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= 009707
(528 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 172 bits (436), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 92/214 (42%), Positives = 124/214 (57%), Gaps = 4/214 (1%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V+++KP G TS V G GHAGTLDPMATG+L++ + +ATK++
Sbjct: 8 IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAAP 67
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y+ RLG+ TST DA+ V+Q P +H+ E I A RGEI QVP SAIKVG
Sbjct: 68 KSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKVG 127
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLI---FRVTCSKGTYIRSLCADF 487
G + Y AR+G S++L R I I +F++ + R LI + CS GTYIR+L D
Sbjct: 128 GRRAYRLARQGRSVQLEARPIRIDRFELL-AARRRDQLIDIDVEIDCSSGTYIRALARDL 186
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEE 521
G ALG H+TALRR +G++ D A +L E
Sbjct: 187 GDALGVGGHVTALRRTRVGRFELDQARSLDDLAE 220
>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 = 139 bits (351), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 81/204 (39%), Positives = 120/204 (58%), Gaps = 5/204 (2%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+++ KPKG TS V GH GTLDP A G+LI+ V + T++++ Y+ +
Sbjct: 5 ILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLK 64
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K
Sbjct: 65 KVYWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKYK 123
Query: 431 GEKMYDKARRGESIELSPRRISIFQF-DIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
GE++Y AR G+ I L P+R+ IF+ D+ ++E R ++ FRV S GTYIRSLC D G
Sbjct: 124 GERLYKLAREGKIINLPPKRVKIFKIWDV--NIEGR-DVSFRVEVSPGTYIRSLCMDIGY 180
Query: 490 ALGSCAHLTALRRDSIGQYSADDA 513
LG A L R+S+G ++ +++
Sbjct: 181 KLGCGATAVELVRESVGPHTIEES 204
>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 = 139 bits (351), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 81/204 (39%), Positives = 120/204 (58%), Gaps = 5/204 (2%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+++ KPKG TS V GH GTLDP A G+LI+ V + T++++ Y+ +
Sbjct: 5 ILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLK 64
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K
Sbjct: 65 KVYWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKYK 123
Query: 431 GEKMYDKARRGESIELSPRRISIFQF-DIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
GE++Y AR G+ I L P+R+ IF+ D+ ++E R ++ FRV S GTYIRSLC D G
Sbjct: 124 GERLYKLAREGKIINLPPKRVKIFKIWDV--NIEGR-DVSFRVEVSPGTYIRSLCMDIGY 180
Query: 490 ALGSCAHLTALRRDSIGQYSADDA 513
LG A L R+S+G ++ +++
Sbjct: 181 KLGCGATAVELVRESVGPHTIEES 204
>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 = 139 bits (351), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 81/204 (39%), Positives = 120/204 (58%), Gaps = 5/204 (2%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+++ KPKG TS V GH GTLDP A G+LI+ V + T++++ Y+ +
Sbjct: 5 ILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLK 64
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K
Sbjct: 65 KVYWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKYK 123
Query: 431 GEKMYDKARRGESIELSPRRISIFQF-DIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
GE++Y AR G+ I L P+R+ IF+ D+ ++E R ++ FRV S GTYIRSLC D G
Sbjct: 124 GERLYKLAREGKIINLPPKRVKIFKIWDV--NIEGR-DVSFRVEVSPGTYIRSLCMDIGY 180
Query: 490 ALGSCAHLTALRRDSIGQYSADDA 513
LG A L R+S+G ++ +++
Sbjct: 181 KLGCGATAVELVRESVGPHTIEES 204
>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 = 138 bits (348), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 80/204 (39%), Positives = 120/204 (58%), Gaps = 5/204 (2%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+++ KPKG TS V GH GTLDP A G+LI+ V + T++++ Y+ +
Sbjct: 5 ILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLK 64
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K + RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K
Sbjct: 65 KVFWVKMRLGLITETFDITGEVVEEREC-NVTEEEIREAIFSFVGEYDQVPPAYSAKKYK 123
Query: 431 GEKMYDKARRGESIELSPRRISIFQF-DIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
GE++Y AR G+ I L P+R+ IF+ D+ ++E R ++ FRV S GTYIRSLC D G
Sbjct: 124 GERLYKLAREGKIINLPPKRVKIFKIWDV--NIEGR-DVSFRVEVSPGTYIRSLCMDIGY 180
Query: 490 ALGSCAHLTALRRDSIGQYSADDA 513
LG A L R+S+G ++ +++
Sbjct: 181 KLGCGATAVELVRESVGPHTIEES 204
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
Trub Bound To A T Stem-Loop Rna
Length = 327
Score = 137 bits (346), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 73/213 (34%), Positives = 116/213 (54%), Gaps = 3/213 (1%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++L++KP+G +S GH G LDP+ATG+L +C+G+ATK
Sbjct: 27 VLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSD 86
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y + RLG+ T T DAD +++ P E + A +FRG+I Q+P M+SA+K
Sbjct: 87 KRYRVIARLGQRTDTSDADGQIVEERPVT-FSAEQLAAALDTFRGDIEQIPSMYSALKYQ 145
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKA 490
G+K+Y+ AR+G + R I++++ R + L + CSKGTYIR++ D G+
Sbjct: 146 GKKLYEYARQGIEVPREARPITVYELLFIR--HEGNELELEIHCSKGTYIRTIIDDLGEK 203
Query: 491 LGSCAHLTALRRDSIGQYSADDAWEFKELEEAI 523
LG AH+ LRR ++ +Y + + L E +
Sbjct: 204 LGCGAHVIYLRRLAVSKYPVERMVTLEHLRELV 236
>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 = 137 bits (345), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 73/213 (34%), Positives = 116/213 (54%), Gaps = 3/213 (1%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++L++KP+G +S GH G LDP+ATG+L +C+G+ATK
Sbjct: 14 VLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSD 73
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y + RLG+ T T DAD +++ P E + A +FRG+I Q+P M+SA+K
Sbjct: 74 KRYRVIARLGQRTDTSDADGQIVEERPVT-FSAEQLAAALDTFRGDIEQIPSMYSALKYQ 132
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKA 490
G+K+Y+ AR+G + R I++++ R + L + CSKGTYIR++ D G+
Sbjct: 133 GKKLYEYARQGIEVPREARPITVYELLFIR--HEGNELELEIHCSKGTYIRTIIDDLGEK 190
Query: 491 LGSCAHLTALRRDSIGQYSADDAWEFKELEEAI 523
LG AH+ LRR ++ +Y + + L E +
Sbjct: 191 LGCGAHVIYLRRLAVSKYPVERMVTLEHLRELV 223
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
Length = 327
Score = 136 bits (342), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 72/213 (33%), Positives = 116/213 (54%), Gaps = 3/213 (1%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++L++KP+G +S GH G L+P+ATG+L +C+G+ATK
Sbjct: 27 VLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALNPLATGMLPICLGEATKFSQYLLDSD 86
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y + RLG+ T T DAD +++ P E + A +FRG+I Q+P M+SA+K
Sbjct: 87 KRYRVIARLGQRTDTSDADGQIVEERPVT-FSAEQLAAALDTFRGDIEQIPSMYSALKYQ 145
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKA 490
G+K+Y+ AR+G + R I++++ R + L + CSKGTYIR++ D G+
Sbjct: 146 GKKLYEYARQGIEVPREARPITVYELLFIR--HEGNELELEIHCSKGTYIRTIIDDLGEK 203
Query: 491 LGSCAHLTALRRDSIGQYSADDAWEFKELEEAI 523
LG AH+ LRR ++ +Y + + L E +
Sbjct: 204 LGCGAHVIYLRRLAVSKYPVERMVTLEHLRELV 236
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5
Nop10 Complex
Length = 357
Score = 102 bits (254), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 68/213 (31%), Positives = 100/213 (46%), Gaps = 39/213 (18%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V+V+KP+G TS V GH GTLDP TG+L V + +ATK + +
Sbjct: 68 VVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPP 127
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y + L S +EDI + F G I+Q PP+ +A+K
Sbjct: 128 KEYVCLMHLHRDAS------------------EEDILRVFKEFTGRIYQRPPLKAAVK-- 167
Query: 431 GEKMYDKARRGESIELSPRRISIFQF-DIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
RR+ I + ++E +D ++++FRV C GTYIR LC D G+
Sbjct: 168 ------------------RRLRIRKIHELELLDKDGKDVLFRVKCQSGTYIRKLCEDIGE 209
Query: 490 ALGSCAHLTALRRDSIGQYSADDAWEFKELEEA 522
ALG+ AH+ LRR G + DA ++L +A
Sbjct: 210 ALGTSAHMQELRRTKSGCFEEKDAVYLQDLLDA 242
>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 = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 64/203 (31%), Positives = 97/203 (47%), Gaps = 36/203 (17%)
Query: 311 MVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP +S V GH+GTLDP TG LIVC+ +AT+LV QG
Sbjct: 61 VINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAG 120
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDE-DIRKAAASFRGEIWQVPPMFSAIKV 429
K Y + RL +A +KDE D+ ++ + G ++Q PP+ SA+K
Sbjct: 121 KEYVCIVRLHDA------------------LKDEKDLGRSLENLTGALFQRPPLISAVK- 161
Query: 430 GGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGK 489
+ R +I S ++ +FD +R+L +F +C GTY+R+LC G
Sbjct: 162 -------RQLRVRTIYES----NLIEFDNKRNLG-----VFWASCEAGTYMRTLCVHLGM 205
Query: 490 ALGSCAHLTALRRDSIGQYSADD 512
LG H+ LRR G S +D
Sbjct: 206 LLGVGGHMQELRRVRSGALSEND 228
>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 = 84.3 bits (207), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 64/199 (32%), Positives = 87/199 (43%), Gaps = 37/199 (18%)
Query: 314 VNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
++KP G TS V GH GTLDP +G+L V + +AT++V K Y
Sbjct: 51 LDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEY 110
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEK 433
+ L D P ++ IR F GEI Q PP+ SA+K
Sbjct: 111 VALMHL-------HGDVP-----------EDKIRAVMKEFEGEIIQRPPLRSAVK----- 147
Query: 434 MYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADFGKALGS 493
RR L R++ + IE D ++++FRV GTYIRSL G ALG
Sbjct: 148 -----RR-----LRTRKV----YYIEILEIDGRDVLFRVGVEAGTYIRSLIHHIGLALGV 193
Query: 494 CAHLTALRRDSIGQYSADD 512
AH+ LRR G + D+
Sbjct: 194 GAHMAELRRTRSGPFKEDE 212
>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 = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 69/221 (31%), Positives = 96/221 (43%), Gaps = 40/221 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTLDP +G+L V + KAT++V
Sbjct: 46 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALL 104
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 105 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 146
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 147 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 187
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
G ALG AH++ LRR G + D+ L + + YF
Sbjct: 188 GLALGVGAHMSELRRTRSGPFKEDET--LITLHDLVDYYYF 226
>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 = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 69/221 (31%), Positives = 96/221 (43%), Gaps = 40/221 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTLDP +G+L V + KAT++V
Sbjct: 46 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALL 104
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 105 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 146
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 147 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 187
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
G ALG AH++ LRR G + D+ L + + YF
Sbjct: 188 GLALGVGAHMSELRRTRSGPFKEDET--LITLHDLVDYYYF 226
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 69/221 (31%), Positives = 96/221 (43%), Gaps = 40/221 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTLDP +G+L V + KAT++V
Sbjct: 39 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALL 97
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 98 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 139
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 140 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 180
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
G ALG AH++ LRR G + D+ L + + YF
Sbjct: 181 GLALGVGAHMSELRRTRSGPFKEDET--LITLHDLVDYYYF 219
>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 = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 69/221 (31%), Positives = 96/221 (43%), Gaps = 40/221 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTLDP +G+L V + KAT++V
Sbjct: 46 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALL 104
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 105 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 146
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 147 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 187
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
G ALG AH++ LRR G + D+ L + + YF
Sbjct: 188 GLALGVGAHMSELRRTRSGPFKEDET--LITLHDLVDYYYF 226
>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 = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 69/221 (31%), Positives = 96/221 (43%), Gaps = 40/221 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTLDP +G+L V + KAT++V
Sbjct: 39 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALL 97
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 98 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 139
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 140 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 180
Query: 488 GKALGSCAHLTALRRDSIGQYSADDAWEFKELEEAITKNYF 528
G ALG AH++ LRR G + D+ L + + YF
Sbjct: 181 GLALGVGAHMSELRRTRSGPFKEDET--LITLHDLVDYYYF 219
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 65/205 (31%), Positives = 90/205 (43%), Gaps = 38/205 (18%)
Query: 308 FGTMVLVNKPKGWTSFTVCGXXXXXXXXXXXGHAGTLDPMATGLLIVCVGKATKLVDRYQ 367
FG + L +KP G TS V GH GTL P +G+L V + KAT++V
Sbjct: 42 FGVINL-DKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLPVALEKATRVVQALL 100
Query: 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAI 427
K Y + L D P ++ I + F GEI Q PP+ SA+
Sbjct: 101 PAGKEYVALMHL-------HGDVP-----------EDKIIQVMKEFEGEIIQRPPLRSAV 142
Query: 428 KVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRQNLIFRVTCSKGTYIRSLCADF 487
K RR L R++ + IE + ++++FRV GTYIRSL
Sbjct: 143 K----------RR-----LRTRKV----YYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHI 183
Query: 488 GKALGSCAHLTALRRDSIGQYSADD 512
G ALG AH++ LRR G + D+
Sbjct: 184 GLALGVGAHMSELRRTRSGPFKEDE 208
>pdb|3LXU|X Chain X, Crystal Structure Of Tripeptidyl Peptidase 2 (Tpp Ii)
Length = 1354
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 344 LDPMATGLLIVCVGKATKLVDRY 366
+DP ATGL +C GK K+++RY
Sbjct: 47 VDPRATGLETLCDGKTVKVIERY 69
>pdb|4ESW|A Chain A, Crystal Structure Of C. Albicans Thi5 H66g Mutant
pdb|4ESW|B Chain B, Crystal Structure Of C. Albicans Thi5 H66g Mutant
Length = 342
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 174 TFAYPWEKDKHYKMVYQLE-KKYFPDQCLDKAFLDPSADQNVKKM 217
TF WE ++ VY K YF D+ LD A L+PS +V ++
Sbjct: 10 TFLLNWEAAPYHIPVYLANIKGYFKDENLDIAILEPSNPSDVTEL 54
>pdb|4ESX|A Chain A, Crystal Structure Of C. Albicans Thi5 Complexed With Plp
pdb|4ESX|B Chain B, Crystal Structure Of C. Albicans Thi5 Complexed With Plp
Length = 342
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 174 TFAYPWEKDKHYKMVYQLE-KKYFPDQCLDKAFLDPSADQNVKKM 217
TF WE ++ VY K YF D+ LD A L+PS +V ++
Sbjct: 10 TFLLNWEAAPYHIPVYLANIKGYFKDENLDIAILEPSNPSDVTEL 54
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 0.134 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,993,768
Number of Sequences: 62578
Number of extensions: 613182
Number of successful extensions: 1527
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1474
Number of HSP's gapped (non-prelim): 23
length of query: 528
length of database: 14,973,337
effective HSP length: 103
effective length of query: 425
effective length of database: 8,527,803
effective search space: 3624316275
effective search space used: 3624316275
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 54 (25.4 bits)