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= 007467
(602 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 = 572 bits (1475), Expect = e-163, Method: Compositional matrix adjust.
Identities = 264/382 (69%), Positives = 317/382 (82%)
Query: 49 FIIKPQSFTPSIDTSQWPILLKNYDRLNVRTGHYTPLPNGYSPLKRPLVDYIRYGIINLD 108
F+IKP++ S DTS+WP+LLKN+D+L VR+GHYTP+P G SPLKR L YI G+INLD
Sbjct: 6 FVIKPEAAGASTDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLD 65
Query: 109 KPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQQGAGKEYVC 168
KP+NPSSHEVVAWIKRILR EKTGHSGTLDPKVTG LIVCIDRATRLVKSQQGAGKEYVC
Sbjct: 66 KPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVC 125
Query: 169 VARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQLRIRTIYESKLLEYDVDRHLVV 228
+ RLHD + D + R+LE LTGA+FQRPPLISAVKRQLR+RTIYES L+E+D R+L V
Sbjct: 126 IVRLHDALKDEKDLGRSLENLTGALFQRPPLISAVKRQLRVRTIYESNLIEFDNKRNLGV 185
Query: 229 FWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDN 288
FW SCEAGTY+RT+C MQELRRVRSG L ENDNMVT+HDVMDAQW+YDN
Sbjct: 186 FWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDN 245
Query: 289 YRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVL 348
RDE+YLR +I PLE LL YKR+VVKD+ VNA+CYGAKLMIPGLLR+E IE+ +E+VL
Sbjct: 246 TRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVL 305
Query: 349 MTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRDTYPRKWGLGPRASMKKKLIAE 408
+TTKGEA+A+ IA+M+T +A+CDHGVVA +KR +M+RD YPR+WGLGP A KK++ A+
Sbjct: 306 ITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKAD 365
Query: 409 GKLDKHGKLNEKTPQEWARNVV 430
GKLDK+G++NE TP++W + V
Sbjct: 366 GKLDKYGRVNENTPEQWKKEYV 387
>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 = 263 bits (673), Expect = 2e-70, Method: Compositional matrix adjust.
Identities = 135/306 (44%), Positives = 194/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I+YG+INLDKP P+SHEVVAWIKRIL +EK GH GTLDPKV+G L V
Sbjct: 32 GFPPDKRPIELHIQYGVINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPV 91
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
++RATR+V++ AGKEYV + LH VP+ K+ ++ G + QRPPL SAVKR+L
Sbjct: 92 ALERATRVVQALLPAGKEYVALMHLHGDVPE-DKIRAVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE +D V+F + EAGTY+R++ M ELRR RSG
Sbjct: 151 RTRKVYYIEILE--IDGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMAELRRTRSGPF 208
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ +VT+HD++D + E Y+R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 209 KEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIKDSAVAAVAHGAN 268
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+++ I+ G+ V +MT K E VALG A M+T M G+ +++V M RD
Sbjct: 269 LTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGIAVDVEKVFMPRD 328
Query: 388 TYPRKW 393
YP+ W
Sbjct: 329 WYPKLW 334
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5
Nop10 Complex
Length = 357
Score = 261 bits (666), Expect = 1e-69, Method: Compositional matrix adjust.
Identities = 137/306 (44%), Positives = 190/306 (62%), Gaps = 4/306 (1%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G +P +R + D I+YG++ +DKP P+SHEV W+K+IL ++K GH GTLDPKVTG L V
Sbjct: 52 GCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPV 111
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
++RAT+ + KEYVC+ LH + + R + TG ++QRPPL +AVKR+L
Sbjct: 112 ALERATKTIPMWHIPPKEYVCLMHLHRDASE-EDILRVFKEFTGRIYQRPPLKAAVKRRL 170
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
RIR I+E +LL D D V+F + C++GTY+R +C MQELRR +SG
Sbjct: 171 RIRKIHELELL--DKDGKDVLFRVKCQSGTYIRKLCEDIGEALGTSAHMQELRRTKSGCF 228
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E D V + D++DA + DE LRRVI P+E L K++VVKD+ V+AIC+GA
Sbjct: 229 EEKD-AVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGLRHLKKVVVKDSAVDAICHGAD 287
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
+ + G+ + I GE V++ T KGEAVA+G A M T + D GV ++RV MDR
Sbjct: 288 VYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGVAVDVERVYMDRG 347
Query: 388 TYPRKW 393
TYPR W
Sbjct: 348 TYPRMW 353
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
Aca Trinucleotide
Length = 328
Score = 260 bits (664), Expect = 2e-69, Method: Compositional matrix adjust.
Identities = 130/306 (42%), Positives = 194/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTLDPKV+G L V
Sbjct: 25 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPV 84
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 85 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 143
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 144 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 201
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 202 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 261
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 262 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 321
Query: 388 TYPRKW 393
YP+ W
Sbjct: 322 WYPKLW 327
>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 = 259 bits (663), Expect = 2e-69, Method: Compositional matrix adjust.
Identities = 130/306 (42%), Positives = 194/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTLDPKV+G L V
Sbjct: 25 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPV 84
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 85 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 143
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 144 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 201
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 202 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 261
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 262 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 321
Query: 388 TYPRKW 393
YP+ W
Sbjct: 322 WYPKLW 327
>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 = 259 bits (662), Expect = 3e-69, Method: Compositional matrix adjust.
Identities = 130/306 (42%), Positives = 194/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTLDPKV+G L V
Sbjct: 32 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPV 91
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 92 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 151 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 208
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 209 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 268
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 269 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 328
Query: 388 TYPRKW 393
YP+ W
Sbjct: 329 WYPKLW 334
>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 = 259 bits (662), Expect = 3e-69, Method: Compositional matrix adjust.
Identities = 130/306 (42%), Positives = 194/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTLDPKV+G L V
Sbjct: 32 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPV 91
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 92 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 151 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 208
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 209 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 268
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 269 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 328
Query: 388 TYPRKW 393
YP+ W
Sbjct: 329 WYPKLW 334
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 256 bits (654), Expect = 2e-68, Method: Compositional matrix adjust.
Identities = 129/306 (42%), Positives = 193/306 (63%), Gaps = 3/306 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTL PKV+G L V
Sbjct: 28 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLPV 87
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 88 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 146
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 147 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 204
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 205 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 264
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 265 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 324
Query: 388 TYPRKW 393
YP+ W
Sbjct: 325 WYPKLW 330
>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 = 256 bits (654), Expect = 3e-68, Method: Compositional matrix adjust.
Identities = 129/304 (42%), Positives = 193/304 (63%), Gaps = 3/304 (0%)
Query: 88 GYSPLKRPLVDYIRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIV 147
G+ P KRP+ +I++G+INLDKP P+SHEVVAWIK+IL +EK GH GTLDPKV+G L V
Sbjct: 32 GFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPV 91
Query: 148 CIDRATRLVKSQQGAGKEYVCVARLHDKVPDVAKVARALEALTGAVFQRPPLISAVKRQL 207
+++ATR+V++ AGKEYV + LH VP+ K+ + ++ G + QRPPL SAVKR+L
Sbjct: 92 ALEKATRVVQALLPAGKEYVALMHLHGDVPE-DKIIQVMKEFEGEIIQRPPLRSAVKRRL 150
Query: 208 RIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXXXXXXXXXMQELRRVRSGIL 267
R R +Y ++LE ++ V+F + EAGTY+R++ M ELRR RSG
Sbjct: 151 RTRKVYYIEVLE--IEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPF 208
Query: 268 GENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTSYKRLVVKDTTVNAICYGAK 327
E++ ++T+HD++D + + E Y R+ I P+E + ++ +KD+ V A+ +GA
Sbjct: 209 KEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGAD 268
Query: 328 LMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARIKRVVMDRD 387
L +PG+ + I+ G+ V +MT K E VALG A MT+ M G+ +++V M RD
Sbjct: 269 LAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRD 328
Query: 388 TYPR 391
YP+
Sbjct: 329 WYPK 332
>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 = 186 bits (472), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 81/128 (63%), Positives = 108/128 (84%)
Query: 301 PLEVLLTSYKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGI 360
PLE LL YKR+VVKD+ VNA+CYGAKLMIPGLLR+E IE+ +E+VL+TTKGEA+A+ I
Sbjct: 67 PLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAI 126
Query: 361 AEMTTAVMATCDHGVVARIKRVVMDRDTYPRKWGLGPRASMKKKLIAEGKLDKHGKLNEK 420
A+M+T +A+CDHGVVA +KR +M+RD YPR+WGLGP A KK++ A+GKLDK+G++NE
Sbjct: 127 AQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNEN 186
Query: 421 TPQEWARN 428
TP++W +
Sbjct: 187 TPEQWKKE 194
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 34/55 (61%), Positives = 43/55 (78%)
Query: 49 FIIKPQSFTPSIDTSQWPILLKNYDRLNVRTGHYTPLPNGYSPLKRPLVDYIRYG 103
F+IKP++ S DTS+WP+LLKN+D+L VR+GHYTP+P G SPLKR L YI G
Sbjct: 12 FVIKPEAAGASTDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSG 66
>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 = 79.0 bits (193), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 68/229 (29%), Positives = 100/229 (43%), Gaps = 38/229 (16%)
Query: 103 GIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQQGA 162
GI+ +DKPA +SH+VV +RI + GH+GTLDP TG L++ I+RAT+++ A
Sbjct: 7 GIVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERATKILGLLTAA 66
Query: 163 GKEYVCVARLH-------------DKVP----DVAKVARALEALTGAVFQRPPLISAVK- 204
K Y RL VP + + A+E L G + Q P +SA+K
Sbjct: 67 PKSYAATIRLGQTTSTEDAEGQVLQSVPAKHLTIEAIDAAMERLRGEIRQVPSSVSAIKV 126
Query: 205 ---RQLRIRTIYESKLLE---YDVDRHLVV------------FWISCEAGTYVRTMCXXX 246
R R+ S LE +DR ++ I C +GTY+R +
Sbjct: 127 GGRRAYRLARQGRSVQLEARPIRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDL 186
Query: 247 XXXXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDNYRDEAYL 295
+ LRR R G E D ++ D+ + L + DEA L
Sbjct: 187 GDALGVGGHVTALRRTRVGRF-ELDQARSLDDLAERPALSLSL-DEACL 233
>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 = 77.0 bits (188), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 74/302 (24%), Positives = 134/302 (44%), Gaps = 44/302 (14%)
Query: 100 IRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQ 159
+++GI+ KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++
Sbjct: 1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFY 60
Query: 160 QGAGKEYVCVARL------HDKVPDVA----------KVARALEALTGAVFQRPPLISAV 203
+ K Y RL D +V ++ A+ + G Q PP SA
Sbjct: 61 KDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAK 120
Query: 204 K----------RQLRI-----RTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXX 248
K R+ +I + + K+ + +++ V F + GTY+R++C
Sbjct: 121 KYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGY 180
Query: 249 XXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTS 308
EL R V H + ++ +++ +E R I+PLE L
Sbjct: 181 KLGCGATAVELVR----------ESVGPHTIEESLNVFEAAPEEIENR--IIPLEKCLEW 228
Query: 309 YKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVM 368
R+VV + I G+++ + +L+ + + GE V + +G +AL AE ++ +
Sbjct: 229 LPRVVVHQESTKMILNGSQIHLE-MLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFL 287
Query: 369 AT 370
T
Sbjct: 288 ET 289
>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 = 77.0 bits (188), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 78/321 (24%), Positives = 141/321 (43%), Gaps = 46/321 (14%)
Query: 100 IRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQ 159
+++GI+ KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++
Sbjct: 1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFY 60
Query: 160 QGAGKEYVCVARL------HDKVPDVA----------KVARALEALTGAVFQRPPLISAV 203
+ K Y RL D +V ++ A+ + G Q PP SA
Sbjct: 61 KDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAK 120
Query: 204 K----------RQLRI-----RTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXX 248
K R+ +I + + K+ + +++ V F + GTY+R++C
Sbjct: 121 KYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGY 180
Query: 249 XXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTS 308
EL R V H + ++ +++ +E R I+PLE L
Sbjct: 181 KLGCGATAVELVR----------ESVGPHTIEESLNVFEAAPEEIENR--IIPLEKCLEW 228
Query: 309 YKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVM 368
R+VV + I G+++ + +L+ + + GE V + +G +AL AE ++ +
Sbjct: 229 LPRVVVHQESTKMILNGSQIHLE-MLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFL 287
Query: 369 ATCDHGVVARIKRVVMDRDTY 389
T R +RV+ R +
Sbjct: 288 ETLRKH--ERQRRVLTLRKVF 306
>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 = 77.0 bits (188), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 74/302 (24%), Positives = 134/302 (44%), Gaps = 44/302 (14%)
Query: 100 IRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQ 159
+++GI+ KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++
Sbjct: 1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFY 60
Query: 160 QGAGKEYVCVARL------HDKVPDVA----------KVARALEALTGAVFQRPPLISAV 203
+ K Y RL D +V ++ A+ + G Q PP SA
Sbjct: 61 KDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAK 120
Query: 204 K----------RQLRI-----RTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXX 248
K R+ +I + + K+ + +++ V F + GTY+R++C
Sbjct: 121 KYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGY 180
Query: 249 XXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTS 308
EL R V H + ++ +++ +E R I+PLE L
Sbjct: 181 KLGCGATAVELVR----------ESVGPHTIEESLNVFEAAPEEIENR--IIPLEKCLEW 228
Query: 309 YKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVM 368
R+VV + I G+++ + +L+ + + GE V + +G +AL AE ++ +
Sbjct: 229 LPRVVVHQESTKMILNGSQIHLE-MLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFL 287
Query: 369 AT 370
T
Sbjct: 288 ET 289
>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 = 75.5 bits (184), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 73/302 (24%), Positives = 134/302 (44%), Gaps = 44/302 (14%)
Query: 100 IRYGIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQ 159
+++GI+ KP P+SH+VV +++ L+ K GH GTLDP G LI+ +++ TR+++
Sbjct: 1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFY 60
Query: 160 QGAGKEYVCVARL------HDKVPDVA----------KVARALEALTGAVFQRPPLISAV 203
+ K + RL D +V ++ A+ + G Q PP SA
Sbjct: 61 KDLKKVFWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAK 120
Query: 204 K----------RQLRI-----RTIYESKLLEYDVDRHLVVFWISCEAGTYVRTMCXXXXX 248
K R+ +I + + K+ + +++ V F + GTY+R++C
Sbjct: 121 KYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGY 180
Query: 249 XXXXXXXMQELRRVRSGILGENDNMVTMHDVMDAQWLYDNYRDEAYLRRVIMPLEVLLTS 308
EL R V H + ++ +++ +E R I+PLE L
Sbjct: 181 KLGCGATAVELVR----------ESVGPHTIEESLNVFEAAPEEIENR--IIPLEKCLEW 228
Query: 309 YKRLVVKDTTVNAICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVM 368
R+VV + I G+++ + +L+ + + GE V + +G +AL AE ++ +
Sbjct: 229 LPRVVVHQESTKMILNGSQIHLE-MLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFL 287
Query: 369 AT 370
T
Sbjct: 288 ET 289
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase
Trub Bound To A T Stem-Loop Rna
Length = 327
Score = 72.4 bits (176), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 48/173 (27%), Positives = 78/173 (45%), Gaps = 35/173 (20%)
Query: 103 GIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQQGA 162
G++ LDKP SS++ + +KRI + GH+G LDP TG L +C+ AT+ + +
Sbjct: 26 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDS 85
Query: 163 GKEYVCVARLHDKVP----------------DVAKVARALEALTGAVFQRPPLISAVK-- 204
K Y +ARL + ++A AL+ G + Q P + SA+K
Sbjct: 86 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQ 145
Query: 205 ---------------RQLRIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTM 242
R+ R T+YE + ++ + + I C GTY+RT+
Sbjct: 146 GKKLYEYARQGIEVPREARPITVYELLFIRHEGNE--LELEIHCSKGTYIRTI 196
>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 = 72.4 bits (176), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 48/173 (27%), Positives = 78/173 (45%), Gaps = 35/173 (20%)
Query: 103 GIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQQGA 162
G++ LDKP SS++ + +KRI + GH+G LDP TG L +C+ AT+ + +
Sbjct: 13 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDS 72
Query: 163 GKEYVCVARLHDKVP----------------DVAKVARALEALTGAVFQRPPLISAVK-- 204
K Y +ARL + ++A AL+ G + Q P + SA+K
Sbjct: 73 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQ 132
Query: 205 ---------------RQLRIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTM 242
R+ R T+YE + ++ + + I C GTY+RT+
Sbjct: 133 GKKLYEYARQGIEVPREARPITVYELLFIRHEGNE--LELEIHCSKGTYIRTI 183
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding
Length = 327
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 47/173 (27%), Positives = 78/173 (45%), Gaps = 35/173 (20%)
Query: 103 GIINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGNLIVCIDRATRLVKSQQGA 162
G++ LDKP SS++ + +KRI + GH+G L+P TG L +C+ AT+ + +
Sbjct: 26 GVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALNPLATGMLPICLGEATKFSQYLLDS 85
Query: 163 GKEYVCVARLHDKVP----------------DVAKVARALEALTGAVFQRPPLISAVK-- 204
K Y +ARL + ++A AL+ G + Q P + SA+K
Sbjct: 86 DKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQ 145
Query: 205 ---------------RQLRIRTIYESKLLEYDVDRHLVVFWISCEAGTYVRTM 242
R+ R T+YE + ++ + + I C GTY+RT+
Sbjct: 146 GKKLYEYARQGIEVPREARPITVYELLFIRHEGNE--LELEIHCSKGTYIRTI 196
>pdb|1Q7H|A Chain A, Structure Of A Conserved Pua Domain Protein From
Thermoplasma Acidophilum
Length = 153
Score = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 322 ICYGAKLMIPGLLRFENDIEVGEEVVLMTTKGEAVALGIAEMTTAVMATCDHGVVARI 379
I G+ L PG++ ++ I G+ + + ++KG +A+G AE + G ARI
Sbjct: 83 ILNGSDLFAPGIVSXDDSIRKGDXIFVKSSKGYFIAVGXAEXDAGEVXATKRGKAARI 140
>pdb|2ZHX|A Chain A, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|C Chain C, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|E Chain E, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|G Chain G, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|I Chain I, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|K Chain K, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|2ZHX|M Chain M, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis In Complex With A
Proteinaceous Inhibitor
pdb|3A7N|A Chain A, Crystal Structure Of Uracil-Dna Glycosylase From
Mycobacterium Tuberculosis
Length = 238
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 55 SFTPSIDTSQWPILLKN-YDRLNVRTGHYTPLPNGYSPLKRPLVDYIRYGIINLDK---- 109
SF+ + D WP L N +D G+ PLP+ L + + G++ L++
Sbjct: 91 SFSVAPDVRPWPRSLANIFDEYTADLGY--PLPSNGD-----LTPWAQRGVLLLNRVLTV 143
Query: 110 -PANPSSHEVVAW 121
P+NP+SH W
Sbjct: 144 RPSNPASHRGKGW 156
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 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,042,771
Number of Sequences: 62578
Number of extensions: 498972
Number of successful extensions: 1142
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1096
Number of HSP's gapped (non-prelim): 21
length of query: 602
length of database: 14,973,337
effective HSP length: 104
effective length of query: 498
effective length of database: 8,465,225
effective search space: 4215682050
effective search space used: 4215682050
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: 54 (25.4 bits)