna-Protein Recognition Through A
Combination Of Rigid Docking And Induced Fit
Length = 314
Score = 60.5 bits (145), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 52/191 (27%), Positives = 82/191 (42%), Gaps = 23/191 (12%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP SS++ + +KRI + GH+G LDP +G L +C+ AT+ + +
Sbjct: 13 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDS 72
Query: 93 GKEYISIFKL------HSAVENVAKASKKKMMIKQ--GLLDKHGKPNENTPASYLAELEA 144
K Y I +L A + + +Q LD E P+ Y A L+
Sbjct: 73 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSA-LKY 131
Query: 145 APNKKPTYMKSNL----ISSDVTLSTGI----------IWLKCQAGTYVRTYCVHMGLVL 190
K Y + + + +T+ + + + C GTY+RT +G L
Sbjct: 132 QGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKL 191
Query: 191 GVGAQMIELRR 201
G GA +I LRR
Sbjct: 192 GCGAHVIYLRR 202
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
Length = 327
Score = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 51/191 (26%), Positives = 82/191 (42%), Gaps = 23/191 (12%)
Query: 33 GYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSA 92
G + LDKP SS++ + +KRI + GH+G L+P +G L +C+ AT+ + +
Sbjct: 26 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALNPLATGMLPICLGEATKFSQYLLDS 85
Query: 93 GKEYISIFKL------HSAVENVAKASKKKMMIKQ--GLLDKHGKPNENTPASYLAELEA 144
K Y I +L A + + +Q LD E P+ Y A L+
Sbjct: 86 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSA-LKY 144
Query: 145 APNKKPTYMKSNL----ISSDVTLSTGI----------IWLKCQAGTYVRTYCVHMGLVL 190
K Y + + + +T+ + + + C GTY+RT +G L
Sbjct: 145 QGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKL 204
Query: 191 GVGAQMIELRR 201
G GA +I LRR
Sbjct: 205 GCGAHVIYLRR 215
>pdb|3ZV0|C Chain C, Structure Of The Shq1p-Cbf5p Complex
pdb|3ZV0|D Chain D, Structure Of The Shq1p-Cbf5p Complex
Length = 195
Score = 57.4 bits (137), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 51/170 (30%), Positives = 71/170 (41%), Gaps = 38/170 (22%)
Query: 1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAG-----------YVNLDKPSNPSSHEVV 49
NFDKL VR+ HYTP+P G SPL+R ++ YI +G V D N +
Sbjct: 34 NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAK 93
Query: 50 AWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKL-HSAVEN 108
I +LR E+ ++ LI A + +Q S + + H V +
Sbjct: 94 LMIPGLLRYEE-----GIELYDEIVLITTKGEAIAVAIAQMST----VDLASCDHGVVAS 144
Query: 109 VAK-----------------ASKKKMMIKQGLLDKHGKPNENTPASYLAE 141
V + A KKK M G LDK+G+ NENTP + E
Sbjct: 145 VKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNENTPEQWKKE 194
>pdb|3U3P|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3Q|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3S|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3T|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
pdb|3U3V|A Chain A, The S-Sad Phased Crystal Structure Of The Ecto-Domain Of
Death Receptor 6 (Dr6)
Length = 313
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 149 KPTYMKSNLISS--DVTLSTGIIWL--KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRS 204
+P SNLI + V +TG + KC AGTYV +C + L + + R+ +
Sbjct: 1 QPEQKASNLIGTYRHVDRATGQVLTCDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHEN 60
Query: 205 GIQSEED 211
GI+ D
Sbjct: 61 GIEKCHD 67
>pdb|3QO4|A Chain A, The Crystal Structure Of Death Receptor 6
Length = 181
Score = 30.8 bits (68), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 149 KPTYMKSNLISS--DVTLSTGIIWL--KCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRS 204
+P SNLI + V +TG + KC AGTYV +C + L + + R+ +
Sbjct: 5 QPEQKASNLIGTYRHVDRATGQVLTCDKCPAGTYVSEHCTNTSLRVCSSCPVGTFTRHEN 64
Query: 205 GIQSEED 211
GI+ D
Sbjct: 65 GIEKCHD 71
>pdb|3PM6|A Chain A, Crystal Structure Of A Putative Fructose-1,6-Biphosphate
Aldolase From Coccidioides Immitis Solved By Combined
Sad Mr
pdb|3PM6|B Chain B, Crystal Structure Of A Putative Fructose-1,6-Biphosphate
Aldolase From Coccidioides Immitis Solved By Combined
Sad Mr
Length = 306
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 13/72 (18%)
Query: 68 DPKTSGCLIVCIDRATRLVKSQQSAGKEYISIF----------KLHSAVENVAKASKKKM 117
DP T CI+R V ++ EY+ + +LH V N +A+ +K+
Sbjct: 230 DPFTKEIFEKCIERGVAKVNVNRAVNNEYVKVMREKAGSLPITRLHEEVTNAMQAAVEKI 289
Query: 118 MIKQGLLDKHGK 129
M ++D GK
Sbjct: 290 M---DMIDSTGK 298
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 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,045,049
Number of Sequences: 62578
Number of extensions: 268835
Number of successful extensions: 516
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 477
Number of HSP's gapped (non-prelim): 34
length of query: 232
length of database: 14,973,337
effective HSP length: 96
effective length of query: 136
effective length of database: 8,965,849
effective search space: 1219355464
effective search space used: 1219355464
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)