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= 026142
(243 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 331 bits (848), Expect = 3e-91, Method: Compositional matrix adjust.
Identities = 161/239 (67%), Positives = 192/239 (80%), Gaps = 1/239 (0%)
Query: 1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
ME RADGRNPNQLRP +C+ + L RAHGSA W+QGDT VLAAVYGPK GT+K ENPEKA
Sbjct: 1 MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60
Query: 61 SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
SIEV+WKP TGQIGK EKEYE+ LKRTLQSIC+LT++PNTTTSVI+QVV +DG+LLPCAI
Sbjct: 61 SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAI 120
Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
NA CAALV AGIP+KHLAVAI C E G ILD K EEQ++K FA+LVFPNS S
Sbjct: 121 NACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180
Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL 239
+ + + E E G+ITS+THG MS +DYF C+ERG AAS+++SDF+R +LQ + PGD+
Sbjct: 181 KEPNQKE-EDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDV 238
>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 = 135 bits (340), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 71/164 (43%), Positives = 101/164 (61%), Gaps = 3/164 (1%)
Query: 9 RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
R P LR AC ++L R GSAS+ QGDT VLA VYGP E KA++EVI +
Sbjct: 24 RGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 83
Query: 68 PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
P+ G G EK E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct: 84 PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMAL 143
Query: 128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
VDAG+PM+ L + C G +LDPT +E++ + A L F
Sbjct: 144 VDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR--AVLTF 185
>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 = 90.5 bits (223), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 13/186 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
R DGR ++LRP+ S+L RA GS G KV+AAV+GP+ ++ ++P KA I
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIR 76
Query: 64 VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
+ + G + EI + K +++ + + P + + ++V+ D
Sbjct: 77 YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG---FAYLVFP 172
+NAA ALVDAG+PMK + ++ A+ G +LDP K E+ + FA+L+
Sbjct: 137 RTACLNAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDNFGEADMPFAFLIRN 195
Query: 173 NSILSV 178
I S+
Sbjct: 196 GKIESI 201
>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 = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 13/186 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
R DGR ++LRP+ S+L RA GS G KV+AAV+GP+ ++ ++P KA I
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIR 76
Query: 64 VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
+ + G + EI + K +++ + + P + + ++V+ D
Sbjct: 77 YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG---FAYLVFP 172
+NAA ALVDAG+PMK + ++ A+ G +LDP K E+ + FA+L+
Sbjct: 137 RTACLNAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDNFGEADMPFAFLIRN 195
Query: 173 NSILSV 178
I S+
Sbjct: 196 GKIESI 201
>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 = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 51/169 (30%), Positives = 85/169 (50%), Gaps = 16/169 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
R DGR +LR + + +A GSA QG+TK LA VYGP G++ P++A +
Sbjct: 17 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76
Query: 63 EVIWKPRTGQIGKPEK---------EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
+ T G+ ++ E + L++T ++ + ++P + + +QV+ DG
Sbjct: 77 NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 136
Query: 114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEE 160
+NAA A++DAGIPM+ +C CSA G + D + +EE
Sbjct: 137 GTYAACVNAATLAVLDAGIPMRDF---VCACSAGFVDGTALADLSHVEE 182
>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 = 87.0 bits (214), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 57/165 (34%), Positives = 81/165 (49%), Gaps = 10/165 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
R DGR +LRP+ +L A+GSA G K++AAVYGP+ K+ + P++A +
Sbjct: 17 RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76
Query: 64 VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
V + + G + EI ++K L+ IL + P T V I+V+ D
Sbjct: 77 VRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGT 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
I AA AL DAGIPM+ L VA C G +LD K E+
Sbjct: 137 RVAGITAASLALADAGIPMRDL-VAACAAGKIEGEIVLDLNKEED 180
>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|D Chain D, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|F Chain F, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|H Chain H, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|J Chain J, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|L Chain L, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|N Chain N, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|P Chain P, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|R Chain R, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|T Chain T, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|V Chain V, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|X Chain X, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
Length = 248
Score = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 10/165 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
R DGR P++LR + +L A GSA + G+TK +AAVYGPK ++ + P++A +
Sbjct: 19 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 78
Query: 64 VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
V + + + + E E +++ L+S ++ + P T V +++ D
Sbjct: 79 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 138
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
++ AA AL DAGIPM+ L + A+ G ILD + E+
Sbjct: 139 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETED 182
>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|E Chain E, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|H Chain H, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 245
Score = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 10/165 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
R DGR P++LR + +L A GSA + G+TK +AAVYGPK ++ + P++A +
Sbjct: 16 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 75
Query: 64 VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
V + + + + E E +++ L+S ++ + P T V +++ D
Sbjct: 76 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 135
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
++ AA AL DAGIPM+ L + A+ G ILD + E+
Sbjct: 136 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETED 179
>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 250
Score = 84.3 bits (207), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 50/164 (30%), Positives = 83/164 (50%), Gaps = 10/164 (6%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
R DGR P++LR + +L A GSA + G+TK +AAVYGPK ++ + P++A +
Sbjct: 21 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 80
Query: 64 VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
V + + + + E E +++ L+S ++ + P T V +++ D
Sbjct: 81 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 140
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLE 159
++ AA AL DAGIPM+ L + A+ G ILD + E
Sbjct: 141 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 183
>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 = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 56/167 (33%), Positives = 81/167 (48%), Gaps = 10/167 (5%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK-AGTKKNENPEKASIE 63
R DGR ++LRPL IL RA GS+ G K+L AVYGP+ A +K + P++A I
Sbjct: 17 REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIR 76
Query: 64 VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
+ + G + EI I L+ IL P + V I+V+ +G
Sbjct: 77 CRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGT 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQK 162
I AA AL DAGIPM+ + VA C +LD ++ E+++
Sbjct: 137 RCAGITAASVALADAGIPMRDMVVA-CAAGKVGDQVVLDLSEEEDKE 182
>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 = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 46/156 (29%), Positives = 78/156 (50%), Gaps = 9/156 (5%)
Query: 13 QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQ 72
+LR + C S L A GSA +SQG T + A+ GP + E ++++ ++ G
Sbjct: 4 RLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG- 62
Query: 73 IGKPEKEYEI---ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVD 129
+ ++ + I+ TL + L + P+TT SV + + DDG++ AIN AC AL+D
Sbjct: 63 ----DNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLD 118
Query: 130 AGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG 165
G+P + + + + I+DPT +E G
Sbjct: 119 NGMPFETVFCGVLIVRVKDEL-IIDPTAKQEAASTG 153
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 68.2 bits (165), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 62/240 (25%), Positives = 99/240 (41%), Gaps = 20/240 (8%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIE 63
+R D + + IL GS+ + DTKV+ +V GP + E P + ++E
Sbjct: 12 NRLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALE 71
Query: 64 VIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVV---HDDGAL----L 116
+I +P G EK E L+ L + P + Q++ D+ L
Sbjct: 72 IIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLREL 131
Query: 117 PCAINAACAALVDAGIPMKHLAVAI-CCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI 175
C INAA ALVDAGI + + +I ++ I+DPT E+ K+
Sbjct: 132 SCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTA-EQLKIS----------- 179
Query: 176 LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 235
LSV V G + ++ ++G + D F LE G +L +RR +Q +
Sbjct: 180 LSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNI 239
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 68.2 bits (165), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 13/171 (7%)
Query: 5 RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASI 62
R DGR N+LR S + H A GS+ QG+ K++ V GPK K++ + KA +
Sbjct: 15 RLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALL 74
Query: 63 EV---IWK----PRTGQIGKPEK---EYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 112
V I K R+ K E+ E + L R + +L I P T + I V+ D
Sbjct: 75 NVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQD 134
Query: 113 GALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKM 163
G ++ IN AL+DAGI M I ++ +LD LEE M
Sbjct: 135 GGIMGSLINGITLALIDAGISMFDYISGISVGLYDT-TPLLDTNSLEENAM 184
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 13/171 (7%)
Query: 5 RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASI 62
R DGR N+LR S + H A GS+ QG+ K++ V GPK K++ + KA +
Sbjct: 13 RLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALL 72
Query: 63 EV---IWK----PRTGQIGKPEK---EYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 112
V I K R+ K E+ E + L R + +L I P T + I V+ D
Sbjct: 73 NVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQD 132
Query: 113 GALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKM 163
G ++ IN AL+DAGI M I ++ +LD LEE M
Sbjct: 133 GGIMGSLINGITLALIDAGISMFDYISGISVGLYDT-TPLLDTNSLEENAM 182
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
R DGR + +R L +L R HGSA +++G+T+ L GT ++ E
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 377
Query: 56 NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
+ + P TG +G P K EI R L +L + P+ T V+
Sbjct: 378 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 435
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
++ +G+ ++ A AL+DAG+P+K I + G Y +L
Sbjct: 436 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 484
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
R DGR + +R L +L R HGSA +++G+T+ L GT ++ E
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 377
Query: 56 NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
+ + P TG +G P K EI R L +L + P+ T V+
Sbjct: 378 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 435
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
++ +G+ ++ A AL+DAG+P+K I + G Y +L
Sbjct: 436 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 484
>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 = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
R DGR + +R L +L R HGSA +++G+T+ L GT ++ E
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 371
Query: 56 NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
+ + P TG +G P K EI R L +L + P+ T V+
Sbjct: 372 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 429
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
++ +G+ ++ A AL+DAG+P+K I + G Y +L
Sbjct: 430 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 478
>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 = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
R DGR + +R L +L R HGSA +++G+T+ L GT ++ E
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 371
Query: 56 NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
+ + P TG +G P K EI R L +L + P+ T V+
Sbjct: 372 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 429
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
++ +G+ ++ A AL+DAG+P+K I + G Y +L
Sbjct: 430 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 478
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 54/177 (30%), Positives = 75/177 (42%), Gaps = 24/177 (13%)
Query: 9 RNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI------ 62
R+P +LRP+ +L +A GSA G TKVL AV GP+ A
Sbjct: 31 RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPA 90
Query: 63 --------EVIWKPRTGQI------GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQV 108
+ P G+ G E+E + L+ L+ L P V +
Sbjct: 91 ALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALL 150
Query: 109 VHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYC---ILDPTKLEEQK 162
+ D G+ L A+ AA AL DAG+ M L V C S G +LDPT+LEE++
Sbjct: 151 LEDGGSALAAALTAAALALADAGVEMYDLVVG-CGLSLAPGPAPTWLLDPTRLEEER 206
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 72/182 (39%), Gaps = 25/182 (13%)
Query: 3 VDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK--KNENPEKA 60
++R GR +QLRP+ + A GS GDTKV+ V + K +
Sbjct: 1 MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWL 60
Query: 61 SIEVIWKPRT-----------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVV 109
+ E PR+ G+ G E + ++ R+L++ L+ T + V+
Sbjct: 61 TAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVI 120
Query: 110 HDDGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAESGYCILDPTKL 158
DG +I A AL+DA G P+K + VA G +LD L
Sbjct: 121 QADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQM-VAAVSVGIYQGVPVLDLDYL 179
Query: 159 EE 160
E+
Sbjct: 180 ED 181
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
R DGR+ +RP+ IL R HGSA +++G+T+ A+ GT +E A +E
Sbjct: 322 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 377
Query: 65 IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
+K TG++G P E + + R L+ + + T ++ +
Sbjct: 378 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 437
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
+ +G+ + + A++DAG+P+ +A+ + G+ +L
Sbjct: 438 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 485
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
R DGR+ +RP+ IL R HGSA +++G+T+ A+ GT +E A +E
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 386
Query: 65 IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
+K TG++G P E + + R L+ + + T ++ +
Sbjct: 387 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 446
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
+ +G+ + + A++DAG+P+ +A+ + G+ +L
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 494
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
R DGR+ +RP+ IL R HGSA +++G+T+ A+ GT +E A +E
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 386
Query: 65 IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
+K TG++G P E + + R L+ + + T ++ +
Sbjct: 387 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 446
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
+ +G+ + + A++DAG+P+ +A+ + G+ +L
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 494
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
R+DGR +QLRP++ L GS S G TKV+ A+V G G
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P I + G+IG E + ++ R +++ LT T V V+
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
DG AI A A+ DA I +
Sbjct: 122 DGGTRTAAITGAFVAVADAIIKL 144
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
R+DGR +QLRP++ L GS S G TKV+ A+V G G
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P I + G+IG E + ++ R +++ LT T V V+
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
DG AI A A+ DA I +
Sbjct: 122 DGGTATAAITGAFVAVADAIIKL 144
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
R+DGR +QLRP++ L GS S G TKV+ A+V G G
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P I + G+IG E + ++ R +++ LT T V V+
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
DG AI A A+ DA I +
Sbjct: 122 DGGTRTAAITGAFVAVADAIIKL 144
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
R+DGR +QLRP++ L GS S G TKV+ A+V G G
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P I + G+IG E + ++ R +++ LT T V V+
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
DG AI A A+ DA I +
Sbjct: 122 DGGARTAAITGAFVAVADAIIKL 144
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 48/189 (25%), Positives = 69/189 (36%), Gaps = 41/189 (21%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKV---------------------LA 42
+R GR +QLRP+ + A GS GDTKV L
Sbjct: 2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLT 61
Query: 43 AVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTT 102
A YG + N +AS G+ G E + ++ R+L++ L+ T
Sbjct: 62 AEYGXLPRSTGERNQREAS--------RGKQGGRTLEIQRLIGRSLRAALDLSKLGENTL 113
Query: 103 SVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAESGYC 151
+ V+ DG +I A AL+DA G P+K VA G
Sbjct: 114 YIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQ-XVAAVSVGIYQGVP 172
Query: 152 ILDPTKLEE 160
+LD LE+
Sbjct: 173 VLDLDYLED 181
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
E R DGR+ LR ++C + HGSA + +G T+VL V
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTV 358
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL 41
E R DGR +R LA + R HGSA + +G+T++L
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQIL 392
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 42/182 (23%), Positives = 64/182 (35%), Gaps = 24/182 (13%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAA----------VYGPKAGTKKN 54
R DGR +LR + + L GS GDTKV+ + + G G
Sbjct: 12 RVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTA 71
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P I + G++ E + ++ R L+++ L T + V+
Sbjct: 72 EYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQA 131
Query: 112 DGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAESGYCILDPTKLEE 160
DG +I A A+V A IP+K A E +LD E+
Sbjct: 132 DGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYAED 191
Query: 161 QK 162
K
Sbjct: 192 SK 193
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 56/136 (41%), Gaps = 13/136 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAV--------YGPKAGTKKN 54
R DGR ++LRP+ + GS + G+TKV+ A+V G G
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P+ + + I + G+I E + ++ R L+++ L T + V+
Sbjct: 62 EYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQA 121
Query: 112 DGALLPCAINAACAAL 127
DG +I A A+
Sbjct: 122 DGGTRTASITGAFLAM 137
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 35.0 bits (79), Expect = 0.033, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLA 42
E R DGR +R LA + R HGSA + +G+T++L
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILG 393
>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 = 35.0 bits (79), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI 62
+R DGR+ ++ R ++ ++ +A GS+ G+T+++ V P+ G + PE I
Sbjct: 24 ERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVK-PQIGEPFPDTPEMGVI 81
>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 = 34.3 bits (77), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 54/136 (39%), Gaps = 13/136 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAV--------YGPKAGTKKN 54
R DGR ++LRP+ + GS + G+TKV+ A+V G G
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61
Query: 55 EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P + I + G+I E + ++ R L+++ L T + V+
Sbjct: 62 EYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQA 121
Query: 112 DGALLPCAINAACAAL 127
DG +I A A+
Sbjct: 122 DGGTRTASITGAFLAM 137
>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 = 33.9 bits (76), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 61/266 (22%), Positives = 100/266 (37%), Gaps = 63/266 (23%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK--NENPEKAS- 61
R DGR RPL+ + +A GSA G T VLA G K K + P + +
Sbjct: 28 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA---GTKLEIDKPYEDTPNQGNL 84
Query: 62 -IEVIWKP---RTGQIGKPEK---EYEIILKRTLQ-----SICILTINPNTTTSVI---I 106
+ V P T + G P++ E ++ R+L+ + L I P + + +
Sbjct: 85 IVNVELLPLAYTTFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDV 144
Query: 107 QVVHDDGALLPCAINAACAALVDAGI-----------------PMKHLAVAICCCSAESG 149
V+ G +L A+ AAL + + P+ + V I +
Sbjct: 145 YVLDYGGNVLDACTLASVAALYNTKVYKVEQISVNKNEVVGKLPLNYPVVTISVAKVDK- 203
Query: 150 YCILDPTKLEEQKMKG---FAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTHGAMS 205
Y ++DP EE M F+Y P+ I+ + G G+MS
Sbjct: 204 YLVVDPDLDEESIMDAKISFSYT--PDLKIVGIQKSG------------------KGSMS 243
Query: 206 VDDYFHCLERGRAASAKLSDFLRRSL 231
+ D R+ + KL + L++ L
Sbjct: 244 LQDIDQAENTARSTAVKLLEELKKHL 269
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
+R DGR ++ R + +++ +A GSA GDT+V+ V
Sbjct: 22 ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 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 = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
+R DGR ++ R + +++ +A GSA GDT+V+ V
Sbjct: 22 ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 62
>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 = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 61/270 (22%), Positives = 100/270 (37%), Gaps = 67/270 (24%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK--NENPEKAS- 61
R DGR RPL+ + +A GSA G T VLA G K K + P + +
Sbjct: 30 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA---GTKLEIDKPYEDTPNQGNL 86
Query: 62 -IEVIWKP---RTGQIGKPEK---EYEIILKRTLQ-----SICILTINPNTTTSVI---I 106
+ V P T + G P++ E ++ R+L+ + L I P + + +
Sbjct: 87 IVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDV 146
Query: 107 QVVHDDGALLPCAINAACAALVDAGI---------------------PMKHLAVAICCCS 145
V+ G +L A+ AAL + + P+ + V I
Sbjct: 147 YVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAK 206
Query: 146 AESGYCILDPTKLEEQKMKG---FAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTH 201
+ Y ++DP EE M F+Y P+ I+ + G
Sbjct: 207 VDK-YLVVDPDLDEESIMDAKISFSYT--PDLKIVGIQKSG------------------K 245
Query: 202 GAMSVDDYFHCLERGRAASAKLSDFLRRSL 231
G+MS+ D R+ + KL + L++ L
Sbjct: 246 GSMSLQDIDQAENTARSTAVKLLEELKKHL 275
>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 = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 61/270 (22%), Positives = 100/270 (37%), Gaps = 67/270 (24%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK--NENPEKAS- 61
R DGR RPL+ + +A GSA G T VLA G K K + P + +
Sbjct: 28 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA---GTKLEIDKPYEDTPNQGNL 84
Query: 62 -IEVIWKP---RTGQIGKPEK---EYEIILKRTLQ-----SICILTINPNTTTSVI---I 106
+ V P T + G P++ E ++ R+L+ + L I P + + +
Sbjct: 85 IVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDV 144
Query: 107 QVVHDDGALLPCAINAACAALVDAGI---------------------PMKHLAVAICCCS 145
V+ G +L A+ AAL + + P+ + V I
Sbjct: 145 YVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAK 204
Query: 146 AESGYCILDPTKLEEQKMKG---FAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTH 201
+ Y ++DP EE M F+Y P+ I+ + G
Sbjct: 205 VDK-YLVVDPDLDEESIMDAKISFSYT--PDLKIVGIQKSG------------------K 243
Query: 202 GAMSVDDYFHCLERGRAASAKLSDFLRRSL 231
G+MS+ D R+ + KL + L++ L
Sbjct: 244 GSMSLQDIDQAENTARSTAVKLLEELKKHL 273
>pdb|4FDW|A Chain A, Crystal Structure Of A Leucine Rich Hypothetical Protein
(Bacova_01565) From Bacteroides Ovatus Atcc 8483 At 2.05
A Resolution
Length = 401
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 110 HDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI-LDPTKLEE----QKMK 164
+DDG P + + + + +P+ V I + + + + P ++E + +K
Sbjct: 54 YDDGKQRPVKVTSEQISGFSSSVPVDKQEVTITIEGKQKSFSVHISPVRVENGVLTEILK 113
Query: 165 GFAYLVFPNSILSV 178
G+ ++ PNS+ S+
Sbjct: 114 GYNEIILPNSVKSI 127
>pdb|1UJN|A Chain A, Crystal Structure Of Dehydroquinate Synthase From Thermus
Thermophilus Hb8
pdb|1UJN|B Chain B, Crystal Structure Of Dehydroquinate Synthase From Thermus
Thermophilus Hb8
Length = 348
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 44/104 (42%), Gaps = 31/104 (29%)
Query: 163 MKGFAYLVFPNSILSV------------LPEGSSLV------QG-------------EPM 191
++G AYL FP + L++ LPEG +LV QG
Sbjct: 108 LRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTF 167
Query: 192 EHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 235
+ G++ + HG ++ D+ +E S +L FL R++ K+
Sbjct: 168 KEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKV 211
>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 = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
R D R RP+ ++ +A GSA G T+VL +
Sbjct: 27 RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGI 66
>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 = 1.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
R DGR R + ++ GSA G T +L V + GT K E P + +E
Sbjct: 37 RVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA-EMGTPKLEKPNEGYLEF 95
Query: 65 I 65
Sbjct: 96 F 96
>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 = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 35/139 (25%), Positives = 53/139 (38%), Gaps = 13/139 (9%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVYGPKAGTKKNENPEKASI 62
R DGR ++LRP+ + GS G TKVL A+V +K +
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66
Query: 63 EVIWKPRT-----------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
E P G++ +E ++ R+L++ L T ++ V+
Sbjct: 67 EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126
Query: 112 DGALLPCAINAACAALVDA 130
DG AI A AL DA
Sbjct: 127 DGGTRTAAITGAYVALADA 145
>pdb|2RC5|A Chain A, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|B Chain B, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|C Chain C, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC5|D Chain D, Refined Structure Of Fnr From Leptospira Interrogans
pdb|2RC6|A Chain A, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|B Chain B, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|C Chain C, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
pdb|2RC6|D Chain D, Refined Structure Of Fnr From Leptospira Interrogans Bound
To Nadp+
Length = 314
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 13/98 (13%)
Query: 47 PKAGTKKNENPEKASI--EVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSV 104
P+ K NP KA + V+ P TG +P+KE E ++ R +L I+ + V
Sbjct: 11 PQINLFKKSNPYKAKVISNVLLTPETGTGKRPKKEGEALVHR-----IVLAIDHSAYPYV 65
Query: 105 IIQVVHDDGALLPCAINAACAA--LVDAGIPMKHLAVA 140
I Q G ++P + A L D G ++ ++A
Sbjct: 66 IGQ----SGGVIPPGEDPEKKAKGLADVGYTVRLYSIA 99
>pdb|4IFD|F Chain F, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 250
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 28/127 (22%), Positives = 51/127 (40%), Gaps = 28/127 (22%)
Query: 38 TKVLAAVYGPKAGTKKNENPEKASIEV----IWKPRTGQIGKPEKEYEIILKRTLQSICI 93
T +++AVYGP++ + SI++ + K T ++ KE L S+
Sbjct: 71 TSLISAVYGPRSIRGSFTSQGTISIQLKNGLLEKYNTNEL----KEVSSFLMGIFNSVVN 126
Query: 94 LTINPNTTTSVIIQVVHDD--------------------GALLPCAINAACAALVDAGIP 133
L+ P + + + + +D +L+P I + AL DAGI
Sbjct: 127 LSRYPKSGIDIFVYLTYDKDLTNNPQDDDSQSKMTSSQISSLIPHCITSITLALADAGIE 186
Query: 134 MKHLAVA 140
+ +A A
Sbjct: 187 LVDMAGA 193
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 0.133 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,352,822
Number of Sequences: 62578
Number of extensions: 288185
Number of successful extensions: 611
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 537
Number of HSP's gapped (non-prelim): 53
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)