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= 024906
(260 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 130 bits (328), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 70/221 (31%), Positives = 120/221 (54%), Gaps = 4/221 (1%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIGRL 95
+R D R F + RP G + A GS+Y EFG K++V+V+GPRE++ + + + +
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75
Query: 96 NCNVSYTTFATPVRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVLESGGS 152
C + F+ R + G D + + S + +AL A+ILE FP++ +DVF VLE+ G
Sbjct: 76 RCRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGG 135
Query: 153 DLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMPSR 212
I+ ASVALADAGI M D+V + + +G +++D EE+ + +A +P
Sbjct: 136 TRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPRT 195
Query: 213 YEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLKE 253
E+T L G + F A+ L ++ ++ ++ + L++
Sbjct: 196 REITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRK 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 = 130 bits (327), Expect = 7e-31, Method: Compositional matrix adjust.
Identities = 76/225 (33%), Positives = 124/225 (55%), Gaps = 4/225 (1%)
Query: 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE-SKKAMMYSN 91
D + R D R ++ RP G + +A+GSAY E+G K+I +V+GPRE K + +
Sbjct: 12 DENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPD 71
Query: 92 IGRLNCNVSYTTFATPVRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVLE 148
L + F+ R + G D + + S ++ ALE A+ILE FP+T +DVF VL+
Sbjct: 72 RAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQ 131
Query: 149 SGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIAC 208
+ I+ AS+ALADAGI M DLVA+ + + +++D EE++Y + + +A
Sbjct: 132 ADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAI 191
Query: 209 MPSRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLKE 253
MP + ++T L + G + F EA++L + + + + R LKE
Sbjct: 192 MPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKE 236
>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 = 113 bits (282), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 70/222 (31%), Positives = 112/222 (50%), Gaps = 4/222 (1%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE-SKKAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 13 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 72
Query: 94 RLNCNVSYTTFATPVRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLESG 150
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 73 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 132
Query: 151 GSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMP 210
V + AS+ALADAGI M DL+A V+V +++D E+ + + + IA MP
Sbjct: 133 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMP 192
Query: 211 SRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLK 252
S +VT + G + F +A L + + + R LK
Sbjct: 193 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALK 234
>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 = 112 bits (281), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 70/222 (31%), Positives = 112/222 (50%), Gaps = 4/222 (1%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE-SKKAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 16 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 75
Query: 94 RLNCNVSYTTFATPVRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLESG 150
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 76 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 135
Query: 151 GSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMP 210
V + AS+ALADAGI M DL+A V+V +++D E+ + + + IA MP
Sbjct: 136 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMP 195
Query: 211 SRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLK 252
S +VT + G + F +A L + + + R LK
Sbjct: 196 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALK 237
>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 = 112 bits (279), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 70/222 (31%), Positives = 111/222 (50%), Gaps = 4/222 (1%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE-SKKAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77
Query: 94 RLNCNVSYTTFATPVRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLESG 150
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 78 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 137
Query: 151 GSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMP 210
V + AS+ALADAGI M DL+A V+V +++D E + + + IA MP
Sbjct: 138 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMP 197
Query: 211 SRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLK 252
S +VT + G + F +A L + + + R LK
Sbjct: 198 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALK 239
>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 = 103 bits (256), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 65/227 (28%), Positives = 112/227 (49%), Gaps = 11/227 (4%)
Query: 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMY---S 90
VD LR D R F + RP + A GS Y E G KVI +VFGPRE +
Sbjct: 13 VDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSK 72
Query: 91 NIGRLNCNVSYTTFATPVRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVL 147
I R N++ F+ R + G D + + S + +A E I+ E FP++ +D+F VL
Sbjct: 73 AIIRYRYNMA--PFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVL 130
Query: 148 ESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIA 207
++ ++ ASVAL DAG+ M ++ SV+V L++DP+ EE+++ + + A
Sbjct: 131 QADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFA 190
Query: 208 CMPSRYEVTQ---LTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCL 251
+ ++ L + G + +A++L + ++ ++ R +
Sbjct: 191 FLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAI 237
>pdb|2BA0|F Chain F, Archaeal Exosome Core
pdb|2BA0|E Chain E, Archaeal Exosome Core
pdb|2BA0|D Chain D, Archaeal Exosome Core
pdb|2BA1|D Chain D, Archaeal Exosome Core
pdb|2BA1|E Chain E, Archaeal Exosome Core
pdb|2BA1|F Chain F, Archaeal Exosome Core
Length = 258
Score = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 65/227 (28%), Positives = 112/227 (49%), Gaps = 11/227 (4%)
Query: 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMY---S 90
VD LR D R F + RP + A GS Y E G KVI +VFGPRE +
Sbjct: 13 VDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSK 72
Query: 91 NIGRLNCNVSYTTFATPVRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVL 147
I R N++ F+ R + G D + + S + +A E I+ E FP++ +D+F VL
Sbjct: 73 AIIRYRYNMA--PFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVL 130
Query: 148 ESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIA 207
++ ++ ASVAL DAG+ M ++ SV+V L++DP+ EE+++ + + A
Sbjct: 131 QADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFA 190
Query: 208 CMPSRYEVTQ---LTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCL 251
+ ++ L + G + +A++L + ++ ++ R +
Sbjct: 191 FLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAI 237
>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 = 95.1 bits (235), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 12/229 (5%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK--KAMMYSNIGRL 95
R D R + R R G A GSAY E GNTK + V+GP E + +A + +
Sbjct: 17 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76
Query: 96 NCNVSYTTFATPVRGQGSDHKDFSS-----MLHKALEGAIILETFPKTTVDVFALVLESG 150
NC S TF+T R + H D S L + E AI+ + P++ +D++ VL++
Sbjct: 77 NCQYSSATFSTGERKR-RPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQAD 135
Query: 151 GSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMP 210
G ++ A++A+ DAGI M D V + S + L D EE+ L +A +P
Sbjct: 136 GGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLP 195
Query: 211 SRYEVTQLTVTGEWSTPHFNE----AMQLCLDASAKLGKIMRSCLKEAA 255
+ ++ L + H A Q D L +++R ++EA+
Sbjct: 196 ASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREAS 244
>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 = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 78/248 (31%), Positives = 122/248 (49%), Gaps = 20/248 (8%)
Query: 23 KTRPPIFSGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE 82
+++PP +D + P +R + RP + R G ++ A GSAY E G TKV+ +V GPR+
Sbjct: 13 ESQPPQLYAADEEEA-PGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQ 71
Query: 83 SKKAMMYSNI------------GRLNCNVSYTTFATPVRGQ---GSDHKDFSSMLHKALE 127
++ GRL C+ FA R G + ++ + L +ALE
Sbjct: 72 AEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALE 131
Query: 128 GAIILETFPKTTVDVFALVLESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCL--- 184
A+ L +P+ ++V AL+LE GGS L ++ A++ALADAG+ MYDLV +S
Sbjct: 132 PAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGP 191
Query: 185 GKNLLIDPVLEEESYQDGSLMIACMPSRYEVT-QLTVTGEWSTPHFNEAMQLCLDASAKL 243
L+DP EE L +A MP +V L T + EA++L L+ +L
Sbjct: 192 APTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRL 251
Query: 244 GKIMRSCL 251
+++ L
Sbjct: 252 YPVLQQSL 259
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 56/175 (32%), Positives = 95/175 (54%), Gaps = 15/175 (8%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNS----ASGSAYAEFGNTKVIVSVFGPRESK-KAMMY 89
+ LR D R +++ R F + ++N+ A GS+Y E GN K+I V GP+E + K+ M
Sbjct: 12 EGLRLDGRRWNELRR--FES-SINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMD 68
Query: 90 SNIGRLNCNVSYTTFATPVRGQGSDHKDFSSMLH------KALEGAIILETFPKTTVDVF 143
++ LN +V+ T F+ R + S HK+ +L + E ++L +P+T +D+
Sbjct: 69 TSKALLNVSVNITKFSKFERSKSS-HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIE 127
Query: 144 ALVLESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEES 198
VLE G + +I+ ++AL DAGI M+D ++ +SV L+D EE+
Sbjct: 128 IHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN 182
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 78.2 bits (191), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 55/173 (31%), Positives = 93/173 (53%), Gaps = 15/173 (8%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNS----ASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSN 91
LR D R +++ R F + ++N+ A GS+Y E GN K+I V GP+E + K+ M ++
Sbjct: 12 LRLDGRRWNELRR--FES-SINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTS 68
Query: 92 IGRLNCNVSYTTFATPVRGQGSDHKDFSSMLH------KALEGAIILETFPKTTVDVFAL 145
LN +V+ F+ R + S HK+ +L + E ++L +P+T +D+
Sbjct: 69 KALLNVSVNINKFSKFERSKSS-HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIH 127
Query: 146 VLESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEES 198
VLE G + +I+ ++AL DAGI M+D ++ +SV L+D EE+
Sbjct: 128 VLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN 180
>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 = 61.6 bits (148), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 60/237 (25%), Positives = 95/237 (40%), Gaps = 26/237 (10%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNC 97
R D R +Q RP ++ A GSA G+T V+ +V+GP+ + G
Sbjct: 5 RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK------GENPE 58
Query: 98 NVSYTTFATPVRGQ-GSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSDLPV 156
S P+ GQ G K++ L + L+ +L P TT V V+ + GS LP
Sbjct: 59 KASIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPC 118
Query: 157 VISCASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMPS----- 211
I+ AL AGI + L ++ L +I + E Q S P+
Sbjct: 119 AINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSA 178
Query: 212 -------------RYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLKEAA 255
R +T +T G S + ++ L AS+++ MR+ L++ A
Sbjct: 179 SSKEPNQKEEDSERGLITSIT-HGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQA 234
>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 = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 57/224 (25%), Positives = 92/224 (41%), Gaps = 28/224 (12%)
Query: 46 QCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGP------RESKKAMMYSNIGRLNCNV 99
+C +F + +A GSA G T + S GP + S +AM R NC
Sbjct: 9 RCELSFLK-----NADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG- 62
Query: 100 SYTTFATPVRGQGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSDLPVVIS 159
+ ++++H L AI LE FP TT+ V ++ GS V I+
Sbjct: 63 ------------DNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAIN 110
Query: 160 CASVALADAGIMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIA-CMPS--RYEVT 216
A AL D G+ + V + + L+IDP ++E+ G ++ + C S EV
Sbjct: 111 GACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVC 170
Query: 217 QLTVTGEWSTPHFNEAMQLCLDASAKLGKIMRSCLKEAAS-DEQ 259
+ G W A L +++ + ++ +K S DEQ
Sbjct: 171 AMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVDEQ 214
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 25/184 (13%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS----------VFGPRESKKA 86
+R D R Q RP + + GS FG TKVI + + G +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60
Query: 87 MMYSNIGRLNCNVSYTTFATPVRGQ-GSDHKDFSSMLHKALEGAIILETFPKTTVDVFAL 145
YS + R T V+G+ G + M+ +A+ A+ L + T+ V
Sbjct: 61 AEYSMLPRAT---QQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCD 117
Query: 146 VLESGGSDLPVVISCASVALADAGIMMY-----------DLVASVSVSCLGKNLLIDPVL 194
V+++ G I+ A VA+ADA I ++ D VA+VSV + +L+D
Sbjct: 118 VIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNF 177
Query: 195 EEES 198
EE+S
Sbjct: 178 EEDS 181
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 25/184 (13%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS----------VFGPRESKKA 86
+R D R Q RP + + GS FG TKVI + + G +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60
Query: 87 MMYSNIGRLNCNVSYTTFATPVRGQ-GSDHKDFSSMLHKALEGAIILETFPKTTVDVFAL 145
YS + R T V+G+ G + M+ +A+ A+ L + T+ V
Sbjct: 61 AEYSMLPRAT---QQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCD 117
Query: 146 VLESGGSDLPVVISCASVALADAGIMMY-----------DLVASVSVSCLGKNLLIDPVL 194
V+++ G I+ A VA+ADA I ++ D VA+VSV + +L+D
Sbjct: 118 VIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNF 177
Query: 195 EEES 198
EE+S
Sbjct: 178 EEDS 181
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 50/185 (27%), Positives = 79/185 (42%), Gaps = 27/185 (14%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS----------VFGPRESKKA 86
+R D R Q RP + + GS FG TKVI + + G +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60
Query: 87 MMYSNIGRLNCNVSYTTFATPVRGQ--GSDHKDFSSMLHKALEGAIILETFPKTTVDVFA 144
YS + R T V+G+ G+ H + M+ +A+ A+ L + T+ V
Sbjct: 61 AEYSMLPRAT---QQRTIRESVQGRIGGATH-EIQRMIGRAMRTAVELTKIGERTIWVDC 116
Query: 145 LVLESGGSDLPVVISCASVALADAGIMMY-----------DLVASVSVSCLGKNLLIDPV 193
V+++ G I+ A VA+ADA I ++ D VA+VSV + +L+D
Sbjct: 117 DVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLN 176
Query: 194 LEEES 198
EE+S
Sbjct: 177 FEEDS 181
>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 = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 52/209 (24%), Positives = 89/209 (42%), Gaps = 21/209 (10%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNC 97
R D R H+ RP G + +GS EFG+TKV+ + + + +G L
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66
Query: 98 NVSYTTFAT-------PVRGQGSDH-KDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
+ AT VRG+ S ++ S ++ ++L I L + T+ + VL++
Sbjct: 67 EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126
Query: 150 GGSDLPVVISCASVALADAGIMMYD------------LVASVSVSCLGKNLLIDPVLEEE 197
G I+ A VALADA + +A+VSV + + +D EE+
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEED 186
Query: 198 SYQDGSLMIACMPSRYEVTQLTVTGEWST 226
S + + + + V ++ TGE +T
Sbjct: 187 SRAEVDMNVVATDTGTLV-EIQGTGEGAT 214
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 25/184 (13%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS----------VFGPRESKKA 86
+R D R Q RP + + GS FG TKVI + + G +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60
Query: 87 MMYSNIGRLNCNVSYTTFATPVRGQ-GSDHKDFSSMLHKALEGAIILETFPKTTVDVFAL 145
YS + R T V+G+ G + M+ +A+ A+ L + T+ V
Sbjct: 61 AEYSMLPRAT---QQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCD 117
Query: 146 VLESGGSDLPVVISCASVALADAGIMMY-----------DLVASVSVSCLGKNLLIDPVL 194
V+++ G I+ A VA+ADA I ++ D VA+VSV + +L+D
Sbjct: 118 VIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNF 177
Query: 195 EEES 198
EE+S
Sbjct: 178 EEDS 181
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 59/237 (24%), Positives = 94/237 (39%), Gaps = 21/237 (8%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFG----PRESK---KAMMYS 90
RP R Q RP A GS EFG+TKVI +V PR K + + +
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 91 NIGRLNCNVSYTTFATPVRG-QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
G L + RG QG + ++ ++L A+ L + T+ + V+++
Sbjct: 63 EYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122
Query: 150 GGSDLPVVISCASVALADA-----------GIMMYDLVASVSVSCLGKNLLIDPVLEEES 198
G I+ A+VAL DA G + VA+VSV ++D E+S
Sbjct: 123 DGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVPVLDLDYLEDS 182
Query: 199 YQDGSL-MIACMPSRYEVTQLTVTGEWSTP-HFNEAMQLCLDASAKLGKIMRSCLKE 253
+ L ++ + Q T G P N ++L +L ++ R+ L E
Sbjct: 183 AAETDLNVVXTDAGGFIEVQGTAEGAPFRPAELNAXLELAQQGXQELFELQRAALAE 239
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 59/237 (24%), Positives = 95/237 (40%), Gaps = 21/237 (8%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFG----PRESK---KAMMYS 90
RP R Q RP A GS EFG+TKVI +V PR K + + +
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 91 NIGRLNCNVSYTTFATPVRG-QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
G L + RG QG + ++ ++L A+ L + T+ + V+++
Sbjct: 63 EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122
Query: 150 GGSDLPVVISCASVALADA-----------GIMMYDLVASVSVSCLGKNLLIDPVLEEES 198
G I+ A+VAL DA G + +VA+VSV ++D E+S
Sbjct: 123 DGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLEDS 182
Query: 199 YQDGSLMIACMPS-RYEVTQLTVTGEWSTP-HFNEAMQLCLDASAKLGKIMRSCLKE 253
+ L + + + Q T G P N ++L +L ++ R+ L E
Sbjct: 183 AAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 39/152 (25%), Positives = 65/152 (42%), Gaps = 16/152 (10%)
Query: 55 GAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPVRGQGSD 114
G ++ GS+ +TKVI SV GP E K L ++ P +G +
Sbjct: 30 GILDHVDGSSEFVSQDTKVICSVTGPIEPKARQ------ELPTQLALEIIVRPAKGVATT 83
Query: 115 -HKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSD-------LPVVISCASVALA 166
K L L I +P+ + +LESG + L I+ A +AL
Sbjct: 84 REKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALV 143
Query: 167 DAGIMMYDLVASVSVSCLG--KNLLIDPVLEE 196
DAGI + + AS+ ++ + ++++DP E+
Sbjct: 144 DAGIALNSMCASIPIAIIKDTSDIIVDPTAEQ 175
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 39/147 (26%), Positives = 62/147 (42%), Gaps = 6/147 (4%)
Query: 62 GSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPVRGQGSDHKDFSSM 121
GSA G+T V+ V+GP E K + N L + P G K +
Sbjct: 45 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEV-ILRPKIGLP----GVAEKSRERL 99
Query: 122 LHKALEGAIILETFPKTTVDVFALVLESGGSDLPVVISCASVALADAGIMMYDLVASVSV 181
+ E ++ P+T++ V V+ GS L ++ A +AL DAG+ M L V+
Sbjct: 100 IRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVAC 159
Query: 182 SCLGK-NLLIDPVLEEESYQDGSLMIA 207
+ L++DP ++E L A
Sbjct: 160 ALDSDGTLVLDPTSKQEKEARAVLTFA 186
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 11/75 (14%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMM-----YSNI 92
R D RGF RP G + A GSA + G+T+V+V + K ++ N+
Sbjct: 27 RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGI------KTSLGEPFPDTPNM 80
Query: 93 GRLNCNVSYTTFATP 107
G + NV A+P
Sbjct: 81 GVMTTNVELVPLASP 95
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
R D R H+ R TG ++ A GS+ + GNT++IV V
Sbjct: 25 RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 60/261 (22%), Positives = 111/261 (42%), Gaps = 42/261 (16%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLN 96
LR D RG R T V++ SGSA + G+T ++V V + K + N G L
Sbjct: 36 LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPK-LEKPNEGYLE 94
Query: 97 CNVSYTTFATP-VRGQGSDH--KDFSSMLHKAL--EGAIILETF---PKT---TVDVFAL 145
V + ATP G+G D + ++ L++ + ++ L+T P+ + V L
Sbjct: 95 FFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVL 154
Query: 146 VLESGGSDLPVVISCASVALADAGIMM-------------------YDLV--------AS 178
+LE GG+ + AL + I YD +
Sbjct: 155 LLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCI 214
Query: 179 VSVSCLGKNLLIDPVLEEESYQDGSLMIACMPSRYEVTQLTVTGEWSTPHFNEAMQLCLD 238
V++ +G ++D L+EE+ SL+++ + S+ VT + G+ S E++ ++
Sbjct: 215 VTLCKIGYRHVVDATLQEEACSLASLLVS-VTSKGVVTCMRKVGKGSLD--PESIFEMME 271
Query: 239 ASAKLGKIMRSCLKEAASDEQ 259
++GK++ + L+ E+
Sbjct: 272 TGKRVGKVLHASLQSVVHKEE 292
>pdb|4IFD|F Chain F, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 250
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 68/151 (45%), Gaps = 29/151 (19%)
Query: 52 FRTGAVNSASGSAYAE---FGN-TKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATP 107
TG + + +GSA E G+ T +I +V+GPR + + +++ G ++ +
Sbjct: 48 LHTGFIENCNGSALVEARSLGHQTSLISAVYGPRSIRGS--FTSQGTISIQLKNGLLE-- 103
Query: 108 VRGQGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALV-----LESGGSD--------- 153
+ ++ K+ SS L + L +PK+ +D+F + L + D
Sbjct: 104 -KYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMTS 162
Query: 154 ------LPVVISCASVALADAGIMMYDLVAS 178
+P I+ ++ALADAGI + D+ +
Sbjct: 163 SQISSLIPHCITSITLALADAGIELVDMAGA 193
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 52/206 (25%), Positives = 75/206 (36%), Gaps = 41/206 (19%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV-FGPRESKKAMMYSNIG 93
D R D RGF + R + A GSA + G+T+V+V V P E A + G
Sbjct: 20 DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEP--APDTPDRG 77
Query: 94 RLNCNVSYTTFATPVRGQGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSD 153
+ N A+P G ++ S L + ++ I VD+ LV+E G
Sbjct: 78 VIIVNAELVPLASPTFEPGPPDEN-SIELARVVDRGI----RESEAVDLSKLVIEEGEKV 132
Query: 154 LPVVISCASVALADAG-------------------------------IMMYDLVASVSVS 182
V + AL D G + + DL SV+
Sbjct: 133 WIVFVDIH--ALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSL 190
Query: 183 CLGKNLLIDPVLEEESYQDGSLMIAC 208
+G L+DP EE S D +L I
Sbjct: 191 IVGNKYLVDPSREEMSVGDTTLTITT 216
>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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 51/206 (24%), Positives = 74/206 (35%), Gaps = 41/206 (19%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV-FGPRESKKAMMYSNIG 93
D R D RGF + R + A GSA + G+T+V+V V P E + G
Sbjct: 20 DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDT--PDRG 77
Query: 94 RLNCNVSYTTFATPVRGQGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSD 153
+ N A+P G ++ S L + ++ I VD+ LV+E G
Sbjct: 78 VIIVNAELVPLASPTFEPGPPDEN-SIELARVVDRGI----RESEAVDLSKLVIEEGEKV 132
Query: 154 LPVVISCASVALADAG-------------------------------IMMYDLVASVSVS 182
V + AL D G + + DL SV+
Sbjct: 133 WIVFVDIH--ALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSL 190
Query: 183 CLGKNLLIDPVLEEESYQDGSLMIAC 208
+G L+DP EE S D +L I
Sbjct: 191 IVGNKYLVDPSREEMSVGDTTLTITT 216
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 48/210 (22%), Positives = 86/210 (40%), Gaps = 21/210 (10%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGP-------RESKKAMMY 89
+R D R + RP F ++ GS GNTKVI + R K +
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60
Query: 90 SNIGRLNCNVSYTTFATPVRGQGSDHK-DFSSMLHKALEGAIILETFPKTTVDVFALVLE 148
+ L + T +G+ S + ++ +AL + LE + T+ + V++
Sbjct: 61 AEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQ 120
Query: 149 SGGSDLPVVISCASVALA-------DAGIM----MYDLVASVSVSC-LGKNLLIDPVLEE 196
+ G I+ A +A+A AG + + D +A++SV + +L+D EE
Sbjct: 121 ADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEE 180
Query: 197 ESYQDGSLMIACMPSRYEVTQLTVTGEWST 226
+S + + + M +L TGE +T
Sbjct: 181 DSSAEVDMNV-IMTGSGRFVELQGTGEEAT 209
>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 = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 48/210 (22%), Positives = 86/210 (40%), Gaps = 21/210 (10%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGP-------RESKKAMMY 89
+R D R + RP F ++ GS GNTKVI + R K +
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60
Query: 90 SNIGRLNCNVSYTTFATPVRGQGSDHK-DFSSMLHKALEGAIILETFPKTTVDVFALVLE 148
+ L + T +G+ S + ++ +AL + LE + T+ + V++
Sbjct: 61 AEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQ 120
Query: 149 SGGSDLPVVISCASVALA-------DAGIM----MYDLVASVSVSC-LGKNLLIDPVLEE 196
+ G I+ A +A+A AG + + D +A++SV + +L+D EE
Sbjct: 121 ADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEE 180
Query: 197 ESYQDGSLMIACMPSRYEVTQLTVTGEWST 226
+S + + + M +L TGE +T
Sbjct: 181 DSSAEVDMNV-IMTGSGRFVELQGTGEEAT 209
>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 = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
RPD R + R G++++A GSA + GNT VI V
Sbjct: 25 RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGV 64
>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 = 0.051, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 97/252 (38%), Gaps = 46/252 (18%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVI----VSVFGPRESKKAMMYSNI 92
+R D R RP A GSA + G T V+ + + P E N
Sbjct: 27 IRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT-----PNQ 81
Query: 93 GRLNCNV-----SYTTFATPVRGQGSDH----KDFSSMLHKALE-GAIILETFPKTTV-- 140
G L NV +YTTF + + D S KAL+ +++E P +V
Sbjct: 82 GNLIVNVELLPLAYTTFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIE--PGKSVWT 139
Query: 141 ---DVFALVLESGGSDLPVVISCASVALADAGIMMYDL-----------------VASVS 180
DV+ VL+ GG+ L + AL + + + V ++S
Sbjct: 140 VWLDVY--VLDYGGNVLDACTLASVAALYNTKVYKVEQISVNKNEVVGKLPLNYPVVTIS 197
Query: 181 VSCLGKNLLIDPVLEEESYQDGSLMIACMPSRYEV-TQLTVTGEWSTPHFNEAMQLCLDA 239
V+ + K L++DP L+EES D + + P V Q + G S ++A
Sbjct: 198 VAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTARST 257
Query: 240 SAKLGKIMRSCL 251
+ KL + ++ L
Sbjct: 258 AVKLLEELKKHL 269
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 53/243 (21%), Positives = 91/243 (37%), Gaps = 24/243 (9%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLN 96
+R D R + R T + GS E G+TKVI S M G +
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVT 70
Query: 97 CNVSYTTFATPVRGQGSDHK--------DFSSMLHKALEGAIILETFPKTTVDVFALVLE 148
+ AT R K + ++ +AL + LE + TV + V++
Sbjct: 71 AEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQ 130
Query: 149 SGGSDLPVVISCASVALADA-----------GIMMYDLVASVSVSCL-GKNLLIDPVLEE 196
+ G I+ A VA+ A I + D +A+ SV + + +++D E
Sbjct: 131 ADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYAE 190
Query: 197 ESYQDGSLMIACMPSRYEVTQLTVTGE---WSTPHFNEAMQLCLDASAKLGKIMRSCLKE 253
+S D + + M + + ++ TGE +S NE + +L I + L +
Sbjct: 191 DSKADVDMNV-IMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDIQKEALGD 249
Query: 254 AAS 256
S
Sbjct: 250 IVS 252
>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 = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 55/254 (21%), Positives = 93/254 (36%), Gaps = 46/254 (18%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVI----VSVFGPRESKKAMMYSNI 92
+R D R RP A GSA + G T V+ + + P E N
Sbjct: 27 IRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT-----PNQ 81
Query: 93 GRLNCNVSYTTFATPVRGQG---SDHKDFSSMLHKALEGAIILETF-----PKTTV---- 140
G L NV A G + + + ++ ++L + L+ P +V
Sbjct: 82 GNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVW 141
Query: 141 -DVFALVLESGGSDLPVVISCASVALADAGIMMYDL---------------------VAS 178
DV+ VL+ GG+ L + AL + + + V +
Sbjct: 142 LDVY--VLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVT 199
Query: 179 VSVSCLGKNLLIDPVLEEESYQDGSLMIACMPSRYEV-TQLTVTGEWSTPHFNEAMQLCL 237
+SV+ + K L++DP L+EES D + + P V Q + G S ++A
Sbjct: 200 ISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTAR 259
Query: 238 DASAKLGKIMRSCL 251
+ KL + ++ L
Sbjct: 260 STAVKLLEELKKHL 273
>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 = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 55/254 (21%), Positives = 93/254 (36%), Gaps = 46/254 (18%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVI----VSVFGPRESKKAMMYSNI 92
+R D R RP A GSA + G T V+ + + P E N
Sbjct: 29 IRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT-----PNQ 83
Query: 93 GRLNCNVSYTTFATPVRGQG---SDHKDFSSMLHKALEGAIILETF-----PKTTV---- 140
G L NV A G + + + ++ ++L + L+ P +V
Sbjct: 84 GNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVW 143
Query: 141 -DVFALVLESGGSDLPVVISCASVALADAGIMMYDL---------------------VAS 178
DV+ VL+ GG+ L + AL + + + V +
Sbjct: 144 LDVY--VLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVT 201
Query: 179 VSVSCLGKNLLIDPVLEEESYQDGSLMIACMPSRYEV-TQLTVTGEWSTPHFNEAMQLCL 237
+SV+ + K L++DP L+EES D + + P V Q + G S ++A
Sbjct: 202 ISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTAR 261
Query: 238 DASAKLGKIMRSCL 251
+ KL + ++ L
Sbjct: 262 STAVKLLEELKKHL 275
>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 = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 52/222 (23%), Positives = 90/222 (40%), Gaps = 18/222 (8%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTK-VIVSVFGPRESKKAM-----MYS 90
LR D R RP G + GSA G T+ ++V+ G + ++ + Y
Sbjct: 321 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 380
Query: 91 NIGRLNCNV-SYTTFATPVRGQ-GSDHKDFSSMLHKALEGAI-ILETFPKTTVDVFALVL 147
L+ N Y+ T G G + +AL + E FP T+ + + +
Sbjct: 381 ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFP-YTIRLVSEIT 439
Query: 148 ESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCL----GKNLLIDPVLEEESYQDGS 203
ES GS + +S+A+ DAG+ + V+ +++ + G +L D + +E+ D
Sbjct: 440 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMD 499
Query: 204 LMIACMPSRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGK 245
+A Q+ + TP M+ L A AK G+
Sbjct: 500 FKVAGTSEGLTSLQMDIKIAGITPAI---MEQAL-AQAKEGR 537
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 52/222 (23%), Positives = 90/222 (40%), Gaps = 18/222 (8%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTK-VIVSVFGPRESKKAM-----MYS 90
LR D R RP G + GSA G T+ ++V+ G + ++ + Y
Sbjct: 330 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 389
Query: 91 NIGRLNCNV-SYTTFATPVRGQ-GSDHKDFSSMLHKALEGAI-ILETFPKTTVDVFALVL 147
L+ N Y+ T G G + +AL + E FP T+ + + +
Sbjct: 390 ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFP-YTIRLVSEIT 448
Query: 148 ESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCL----GKNLLIDPVLEEESYQDGS 203
ES GS + +S+A+ DAG+ + V+ +++ + G +L D + +E+ D
Sbjct: 449 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMD 508
Query: 204 LMIACMPSRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGK 245
+A Q+ + TP M+ L A AK G+
Sbjct: 509 FKVAGTSEGLTSLQMDIKIAGITPAI---MEQAL-AQAKEGR 546
>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 = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 52/222 (23%), Positives = 90/222 (40%), Gaps = 18/222 (8%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTK-VIVSVFGPRESKKAM-----MYS 90
LR D R RP G + GSA G T+ ++V+ G + ++ + Y
Sbjct: 330 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 389
Query: 91 NIGRLNCNV-SYTTFATPVRGQ-GSDHKDFSSMLHKALEGAI-ILETFPKTTVDVFALVL 147
L+ N Y+ T G G + +AL + E FP T+ + + +
Sbjct: 390 ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFP-YTIRLVSEIT 448
Query: 148 ESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCL----GKNLLIDPVLEEESYQDGS 203
ES GS + +S+A+ DAG+ + V+ +++ + G +L D + +E+ D
Sbjct: 449 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGDMD 508
Query: 204 LMIACMPSRYEVTQLTVTGEWSTPHFNEAMQLCLDASAKLGK 245
+A Q+ + TP M+ L A AK G+
Sbjct: 509 FKVAGTSEGLTSLQMDIKIAGITPAI---MEQAL-AQAKEGR 546
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 30.4 bits (67), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 43/106 (40%), Gaps = 16/106 (15%)
Query: 111 QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGGSDLPVVISCASVALADAG- 169
+G D S LHK++ G+ P + +A ++ +GG L V C ++A D G
Sbjct: 251 KGDRFYDLISALHKSVRGSA-----PDAALYWYARIITAGGDPLYVARRCLAIASEDVGN 305
Query: 170 ----IMMYDLVASVSVSCLGKNLLIDPVLEEESYQDGSLMIACMPS 211
M VA + C + + P E + + +AC P
Sbjct: 306 ADPRAMQ---VAIAAWDCFTR---VGPAEGERAIAQAIVYLACAPK 345
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 72/164 (43%), Gaps = 14/164 (8%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV-FGPRES--KKAMMYSN 91
++ R D R R + GSA + G T+V+ +V F ES K + +
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA 375
Query: 92 IGRLN-----CNVSYTTFATPVRGQ--GSDHKDFS--SMLHKALEGAIILETFPKTTVDV 142
I + + + +AT G+ G + ++ ++ KAL +I FP T+ V
Sbjct: 376 INGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALY-PVIPRDFP-FTIRV 433
Query: 143 FALVLESGGSDLPVVISCASVALADAGIMMYDLVASVSVSCLGK 186
+ VLES GS S+AL D+G+ + VA V++ + K
Sbjct: 434 TSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTK 477
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 42 RGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPR--ESKKAMMYSNIGRLNCNV 99
RG + R + + S + GN + ++ P + + ++ RLN N
Sbjct: 293 RGLNYLRVLNVSGNQLTTLEESVFHSVGNLETLILDSNPLACDCRLLWVFRRRWRLNFNR 352
Query: 100 SYTTFATPVRGQGSDHKDFSSML 122
T ATP QG + KDF +L
Sbjct: 353 QQPTCATPEFVQGKEFKDFPDVL 375
>pdb|2K1S|A Chain A, Solution Nmr Structure Of The Folded C-Terminal Fragment
Of Yiad From Escherichia Coli. Northeast Structural
Genomics Consortium Target Er553
Length = 149
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 129 AIILETFPKTTVDVFALVLESGGSDLPVVIS 159
A++L+ +PKT V+V +GG DL + +S
Sbjct: 57 AMVLKEYPKTAVNVIGYTDSTGGHDLNMRLS 87
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.132 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,039,410
Number of Sequences: 62578
Number of extensions: 271794
Number of successful extensions: 627
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 569
Number of HSP's gapped (non-prelim): 49
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)