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= psy3754
(755 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 808 bits (2088), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 380/690 (55%), Positives = 529/690 (76%), Gaps = 1/690 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
L N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 7 LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 67 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 247 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 305
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 306 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 365
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 366 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 425
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 426 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 485
Query: 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 603
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 486 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 545
Query: 604 EVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIAS 663
+ + ++S+FAPR+ TIKI+P KI+DVIGKGGS IR LTEETGT I+I D+G + IA+
Sbjct: 546 AINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAA 605
Query: 664 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 723
+ + A RRIE++T +++G+VYTG V R+ DFGA + I GK+GL+HISQI+ KRV
Sbjct: 606 TDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRV 665
Query: 724 NIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
+TD+L+ Q+V VKVL +D +GRI+LS+
Sbjct: 666 EKVTDYLQMGQEVPVKVLEVDRQGRIRLSI 695
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 700 bits (1807), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 347/692 (50%), Positives = 489/692 (70%), Gaps = 3/692 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+F+ K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 74
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 75 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 134
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 135 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 194
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 195 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 253
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 361
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 254 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 313
Query: 362 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 421
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 314 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 373
Query: 422 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 481
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 433
Query: 482 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 541
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 434 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 493
Query: 542 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 494 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 553
Query: 602 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 661
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 554 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 613
Query: 662 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 721
++ + + A I+ +T+ +IGK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 722 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 674 RVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 705
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 700 bits (1806), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 346/692 (50%), Positives = 489/692 (70%), Gaps = 3/692 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+F+ K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 74
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 75 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 134
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 135 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 194
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 195 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 253
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 361
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 254 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 313
Query: 362 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 421
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 314 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 373
Query: 422 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 481
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 433
Query: 482 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 541
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 434 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 493
Query: 542 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 494 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 553
Query: 602 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 661
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 554 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 613
Query: 662 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 721
++ + + A I+ +T+ ++GK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 722 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 674 RVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 705
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 700 bits (1806), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 346/692 (50%), Positives = 489/692 (70%), Gaps = 3/692 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+F+ K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 6 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 65
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 66 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 125
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 126 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 185
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 186 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 244
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 361
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 245 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 304
Query: 362 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 421
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 305 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 364
Query: 422 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 481
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 365 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 424
Query: 482 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 541
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 425 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 484
Query: 542 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 485 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 544
Query: 602 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 661
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 545 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 604
Query: 662 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 721
++ + + A I+ +T+ ++GK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 605 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 664
Query: 722 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 753
RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 665 RVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 696
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 649 bits (1673), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 300/550 (54%), Positives = 421/550 (76%), Gaps = 1/550 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+ N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 299
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 603
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 604 EVPKCKNELS 613
+ + ++S
Sbjct: 540 AINAPRGDIS 549
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 648 bits (1672), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 300/550 (54%), Positives = 421/550 (76%), Gaps = 1/550 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
+ N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 299
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 603
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 604 EVPKCKNELS 613
+ + ++S
Sbjct: 540 AINAPRGDIS 549
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 647 bits (1669), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 300/542 (55%), Positives = 417/542 (76%), Gaps = 1/542 (0%)
Query: 64 LFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 123
L N I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 7 LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 124 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 183
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 67 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 184 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 243
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 244 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 303
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 304 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 363
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 247 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 305
Query: 364 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 423
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 306 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 365
Query: 424 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 483
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 366 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 425
Query: 484 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 543
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 426 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 485
Query: 544 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 603
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 486 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 545
Query: 604 EV 605
+
Sbjct: 546 AI 547
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 461 bits (1187), Expect = e-130, Method: Compositional matrix adjust.
Identities = 275/714 (38%), Positives = 408/714 (57%), Gaps = 34/714 (4%)
Query: 68 IIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVSCKDPTSTYNFFPLTVDY 126
+I + +G+ I E G +ARQA S + ++D T++L+ + K+P +FFPLTVD
Sbjct: 28 VIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDV 87
Query: 127 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 186
E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G NEIQ+V ++++NP
Sbjct: 88 EERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPD 147
Query: 187 IDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG-- 244
D+ +I S + ++ LPF GP+G +V I G+++ PT +L+ + D++VAG
Sbjct: 148 HLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRV 207
Query: 245 ---------------TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 289
TEK I V+ ++ E+++ + +K+ A +L
Sbjct: 208 LEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKA 267
Query: 290 GQKKVNWDPIVKD--KTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN 347
+ + P+ D ++ + ++ A I KQ R+ + L+
Sbjct: 268 AKPTGEF-PVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLL-- 324
Query: 348 ENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLF 407
+I+ L ++R++++ + RID RGV DIR ++ +PR HGS+LF
Sbjct: 325 PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALF 384
Query: 408 TRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGH 467
RG+TQ L V TL R EQ++D L +M +YN PP++ G+ GR+G PKRREIGH
Sbjct: 385 ERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGH 444
Query: 468 GRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAG 527
G LA+RA++PVLP +F Y+IR VSE SNGS+SM SVC ++LL+AGVP+ VAG
Sbjct: 445 GALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAG 504
Query: 528 IAMGLIK---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 583
IAMGLI +GE V L+DILG ED GDMDFKVAGT +TALQ+D K+ GI ++
Sbjct: 505 IAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 584 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTL 643
AL +A+ +IL+ M E +E+S APR+IT+KI KI +VIG I +
Sbjct: 565 AAALKQARDARLHILDVM-MEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQI 623
Query: 644 TEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVLRLFDFGA 701
E+TG +I I D+G I I + + + + A+ I + S ++G+ G V++ FGA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 702 IIRILSGKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 751
+ +L GKDGLLHISQI KRV + D L QKV+V++ ID RG++ L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 431 bits (1108), Expect = e-121, Method: Compositional matrix adjust.
Identities = 270/714 (37%), Positives = 399/714 (55%), Gaps = 34/714 (4%)
Query: 68 IIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVSCKDPTSTYNFFPLTVDY 126
+I + +G+ I E G +ARQA S + ++D T +L+ + K+P +FFPLTVD
Sbjct: 28 VIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTXVLSATTASKNPKDQLDFFPLTVDV 87
Query: 127 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 186
E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G NEIQ+V + ++NP
Sbjct: 88 EERXYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIXALNPD 147
Query: 187 IDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG-- 244
D+ +I S + ++ LPF GP+G +V I G+++ PT +L+ + D +VAG
Sbjct: 148 HLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDXVVAGRV 207
Query: 245 ---------------TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 289
TEK I V+ ++ E+++ + +K+ A +L
Sbjct: 208 LEDGDVAIXXVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKA 267
Query: 290 GQKKVNWDPIVKD--KTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN 347
+ + P+ D ++ + ++ A I KQ R+ + L+
Sbjct: 268 AKPTGEF-PVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLL-- 324
Query: 348 ENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLF 407
+I+ L ++R++++ + RID RGV DIR ++ +PR HGS+LF
Sbjct: 325 PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALF 384
Query: 408 TRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGH 467
RG+TQ L V TL R EQ++D L + +YN PP++ G+ GR+G PKRREIGH
Sbjct: 385 ERGETQILGVTTLNXLRXEQQLDTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGH 444
Query: 468 GRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAG 527
G LA+RA++PVLP +F Y+IR VSE SNGS+S SVC +LL+AGVP+ VAG
Sbjct: 445 GALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAG 504
Query: 528 IAMGLIK---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 583
IA GLI +GE V L+DILG ED GD DFKVAGT +TALQ+D K+ GI ++
Sbjct: 505 IAXGLISQEINGETHYVALTDILGAEDAFGDXDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 584 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTL 643
AL +A+ +IL+ + E +E S APR+IT+KI KI +VIG I +
Sbjct: 565 AAALKQARDARLHILD-VXXEAIDTPDEXSPNAPRIITVKIPVDKIGEVIGPKRQXINQI 623
Query: 644 TEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVLRLFDFGA 701
E+TG +I I D+G I I + + + + A+ I + S ++G+ G V++ FGA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 702 IIRILSGKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 751
+ +L GKDGLLHISQI KRV + D L QKV+V++ ID RG++ L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737
>pdb|3U1K|A Chain A, Crystal Structure Of Human Pnpase
pdb|3U1K|C Chain C, Crystal Structure Of Human Pnpase
pdb|3U1K|B Chain B, Crystal Structure Of Human Pnpase
pdb|3U1K|D Chain D, Crystal Structure Of Human Pnpase
Length = 630
Score = 375 bits (962), Expect = e-104, Method: Compositional matrix adjust.
Identities = 235/626 (37%), Positives = 355/626 (56%), Gaps = 27/626 (4%)
Query: 75 GSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAG 134
G+ K+ I G++AR A S +V DT ++ T VS P+ + F PL VDY +KA AAG
Sbjct: 13 GNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPS-QFMPLVVDYRQKAAAAG 71
Query: 135 RIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASI 194
RIP ++ +RE S++E + SR+IDR IRPLFP GY + Q++ +L+V+ +PD+ +I
Sbjct: 72 RIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLAI 131
Query: 195 IGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVE 253
G S ALS+S++P+ GP+G ++G IDG+Y++NPT +++ S L+L+VAG K+ I+ +E
Sbjct: 132 NGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVMLE 191
Query: 254 SESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINIS 313
+ ++ + + +AI G + + I I +LV+ G K + I K
Sbjct: 192 ASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYT--- 248
Query: 314 EHKI--RKAYQI-----KNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLES 366
HK+ + Y + +K RD I D L + D +I +
Sbjct: 249 -HKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQL-KEKFPEADPYEIIESFNVVAK 306
Query: 367 KIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS--- 423
++ R +L++ R D R + +R +S + HGS+LF RG TQ L T +
Sbjct: 307 EVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESG 366
Query: 424 -RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNN 482
+ +Q I A+ G +FMLHY PP+AT +IG++ RRE+GHG LA++AL PV+P +
Sbjct: 367 IKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRD 426
Query: 483 NKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLI--KDGEKVV 540
F ++IR+ SE+ ESNGSSSMAS CGG LAL+D+GVPIS VAG+A+GL+ D EK
Sbjct: 427 --FPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGE 484
Query: 541 I-----LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLS 595
I L+DILG ED GDMDFK+AGT GITALQ DIK+ GI I+ A+ +A
Sbjct: 485 IEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKK 544
Query: 596 YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 655
IL+ M + K + + P + T+++ SK +G GG ++ L ETG I D
Sbjct: 545 EILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD 604
Query: 656 EGIITIASFNSVSGQEAKRRIEKLTE 681
E ++ + + EA+ I ++ +
Sbjct: 605 EETFSVFAPTPSAMHEARDFITEICK 630
>pdb|3M7N|D Chain D, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|E Chain E, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|F Chain F, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M85|D Chain D, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|E Chain E, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|F Chain F, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
Length = 258
Score = 86.7 bits (213), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 72/240 (30%), Positives = 114/240 (47%), Gaps = 17/240 (7%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K I+D GLR+D R +++RPI I +L R GS G + ++ A G E +
Sbjct: 10 KLIVD-GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNK-VIAAVFGPR--EVHPE 65
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
L YNM PF+ + R G P RR I +++K A V+ +I
Sbjct: 66 HLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELFPRSAID 124
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ E+ +++ S A + +AL+DAGVP+ + +A+G DG+ V+ D + +ED
Sbjct: 125 IFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGK-ADGQLVL---DPMKEED 180
Query: 551 RCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
G+ D A G + I LQMD + +T D ++ A+ AKKG I E + +
Sbjct: 181 NFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYEMQREAI 237
>pdb|2BA0|F Chain F, Archaeal Exosome Core
pdb|2BA0|E Chain E, Archaeal Exosome Core
pdb|2BA0|D Chain D, Archaeal Exosome Core
pdb|2BA1|D Chain D, Archaeal Exosome Core
pdb|2BA1|E Chain E, Archaeal Exosome Core
pdb|2BA1|F Chain F, Archaeal Exosome Core
Length = 258
Score = 85.1 bits (209), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 72/240 (30%), Positives = 113/240 (47%), Gaps = 17/240 (7%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K I+D GLR+D R +++RPI I +L R GS G + ++ A G E
Sbjct: 10 KLIVD-GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNK-VIAAVFGPR--EVHPR 65
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
L YNM PF+ + R G P RR I +++K A V+ +I
Sbjct: 66 HLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELFPRSAID 124
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ E+ +++ S A + +AL+DAGVP+ + +A+G DG+ V+ D + +ED
Sbjct: 125 IFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-DGQLVL---DPMKEED 180
Query: 551 RCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 605
G+ D A G + I LQMD + +T D ++ A+ AKKG I E + +
Sbjct: 181 NFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYEMQREAI 237
>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|E Chain E, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|H Chain H, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 245
Score = 85.1 bits (209), Expect = 1e-16, Method: Composition-based stats.
Identities = 75/247 (30%), Positives = 125/247 (50%), Gaps = 17/247 (6%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 8 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 66
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 67 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 123
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ ED
Sbjct: 124 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETED 179
Query: 551 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 604
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 180 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 236
Query: 605 VPKCKNE 611
+ K E
Sbjct: 237 YVEFKEE 243
>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|D Chain D, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|F Chain F, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|H Chain H, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|J Chain J, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|L Chain L, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|N Chain N, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|P Chain P, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|R Chain R, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|T Chain T, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|V Chain V, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|X Chain X, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
Length = 248
Score = 85.1 bits (209), Expect = 1e-16, Method: Composition-based stats.
Identities = 75/247 (30%), Positives = 125/247 (50%), Gaps = 17/247 (6%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 11 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 69
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 70 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 126
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ ED
Sbjct: 127 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETED 182
Query: 551 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 604
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 183 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 239
Query: 605 VPKCKNE 611
+ K E
Sbjct: 240 YVEFKEE 246
>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 250
Score = 82.4 bits (202), Expect = 8e-16, Method: Composition-based stats.
Identities = 74/247 (29%), Positives = 124/247 (50%), Gaps = 17/247 (6%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 13 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 71
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 72 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 128
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ E
Sbjct: 129 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETEA 184
Query: 551 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 604
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 185 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 241
Query: 605 VPKCKNE 611
+ K E
Sbjct: 242 YVEFKEE 248
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 81.3 bits (199), Expect = 2e-15, Method: Composition-based stats.
Identities = 39/71 (54%), Positives = 56/71 (78%)
Query: 683 VQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLG 742
+++G+VYTG V R+ DFGA + I GK+GL+HISQI+ KRV +TD+L+ Q+V VKVL
Sbjct: 3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLE 62
Query: 743 IDDRGRIKLSM 753
+D +GRI+LS+
Sbjct: 63 VDRQGRIRLSI 73
>pdb|2WNR|B Chain B, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|D Chain D, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|F Chain F, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
Length = 240
Score = 78.6 bits (192), Expect = 1e-14, Method: Composition-based stats.
Identities = 65/197 (32%), Positives = 92/197 (46%), Gaps = 10/197 (5%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R +++RP+ I GIL R GSS G + L VA G E +I L
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKIL-VAVYGPR--EAQIRKLQRPDR 72
Query: 438 DSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITE 497
YNM PF+ + R G P RR + ++ AL P L I + E+ E
Sbjct: 73 AVIRCRYNMAPFSVEERKRPG-PDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLE 131
Query: 498 SNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDF 557
+ G + A + +AL DAG+P+ + V A G K G++VV+ D+ +ED+ G D
Sbjct: 132 AEGGTRCAGITAASVALADAGIPMRDMVVACAAG--KVGDQVVL--DLSEEEDKEGQADV 187
Query: 558 KVA--GTVNGITALQMD 572
VA IT LQ D
Sbjct: 188 PVAILPRTREITLLQSD 204
>pdb|2PNZ|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Udp And Gmp
pdb|2PO0|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Adp In Double Conformation
pdb|2PO1|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With A Single Stranded 10-Mer Poly(A) Rna
pdb|2PO2|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Cdp
Length = 249
Score = 76.6 bits (187), Expect = 4e-14, Method: Composition-based stats.
Identities = 66/204 (32%), Positives = 99/204 (48%), Gaps = 10/204 (4%)
Query: 371 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 430
K I + G RID R ++RPI + G+L +GS+ G + ++ A G K
Sbjct: 9 KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNK-IIAAVYGPRELHPK-- 65
Query: 431 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
L + YNM PF+ + + G P RR I ++ K AL P L +I
Sbjct: 66 HLQRPDRAILRVRYNMAPFSVEERKKPG-PDRRSIEISKVIKGALEPALILEMFPRTAID 124
Query: 491 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 550
+ E+ +++ + +A + LAL DAG+P+ + VA A G I +GE I+ D+ +ED
Sbjct: 125 VFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKI-EGE---IVLDLNKEED 180
Query: 551 RCGDMDFKVA--GTVNGITALQMD 572
G+ D VA N IT LQMD
Sbjct: 181 NYGEADVPVAIMPLKNDITLLQMD 204
>pdb|1QD7|H Chain H, Partial Model For 30s Ribosomal Subunit
Length = 85
Score = 69.3 bits (168), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 32/61 (52%), Positives = 44/61 (72%), Gaps = 6/61 (9%)
Query: 19 KNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGN------FLFNKIIKSF 72
+NDTGSPEVQ+A+LT +IN+LN H ++H KDHHSRRGL+ M G +L NK + +
Sbjct: 17 ENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVGKRRRLLAYLRNKDVARY 76
Query: 73 K 73
+
Sbjct: 77 R 77
>pdb|1FKA|O Chain O, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
Length = 89
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 35/61 (57%), Positives = 41/61 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M I K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM
Sbjct: 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 G 61
G
Sbjct: 61 G 61
>pdb|1EG0|F Chain F, Fitting Of Components With Known Structure Into An 11.5
A Cryo-Em Map Of The E.Coli 70s Ribosome
pdb|1FJG|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin, And Paromomycin
pdb|1HR0|O Chain O, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNW|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1HNZ|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1GIX|R Chain R, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1IBK|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1IBL|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1IBM|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1JGO|R Chain R, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgo, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
pdb|1JGP|R Chain R, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgp, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
pdb|1JGQ|R Chain R, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgq, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
pdb|1ML5|R Chain R, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1XMO|O Chain O, Crystal Structure Of Mnm5u34t6a37-Trnalysuuu Complexed
With Aag-Mrna In The Decoding Center
pdb|1XMQ|O Chain O, Crystal Structure Of T6a37-Asllysuuu Aaa-Mrna Bound To
The Decoding Center
pdb|1XNQ|O Chain O, Structure Of An Inosine-Adenine Wobble Base Pair Complex
In The Context Of The Decoding Center
pdb|1XNR|O Chain O, Crystal Structure Of An Inosine-Cytosine Wobble Base
Pair In The Context Of The Decoding Center
pdb|1YL4|R Chain R, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. 30s Subunit. The Coordinates For The 50s Subunit
Are In The Pdb Entry 1yl3
pdb|2B64|O Chain O, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor
Rf1 From A Crystal Structure Of The Whole Ribosomal
Complex. This File Contains The 30s Subunit, Trnas,
Mrna And Release Factor Rf1 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf1 And Is Described In Remark 400.
pdb|2B9M|O Chain O, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor
Rf2 From A Crystal Structure Of The Whole Ribosomal
Complex. This File Contains The 30s Ribosomal Subunit,
Trnas, Mrna And Release Factor Rf2 From A Crystal
Structure Of The Whole Ribosomal Complex". The Entire
Crystal Structure Contains One 70s Ribosome, Trnas,
Mrna And Release Factor Rf2 And Is Described In Remark
400.
pdb|2B9O|O Chain O, 30s Ribosomal Subunit, Trnas And Mrna From A Crystal
Structure Of The Whole Ribosomal Complex With A Stop
Codon In The A-Site. This File Contains The 30s
Subunit, Trnas And Mrna From A Crystal Structure Of The
Whole Ribosomal Complex With A Stop Codon In The A-Site
And Is Described In Remark 400.
pdb|2F4V|O Chain O, 30s Ribosome + Designer Antibiotic
pdb|2HHH|O Chain O, Crystal Structure Of Kasugamycin Bound To The 30s
Ribosomal Subunit
pdb|2J00|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 1 Of
4). This File Contains The 30s Subunit, Mrna, A-, P-
And E-Site Trnas And Paromomycin For Molecule I.
pdb|2J02|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 3 Of 4)
This File Contains The 30s Subunit, Mrna, A-, P- And
E-Site Trnas And Paromomycin For Molecule Ii.
pdb|2HGI|R Chain R, Crystal Structure Of The 70s Thermus Thermophilus
Ribosome Showing How The 16s 3'-End Mimicks Mrna E And
P Codons. This Entry 2hgi Contains 30s Ribosomal
Subunit. The 50s Ribosomal Subunit Can Be Found In Pdb
Entry 2hgj.
pdb|2HGP|R Chain R, Crystal Structure Of The 70s Thermus Thermophilus
Ribosome With Translocated And Rotated Shine-Dalgarno
Duplex. This Entry 2hgp Contains 30s Ribosomal Subunit.
The 50s Ribosomal Subunit Can Be Found In Pdb Entry
2hgq.
pdb|2HGR|R Chain R, 70s T.Th. Ribosome Functional Complex With Mrna And E-
And P-Site Trnas At 4.5a. This Entry 2hgr Contains 30s
Ribosomal Subunit. The 50s Ribosomal Subunit Can Be
Found In Pdb Entry 2hgu.
pdb|2OW8|PP Chain p, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
Functional Interactions And Rearrangements. This File,
2ow8, Contains The 30s Ribosome Subunit, Two Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File
1vsa.
pdb|2UU9|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-asl With Cmo5u In
Position 34 Bound To An Mrna With A Gug-codon In The
A-site And Paromomycin.
pdb|2UUA|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-Asl With Cmo5u In
Position 34 Bound To An Mrna With A Guc-Codon In The
A-Site And Paromomycin.
pdb|2UUB|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-Asl With Cmo5u In
Position 34 Bound To An Mrna With A Guu-Codon In The
A-Site And Paromomycin.
pdb|2UUC|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-asl With Cmo5u In
Position 34 Bound To An Mrna With A Gua-codon In The
A-site And Paromomycin.
pdb|2UXC|O Chain O, Crystal Structure Of An Extended Trna Anticodon Stem
Loop In Complex With Its Cognate Mrna Ucgu In The
Context Of The Thermus Thermophilus 30s Subunit.
pdb|2UXB|O Chain O, Crystal Structure Of An Extended Trna Anticodon Stem
Loop In Complex With Its Cognate Mrna Gggu In The
Context Of The Thermus Thermophilus 30s Subunit.
pdb|2V46|O Chain O, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe
And Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|O Chain O, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe
And Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2UXD|O Chain O, Crystal Structure Of An Extended Trna Anticodon Stem
Loop In Complex With Its Cognate Mrna Cggg In The
Context Of The Thermus Thermophilus 30s Subunit.
pdb|2QNH|PP Chain p, Interactions And Dynamics Of The Shine-Dalgarno Helix In
The 70s Ribosome. This File, 2qnh, Contains The 30s
Ribosome Subunit, Two Trna, And Mrna Molecules. 50s
Ribosome Subunit Is In The File 1vsp.
pdb|2VQE|O Chain O, Modified Uridines With C5-methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-g
Wobble Pairing During Decoding
pdb|2VQF|O Chain O, Modified Uridines With C5-Methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-G
Wobble Pairing During Decoding
pdb|2ZKQ|OO Chain o, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
pdb|3D5A|O Chain O, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|O Chain O, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3F1E|O Chain O, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|O Chain O, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|2WDG|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule I.
pdb|2WDH|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule Ii.
pdb|2WDK|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule I.
pdb|2WDM|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule Ii.
pdb|2WH1|O Chain O, Insights Into Translational Termination From The
Structure Of Rf2 Bound To The Ribosome
pdb|2WH3|O Chain O, Insights Into Translational Termination From The
Structure Of Rf2 Bound To The Ribosome). This File
Contains The 30s Subunit.
pdb|3HUW|O Chain O, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P
For Molecule I.
pdb|3HUY|O Chain O, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P
For Molecule Ii.
pdb|2WRI|O Chain O, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 1 Of
4).
pdb|2WRK|O Chain O, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 3 Of
4).
pdb|2WRN|O Chain O, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 1 Of 4).
pdb|2WRQ|O Chain O, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 3 Of 4).
pdb|3KIQ|OO Chain o, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 1 Of 4)
pdb|3KIS|OO Chain o, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 3 Of 4)
pdb|3KIU|OO Chain o, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 1 Of 4)
pdb|3KIX|OO Chain o, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 3 Of 4)
pdb|3KNH|O Chain O, The Structures Of Viomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule I
pdb|3KNJ|O Chain O, The Structures Of Viomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule Ii'
pdb|3KNL|O Chain O, The Structures Of Capreomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule I
pdb|3KNN|O Chain O, The Structures Of Capreomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule Ii
pdb|3I8G|R Chain R, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8g Contains 30s Ribosomal Subnit.The 50s
Ribosomal Can Be Found In Pdb Entry 3i8f. Molecule B In
The Same Asym Unit Is Deposited As 3i8g (30s) And 3i8f
(50s).
pdb|3I8H|R Chain R, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8h Contains 30s Ribosomal Subnit. The 50s
Ribosomal Can Be Found In Pdb Entry 3i8i. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I9B|R Chain R, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9b Contains 30s Ribosomal Subunit Of Molecule
B. The 50s Subunit Can Be Found In Pdb Entry 3i9c.
Molecule A In The S Asymmetric Unit Is Deposited As
3i9d (30s) And 3i9e (50s)
pdb|3I9D|R Chain R, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9d Contains 30s Ribosomal Subunit Of Molecule
A. The 50s Subunit Can Be Found In Pdb Entry 3i9e.
Molecule B In The S Asymmetric Unit Is Deposited As
3i9b (30s) And 3i9c (50s)
pdb|2X9R|O Chain O, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|O Chain O, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XFZ|O Chain O, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 1 Of 4)
pdb|2XG1|O Chain O, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 3 Of 4)
pdb|3OTO|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From A
Ksga Mutant Of Thermus Thermophilus (Hb8)
pdb|3OGE|O Chain O, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OGY|O Chain O, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OHC|O Chain O, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OHD|O Chain O, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OHY|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI0|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI2|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI4|O Chain O, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2XQD|O Chain O, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The
70s Ribosome With A Gtp Analog
pdb|2XSY|O Chain O, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUY|O Chain O, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0U|O Chain O, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y0W|O Chain O, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Y|O Chain O, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound
To A Near-Cognate Codon On The 70s Ribosome
pdb|2Y10|O Chain O, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y12|O Chain O, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound
To A Near-Cognate Codon On The 70s Ribosome
pdb|2Y14|O Chain O, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound
To A Cognate Codon On The 70s Ribosome.
pdb|2Y16|O Chain O, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound
To A Cognate Codon On The 70s Ribosome.
pdb|2Y18|O Chain O, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|3ZVO|O Chain O, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release
Factor 3
pdb|3T1H|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aaa-Codon In The A-Site And Paromomycin
pdb|3T1Y|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aag-Codon In The A-Site And Paromomycin
pdb|3UXS|O Chain O, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UXT|O Chain O, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.'
pdb|3TVF|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3TVG|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3UYD|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Leu Complex
pdb|3UYF|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Leu Complex
pdb|3UZ3|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Leu Complex With Paromomycin.
pdb|3UZ4|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Leu Complex With Paromomycin.
pdb|3UZ6|R Chain R, Structure Analysis Of Ribosomal Decoding. This Entry
Contains The 30s Ribosomal Subunit Of The First 70s
Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex
pdb|3UZ7|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZG|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Tyr Complex
pdb|3UZI|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Tyr Complex
pdb|3UZL|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The
Near-Cognate Trna-Tyr Complex With Paromomycin
pdb|3UZM|R Chain R, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The
Near-cognate Trna-tyr Complex With Paromomycin
pdb|4ABR|O Chain O, Complex Of Smpb, A Tmrna Fragment And
Ef-Tu-Gdp-Kirromycin With The 70s Ribosome
pdb|4DH9|O Chain O, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHB|O Chain O, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V22|O Chain O, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Rmf Of The 1st Ribosome In The Asu
pdb|3V24|O Chain O, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Rmf Of The 2nd Ribosome In The Asu
pdb|3V26|O Chain O, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Hpf Of The 1st Ribosome In The Asu
pdb|3V28|O Chain O, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Hpf Of The 2nd Ribosome In The Asu
pdb|3V2C|O Chain O, Crystal Structure Of Yfia Bound To The 70s Ribosome.
This Pdb Entry Contains Coordinates For The 30s Subunit
With Bound Yfia Of The 1st Ribosome In The Asu
pdb|3V2E|O Chain O, Crystal Structure Of Yfia Bound To The 70s Ribosome.
This Pdb Entry Contains Coordinates For The 30s Subunit
With Bound Yfia Of The 2nd Ribosome In The Asu
pdb|4DR1|O Chain O, Crystal Structure Of The Apo 30s Ribosomal Subunit From
Thermus Thermophilus (hb8)
pdb|4DR2|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Multiple Copies Of Paromomycin
Molecules Bound
pdb|4DR3|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Streptomycin Bound
pdb|4DR4|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Cognate Transfer Rna
Anticodon Stem-loop And Multiple Copies Of Paromomycin
Molecules Bound
pdb|4DR5|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Crystallographically
Disordered Cognate Transfer Rna Anticodon Stem-loop And
Streptomycin Bound
pdb|4DR6|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Near-cognate Transfer Rna
Anticodon Stem-loop Mismatched At The First Codon
Position And Streptomycin Bound
pdb|4DR7|O Chain O, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Crystallographically
Disordered Near-cognate Transfer Rna Anticodon
Stem-loop Mismatched At The Second Codon Position, And
Streptomycin Bound
pdb|4G5K|R Chain R, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 30s Subunit Of Molecule A.
pdb|4G5M|R Chain R, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 30s Subunit Of Molecule B.
pdb|4G5T|R Chain R, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 30s Subunit Of Molecule A.
pdb|4G5V|R Chain R, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 30s Subunit Of Molecule B.
pdb|4DUY|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U13c
pdb|4DUZ|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U13c, Bound
With Streptomycin
pdb|4DV0|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U20g
pdb|4DV1|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U20g, Bound
With Streptomycin
pdb|4DV2|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, C912a
pdb|4DV3|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, C912a,
Bound With Streptomycin
pdb|4DV4|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A914g
pdb|4DV5|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A914g,
Bound With Streptomycin
pdb|4DV6|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A915g
pdb|4DV7|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A915g,
Bound With Streptomycin
Length = 89
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 35/61 (57%), Positives = 41/61 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M I K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM
Sbjct: 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 G 61
G
Sbjct: 61 G 61
>pdb|2QOU|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The First 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOW|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOY|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
First 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QP0|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QAL|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The First 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QAN|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QB9|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The First 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBB|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBD|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
First 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBF|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBH|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBJ|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2VAZ|F Chain F, Model Of The S15-Mrna Complex Fitted Into The Cryo-Em
Map Of The 70s Entrapment Complex.
pdb|2Z4K|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4M|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With
Paromomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|3I1M|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|O Chain O, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3OR9|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3ORA|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3SFS|O Chain O, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|O Chain O, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
(Without Viomycin)
pdb|4GAQ|O Chain O, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|O Chain O, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 89
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 33/59 (55%), Positives = 40/59 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
M++ A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 1 MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRM 59
>pdb|2AVY|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File
Contains The 30s Subunit Of One 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes And
Is Described In Remark 400.
pdb|2AW7|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File
Contains The 30s Subunit Of The Second 70s Ribosome.
The Entire Crystal Structure Contains Two 70s Ribosomes
And Is Described In Remark 400.
pdb|1VS5|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|1VS7|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|2VHO|O Chain O, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|O Chain O, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This
File Contains The 30s Subunit Of The First 70s
Ribosome, With Hygromycin B Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3DF3|O Chain O, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Hygromycin B Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3E1A|H Chain H, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Pre- Accommodation State
pdb|3E1C|H Chain H, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Post-Accommodation State
pdb|3KC4|O Chain O, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be
Found In Pdb Entry 3kcr
pdb|3IZV|S Chain S, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Small Subunit Of A Ribosome Programmed With A
Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
Ef-Tu
pdb|3IZW|S Chain S, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding.This Entry Contains The
Small Subunit Of A Ribosome Programmed With A Cognate
Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
pdb|4ADV|O Chain O, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
Length = 89
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 33/59 (55%), Positives = 40/59 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
M++ A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 1 MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRM 59
>pdb|1KUQ|A Chain A, Crystal Structure Of T3c Mutant S15 Ribosomal Protein In
Complex With 16s Rrna
Length = 87
Score = 67.4 bits (163), Expect = 3e-11, Method: Composition-based stats.
Identities = 35/61 (57%), Positives = 41/61 (67%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M I K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM
Sbjct: 1 MPICKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMV 60
Query: 61 G 61
G
Sbjct: 61 G 61
>pdb|1A32|A Chain A, Ribosomal Protein S15 From Bacillus Stearothermophilus
Length = 88
Score = 67.0 bits (162), Expect = 4e-11, Method: Composition-based stats.
Identities = 35/72 (48%), Positives = 47/72 (65%), Gaps = 6/72 (8%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKGN----- 62
K II +NDTGSPEVQ+A+LT +IN+LN H ++H KDHHSRRGL+ M G
Sbjct: 7 KREIIEQFKVHENDTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVGKRRRLL 66
Query: 63 -FLFNKIIKSFK 73
+L NK + ++
Sbjct: 67 AYLRNKDVARYR 78
>pdb|1G1X|B Chain B, Structure Of Ribosomal Proteins S15, S6, S18, And 16s
Ribosomal Rna
pdb|1G1X|G Chain G, Structure Of Ribosomal Proteins S15, S6, S18, And 16s
Ribosomal Rna
Length = 88
Score = 66.2 bits (160), Expect = 6e-11, Method: Composition-based stats.
Identities = 33/54 (61%), Positives = 39/54 (72%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM G
Sbjct: 7 KQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVG 60
>pdb|1I94|O Chain O, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I95|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
pdb|1I96|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|O Chain O, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1J5E|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1N32|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The First Codon
Position At The A Site With Paromomycin
pdb|1N33|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The Second Codon
Position At The A Site With Paromomycin
pdb|1N34|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Codon And
Crystallographically Disordered Near-Cognate Transfer
Rna Anticodon Stem-Loop Mismatched At The First Codon
Position
pdb|1N36|O Chain O, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Crystallographically
Disordered Codon And Near-cognate Transfer Rna
Anticodon Stem-loop Mismatched At The Second Codon
Position
pdb|1PNS|O Chain O, Crystal Structure Of A Streptomycin Dependent Ribosome
From E. Coli, 30s Subunit Of 70s Ribosome. This File,
1pns, Contains The 30s Subunit, Two Trnas, And One Mrna
Molecule. The 50s Ribosomal Subunit Is In File 1pnu.
pdb|1PNX|O Chain O, Crystal Structure Of The Wild Type Ribosome From E.
Coli, 30s Subunit Of 70s Ribosome. This File, 1pnx,
Contains Only Molecules Of The 30s Ribosomal Subunit.
The 50s Subunit Is In The Pdb File 1pny.
pdb|1VOQ|O Chain O, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOS|O Chain O, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOV|O Chain O, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOX|O Chain O, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOZ|O Chain O, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|2E5L|O Chain O, A Snapshot Of The 30s Ribosomal Subunit Capturing Mrna
Via The Shine- Dalgarno Interaction
pdb|3FIC|O Chain O, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 30s Subunit
And The Ligands
pdb|2ZM6|O Chain O, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit
pdb|1AB3|A Chain A, Ribosomal Protein S15 From Thermus Thermophilus, Nmr, 26
Structures
pdb|2FKX|A Chain A, Ribosomal Protein S15 From Thermus Thermophilus, Nmr
Recalculated Structure
pdb|3MR8|O Chain O, Recognition Of The Amber Stop Codon By Release Factor
Rf1. This Entry 3mr8 Contains 30s Ribosomal Subunit.
The 50s Ribosomal Subunit Can Be Found In Pdb Entry
3ms1. Molecule B In The Same Asymmetric Unit Is
Deposited As 3mrz (50s) And 3ms0 (30s).
pdb|3MS0|O Chain O, Recognition Of The Amber Stop Codon By Release Factor
Rf1. This Entry 3ms0 Contains 30s Ribosomal Subunit.
The 50s Ribosomal Subunit Can Be Found In Pdb Entry
3mrz. Molecule A In The Same Asymmetric Unit Is
Deposited As 3mr8 (30s) And 3ms1 (50s).
pdb|3PYN|O Chain O, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The First 70s
Ribosome.
pdb|3PYQ|O Chain O, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The Second 70s
Ribosome.
pdb|3PYS|O Chain O, Crystal Structure Of A Complex Containing Domain 3 Of
Crpv Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The First 70s Ribosome.
pdb|3PYU|O Chain O, Crystal Structure Of A Complex Containing Domain 3 Of
Crpv Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The Second 70s Ribosome.
pdb|4AQY|O Chain O, Structure Of Ribosome-Apramycin Complexes
Length = 88
Score = 66.2 bits (160), Expect = 7e-11, Method: Composition-based stats.
Identities = 33/54 (61%), Positives = 39/54 (72%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K +I + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+MM G
Sbjct: 7 KQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVG 60
>pdb|1P6G|O Chain O, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P87|O Chain O, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|3OFO|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFP|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3OFA|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OFB|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3OFX|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFY|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome
pdb|3OAQ|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OAR|O Chain O, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|2YKR|O Chain O, 30s Ribosomal Subunit With Rsga Bound In The Presence Of
Gmppnp
pdb|3J18|O Chain O, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And
Mld-Loading (30s Subunit)
pdb|4GD1|O Chain O, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4GD2|O Chain O, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4A5U|B Chain B, Turnip Yellow Mosaic Virus Proteinase And Escherichia
Coli 30s Ribosomal S15
Length = 88
Score = 65.5 bits (158), Expect = 1e-10, Method: Composition-based stats.
Identities = 32/58 (55%), Positives = 39/58 (67%)
Query: 2 TIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
++ A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 1 SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRM 58
>pdb|2GY9|O Chain O, Structure Of The 30s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYB|O Chain O, Structure Of The 30s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
Length = 86
Score = 65.5 bits (158), Expect = 1e-10, Method: Composition-based stats.
Identities = 32/51 (62%), Positives = 37/51 (72%)
Query: 9 ASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 7 AKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRM 57
>pdb|2I2P|O Chain O, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|2I2U|O Chain O, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|3FIH|O Chain O, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 30s Subunit, Trnas And The Ternary
Complex.
pdb|3IY8|O Chain O, Leishmania Tarentolae Mitonchondrial Ribosome Small
Subunit
pdb|2WWL|O Chain O, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 30s, The P-Site
Trna And The Tnac Leader Peptide (Part 1 Of 2).
pdb|3J00|O Chain O, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|4A2I|O Chain O, Cryo-Electron Microscopy Structure Of The 30s Subunit In
Complex With The Yjeq Biogenesis Factor
pdb|3J0U|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|R Chain R, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
Length = 88
Score = 65.5 bits (158), Expect = 1e-10, Method: Composition-based stats.
Identities = 32/58 (55%), Positives = 39/58 (67%)
Query: 2 TIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMM 59
++ A I+ + R NDTGS EVQVALLT++IN L HF H KDHHSRRGL+ M
Sbjct: 1 SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRM 58
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 112/247 (45%), Gaps = 36/247 (14%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 438 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 491 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 539
+ ++ +++G ++ A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 595
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 596 YILEKMK 602
++E K
Sbjct: 227 ELIELQK 233
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 111/247 (44%), Gaps = 36/247 (14%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 438 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 491 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 539
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 595
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 596 YILEKMK 602
++E K
Sbjct: 227 ELIELQK 233
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 111/247 (44%), Gaps = 36/247 (14%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 438 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 491 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 539
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 595
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 596 YILEKMK 602
++E K
Sbjct: 227 ELIELQK 233
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 110/247 (44%), Gaps = 36/247 (14%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 437
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 438 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 490
Y+M P AT GRIG EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GATHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 491 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 539
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 595
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 596 YILEKMK 602
++E K
Sbjct: 227 ELIELQK 233
>pdb|1F7Y|A Chain A, The Crystal Structure Of Two Uucg Loops Highlights The
Role Played By 2'-Hydroxyl Groups In Its Unusual
Stability
Length = 89
Score = 60.8 bits (146), Expect = 3e-09, Method: Composition-based stats.
Identities = 32/61 (52%), Positives = 38/61 (62%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M I K + + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+
Sbjct: 1 MPITKEEKQKVXQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLXXV 60
Query: 61 G 61
G
Sbjct: 61 G 61
>pdb|1DK1|A Chain A, Detailed View Of A Key Element Of The Ribosome Assembly:
Crystal Structure Of The S15-Rrna Complex
Length = 86
Score = 58.9 bits (141), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/54 (55%), Positives = 36/54 (66%)
Query: 8 KASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMKG 61
K + + +R DTGS EVQVALLT RIN L+ H K+H KDHHS RGL+ G
Sbjct: 7 KQKVXQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLXXVG 60
>pdb|2NN6|B Chain B, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 249
Score = 58.9 bits (141), Expect = 1e-08, Method: Composition-based stats.
Identities = 53/231 (22%), Positives = 103/231 (44%), Gaps = 12/231 (5%)
Query: 375 DKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMG 434
D+G R+D R ++R I R G+ + GS+ +G+T+AL V + AL
Sbjct: 13 DQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARAL-- 70
Query: 435 EFTDSFMLH--YNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 492
D +++ Y+ F+TG+ R R+ G ++ + I +
Sbjct: 71 --PDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIY 128
Query: 493 SEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRC 552
++ +++G + A V LA+LDAG+P+ + V + G + DG + LS + E+
Sbjct: 129 VQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-DGTALADLSHV---EEAA 184
Query: 553 GDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 601
G +A I L+MD ++ + + A +A + + +L+++
Sbjct: 185 GGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRV 235
>pdb|3HKM|A Chain A, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|B Chain B, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|C Chain C, Crystal Structure Of Rice(Oryza Sativa) Rrp46
Length = 246
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 438
R D R N +RP S L R HGS+ + +GDT ++ A G +K GE +
Sbjct: 5 RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDT-IVLAAVYGPKPGTRK-----GENPE 58
Query: 439 SFMLHYNMPPFATGDIGRIGVPKRREIGHGR-LAKRALLPVLPNNNKFNYSIRLVSEITE 497
+ P TG IG+ K E+ R L LL V PN + ++ ++
Sbjct: 59 KASIEVVWKPM-TGQIGK--QEKEYEMTLKRTLQSICLLTVHPNT-----TTSVILQVVG 110
Query: 498 SNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGE 537
++GS ++ C AL+ AG+P+ I G+++DGE
Sbjct: 111 NDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGE 150
>pdb|4IYL|A Chain A, 30s Ribosomal Protein S15 From Campylobacter Jejuni
Length = 93
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/62 (45%), Positives = 39/62 (62%)
Query: 1 MTIKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGLIMMK 60
M + + KA I+ ++ DTGS EVQVALLT+RI +L H K++ KD SR GL+ +
Sbjct: 4 MALDSAKKAEIVAKFAKKPGDTGSTEVQVALLTARIAELTEHLKIYKKDFSSRLGLLKLV 63
Query: 61 GN 62
G
Sbjct: 64 GQ 65
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 678 KLTESVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQK 735
K E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE QK
Sbjct: 4 KAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQK 63
Query: 736 VRVKVLGIDDR-GRIKLSM 753
V KV+ +D R G I LS+
Sbjct: 64 VVAKVIRVDPRKGHIDLSL 82
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 678 KLTESVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQK 735
+ E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE QK
Sbjct: 3 RAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQK 62
Query: 736 VRVKVLGIDDR-GRIKLSM 753
V KV+ +D R G I LS+
Sbjct: 63 VVAKVIRVDPRKGHIDLSL 81
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 53/204 (25%), Positives = 92/204 (45%), Gaps = 24/204 (11%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEF 436
+R+D R ++R I I T L GS L GDT+ + AT+ E+++ M GE
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI-----EERVPPFMRGEG 65
Query: 437 TDSFMLHYNMPPFATGDI----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 492
Y M P AT G R + RL RAL V+ ++ +
Sbjct: 66 KGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWID 125
Query: 493 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 541
++ +++G + AS+ G +A++ A +P+ +++A ++G+++ E+ V+
Sbjct: 126 CDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVE--EQGVV 183
Query: 542 LSDILGDEDRCGDMDFKVAGTVNG 565
L D+ ED D+D V T G
Sbjct: 184 L-DLNYAEDSKADVDMNVIMTGKG 206
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 62/245 (25%), Positives = 113/245 (46%), Gaps = 31/245 (12%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEF 436
+R D R +++RPI+ + GS L T G+T+ + A++ E ++ + G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV-----EDRVPPFLRGGG 55
Query: 437 TDSFMLHYNMPPFATGDI-------GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSI 489
Y+M P AT G+I R + RL RAL V+ +I
Sbjct: 56 KGWITAEYSMLPQATNQQTIQESSKGKI---SGRTMEIQRLIGRALRAVVDLEKLGERTI 112
Query: 490 RLVSEITESNGSSSMASVCGGCLA-------LLDAGV----PISEHVAGIAMGLIKDGEK 538
+ ++ +++G + AS+ G LA L+ AG PI++ +A I++G+ D E+
Sbjct: 113 WIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI--DKEQ 170
Query: 539 VVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYI 597
++L D+ +ED ++D V T +G LQ + + + + L A+KG+ +
Sbjct: 171 GILL-DLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQEL 229
Query: 598 LEKMK 602
++K K
Sbjct: 230 IDKQK 234
>pdb|1OYP|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 62/245 (25%), Positives = 113/245 (46%), Gaps = 31/245 (12%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEF 436
+R D R +++RPI+ + GS L T G+T+ + A++ E ++ + G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV-----EDRVPPFLRGGG 55
Query: 437 TDSFMLHYNMPPFAT-------GDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSI 489
Y+M P AT G+I R + RL RAL V+ +I
Sbjct: 56 KGWITAEYSMLPRATNQRTIRESSKGKI---SGRTMEIQRLIGRALRAVVDLEKLGERTI 112
Query: 490 RLVSEITESNGSSSMASVCGGCLA-------LLDAGV----PISEHVAGIAMGLIKDGEK 538
+ ++ +++G + AS+ G LA L+ AG PI++ +A I++G+ D E+
Sbjct: 113 WIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI--DKEQ 170
Query: 539 VVILSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYI 597
++L D+ +ED ++D V T +G LQ + + + + L A+KG+ +
Sbjct: 171 GILL-DLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQEL 229
Query: 598 LEKMK 602
++K K
Sbjct: 230 IDKQK 234
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 679 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 738
+ ++G VYTG V L +GA + + GL+HIS+++ V I + L +V+V
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 739 KVLGID-DRGRIKLSM 753
KVL +D ++G+I LS+
Sbjct: 61 KVLAVDEEKGKISLSI 76
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 52/204 (25%), Positives = 85/204 (41%), Gaps = 27/204 (13%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGEF 436
R R + +RPI I GS L GDT+ + V A G R L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPR------FLKGQG 56
Query: 437 TDSFMLHYNMPPFATGDIGRIGVPKRREIGHG----RLAKRALLPVLPNNNKFNYSIRLV 492
Y M P +TG+ + + ++ G RL R+L L + ++ +
Sbjct: 57 QGWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYID 116
Query: 493 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 541
++ +++G + AS+ G +AL+DA G P+ + VA +++G I G V+
Sbjct: 117 CDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVG-IYQGVPVLD 175
Query: 542 LSDILGDEDRCGDMDFKVAGTVNG 565
L + ED + D V T G
Sbjct: 176 LDYL---EDSAAETDLNVVMTDAG 196
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 5/91 (5%)
Query: 664 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 723
F + QE +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V
Sbjct: 637 FKTAEFQEG---VESLKD-LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV 692
Query: 724 NIITDFLKENQKVRVKVLGID-DRGRIKLSM 753
+ +K V+VKV+ +D R R+ LSM
Sbjct: 693 KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM 723
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 5/91 (5%)
Query: 664 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 723
F + QE +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V
Sbjct: 638 FKTAEFQEG---VESLKD-LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV 693
Query: 724 NIITDFLKENQKVRVKVLGID-DRGRIKLSM 753
+ +K V+VKV+ +D R R+ LSM
Sbjct: 694 KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM 724
>pdb|2PNZ|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Udp And Gmp
pdb|2PO0|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Adp In Double Conformation
pdb|2PO1|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With A Single Stranded 10-Mer Poly(A) Rna
pdb|2PO2|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Cdp
Length = 277
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 373 ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
+L +G RID+RG D RPI I G++ + GS+L G TQ LV
Sbjct: 21 LLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLV 64
>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 237
Score = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 42/153 (27%), Positives = 64/153 (41%), Gaps = 13/153 (8%)
Query: 388 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMP 447
+R + +L R GS+ F +GDT L G + E K+ E + L +
Sbjct: 30 LRHFACEQNLLSRPDGSASFLQGDTSVLA-GVYGPA--EVKVSK---EIFNKATLEVILR 83
Query: 448 PFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASV 507
P +IG+P E RL + V+ SI +V ++ GS +
Sbjct: 84 P-------KIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCL 136
Query: 508 CGGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 540
C+AL+DAGVP+ G+A L DG V+
Sbjct: 137 NAACMALVDAGVPMRALFCGVACALDSDGTLVL 169
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 51/204 (25%), Positives = 84/204 (41%), Gaps = 27/204 (13%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGEF 436
R R + +RPI I GS L GDT+ + V A G R L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPR------FLKGQG 56
Query: 437 TDSFMLHYNMPPFATGDIGRIGVPKRREIGHG----RLAKRALLPVLPNNNKFNYSIRLV 492
Y P +TG+ + + ++ G RL R+L L + ++ +
Sbjct: 57 QGWLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYID 116
Query: 493 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 541
++ +++G + AS+ G +AL+DA G P+ + VA +++G I G V+
Sbjct: 117 CDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVG-IYQGVPVLD 175
Query: 542 LSDILGDEDRCGDMDFKVAGTVNG 565
L + ED + D V T G
Sbjct: 176 LDYL---EDSAAETDLNVVXTDAG 196
>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha-
Gamma Heterodimer From Sulfolobus Solfataricus Complexed
With Gdpnp
pdb|3CW2|C Chain C, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|D Chain D, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|G Chain G, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|H Chain H, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3V11|B Chain B, Structure Of The Ternary Initiation Complex
Aif2:gdpnp:methionylated Initiator Trna
Length = 266
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 686 GKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 743
G++ V ++FD+G+ + + G L S++SSK V I D LKEN+KV VKV+ +
Sbjct: 12 GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV 71
Query: 744 DDR-GRIKLSM 753
D R G + +S+
Sbjct: 72 DRRKGTVDVSL 82
>pdb|3BBN|O Chain O, Homology Model For The Spinach Chloroplast 30s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 90
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 3 IKNNIKASIILDNSRTKNDTGSPEVQVALLTSRINDLNIHFKLHIKDHHSRRGL 56
+K N S+I D + +N GS E QV T++I L +H +LH KD+ S+RGL
Sbjct: 1 MKKNSFISVISDEKKEENK-GSVEFQVFCFTNKIRRLTLHLELHKKDYSSQRGL 53
>pdb|2WNR|A Chain A, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|C Chain C, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|E Chain E, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
Length = 271
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 33/117 (28%), Positives = 49/117 (41%), Gaps = 9/117 (7%)
Query: 362 YDLESKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 418
D+ +I RK I D RID R +++ R ISI TG++ + GSS G+TQ +V
Sbjct: 5 MDIIPEITRKSITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
Query: 419 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL 475
+ T+S +L P F G P R + R+ R +
Sbjct: 65 KPQIGEPFPDTPEMGVILTNSELLPMASPTFEPGP------PDERSVELSRVVDRCI 115
>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Hypothetical Protein Flj11067
Length = 119
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 4/83 (4%)
Query: 675 RIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSG-KDGLLHISQISSKRVNIITDFLKEN 733
R E + + ++ G V + D+GA I+I K GL+H + +SS RV+ ++ +
Sbjct: 12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVG 71
Query: 734 QKVRVKVLGID---DRGRIKLSM 753
KV VK++G + DR ++ LSM
Sbjct: 72 DKVWVKLIGREMKNDRIKVSLSM 94
>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Atp-Dependent Rna Helicase Dhx8
Length = 103
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 681 ESVQIGKVYTGIVLRLFDFGAIIRILSGK---DGLLHISQISSK-RVNIITDFLKENQKV 736
E IG +Y G V + FG +++ + +GL+HIS++ + RV + D + + Q+V
Sbjct: 8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRV 67
Query: 737 RVKVL 741
+VKVL
Sbjct: 68 KVKVL 72
>pdb|2NN6|E Chain E, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 305
Score = 37.4 bits (85), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 378 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGE 435
LR+D RG D R + + T ++ T GS+ G T L V A +GT + E+ + +
Sbjct: 36 LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEF 95
Query: 436 FTDS 439
F D
Sbjct: 96 FVDC 99
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 36.6 bits (83), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 376 KGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDALMG 434
+GLR+D R N++R P GSS +G+ + + TL E ++ + M
Sbjct: 12 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNK---IITLVKGPKEPRLKSQMD 68
Query: 435 EFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 494
+ N+ F+ + + R + + +L+ + N N R V +
Sbjct: 69 TSKALLNVSVNITKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 125
Query: 495 IT----ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGL 532
I E +G + + G LAL+DAG+ + ++++GI++GL
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 167
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 36.2 bits (82), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 376 KGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDALMG 434
+GLR+D R N++R P GSS +G+ + + TL E ++ + M
Sbjct: 10 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNK---IITLVKGPKEPRLKSQMD 66
Query: 435 EFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 494
+ N+ F+ + + R + + +L+ + N N R V +
Sbjct: 67 TSKALLNVSVNINKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 123
Query: 495 IT----ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGL 532
I E +G + + G LAL+DAG+ + ++++GI++GL
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 165
>pdb|3M85|G Chain G, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|H Chain H, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|I Chain I, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
Length = 259
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 360 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
IL D++ + ++ D RID RG ++ R + I ++ + GS+L GDTQ +V
Sbjct: 5 ILVDIKRDYVLSKLRDNE-RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVV 60
>pdb|2BA0|I Chain I, Archaeal Exosome Core
pdb|2BA0|H Chain H, Archaeal Exosome Core
pdb|2BA0|G Chain G, Archaeal Exosome Core
pdb|2BA1|G Chain G, Archaeal Exosome Core
pdb|2BA1|H Chain H, Archaeal Exosome Core
pdb|2BA1|I Chain I, Archaeal Exosome Core
pdb|3M7N|G Chain G, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|H Chain H, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|I Chain I, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
Length = 259
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 360 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 416
IL D++ + ++ D RID RG ++ R + I ++ + GS+L GDTQ +V
Sbjct: 5 ILVDIKRDYVLSKLRDNE-RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVV 60
>pdb|3L7Z|A Chain A, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|D Chain D, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|G Chain G, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 271
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 368 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 415
II+K+ + +KG+R D R + D RP+SI + GS+L G T L
Sbjct: 13 IIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVL 64
>pdb|2BR2|A Chain A, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|C Chain C, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|E Chain E, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|G Chain G, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|I Chain I, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|K Chain K, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|M Chain M, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|O Chain O, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|S Chain S, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|U Chain U, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|W Chain W, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C38|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
Length = 275
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 368 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 415
II+K+ + +KG+R D R + D RP+SI + GS+L G T L
Sbjct: 13 IIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVL 64
>pdb|2JE6|A Chain A, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 277
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 368 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 415
II+K+ + +KG+R D R + D RP+SI + GS+L G T L
Sbjct: 15 IIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVL 66
>pdb|3B4T|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|E Chain E, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|F Chain F, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
Length = 262
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 51/206 (24%), Positives = 87/206 (42%), Gaps = 30/206 (14%)
Query: 379 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 438
R D R +++RP+ I G GS L G T+ L A++ + +G T
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLT- 65
Query: 439 SFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRL 491
Y M P AT GR+ + +EI RL R+L + +I +
Sbjct: 66 ---AEYAMLPSATHSRSDRESVRGRLS-GRTQEI--SRLIGRSLRACIDLAALGENTIAI 119
Query: 492 VSEITESNGSSSMASVCGGCLALLDAGV------------PISEHVAGIAMGLIKDGEKV 539
++ +++G + A++ G +AL DA P+S +A +++G++ DG
Sbjct: 120 DCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV-DGR-- 176
Query: 540 VILSDILGDEDRCGDMDFKVAGTVNG 565
I D+ +ED ++D V T G
Sbjct: 177 -IRVDLPYEEDSRAEVDMNVVATDTG 201
>pdb|2BA0|A Chain A, Archaeal Exosome Core
pdb|2BA0|B Chain B, Archaeal Exosome Core
pdb|2BA0|C Chain C, Archaeal Exosome Core
Length = 229
Score = 32.3 bits (72), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 622 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 661
+ I+P+++ VIGK GS I+ L E QI + G+I +
Sbjct: 140 VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWV 179
>pdb|3KRN|A Chain A, Crystal Structure Of C. Elegans Cell-Death-Related
Nuclease 5(Crn-5)
pdb|3KRN|B Chain B, Crystal Structure Of C. Elegans Cell-Death-Related
Nuclease 5(Crn-5)
Length = 222
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 465 IGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEH 524
I H L+ L + P+ +I + + +GS ++ G C ALLD G+P
Sbjct: 72 IIHSTLSNAINLELFPHT-----TISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETV 126
Query: 525 VAGIAMGLIKD 535
G+ + +KD
Sbjct: 127 FCGVLIVRVKD 137
>pdb|4GDP|A Chain A, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|B Chain B, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|C Chain C, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|D Chain D, Yeast Polyamine Oxidase Fms1, N195a Mutant
Length = 516
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVS 109
H R + + + +I +SF K+S E+ I R+ + +V V+ ED TV A V
Sbjct: 191 HQGRAAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVI 250
Query: 110 CKDPTSTYNF 119
P S N
Sbjct: 251 ITVPQSVLNL 260
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 686 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-ITDFLKENQKVRVKVLGID 744
G TG V L D+G + I G +GL+H+S++ NI + + V V VL ID
Sbjct: 31 GTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID 90
Query: 745 -DRGRIKLSM 753
+R RI L +
Sbjct: 91 EERRRISLGL 100
>pdb|1RSG|A Chain A, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
pdb|1RSG|B Chain B, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
Length = 516
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVS 109
H R + + + +I +SF K+S E+ I R+ + +V V+ ED TV A V
Sbjct: 191 HQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVI 250
Query: 110 CKDPTSTYN 118
P S N
Sbjct: 251 ITVPQSVLN 259
>pdb|4ECH|A Chain A, Yeast Polyamine Oxidase Fms1, H67q Mutant
pdb|4ECH|B Chain B, Yeast Polyamine Oxidase Fms1, H67q Mutant
Length = 516
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVS 109
H R + + + +I +SF K+S E+ I R+ + +V V+ ED TV A V
Sbjct: 191 HQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVI 250
Query: 110 CKDPTSTYNF 119
P S N
Sbjct: 251 ITVPQSVLNL 260
>pdb|1Z6L|A Chain A, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|1Z6L|B Chain B, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|3BI2|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI2|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BNM|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNM|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNU|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3BNU|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3CN8|B Chain B, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CN8|A Chain A, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CND|B Chain B, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CND|A Chain A, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CNP|B Chain B, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNP|A Chain A, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNS|A Chain A, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNS|B Chain B, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNT|B Chain B, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
pdb|3CNT|A Chain A, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
Length = 516
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVS 109
H R + + + +I +SF K+S E+ I R+ + +V V+ ED TV A V
Sbjct: 191 HQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVI 250
Query: 110 CKDPTSTYNF 119
P S N
Sbjct: 251 ITVPQSVLNL 260
>pdb|1YY5|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1YY5|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|C Chain C, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|D Chain D, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
Length = 513
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 51 HSRRGLIMMKGNFLFNKIIKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVS 109
H R + + + +I +SF K+S E+ I R+ + +V V+ ED TV A V
Sbjct: 191 HQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVI 250
Query: 110 CKDPTSTYNF 119
P S N
Sbjct: 251 ITVPQSVLNL 260
>pdb|3L7Z|C Chain C, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|F Chain F, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|I Chain I, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 249
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 676
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 155 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 214
Query: 677 E 677
E
Sbjct: 215 E 215
>pdb|2JEB|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
Length = 251
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 676
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 157 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 216
Query: 677 E 677
E
Sbjct: 217 E 217
>pdb|2JE6|I Chain I, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|4BA1|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 251
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 620 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 676
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 157 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 216
Query: 677 E 677
E
Sbjct: 217 E 217
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 60/128 (46%), Gaps = 12/128 (9%)
Query: 628 KIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITIASFNSVSGQEAKRRIEKLTESV 683
++ +IGK G +++ + EE+G +I+I++ E IIT+A + + I+KL E +
Sbjct: 15 EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDI 74
Query: 684 QIGKVYTG------IVLRLFDFGAIIRILSGKDG--LLHISQISSKRVNIITDFLKENQK 735
+ + LRL + L GK G + I + + +V + D L + +
Sbjct: 75 SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE 134
Query: 736 VRVKVLGI 743
+ + GI
Sbjct: 135 RAITIAGI 142
Score = 29.3 bits (64), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 586 ALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK--IDPSKIRDVIGKGGSTIRTL 643
A++KA + I++K++ ++ + + +T++ + S+ +IGKGG I+ +
Sbjct: 58 AIFKA---FAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 114
Query: 644 TEETGTQIDI 653
E TG Q+ +
Sbjct: 115 RESTGAQVQV 124
>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2
Length = 308
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 35/58 (60%), Gaps = 3/58 (5%)
Query: 698 DFGAIIRILSGK--DGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 752
+ GA + +L +G++H+S++S +R+ I ++ + VKV+ +D ++G I LS
Sbjct: 26 EMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLS 83
>pdb|4AIB|A Chain A, Crystal Structure Of Ornithine Decarboxylase From
Entamoeba Histolytica.
pdb|4AIB|B Chain B, Crystal Structure Of Ornithine Decarboxylase From
Entamoeba Histolytica.
pdb|4AIB|C Chain C, Crystal Structure Of Ornithine Decarboxylase From
Entamoeba Histolytica.
pdb|4AIB|D Chain D, Crystal Structure Of Ornithine Decarboxylase From
Entamoeba Histolytica
Length = 395
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 361 LYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATL 420
L+D E +I+ K+I DKGL +D + + +H S +FT+ T+A TL
Sbjct: 160 LHDDEVEIVLKEIKDKGLNLD----------GVHFHVGSDSHNSEVFTKALTKARNTVTL 209
Query: 421 G 421
Sbjct: 210 A 210
>pdb|1TUA|A Chain A, 1.5 A Crystal Structure Of A Protein Of Unknown Function
Ape0754 From Aeropyrum Pernix
Length = 191
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 632 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 689
+IG+GG RT+ E T T I++ + + I + AK+ IE L E VY
Sbjct: 112 IIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYE--RAMAAKQAIEMLAEGRMHSTVY 167
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 612 LSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQI--DINDEGIITIASFNSVSG 669
L++ P + + + +IG+GG TIR++ + +G +I D EG + ++ +SG
Sbjct: 9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG 68
Query: 670 QE 671
+
Sbjct: 69 TQ 70
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 39/177 (22%), Positives = 72/177 (40%), Gaps = 23/177 (12%)
Query: 521 ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITY 580
I + AG +G K G+ +V L G + GT + +Q I+ +
Sbjct: 12 IPSYAAGSIIG--KGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVH 69
Query: 581 DIIQIALYKAKKGLS-----YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGK 635
I + + + ++ IL+ T P N++ P S +IGK
Sbjct: 70 GFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPN--------STAGLIIGK 121
Query: 636 GGSTIRTLTEETGTQIDIND--EGIITIASFNSVSGQEAKRR------IEKLTESVQ 684
GG+T++ + E++G + ++ +GI +VSG+ + R I+K+ E Q
Sbjct: 122 GGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 71/177 (40%), Gaps = 23/177 (12%)
Query: 521 ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITY 580
I + AG +G K G+ +V L G + GT + +Q I+ +
Sbjct: 12 IPSYAAGSIIG--KGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVH 69
Query: 581 DII-----QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGK 635
I ++ AK IL+ T P N++ P S +IGK
Sbjct: 70 GFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPN--------STAGLIIGK 121
Query: 636 GGSTIRTLTEETGTQIDIND--EGIITIASFNSVSGQEAKRR------IEKLTESVQ 684
GG+T++ + E++G + ++ +GI +VSG+ + R I+K+ E Q
Sbjct: 122 GGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 29.3 bits (64), Expect = 8.6, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 684 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS 719
Q G G + + DFG I + G DGL+H+S IS
Sbjct: 60 QQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDIS 95
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
0.319 0.139 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,108,011
Number of Sequences: 62578
Number of extensions: 892502
Number of successful extensions: 2687
Number of sequences better than 100.0: 103
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 2534
Number of HSP's gapped (non-prelim): 126
length of query: 755
length of database: 14,973,337
effective HSP length: 106
effective length of query: 649
effective length of database: 8,340,069
effective search space: 5412704781
effective search space used: 5412704781
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)