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= 026672
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 246 bits (627), Expect = 1e-65, Method: Compositional matrix adjust.
Identities = 117/235 (49%), Positives = 169/235 (71%), Gaps = 7/235 (2%)
Query: 1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
+E +S +G R+DGRR E+R+++A +G A+ADGSA E GNTK +A VYGP E++ +++
Sbjct: 8 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67
Query: 60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
+ + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 68 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 127
Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLD------SAGGP 173
+VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L D +AGGP
Sbjct: 128 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 187
Query: 174 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 228
+ + +LP ++ LL+MDA+L + E V++ A + + V + V+ ++ ++
Sbjct: 188 QLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVRE 242
>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 = 210 bits (534), Expect = 6e-55, Method: Compositional matrix adjust.
Identities = 107/231 (46%), Positives = 150/231 (64%), Gaps = 7/231 (3%)
Query: 1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
++ + G R+DGR+ E+R ++ E+G + A+GSA E G K+IAAVYGPRE+ K
Sbjct: 8 LKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHL 67
Query: 61 QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
Q D+A++R Y+MA FS +R +KP DRRS EIS VI+ +E ++ + PR+ ID+F
Sbjct: 68 QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVF 126
Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPD 174
++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG + +L D+ G D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186
Query: 175 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 225
V V I+P + +TLLQMD L + F + ++LAI+G KAV RE L E
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEK 237
>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 = 197 bits (501), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 95/232 (40%), Positives = 146/232 (62%), Gaps = 9/232 (3%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
+G R DGR+P E+R ++ E+G + ADGSA+FEMGNTK IAAVYGP+E+ + + D+A
Sbjct: 16 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 75
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
++R Y M FST +R + P RR E+S VIR+ +E+ +L L PR+ ID+F ++LQA
Sbjct: 76 VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 134
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPDVTVGIL 180
D G+R + AA+LAL DAGIPMRD++ + G + +L D G D+ + ++
Sbjct: 135 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMM 194
Query: 181 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 232
P+L++VTL Q++ + + F LA++G + N RE L +K +E +
Sbjct: 195 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 244
>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 = 197 bits (500), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 95/232 (40%), Positives = 146/232 (62%), Gaps = 9/232 (3%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
+G R DGR+P E+R ++ E+G + ADGSA+FEMGNTK IAAVYGP+E+ + + D+A
Sbjct: 18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
++R Y M FST +R + P RR E+S VIR+ +E+ +L L PR+ ID+F ++LQA
Sbjct: 78 VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLD------SAGGPDVTVGIL 180
D G+R + AA+LAL DAGIPMRD++ + G + +LD G D+ + ++
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMM 196
Query: 181 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 232
P+L++VTL Q++ + + F LA++G + N RE L +K +E +
Sbjct: 197 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 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 = 197 bits (500), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 95/232 (40%), Positives = 146/232 (62%), Gaps = 9/232 (3%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
+G R DGR+P E+R ++ E+G + ADGSA+FEMGNTK IAAVYGP+E+ + + D+A
Sbjct: 13 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 72
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
++R Y M FST +R + P RR E+S VIR+ +E+ +L L PR+ ID+F ++LQA
Sbjct: 73 VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 131
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPDVTVGIL 180
D G+R + AA+LAL DAGIPMRD++ + G + +L D G D+ + ++
Sbjct: 132 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMM 191
Query: 181 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 232
P+L++VTL Q++ + + F LA++G + N RE L +K +E +
Sbjct: 192 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 241
>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 = 189 bits (481), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 99/220 (45%), Positives = 136/220 (61%), Gaps = 7/220 (3%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R DGR E+R L+ E G + +ADGS+ E G K++ AVYGPRE Q + Q D+A++
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75
Query: 69 RCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADG 128
RC Y+MA FS +R R P DRRS EIS + + + ++ PRS ID+F++VL+A+G
Sbjct: 76 RCRYNMAPFSVEERKR-PGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEG 134
Query: 129 GTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPDVTVGILPT 182
GTR A I AA++AL DAGIPMRD+V +C+AG + +L D G DV V ILP
Sbjct: 135 GTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPR 194
Query: 183 LDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
++TLLQ D L FE + LA+EGC + +E L
Sbjct: 195 TREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEAL 234
>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 = 181 bits (460), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 97/226 (42%), Positives = 141/226 (62%), Gaps = 10/226 (4%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
+GLRLDGR+ E+R ++ E + +ADGS EMG KVIAAV+GPREV + Q +A
Sbjct: 14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKA 73
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
++R Y+MA FS +R R P DRRS EIS V ++ EA I+ L PRS IDIFV+VLQA
Sbjct: 74 IIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPDVTVGIL 180
D G+R+AC+NAA++AL DAG+PM+ ++TS + G + +L D+ G D+ L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192
Query: 181 ---PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 223
++ + LLQMD ++ + + ++LA +G + RE +L
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAIL 238
>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 = 181 bits (458), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 97/226 (42%), Positives = 141/226 (62%), Gaps = 10/226 (4%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
+GLRLDGR+ E+R ++ E + +ADGS EMG KVIAAV+GPREV + Q +A
Sbjct: 14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKA 73
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
++R Y+MA FS +R R P DRRS EIS V ++ EA I+ L PRS IDIFV+VLQA
Sbjct: 74 IIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL------DSAGGPDVTVGIL 180
D G+R+AC+NAA++AL DAG+PM+ ++TS + G + +L D+ G D+ L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192
Query: 181 ---PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 223
++ + LLQMD ++ + + ++LA +G + RE +L
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAIL 238
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 154 bits (389), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 86/235 (36%), Positives = 138/235 (58%), Gaps = 7/235 (2%)
Query: 1 MEFVSPEGLRLDGRRPTEMRQLRAEIG-NVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
+E SPEGLRLDGRR E+R+ + I + ADGS+ E GN K+I V GP+E + KS
Sbjct: 6 LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKS 65
Query: 60 QQMSDQALVRCEYSMANFSTGDRMRKP-KGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
Q + +AL+ ++ FS +R + K +RR EI + + E ++ ++ PR+ ID
Sbjct: 66 QMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 125
Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDSAGGPD---- 174
I + VL+ DGG + IN TLAL DAGI M D ++ S G ++TPLLD+ +
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMS 185
Query: 175 -VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 228
VT+G++ +K++LL ++ K+P + E+V+ + I G V + + E L ++ ++
Sbjct: 186 TVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQK 240
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 154 bits (388), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 86/235 (36%), Positives = 138/235 (58%), Gaps = 7/235 (2%)
Query: 1 MEFVSPEGLRLDGRRPTEMRQLRAEIG-NVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
+E SPEGLRLDGRR E+R+ + I + ADGS+ E GN K+I V GP+E + KS
Sbjct: 4 LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKS 63
Query: 60 QQMSDQALVRCEYSMANFSTGDRMRKP-KGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
Q + +AL+ ++ FS +R + K +RR EI + + E ++ ++ PR+ ID
Sbjct: 64 QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123
Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDSAGGPD---- 174
I + VL+ DGG + IN TLAL DAGI M D ++ S G ++TPLLD+ +
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMS 183
Query: 175 -VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 228
VT+G++ +K++LL ++ K+P + E+V+ + I G V + + E L ++ ++
Sbjct: 184 TVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQK 238
>pdb|2NN6|F Chain F, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 272
Score = 78.6 bits (192), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 65/231 (28%), Positives = 115/231 (49%), Gaps = 22/231 (9%)
Query: 14 RRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSD--------- 64
R PT +R + A G +++A GSA E G TKV+ AV GPR+ + +
Sbjct: 31 RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPA 90
Query: 65 --QALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
+ + C++ A F+ G R R P G E++L +++ +E + PR+Q+++
Sbjct: 91 ALRGRLLCDFRRAPFA-GRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSAL 149
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCS---------AGYLNSTPLLDSAGGP 173
+L+ G +A + AA LAL DAG+ M D+V C L+ T L +
Sbjct: 150 LLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAA 209
Query: 174 DVTVGILPTLDKVT-LLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 223
+TV ++P L++V LL T ++ + ++L +EGC+ + +++ L+
Sbjct: 210 GLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLV 260
>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 = 77.0 bits (188), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/138 (34%), Positives = 75/138 (54%), Gaps = 18/138 (13%)
Query: 19 MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA----LVRCEYSM 74
+R E +++ DGSA F G+T V+A VYGP EV+ S+++ ++A ++R + +
Sbjct: 30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK-VSKEIFNKATLEVILRPKIGL 88
Query: 75 ANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSAC 134
+ R R +IR T EA +L L PR+ I + +QV+ G + C
Sbjct: 89 PGVAEKSRER-------------LIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACC 135
Query: 135 INAATLALQDAGIPMRDI 152
+NAA +AL DAG+PMR +
Sbjct: 136 LNAACMALVDAGVPMRAL 153
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 56/178 (31%), Positives = 86/178 (48%), Gaps = 24/178 (13%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG----PREVQNKSQQMSDQ 65
R GR ++R +R A+GS + E G+TKVI V PR ++ + Q
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQ----- 57
Query: 66 ALVRCEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
+ EY M STG+R ++ K R+ EI +I +++ A + + + + I
Sbjct: 58 GWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDC 117
Query: 122 QVLQADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLD 168
V+QADGGTR+A I AT+AL DA G P++ +V + S G P+LD
Sbjct: 118 DVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLD 175
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 70.5 bits (171), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 55/178 (30%), Positives = 84/178 (47%), Gaps = 24/178 (13%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG----PREVQNKSQQMSDQ 65
R GR ++R +R A+GS + E G+TKVI V PR ++ + Q
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQ----- 57
Query: 66 ALVRCEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
+ EY STG+R ++ K R+ EI +I +++ A + + + + I
Sbjct: 58 GWLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDC 117
Query: 122 QVLQADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLD 168
V+QADGGTR+A I AT+AL DA G P++ V + S G P+LD
Sbjct: 118 DVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVPVLD 175
>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 = 67.4 bits (163), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 73/155 (47%), Gaps = 10/155 (6%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
E R DGR P ++R + +A GSA + G+T V+AAVYGP+ K + ++A
Sbjct: 2 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGEN-PEKA 60
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
+ + G ++ E + +++T+++ L + P + + +QV+
Sbjct: 61 SIEVVWKPMTGQIG---------KQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGN 111
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL 161
DG INA AL AGIP++ + + G L
Sbjct: 112 DGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVL 146
>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 = 64.7 bits (156), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 63/134 (47%), Gaps = 12/134 (8%)
Query: 19 MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFS 78
+R++R E+ + ADGSA F G T + A+ GP +V + + SD+A+ +
Sbjct: 5 LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVH--ASKASDEAM----------T 52
Query: 79 TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAA 138
R GD + ++ +I T+ I L P + I + V +Q DG + IN A
Sbjct: 53 LDISYRANCGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGA 112
Query: 139 TLALQDAGIPMRDI 152
AL D G+P +
Sbjct: 113 CFALLDNGMPFETV 126
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 63.9 bits (154), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 56/176 (31%), Positives = 85/176 (48%), Gaps = 18/176 (10%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R DGR+ ++R + + + +GS + G TKVI V N + Q +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69 RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
EYSM +T R +R+ R R+ EI +I + M + LT + R+ I + V
Sbjct: 60 TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLD 168
+QADGGTR+A I A +A+ DA I P++D V + S G +N LLD
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLD 174
>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 = 3e-10, Method: Compositional matrix adjust.
Identities = 55/176 (31%), Positives = 84/176 (47%), Gaps = 18/176 (10%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R DGR+ ++R + + + +GS + G TKVI V N + Q +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69 RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
EYSM +T R +R+ R R+ EI +I + M + LT + R+ I + V
Sbjct: 60 TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLD 168
+QADGG R+A I A +A+ DA I P++D V + S G +N LLD
Sbjct: 119 IQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLD 174
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 54/176 (30%), Positives = 82/176 (46%), Gaps = 18/176 (10%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R DGR+ ++R + + + +GS + G TKVI V N + Q +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69 RCEYSMANFSTGDRMRKPKGDRR----STEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
EYSM +T R + R + EI +I + M + LT + R+ I + V
Sbjct: 60 TAEYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLD 168
+QADGGTR+A I A +A+ DA I P++D V + S G +N LLD
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLD 174
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 47/169 (27%), Positives = 79/169 (46%), Gaps = 16/169 (9%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R+DGR TE+R + + +GS + E+G+TKVI + V + + V
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP-PFMRGEGKGWV 69
Query: 69 RCEYSMANFSTGDRM----RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
EY+M +T R K K R+ EI +I + + A + + + I V+
Sbjct: 70 TAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVI 129
Query: 125 QADGGTRSACINAATLAL-----------QDAGIPMRDIVTSCSAGYLN 162
QADGGTR+A I A +A+ + + IP++D + + S G +
Sbjct: 130 QADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVE 178
>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 = 61.2 bits (147), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 48/140 (34%), Positives = 70/140 (50%), Gaps = 5/140 (3%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
R DGR E+R + G GS + E G+TKV+ V + ++ + +
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP-RWRKATGLGWLT 65
Query: 70 CEYSM---ANFSTGDRMR-KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ 125
EY+M A S DR + + R+ EIS +I +++ ACI + + I I VLQ
Sbjct: 66 AEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQ 125
Query: 126 ADGGTRSACINAATLALQDA 145
ADGGTR+A I A +AL DA
Sbjct: 126 ADGGTRTAAITGAYVALADA 145
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 61.2 bits (147), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 55/176 (31%), Positives = 84/176 (47%), Gaps = 18/176 (10%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
+R DGR+ ++R + + + +GS + G TKVI V N + Q +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69 RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
EYSM +T R +R+ R R+ EI +I + M + LT + R+ I + V
Sbjct: 60 TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLD 168
+QADGGT +A I A +A+ DA I P++D V + S G +N LLD
Sbjct: 119 IQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLD 174
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 68/250 (27%), Positives = 113/250 (45%), Gaps = 33/250 (13%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQM---SDQ 65
+R DGR+ E+R + ++ ++ +GS + GNTKVI V+++ +
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNA----SVEDRVPPFLRGGGK 56
Query: 66 ALVRCEYSMANFSTGDRM----RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
+ EYSM +T R K K R+ EI +I + + A + + I I
Sbjct: 57 GWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 122 QVLQADGGTRSACINAATLA-------LQDAGI----PMRDIVTSCSAGYLNSTPLL--- 167
V+QADGGTR+A I A LA L AG P+ D + + S G +L
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDL 176
Query: 168 ----DSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFED---VMQLAIEGCKAVANYIRE 220
DS+ D+ V I+ + LQ + T + ED ++ LA +G + + + +E
Sbjct: 177 NYEEDSSAEVDMNV-IMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKE 235
Query: 221 VLLENTKQLE 230
VL ++ +L+
Sbjct: 236 VLGDSLPELK 245
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 68/250 (27%), Positives = 112/250 (44%), Gaps = 33/250 (13%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQM---SDQ 65
+R DGR+ E+R + ++ ++ +GS + GNTKVI V+++ +
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNA----SVEDRVPPFLRGGGK 56
Query: 66 ALVRCEYSM----ANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
+ EYSM N T K K R+ EI +I + + A + + I I
Sbjct: 57 GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 122 QVLQADGGTRSACINAATLA-------LQDAGI----PMRDIVTSCSAGYLNSTPLL--- 167
V+QADGGTR+A I A LA L AG P+ D + + S G +L
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDL 176
Query: 168 ----DSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFED---VMQLAIEGCKAVANYIRE 220
DS+ D+ V I+ + LQ + T + ED ++ LA +G + + + +E
Sbjct: 177 NYEEDSSAEVDMNV-IMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKE 235
Query: 221 VLLENTKQLE 230
VL ++ +L+
Sbjct: 236 VLGDSLPELK 245
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 78/165 (47%), Gaps = 23/165 (13%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ---QMSDQA 66
RLD + ++AEIG + DGS+ F +TKVI +V GP E + + + Q++ +
Sbjct: 13 RLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEI 72
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL-- 124
+VR +A +T +++ + K +R + I H PR I Q+L
Sbjct: 73 IVRPAKGVA--TTREKVLEDK-----------LRAVLTPLITRHCYPRQLCQITCQILES 119
Query: 125 ---QADGGTR--SACINAATLALQDAGIPMRDIVTSCSAGYLNST 164
+A+ R S CINAA LAL DAGI + + S + T
Sbjct: 120 GEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDT 164
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 55/224 (24%), Positives = 100/224 (44%), Gaps = 12/224 (5%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
R+DGR +R L G + + GSA+F G T+ V A + R+ Q + M ++
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 380
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
Y+ +S G+ RR + ++ + A + + + ++ ++
Sbjct: 381 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 440
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDSAGGP----DVTVG 178
+G + A + A+LAL DAG+P++ V + G + N L D G D+
Sbjct: 441 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFK 500
Query: 179 ILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
+ + D ++ LQMD K+ T E +MQ+A+ K +I V+
Sbjct: 501 VAGSRDGISALQMDIKIEGITKE-IMQVALNQAKGARLHILGVM 543
>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 = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 54/224 (24%), Positives = 101/224 (45%), Gaps = 12/224 (5%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
R+DGR +R L G + + GSA+F G T+ V A + R+ Q + M ++
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 374
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
Y+ +S G+ RR + ++ + A + + + ++ ++
Sbjct: 375 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 434
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDSAGGP----DVTVG 178
+G + A + A+LAL DAG+P++ V + G + N L D G D+
Sbjct: 435 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFK 494
Query: 179 ILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
+ + D ++ LQMD K+ T +++MQ+A+ K +I V+
Sbjct: 495 VAGSRDGISALQMDIKIEGIT-KEIMQVALNQAKGARLHILGVM 537
>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 = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 54/224 (24%), Positives = 101/224 (45%), Gaps = 12/224 (5%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
R+DGR +R L G + + GSA+F G T+ V A + R+ Q + M ++
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 374
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
Y+ +S G+ RR + ++ + A + + + ++ ++
Sbjct: 375 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 434
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDSAGGP----DVTVG 178
+G + A + A+LAL DAG+P++ V + G + N L D G D+
Sbjct: 435 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFK 494
Query: 179 ILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
+ + D ++ LQMD K+ T +++MQ+A+ K +I V+
Sbjct: 495 VAGSRDGISALQMDIKIEGIT-KEIMQVALNQAKGARLHILGVM 537
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 55/224 (24%), Positives = 100/224 (44%), Gaps = 12/224 (5%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
R+DGR +R L G + + GSA+F G T+ V A + R+ Q + M ++
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 380
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
Y+ +S G+ RR + ++ + A + + + ++ ++
Sbjct: 381 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 440
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDSAGGP----DVTVG 178
+G + A + A+LAL DAG+P++ V + G + N L D G D+
Sbjct: 441 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMDFK 500
Query: 179 ILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
+ + D ++ LQMD K+ T E +MQ+A+ K +I V+
Sbjct: 501 VAGSRDGISALQMDIKIEGITKE-IMQVALNQAKGARLHILGVM 543
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 53.5 bits (127), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 24/242 (9%)
Query: 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
E V E R+DGR T++R L AE+ + + GSA+FE G T+++ + QQ
Sbjct: 348 ERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTT--LNMLRMEQQ 405
Query: 62 MSDQALVRCEYSMAN-----FSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQ 116
+ + V + M N +S G+ R RR + + + + T
Sbjct: 406 LDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYA 465
Query: 117 IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAG-----------YLNSTP 165
I + L ++G T + A+T++L +AG+P++ V + G Y+ T
Sbjct: 466 IRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTD 525
Query: 166 LL---DSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 222
+L D+ G D+ + T + VT LQ+D KL V+ A++ + +I +V+
Sbjct: 526 ILGAEDAFG--DMDFKVAGTKEFVTALQLDTKL-DGIPASVLAAALKQARDARLHILDVM 582
Query: 223 LE 224
+E
Sbjct: 583 ME 584
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 47/199 (23%), Positives = 87/199 (43%), Gaps = 11/199 (5%)
Query: 8 GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
GLR+DGR +R + E+G + + GSA+F G T+ I G E + + +
Sbjct: 320 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 379
Query: 65 QALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
+ Y+ +S G+ R RR + + + + T I + ++
Sbjct: 380 KESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEIT 439
Query: 125 QADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLLDSAGGPDVT 176
+++G + A + ++LA+ DAG+P+ V+ + G + S L D D+
Sbjct: 440 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMD 499
Query: 177 VGILPTLDKVTLLQMDAKL 195
+ T + +T LQMD K+
Sbjct: 500 FKVAGTSEGLTSLQMDIKI 518
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 51/201 (25%), Positives = 88/201 (43%), Gaps = 15/201 (7%)
Query: 8 GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
GLR+DGR +R + E+G + + GSA+F G T+ I G E + + +
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 65 QALVRCEYSMANFSTGD--RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
+ Y+ +S G+ RM P G R L R P + I + +
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 446
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLLDSAGGPD 174
+ +++G + A + ++LA+ DAG+P+ V+ + G + S L D D
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGD 506
Query: 175 VTVGILPTLDKVTLLQMDAKL 195
+ + T + +T LQMD K+
Sbjct: 507 MDFKVAGTSEGLTSLQMDIKI 527
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 51/201 (25%), Positives = 88/201 (43%), Gaps = 15/201 (7%)
Query: 8 GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
GLR+DGR +R + E+G + + GSA+F G T+ I G E + + +
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 65 QALVRCEYSMANFSTGD--RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
+ Y+ +S G+ RM P G R L R P + I + +
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 446
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLLDSAGGPD 174
+ +++G + A + ++LA+ DAG+P+ V+ + G + S L D D
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGD 506
Query: 175 VTVGILPTLDKVTLLQMDAKL 195
+ + T + +T LQMD K+
Sbjct: 507 MDFKVAGTSEGLTSLQMDIKI 527
>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 = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 57/225 (25%), Positives = 92/225 (40%), Gaps = 32/225 (14%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ---- 61
E R DGR T +R + E+ GSA+F+ G T+V+ V + E KS Q
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA 375
Query: 62 ---MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRS--- 115
+ D+ + Y ++T + + +RR + + + I PR
Sbjct: 376 INGIKDKNFM-LHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVI-----PRDFPF 429
Query: 116 QIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTP---------- 165
I + +VL+++G + A +LAL D+G+P+ V + G + T
Sbjct: 430 TIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDYR 489
Query: 166 -LLDSAG----GPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQ 205
L D G D+ I T +T LQ D KLP + VM+
Sbjct: 490 LLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVME 534
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 56/212 (26%), Positives = 94/212 (44%), Gaps = 21/212 (9%)
Query: 2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
E V E R+DGR T++R L AE+ + + GSA+FE G T+++ V ++ + Q
Sbjct: 348 ERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQIL-GVTTLNXLRXEQQL 406
Query: 62 MSDQALVR----CEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQI 117
+ + R Y+ +S G+ R RR + + + + T I
Sbjct: 407 DTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAI 466
Query: 118 DIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAG-----------YLNSTPL 166
+ L ++G T + A+T +L +AG+P++ V + G Y+ T +
Sbjct: 467 RQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAGIAXGLISQEINGETHYVALTDI 526
Query: 167 L---DSAGGPDVTVGILPTLDKVTLLQMDAKL 195
L D+ G D V T + VT LQ+D KL
Sbjct: 527 LGAEDAFGDXDFKVA--GTKEFVTALQLDTKL 556
>pdb|2NN6|C Chain C, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 278
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 58/151 (38%), Gaps = 13/151 (8%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
E R DGR E R IG+++ ADGSA+ ++GNT VI V E S D+
Sbjct: 22 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA--EFAAPSTDAPDKG 79
Query: 67 LVRCEYSMANFSTGDRMRKPKGDRRSTEISLV--------IRQTMEACILT-HLMPRSQI 117
V + + P G+ + I Q + CI L+
Sbjct: 80 YVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYC 139
Query: 118 DIFVQVLQADGGTRSACINAATLALQDAGIP 148
D+ L DG AC A AL++ +P
Sbjct: 140 DLI--CLDYDGNILDACTFALLAALKNVQLP 168
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 55/225 (24%), Positives = 98/225 (43%), Gaps = 36/225 (16%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
+G+R DGR+ T+ R L + KADGSA+ ++G T V+A + P E N+
Sbjct: 25 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 84
Query: 62 MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
+ + L+ Y+ F G D + E++ V+ +++ +A LT L+
Sbjct: 85 IVNVELLPLAYT--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 136
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDSAGGP 173
++ V VL G AC A+ AL + + + ++ + PL P
Sbjct: 137 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQISVNKNEVVGKLPL----NYP 192
Query: 174 DVTVGIL---------PTLDKVTLLQMDAKLPTNTFEDVMQLAIE 209
VT+ + P LD+ ++ MDAK+ + D+ + I+
Sbjct: 193 VVTISVAKVDKYLVVDPDLDEESI--MDAKISFSYTPDLKIVGIQ 235
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 69/154 (44%), Gaps = 21/154 (13%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
+G+R DGR+ T+ R L + KADGSA+ ++G T V+A + P E N+
Sbjct: 25 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 84
Query: 62 MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
+ + L+ Y F G D + E++ V+ +++ +A LT L+
Sbjct: 85 IVNVELLPLAYE--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 136
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGI 147
++ V VL G AC A+ AL + +
Sbjct: 137 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKV 170
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 69/154 (44%), Gaps = 21/154 (13%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
+G+R DGR+ T+ R L + KADGSA+ ++G T V+A + P E N+
Sbjct: 27 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 86
Query: 62 MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
+ + L+ Y F G D + E++ V+ +++ +A LT L+
Sbjct: 87 IVNVELLPLAYE--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 138
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGI 147
++ V VL G AC A+ AL + +
Sbjct: 139 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKV 172
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 27/40 (67%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
R+DGR E R + E G ++KA+GS+ ++GNT++I V
Sbjct: 25 RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
>pdb|4IFD|F Chain F, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 250
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 42/169 (24%), Positives = 70/169 (41%), Gaps = 37/169 (21%)
Query: 20 RQLRAEIGNVAKADGSAVFE---MGN-TKVIAAVYGPREVQNKSQQMSDQALVRCEYSMA 75
++L G + +GSA+ E +G+ T +I+AVYGPR ++ + Q + +
Sbjct: 44 QELSLHTGFIENCNGSALVEARSLGHQTSLISAVYGPRSIRGS---FTSQGTISIQLK-- 98
Query: 76 NFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ--------AD 127
+ + + E+S + + + P+S IDIFV + D
Sbjct: 99 -----NGLLEKYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQD 153
Query: 128 GGTRSA------------CINAATLALQDAGIPMRDIVTSCSAGYLNST 164
++S CI + TLAL DAGI + D+ AG N T
Sbjct: 154 DDSQSKMTSSQISSLIPHCITSITLALADAGIELVDMA---GAGEANGT 199
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 29/43 (67%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
EG R+D R + R + E+G + KA+GSA+ ++G+T+V+ +
Sbjct: 24 EGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGI 66
>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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
R+DGR E R++ + KA+GSA+ ++G+T+V+ V
Sbjct: 23 RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 62
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
R+DGR E R++ + KA+GSA+ ++G+T+V+ V
Sbjct: 23 RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 62
>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 = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
E LR+DGR + R + E V+ GSA ++G+T ++ V
Sbjct: 34 EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGV 76
>pdb|2NN6|A Chain A, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 358
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
E RLDGR+ + R +R G G + E+G T+V+ V
Sbjct: 37 EKKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQV 76
>pdb|3NYD|A Chain A, Crystal Structure Of Kemp Eliminase Hg-2 Complexed With
Transition State Analog 5-Nitro Benzotriazole
pdb|3NYD|B Chain B, Crystal Structure Of Kemp Eliminase Hg-2 Complexed With
Transition State Analog 5-Nitro Benzotriazole
Length = 316
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 145 AGIPMRDIVTSCS------AGYLNSTPLLDSAGGPDVTVGIL 180
AG+P+ I + AG L + PLL SAG P+V++ +L
Sbjct: 197 AGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVSILML 238
>pdb|3NRK|A Chain A, The Crystal Structure Of The Leptospiral Hypothetical
Protein Lic12922
Length = 325
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 9 LRLDGRRPTEMRQLRAEIGNVAKAD 33
L+++G+RPT M LR I N+ D
Sbjct: 259 LKIEGKRPTPMENLRGGIQNILYRD 283
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 0.133 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,415,098
Number of Sequences: 62578
Number of extensions: 240873
Number of successful extensions: 557
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 45
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 456
Number of HSP's gapped (non-prelim): 53
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)