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= psy3755
(692 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 = 803 bits (2074), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 378/686 (55%), Positives = 527/686 (76%), Gaps = 1/686 (0%)
Query: 5 ILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYI 64
I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLTV+Y
Sbjct: 11 IVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQ 70
Query: 65 EKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQI 124
E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SVNPQ+
Sbjct: 71 ERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQV 130
Query: 125 DPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 184
+PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VAGTE
Sbjct: 131 NPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEA 190
Query: 185 AIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLIS 244
A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++ L +
Sbjct: 191 AVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEALNA 250
Query: 245 KIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESK 304
++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+ +E
Sbjct: 251 RVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHAIEKN 309
Query: 305 IIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQ 364
++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+RD Q
Sbjct: 310 VVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQ 369
Query: 365 KIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNY 424
+D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +KF Y
Sbjct: 370 VLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPY 429
Query: 425 SIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILG 484
++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LSDILG
Sbjct: 430 TVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILG 489
Query: 485 DEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 544
DED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+ +
Sbjct: 490 DEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINA 549
Query: 545 CKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSV 604
+ ++S+FAPR+ TIKI+P KI+DVIGKGGS IR LTEETGT I+I D+G + IA+ +
Sbjct: 550 PRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAATDGE 609
Query: 605 SGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIIT 664
+ A RRIE++T +++G+VYTG V R+ DFGA + I GK+GL+HISQI+ KRV +T
Sbjct: 610 KAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVT 669
Query: 665 DFLKENQKVRVKVLGIDDRGRIKLSM 690
D+L+ Q+V VKVL +D +GRI+LS+
Sbjct: 670 DYLQMGQEVPVKVLEVDRQGRIRLSI 695
>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 = 701 bits (1809), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 347/692 (50%), Positives = 488/692 (70%), Gaps = 3/692 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 74
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 75 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 134
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 135 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 194
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 195 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 253
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 298
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 254 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 313
Query: 299 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 358
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 314 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 373
Query: 359 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 418
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 433
Query: 419 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 478
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 434 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 493
Query: 479 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 494 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 553
Query: 539 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 554 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 613
Query: 599 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 658
++ + + A I+ +T+ ++GK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 659 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
RV +D LKE Q V+VK+LG DDRG+ KLSM
Sbjct: 674 RVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSM 705
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 701 bits (1808), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 348/692 (50%), Positives = 488/692 (70%), Gaps = 3/692 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 74
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 75 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 134
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 135 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 194
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 195 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 253
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 298
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 254 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 313
Query: 299 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 358
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 314 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 373
Query: 359 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 418
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 433
Query: 419 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 478
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 434 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 493
Query: 479 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 494 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 553
Query: 539 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 554 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 613
Query: 599 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 658
++ + + A I+ +T+ +IGK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 659 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
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 = 701 bits (1808), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 347/692 (50%), Positives = 488/692 (70%), Gaps = 3/692 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
MF K+ ++G + +E G IARQA +VL ++ +TV+LAT V K +FFPLT
Sbjct: 6 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLT 65
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y EK +AAG+IPG FFKREG+PSE+ET++SRLIDRPIRPLF +G+ NE+Q+VV VL
Sbjct: 66 VNYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQH 125
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
+ + DPDI ++ S AL +S PF+GP+G A+VG++DG Y+LNPT +++K+S +DL+VA
Sbjct: 126 DLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVA 185
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GT A++ VESE ++L E+I+L + F H++M+ I+AI +L ++ ++ ++P D
Sbjct: 186 GTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTD- 244
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSL-IDNENLT-IDINDINCIL 298
+ +K+ ++ I AY+I+ KQ R K ++L + +EN T D + I
Sbjct: 245 AIKAKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIF 304
Query: 299 YDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLG 358
+LE+ ++R+ ILD GLRID R V +RPI GILPRTHGS+LFTRG+TQA+VVATLG
Sbjct: 305 KELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLG 364
Query: 359 TSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPN 418
T DEQ IDAL G + +SF+LHYN PP++ G+ GR+G P RREIGHG+LA RAL P+LP
Sbjct: 365 TGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPT 424
Query: 419 NNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVI 478
F Y+IRLVSEITESNGSSSMA+VCG LA++DAGVP+ V+GIAMGLI + + +
Sbjct: 425 KEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAV 484
Query: 479 LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
LSDILGDED GDMDFKVAGT G+T+LQMDIKI GIT I++ AL +AK+G ++IL +M
Sbjct: 485 LSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEM 544
Query: 539 KTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
+ + ++ FAP++ TI I KIR+VIG GG IR + TG ++DIND+G++ +
Sbjct: 545 NKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKV 604
Query: 599 ASFNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSK 658
++ + + A I+ +T+ ++GK+Y G V+++ DFGA + KDGL+H+SQIS++
Sbjct: 605 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 664
Query: 659 RVNIITDFLKENQKVRVKVLGIDDRGRIKLSM 690
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 = 645 bits (1664), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 300/550 (54%), Positives = 420/550 (76%), Gaps = 1/550 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
M I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 299
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 541 EVPKCKNELS 550
+ + ++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 = 645 bits (1663), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 300/550 (54%), Positives = 420/550 (76%), Gaps = 1/550 (0%)
Query: 1 MFRFILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLT 60
M I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 61 VDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSV 120
V+Y E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SV
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 121 NPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVA 180
NPQ++PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VA
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 181 GTEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDK 240
GTE A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 241 TLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYD 300
L +++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+
Sbjct: 241 ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHA 299
Query: 301 LESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS 360
+E ++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359
Query: 361 RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNN 420
RD Q +D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419
Query: 421 KFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILS 480
KF Y++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LS
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS 479
Query: 481 DILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKT 540
DILGDED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+
Sbjct: 480 DILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQ 539
Query: 541 EVPKCKNELS 550
+ + ++S
Sbjct: 540 AINAPRGDIS 549
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 642 bits (1656), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 298/538 (55%), Positives = 415/538 (77%), Gaps = 1/538 (0%)
Query: 5 ILKSFKYGSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYI 64
I++ F+YG + +++E G +ARQAT++V+VS++DT + TVV K +FFPLTV+Y
Sbjct: 11 IVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQ 70
Query: 65 EKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQI 124
E+ YAAGRIPGSFF+REG+PSE ET+I+RLIDRPIRPLFPEG++NE+Q++ V+SVNPQ+
Sbjct: 71 ERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQV 130
Query: 125 DPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEK 184
+PDI ++IG S ALS+S +PF GP+G A+VGYI+ +Y+LNPT ++LK+S LDL+VAGTE
Sbjct: 131 NPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEA 190
Query: 185 AIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLIS 244
A++ VESE++ L ED +L A++FGHE+ ++ I INELV+ G+ + +W P ++ L +
Sbjct: 191 AVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEALNA 250
Query: 245 KIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLESK 304
++ ++E ++ AY+I +KQ R I + ++L+ E+ T+D N++ IL+ +E
Sbjct: 251 RVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLL-AEDETLDENELGEILHAIEKN 309
Query: 305 IIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQ 364
++R ++L RID R + IR + +RTG+LPRTHGS+LFTRG+TQALV ATLGT+RD Q
Sbjct: 310 VVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQ 369
Query: 365 KIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNY 424
+D LMGE TD+F+ HYN PP++ G+ G +G PKRREIGHGRLAKR +L V+P+ +KF Y
Sbjct: 370 VLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPY 429
Query: 425 SIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILG 484
++R+VSEITESNGSSSMASVCG LAL+DAGVPI VAGIAMGL+K+G+ V+LSDILG
Sbjct: 430 TVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILG 489
Query: 485 DEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
DED GDMDFKVAG+ +GI+ALQMDIKI GIT +I+Q+AL +AK +IL M+ +
Sbjct: 490 DEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAI 547
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 461 bits (1185), Expect = e-130, Method: Compositional matrix adjust.
Identities = 274/714 (38%), Positives = 408/714 (57%), Gaps = 34/714 (4%)
Query: 5 ILKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVSCKDPTSTYNFFPLTVDY 63
++ + +G+ I E G +ARQA S + ++D T++L+ + K+P +FFPLTVD
Sbjct: 28 VIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDV 87
Query: 64 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 123
E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G NEIQ+V ++++NP
Sbjct: 88 EERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPD 147
Query: 124 IDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG-- 181
D+ +I S + ++ LPF GP+G +V I G+++ PT +L+ + D++VAG
Sbjct: 148 HLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRV 207
Query: 182 ---------------TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 226
TEK I V+ ++ E+++ + +K+ A +L
Sbjct: 208 LEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKA 267
Query: 227 GQKKVNWDPIVKD--KTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN 284
+ + P+ D ++ + ++ A I KQ R+ + L+
Sbjct: 268 AKPTGEF-PVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLL-- 324
Query: 285 ENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLF 344
+I+ L ++R++++ + RID RGV DIR ++ +PR HGS+LF
Sbjct: 325 PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALF 384
Query: 345 TRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGH 404
RG+TQ L V TL R EQ++D L +M +YN PP++ G+ GR+G PKRREIGH
Sbjct: 385 ERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGH 444
Query: 405 GRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAG 464
G LA+RA++PVLP +F Y+IR VSE SNGS+SM SVC ++LL+AGVP+ VAG
Sbjct: 445 GALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAG 504
Query: 465 IAMGLIK---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 520
IAMGLI +GE V L+DILG ED GDMDFKVAGT +TALQ+D K+ GI ++
Sbjct: 505 IAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 521 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTL 580
AL +A+ +IL+ M E +E+S APR+IT+KI KI +VIG I +
Sbjct: 565 AAALKQARDARLHILDVM-MEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQI 623
Query: 581 TEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVLRLFDFGA 638
E+TG +I I D+G I I + + + + A+ I + S ++G+ G V++ FGA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 639 IIRILSGKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 688
+ +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 = 430 bits (1106), Expect = e-120, Method: Compositional matrix adjust.
Identities = 269/714 (37%), Positives = 399/714 (55%), Gaps = 34/714 (4%)
Query: 5 ILKSFKYGSYKISIEIGEIARQATSSVLVSIED-TVILATVVSCKDPTSTYNFFPLTVDY 63
++ + +G+ I E G +ARQA S + ++D T +L+ + K+P +FFPLTVD
Sbjct: 28 VIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTXVLSATTASKNPKDQLDFFPLTVDV 87
Query: 64 IEKAYAAGRIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQ 123
E+ YAAG+IPGSFF+REG+PSE + RLIDRP+RP F +G NEIQ+V + ++NP
Sbjct: 88 EERXYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIXALNPD 147
Query: 124 IDPDIASIIGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAG-- 181
D+ +I S + ++ LPF GP+G +V I G+++ PT +L+ + D +VAG
Sbjct: 148 HLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDXVVAGRV 207
Query: 182 ---------------TEKAIITVESESKQLPEDIILNAIIFGHEKMKIAINAINELVQNV 226
TEK I V+ ++ E+++ + +K+ A +L
Sbjct: 208 LEDGDVAIXXVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKA 267
Query: 227 GQKKVNWDPIVKD--KTLISKIINISEHKIRKAYQIKNKQIRDLTFKNISKDIYSSLIDN 284
+ + P+ D ++ + ++ A I KQ R+ + L+
Sbjct: 268 AKPTGEF-PVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLL-- 324
Query: 285 ENLTIDINDINCILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLF 344
+I+ L ++R++++ + RID RGV DIR ++ +PR HGS+LF
Sbjct: 325 PEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALF 384
Query: 345 TRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGH 404
RG+TQ L V TL R EQ++D L + +YN PP++ G+ GR+G PKRREIGH
Sbjct: 385 ERGETQILGVTTLNXLRXEQQLDTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGH 444
Query: 405 GRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAG 464
G LA+RA++PVLP +F Y+IR VSE SNGS+S SVC +LL+AGVP+ VAG
Sbjct: 445 GALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAG 504
Query: 465 IAMGLIK---DGE-KVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDII 520
IA GLI +GE V L+DILG ED GD DFKVAGT +TALQ+D K+ GI ++
Sbjct: 505 IAXGLISQEINGETHYVALTDILGAEDAFGDXDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 521 QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTL 580
AL +A+ +IL+ + E +E S APR+IT+KI KI +VIG I +
Sbjct: 565 AAALKQARDARLHILD-VXXEAIDTPDEXSPNAPRIITVKIPVDKIGEVIGPKRQXINQI 623
Query: 581 TEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTE--SVQIGKVYTGIVLRLFDFGA 638
E+TG +I I D+G I I + + + + A+ I + S ++G+ G V++ FGA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 639 IIRILSGKDGLLHISQI----SSKRVNIITDFLKENQKVRVKVLGIDDRGRIKL 688
+ +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 = 374 bits (961), Expect = e-104, Method: Compositional matrix adjust.
Identities = 235/626 (37%), Positives = 355/626 (56%), Gaps = 27/626 (4%)
Query: 12 GSYKISIEIGEIARQATSSVLVSIEDTVILATVVSCKDPTSTYNFFPLTVDYIEKAYAAG 71
G+ K+ I G++AR A S +V DT ++ T VS P+ + F PL VDY +KA AAG
Sbjct: 13 GNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPS-QFMPLVVDYRQKAAAAG 71
Query: 72 RIPGSFFKREGKPSERETIISRLIDRPIRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASI 131
RIP ++ +RE S++E + SR+IDR IRPLFP GY + Q++ +L+V+ +PD+ +I
Sbjct: 72 RIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLAI 131
Query: 132 IGVSTALSISELPFLGPLGVAKVGYIDGKYILNPTTEQLKKSHLDLLVAGTEKA-IITVE 190
G S ALS+S++P+ GP+G ++G IDG+Y++NPT +++ S L+L+VAG K+ I+ +E
Sbjct: 132 NGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVMLE 191
Query: 191 SESKQLPEDIILNAIIFGHEKMKIAINAINELVQNVGQKKVNWDPIVKDKTLISKIINIS 250
+ ++ + + +AI G + + I I +LV+ G K + I K
Sbjct: 192 ASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYT--- 248
Query: 251 EHKI--RKAYQI-----KNKQIRDLTFKNISKDIYSSLIDNENLTIDINDINCILYDLES 303
HK+ + Y + +K RD I D L + D +I +
Sbjct: 249 -HKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQL-KEKFPEADPYEIIESFNVVAK 306
Query: 304 KIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTS--- 360
++ R +L++ R D R + +R +S + HGS+LF RG TQ L T +
Sbjct: 307 EVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESG 366
Query: 361 -RDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNN 419
+ +Q I A+ G +FMLHY PP+AT +IG++ RRE+GHG LA++AL PV+P +
Sbjct: 367 IKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIPRD 426
Query: 420 NKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLI--KDGEKVV 477
F ++IR+ SE+ ESNGSSSMAS CGG LAL+D+GVPIS VAG+A+GL+ D EK
Sbjct: 427 --FPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGE 484
Query: 478 I-----LSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYKAKKGLS 532
I L+DILG ED GDMDFK+AGT GITALQ DIK+ GI I+ A+ +A
Sbjct: 485 IEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKK 544
Query: 533 YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDIND 592
IL+ M + K + + P + T+++ SK +G GG ++ L ETG I D
Sbjct: 545 EILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD 604
Query: 593 EGIITIASFNSVSGQEAKRRIEKLTE 618
E ++ + + EA+ I ++ +
Sbjct: 605 EETFSVFAPTPSAMHEARDFITEICK 630
>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 = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 75/247 (30%), Positives = 125/247 (50%), Gaps = 17/247 (6%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 11 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 69
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 70 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 126
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ ED
Sbjct: 127 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETED 182
Query: 488 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 541
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 183 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 239
Query: 542 VPKCKNE 548
+ K E
Sbjct: 240 YVEFKEE 246
>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 = 87.4 bits (215), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 75/247 (30%), Positives = 125/247 (50%), Gaps = 17/247 (6%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 8 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 66
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 67 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 123
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ ED
Sbjct: 124 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETED 179
Query: 488 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 541
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 180 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 236
Query: 542 VPKCKNE 548
+ K E
Sbjct: 237 YVEFKEE 243
>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 = 86.3 bits (212), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 72/240 (30%), Positives = 114/240 (47%), Gaps = 17/240 (7%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K I+D GLR+D R +++RPI I +L R GS G + ++ A G E +
Sbjct: 10 KLIVD-GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNK-VIAAVFGPR--EVHPE 65
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
L YNM PF+ + R G P RR I +++K A V+ +I
Sbjct: 66 HLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELFPRSAID 124
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ E+ +++ S A + +AL+DAGVP+ + +A+G DG+ V+ D + +ED
Sbjct: 125 IFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-DGQLVL---DPMKEED 180
Query: 488 RCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
G+ D A G + I LQMD + +T D ++ A+ AKKG I E + +
Sbjct: 181 NFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYEMQREAI 237
Score = 29.3 bits (64), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 35/143 (24%), Positives = 56/143 (39%), Gaps = 30/143 (20%)
Query: 48 KDPTST-----YNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRP---- 98
+DP+ YN P +V+ ++ PG P R IS++
Sbjct: 68 QDPSKAIIRYRYNMAPFSVEERKR-------PG--------PDRRSIEISKVSKEAFEAV 112
Query: 99 -IRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYI 157
++ LFP + I I V VL + A + S AL + +P G + VG
Sbjct: 113 IMKELFPR---SAIDIFVEVLQAD--AGSRTACLNAASVALVDAGVPMKGMITSVAVGKA 167
Query: 158 DGKYILNPTTEQLKKSHLDLLVA 180
DG+ +L+P E+ D+ A
Sbjct: 168 DGQLVLDPMKEEDNFGEADMPFA 190
>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: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K I+D GLR+D R +++RPI I +L R GS G + ++ A G E
Sbjct: 10 KLIVD-GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNK-VIAAVFGPR--EVHPR 65
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
L YNM PF+ + R G P RR I +++K A V+ +I
Sbjct: 66 HLQDPSKAIIRYRYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKELFPRSAID 124
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ E+ +++ S A + +AL+DAGVP+ + +A+G DG+ V+ D + +ED
Sbjct: 125 IFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-DGQLVL---DPMKEED 180
Query: 488 RCGDMDFKVA-----GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEV 542
G+ D A G + I LQMD + +T D ++ A+ AKKG I E + +
Sbjct: 181 NFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYEMQREAI 237
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 35/143 (24%), Positives = 56/143 (39%), Gaps = 30/143 (20%)
Query: 48 KDPTST-----YNFFPLTVDYIEKAYAAGRIPGSFFKREGKPSERETIISRLIDRP---- 98
+DP+ YN P +V+ ++ PG P R IS++
Sbjct: 68 QDPSKAIIRYRYNMAPFSVEERKR-------PG--------PDRRSIEISKVSKEAFEAV 112
Query: 99 -IRPLFPEGYLNEIQIVVYVLSVNPQIDPDIASIIGVSTALSISELPFLGPLGVAKVGYI 157
++ LFP + I I V VL + A + S AL + +P G + VG
Sbjct: 113 IMKELFPR---SAIDIFVEVLQAD--AGSRTACLNAASVALVDAGVPMKGMITSVAVGKA 167
Query: 158 DGKYILNPTTEQLKKSHLDLLVA 180
DG+ +L+P E+ D+ A
Sbjct: 168 DGQLVLDPMKEEDNFGEADMPFA 190
>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 = 84.0 bits (206), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 74/247 (29%), Positives = 124/247 (50%), Gaps = 17/247 (6%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K ILD G R D R +++R I I G+L GS++F G+T+A + A G +
Sbjct: 13 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA-IAAVYGPKEMHPRHL 71
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
+L + Y+M PF+T D + P RREI ++ + AL + +I
Sbjct: 72 SLPDRAV--LRVRYHMTPFST-DERKNPAPSRREIELSKVIREALESAVLVELFPRTAID 128
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ +EI +++ S + S+ LAL DAG+P+ + +AG+A+G DG VI+ D+ E
Sbjct: 129 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK-ADG---VIILDLNETEA 184
Query: 488 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYIL----EKMKTE 541
G+ D +A ++N +T Q++ +T D + A A KG++ I E +K++
Sbjct: 185 MWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKGINIIYNLEREALKSK 241
Query: 542 VPKCKNE 548
+ K E
Sbjct: 242 YVEFKEE 248
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 83.2 bits (204), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 39/72 (54%), Positives = 56/72 (77%)
Query: 619 SVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVL 678
+++G+VYTG V R+ DFGA + I GK+GL+HISQI+ KRV +TD+L+ Q+V VKVL
Sbjct: 2 EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61
Query: 679 GIDDRGRIKLSM 690
+D +GRI+LS+
Sbjct: 62 EVDRQGRIRLSI 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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 76/233 (32%), Positives = 110/233 (47%), Gaps = 15/233 (6%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R +++RP+ I GIL R GSS G + ++VA G E +I L
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNK-ILVAVYGPR--EAQIRKLQRPDR 72
Query: 375 DSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYS-IRLVSEIT 433
YNM PF+ + R G P RR + ++ AL P L KF S I + E+
Sbjct: 73 AVIRCRYNMAPFSVEERKRPG-PDRRSVEISKITAEALRPAL-ILEKFPRSVIDVFIEVL 130
Query: 434 ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMD 493
E+ G + A + +AL DAG+P+ + V A G K G++VV+ D+ +ED+ G D
Sbjct: 131 EAEGGTRCAGITAASVALADAGIPMRDMVVACAAG--KVGDQVVL--DLSEEEDKEGQAD 186
Query: 494 FKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKMKTEVPK 544
VA IT LQ D +T + + AL A +G I E K + K
Sbjct: 187 VPVAILPRTREITLLQSD---GNLTPEEFERALDLAVEGCLRIHEVQKEALRK 236
>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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 66/204 (32%), Positives = 99/204 (48%), Gaps = 10/204 (4%)
Query: 308 KQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKID 367
K I + G RID R ++RPI + G+L +GS+ G + ++ A G K
Sbjct: 9 KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNK-IIAAVYGPRELHPK-- 65
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
L + YNM PF+ + + G P RR I ++ K AL P L +I
Sbjct: 66 HLQRPDRAILRVRYNMAPFSVEERKKPG-PDRRSIEISKVIKGALEPALILEMFPRTAID 124
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ E+ +++ + +A + LAL DAG+P+ + VA A G I +GE I+ D+ +ED
Sbjct: 125 VFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKI-EGE---IVLDLNKEED 180
Query: 488 RCGDMDFKVA--GTVNGITALQMD 509
G+ D VA N IT LQMD
Sbjct: 181 NYGEADVPVAIMPLKNDITLLQMD 204
>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 = 5e-10, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 112/247 (45%), Gaps = 36/247 (14%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 375 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 428 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 476
+ ++ +++G ++ A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 477 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 532
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 533 YILEKMK 539
++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: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 375 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 428 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 476
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 477 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 532
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 533 YILEKMK 539
++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: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 375 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
Y+M P AT GRIG + EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GRTHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 428 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 476
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 477 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 532
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 533 YILEKMK 539
++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 = 2e-09, Method: Compositional matrix adjust.
Identities = 63/247 (25%), Positives = 110/247 (44%), Gaps = 36/247 (14%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFT 374
+R D R + +RP+SI+ L GS L + G T+ + A++ E + L G+
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56
Query: 375 DSFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
Y+M P AT GRIG EI R+ RA+ + +I
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIG-GATHEI--QRMIGRAMRTAVELTKIGERTIW 113
Query: 428 LVSEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKV 476
+ ++ +++G + A++ G +A+ DA PI + VA +++G++ D
Sbjct: 114 VDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND---- 169
Query: 477 VILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITYDIIQIALYK----AKKGLS 532
IL D+ +ED +D V GT +G + ++ G Y + L K A+KG++
Sbjct: 170 RILLDLNFEEDSAAQVDMNVVGTGSGRLS---EVHTMGEEYSFTKDELIKMLDLAQKGIN 226
Query: 533 YILEKMK 539
++E K
Sbjct: 227 ELIELQK 233
>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 = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 53/233 (22%), Positives = 101/233 (43%), Gaps = 16/233 (6%)
Query: 312 DKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA----TLGTSRDEQKID 367
D+G R+D R ++R I R G+ + GS+ +G+T+AL V + SR D
Sbjct: 13 DQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPD 72
Query: 368 ALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIR 427
+ Y+ F+TG+ R R+ G ++ + I
Sbjct: 73 RAL------VNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQID 126
Query: 428 LVSEITESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDED 487
+ ++ +++G + A V LA+LDAG+P+ + V + G + DG + LS + E+
Sbjct: 127 IYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-DGTALADLSHV---EE 182
Query: 488 RCGDMDFKVA--GTVNGITALQMDIKIFGITYDIIQIALYKAKKGLSYILEKM 538
G +A I L+MD ++ + + A +A + + +L+++
Sbjct: 183 AAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRV 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 = 51/174 (29%), Positives = 79/174 (45%), Gaps = 17/174 (9%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 375
R D R N +RP S L R HGS+ + +GDT ++ A G +K GE +
Sbjct: 5 RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDT-IVLAAVYGPKPGTRK-----GENPE 58
Query: 376 SFMLHYNMPPFATGDIGRIGVPKRREIGHGR-LAKRALLPVLPNNNKFNYSIRLVSEITE 434
+ P TG IG+ K E+ R L LL V PN + ++ ++
Sbjct: 59 KASIEVVWKPM-TGQIGK--QEKEYEMTLKRTLQSICLLTVHPNT-----TTSVILQVVG 110
Query: 435 SNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGLIKDGEKVVILSDILGDEDR 488
++GS ++ C AL+ AG+P+ I G+++DGE VIL +E +
Sbjct: 111 NDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGE--VILDTNKAEEQQ 162
>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: 615 KLTESVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQK 672
K E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE QK
Sbjct: 4 KAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQK 63
Query: 673 VRVKVLGIDDR-GRIKLSM 690
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 = 6e-07, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 615 KLTESVQIGKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQK 672
+ E + G+ V R+ ++GA + + GK+ +HIS+++S V I D+LKE QK
Sbjct: 3 RAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQK 62
Query: 673 VRVKVLGIDDR-GRIKLSM 690
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: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALM-GEF 373
+R+D R ++R I I T L GS L GDT+ + AT+ E+++ M GE
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI-----EERVPPFMRGEG 65
Query: 374 TDSFMLHYNMPPFATGDI----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 429
Y M P AT G R + RL RAL V+ ++ +
Sbjct: 66 KGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWID 125
Query: 430 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 478
++ +++G + AS+ G +A++ A +P+ +++A ++G+++ E+ V+
Sbjct: 126 CDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVE--EQGVV 183
Query: 479 LSDILGDEDRCGDMDFKVAGTVNG 502
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 = 9e-06, Method: Compositional matrix adjust.
Identities = 62/242 (25%), Positives = 111/242 (45%), Gaps = 25/242 (10%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDA-LMGEF 373
+R D R +++RPI+ + GS L T G+T+ + A++ E ++ L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV-----EDRVPPFLRGGG 55
Query: 374 TDSFMLHYNMPPFATGDI----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 429
Y+M P AT G R + RL RAL V+ +I +
Sbjct: 56 KGWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWID 115
Query: 430 SEITESNGSSSMASVCGGCLA-------LLDAGV----PISEHVAGIAMGLIKDGEKVVI 478
++ +++G + AS+ G LA L+ AG PI++ +A I++G+ D E+ ++
Sbjct: 116 CDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI--DKEQGIL 173
Query: 479 LSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEK 537
L D+ +ED ++D V T +G LQ + + + + L A+KG+ +++K
Sbjct: 174 L-DLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDK 232
Query: 538 MK 539
K
Sbjct: 233 QK 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 = 62/242 (25%), Positives = 111/242 (45%), Gaps = 25/242 (10%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDA-LMGEF 373
+R D R +++RPI+ + GS L T G+T+ + A++ E ++ L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV-----EDRVPPFLRGGG 55
Query: 374 TDSFMLHYNMPPFATGDI----GRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLV 429
Y+M P AT G R + RL RAL V+ +I +
Sbjct: 56 KGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWID 115
Query: 430 SEITESNGSSSMASVCGGCLA-------LLDAGV----PISEHVAGIAMGLIKDGEKVVI 478
++ +++G + AS+ G LA L+ AG PI++ +A I++G+ D E+ ++
Sbjct: 116 CDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI--DKEQGIL 173
Query: 479 LSDILGDEDRCGDMDFKVAGTVNG-ITALQMDIKIFGITYDIIQIALYKAKKGLSYILEK 537
L D+ +ED ++D V T +G LQ + + + + L A+KG+ +++K
Sbjct: 174 L-DLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDK 232
Query: 538 MK 539
K
Sbjct: 233 QK 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: 616 LTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNIITDFLKENQKVRV 675
+ ++G VYTG V L +GA + + GL+HIS+++ V I + L +V+V
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 676 KVLGID-DRGRIKLSM 690
KVL +D ++G+I LS+
Sbjct: 61 KVLAVDEEKGKISLSI 76
>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: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 660
F + QE +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V
Sbjct: 638 FKTAEFQEG---VESLKD-LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV 693
Query: 661 NIITDFLKENQKVRVKVLGID-DRGRIKLSM 690
+ +K V+VKV+ +D R R+ LSM
Sbjct: 694 KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM 724
>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: 601 FNSVSGQEAKRRIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRV 660
F + QE +E L + ++ G V G+V + +FGA + I +DGL+HIS +S K V
Sbjct: 637 FKTAEFQEG---VESLKD-LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV 692
Query: 661 NIITDFLKENQKVRVKVLGID-DRGRIKLSM 690
+ +K V+VKV+ +D R R+ LSM
Sbjct: 693 KDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM 723
>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 = 21/45 (46%), Positives = 28/45 (62%)
Query: 309 QILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
+L +G RID+RG D RPI I G++ + GS+L G TQ LV
Sbjct: 20 NLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLV 64
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 3/71 (4%)
Query: 623 GKVYTGIVLRLFDFGAIIRI--LSGKDGLLHISQISSKRVNIITDFLKENQKVRVKVLGI 680
G++ V ++FD+G+ + + G L S++SSK V I D LKEN+KV VKV+ +
Sbjct: 12 GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV 71
Query: 681 DDR-GRIKLSM 690
D R G + +S+
Sbjct: 72 DRRKGTVDVSL 82
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 54/204 (26%), Positives = 86/204 (42%), Gaps = 27/204 (13%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGEF 373
R R + +RPI I GS L GDT+ + V A G R L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPR------FLKGQG 56
Query: 374 TDSFMLHYNMPPFATGDIGRIGVPKRREIGH----GRLAKRALLPVLPNNNKFNYSIRLV 429
Y M P +TG+ + + ++ G RL R+L L + ++ +
Sbjct: 57 QGWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYID 116
Query: 430 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 478
++ +++G + AS+ G +AL+DA G P+ + VA +++G I G V+
Sbjct: 117 CDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVG-IYQGVPVLD 175
Query: 479 LSDILGDEDRCGDMDFKVAGTVNG 502
L D L ED + D V T G
Sbjct: 176 L-DYL--EDSAAETDLNVVMTDAG 196
>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 = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 42/153 (27%), Positives = 64/153 (41%), Gaps = 13/153 (8%)
Query: 325 IRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTDSFMLHYNMP 384
+R + +L R GS+ F +GDT L G + E K+ E + L +
Sbjct: 30 LRHFACEQNLLSRPDGSASFLQGDTSVLA-GVYGPA--EVKVSK---EIFNKATLEVILR 83
Query: 385 PFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASV 444
P +IG+P E RL + V+ SI +V ++ GS +
Sbjct: 84 P-------KIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCL 136
Query: 445 CGGCLALLDAGVPISEHVAGIAMGLIKDGEKVV 477
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 = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 53/204 (25%), Positives = 85/204 (41%), Gaps = 27/204 (13%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGEF 373
R R + +RPI I GS L GDT+ + V A G R L G+
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPR------FLKGQG 56
Query: 374 TDSFMLHYNMPPFATGDIGRIGVPKRREIGH----GRLAKRALLPVLPNNNKFNYSIRLV 429
Y P +TG+ + + ++ G RL R+L L + ++ +
Sbjct: 57 QGWLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYID 116
Query: 430 SEITESNGSSSMASVCGGCLALLDA-----------GVPISEHVAGIAMGLIKDGEKVVI 478
++ +++G + AS+ G +AL+DA G P+ + VA +++G I G V+
Sbjct: 117 CDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVG-IYQGVPVLD 175
Query: 479 LSDILGDEDRCGDMDFKVAGTVNG 502
L D L ED + D V T G
Sbjct: 176 L-DYL--EDSAAETDLNVVXTDAG 196
>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: 299 YDLESKIIRKQILD---KGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 355
D+ +I RK I D RID R +++ R ISI TG++ + GSS G+TQ +V
Sbjct: 5 MDIIPEITRKSITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
Query: 356 TLGTSRDEQKIDALMGEFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRAL 412
+ 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: 612 RIEKLTESVQIGKVYTGIVLRLFDFGAIIRILSG-KDGLLHISQISSKRVNIITDFLKEN 670
R E + + ++ G V + D+GA I+I K GL+H + +SS RV+ ++ +
Sbjct: 12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVG 71
Query: 671 QKVRVKVLGID---DRGRIKLSM 690
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 = 0.014, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 618 ESVQIGKVYTGIVLRLFDFGAIIRILSGK---DGLLHISQISSK-RVNIITDFLKENQKV 673
E IG +Y G V + FG +++ + +GL+HIS++ + RV + D + + Q+V
Sbjct: 8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRV 67
Query: 674 RVKVL 678
+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 = 37.0 bits (84), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 315 LRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL--VVATLGTSRDEQKIDALMGE 372
LR+D RG D R + + T ++ T GS+ G T L V A +GT + E+ + +
Sbjct: 36 LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEF 95
Query: 373 FTDS 376
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 = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 313 KGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDALMG 371
+GLR+D R N++R P GSS +G+ + + TL E ++ + M
Sbjct: 12 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNK---IITLVKGPKEPRLKSQMD 68
Query: 372 EFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 431
+ N+ F+ + + R + + +L+ + N N R V +
Sbjct: 69 TSKALLNVSVNITKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 125
Query: 432 IT----ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGL 469
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 = 0.059, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 313 KGLRIDNRGVNDIRPISIRTGILPRT-HGSSLFTRGDTQALVVATLGTSRDEQKIDALMG 371
+GLR+D R N++R P GSS +G+ + + TL E ++ + M
Sbjct: 10 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNK---IITLVKGPKEPRLKSQMD 66
Query: 372 EFTDSFMLHYNMPPFATGDIGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRLVSE 431
+ N+ F+ + + R + + +L+ + N N R V +
Sbjct: 67 TSKALLNVSVNINKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 123
Query: 432 IT----ESNGSSSMASVCGGCLALLDAGVPISEHVAGIAMGL 469
I E +G + + G LAL+DAG+ + ++++GI++GL
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 165
>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 = 0.10, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 297 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
IL D++ + ++ D RID RG ++ R + I ++ + GS+L GDTQ +V
Sbjct: 5 ILVDIKRDYVLSKLRDNE-RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVV 60
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 297 ILYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALV 353
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 = 0.19, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 305 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 352
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 = 0.19, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 305 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 352
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 = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 305 IIRKQ----ILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQAL 352
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 = 0.21, Method: Compositional matrix adjust.
Identities = 51/206 (24%), Positives = 87/206 (42%), Gaps = 30/206 (14%)
Query: 316 RIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATLGTSRDEQKIDALMGEFTD 375
R D R +++RP+ I G GS L G T+ L A++ + +G T
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLT- 65
Query: 376 SFMLHYNMPPFATGD-------IGRIGVPKRREIGHGRLAKRALLPVLPNNNKFNYSIRL 428
Y M P AT GR+ + +EI RL R+L + +I +
Sbjct: 66 ---AEYAMLPSATHSRSDRESVRGRLS-GRTQEI--SRLIGRSLRACIDLAALGENTIAI 119
Query: 429 VSEITESNGSSSMASVCGGCLALLDAGV------------PISEHVAGIAMGLIKDGEKV 476
++ +++G + A++ G +AL DA P+S +A +++G++ DG
Sbjct: 120 DCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV-DGR-- 176
Query: 477 VILSDILGDEDRCGDMDFKVAGTVNG 502
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 = 0.88, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 559 IKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITI 598
+ 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 = 0.98, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 402 IGHGRLAKRALLPVLPNNNKFNYSIRLVSEITESNGSSSMASVCGGCLALLDAGVPISEH 461
I H L+ L + P+ +I + + +GS ++ G C ALLD G+P
Sbjct: 72 IIHSTLSNAINLELFPHT-----TISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETV 126
Query: 462 VAGIAMGLIKD 472
G+ + +KD
Sbjct: 127 FCGVLIVRVKD 137
>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 = 0.99, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 623 GKVYTGIVLRLFDFGAIIRILSGKDGLLHISQISSKRVNI-ITDFLKENQKVRVKVLGID 681
G TG V L D+G + I G +GL+H+S++ NI + + V V VL ID
Sbjct: 31 GTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID 90
Query: 682 -DRGRIKLSM 690
+R RI L +
Sbjct: 91 EERRRISLGL 100
>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: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 613
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 155 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 214
Query: 614 E 614
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 = 1.5, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 613
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 157 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 216
Query: 614 E 614
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: 557 ITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQ---EAKRRI 613
I I I P K+ VIGK S TLT ++G I + + G I + S + EA R+I
Sbjct: 157 IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKI 216
Query: 614 E 614
E
Sbjct: 217 E 217
>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 = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 298 LYDLESKIIRKQILDKGLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVATL 357
L+D E +I+ K+I DKGL +D + + +H S +FT+ T+A TL
Sbjct: 160 LHDDEVEIVLKEIKDKGLNLD----------GVHFHVGSDSHNSEVFTKALTKARNTVTL 209
Query: 358 G 358
Sbjct: 210 A 210
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 60/128 (46%), Gaps = 12/128 (9%)
Query: 565 KIRDVIGKGGSTIRTLTEETGTQIDIND----EGIITIASFNSVSGQEAKRRIEKLTESV 620
++ +IGK G +++ + EE+G +I+I++ E IIT+A + + I+KL E +
Sbjct: 15 EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDI 74
Query: 621 QIGKVYTG------IVLRLFDFGAIIRILSGKDG--LLHISQISSKRVNIITDFLKENQK 672
+ + LRL + L GK G + I + + +V + D L + +
Sbjct: 75 SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE 134
Query: 673 VRVKVLGI 680
+ + 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: 523 ALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIK--IDPSKIRDVIGKGGSTIRTL 580
A++KA + I++K++ ++ + + +T++ + S+ +IGKGG I+ +
Sbjct: 58 AIFKA---FAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 114
Query: 581 TEETGTQIDI 590
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 = 3.4, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 35/58 (60%), Gaps = 3/58 (5%)
Query: 635 DFGAIIRILSGK--DGLLHISQISSKRVNIITDFLKENQKVRVKVLGID-DRGRIKLS 689
+ GA + +L +G++H+S++S +R+ I ++ + VKV+ +D ++G I LS
Sbjct: 26 EMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLS 83
>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 = 3.7, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 569 VIGKGGSTIRTLTEETGTQIDINDEGIITIASFNSVSGQEAKRRIEKLTESVQIGKVY 626
+IG+GG RT+ E T T I++ + + I + AK+ IE L E VY
Sbjct: 112 IIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYE--RAMAAKQAIEMLAEGRMHSTVY 167
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 41/177 (23%), Positives = 71/177 (40%), Gaps = 23/177 (12%)
Query: 458 ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITY 517
I + AG +G K G+ +V L G + GT + +Q I+ +
Sbjct: 12 IPSYAAGSIIG--KGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVH 69
Query: 518 DII-----QIALYKAKKGLSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGK 572
I ++ AK IL+ T P N++ P S +IGK
Sbjct: 70 GFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPN--------STAGLIIGK 121
Query: 573 GGSTIRTLTEETGTQIDIND--EGIITIASFNSVSGQEAKRR------IEKLTESVQ 621
GG+T++ + E++G + ++ +GI +VSG+ + R I+K+ E Q
Sbjct: 122 GGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178
>pdb|2GAG|A Chain A, Heteroteterameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 15/83 (18%)
Query: 531 LSYILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQIDI 590
L ++ E ++TE P + +L T+ + + RDVI K ST +D+
Sbjct: 701 LDWLEEWLQTEWPDLDVTCTSVTEQLATVAVVGPRSRDVIAKLAST-----------VDV 749
Query: 591 NDEGIITIASFNSV---SGQEAK 610
++EG +A F V SG EA+
Sbjct: 750 SNEGFKFMA-FKDVVLDSGIEAR 771
>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 = 5.4, Method: Compositional matrix adjust.
Identities = 39/177 (22%), Positives = 72/177 (40%), Gaps = 23/177 (12%)
Query: 458 ISEHVAGIAMGLIKDGEKVVILSDILGDEDRCGDMDFKVAGTVNGITALQMDIKIFGITY 517
I + AG +G K G+ +V L G + GT + +Q I+ +
Sbjct: 12 IPSYAAGSIIG--KGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVH 69
Query: 518 DIIQIALYKAKKGLS-----YILEKMKTEVPKCKNELSKFAPRLITIKIDPSKIRDVIGK 572
I + + + ++ IL+ T P N++ P S +IGK
Sbjct: 70 GFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPN--------STAGLIIGK 121
Query: 573 GGSTIRTLTEETGTQIDIND--EGIITIASFNSVSGQEAKRR------IEKLTESVQ 621
GG+T++ + E++G + ++ +GI +VSG+ + R I+K+ E Q
Sbjct: 122 GGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDPQ 178
>pdb|4IFD|E Chain E, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 267
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 314 GLRIDNRGVNDIRPISIRTGILPRTHGSSLFTRGDTQALVVA 355
+R D R + RPI I T LP ++GSS D +V+
Sbjct: 22 SIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVS 63
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 549 LSKFAPRLITIKIDPSKIRDVIGKGGSTIRTLTEETGTQI--DINDEGIITIASFNSVSG 606
L++ P + + + +IG+GG TIR++ + +G +I D EG + ++ +SG
Sbjct: 9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG 68
Query: 607 QE 608
+
Sbjct: 69 TQ 70
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 621 QIGKVYTGIVLRLFDFGAIIRILSGKDGLLHISQIS 656
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 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,272,437
Number of Sequences: 62578
Number of extensions: 815523
Number of successful extensions: 2526
Number of sequences better than 100.0: 89
Number of HSP's better than 100.0 without gapping: 61
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 2390
Number of HSP's gapped (non-prelim): 110
length of query: 692
length of database: 14,973,337
effective HSP length: 106
effective length of query: 586
effective length of database: 8,340,069
effective search space: 4887280434
effective search space used: 4887280434
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)