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= 024064
(273 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 = 315 bits (806), Expect = 2e-86, Method: Compositional matrix adjust.
Identities = 161/269 (59%), Positives = 192/269 (71%), Gaps = 31/269 (11%)
Query: 1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFC 60
ME RADGRNPNQLRP +C+ + L RAHGSA W+QG
Sbjct: 1 MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQG------------------------ 36
Query: 61 YWVGSGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
DT VLAAVYGPK GT+K ENPEKASIEV+WKP TGQIGK EKEYE+ LKRTLQS
Sbjct: 37 ------DTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTGQIGKQEKEYEMTLKRTLQS 90
Query: 121 ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGY 180
IC+LT++PNTTTSVI+QVV +DG+LLPCAINA CAALV AGIP+KHLAVAI C E G
Sbjct: 91 ICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGE 150
Query: 181 CILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYF 240
ILD K EEQ++K FA+LVFPNS S + + + E E G+ITS+THG MS +DYF
Sbjct: 151 VILDTNKAEEQQLKSFAHLVFPNSRKSASSKEPNQKE-EDSERGLITSITHGVMSEEDYF 209
Query: 241 HCLERGRAASAKLSDFLRRSLQSKLPGDL 269
C+ERG AAS+++SDF+R +LQ + PGD+
Sbjct: 210 SCIERGLAASSRISDFMRTTLQKQAPGDV 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 = 119 bits (299), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 71/194 (36%), Positives = 101/194 (52%), Gaps = 33/194 (17%)
Query: 9 RNPN-QLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGD 67
R P LR AC ++L R GSAS+ QG D
Sbjct: 24 RGPGCSLRHFACEQNLLSRPDGSASFLQG------------------------------D 53
Query: 68 TKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTIN 127
T VLA VYGP E KA++EVI +P+ G G EK E +++ T +++ + T++
Sbjct: 54 TSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLH 113
Query: 128 PNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTK 187
P T+ +V++QVV D G+LL C +NAAC ALVDAG+PM+ L + C G +LDPT
Sbjct: 114 PRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTS 173
Query: 188 LEEQKMKGFAYLVF 201
+E++ + A L F
Sbjct: 174 KQEKEAR--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 = 77.8 bits (190), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 65/269 (24%), Positives = 114/269 (42%), Gaps = 60/269 (22%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR ++LRP+ S+L RA GS CY
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGS--------------------------CYLEM--- 47
Query: 65 SGDTKVLAAVYGPKAGTKKN-ENPEKASIEVIWK------PRTGQIGKPEKEYEI--ILK 115
G KV+AAV+GP+ ++ ++P KA I + + G + EI + K
Sbjct: 48 -GKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSK 106
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+++ + + P + + ++V+ D +NAA ALVDAG+PMK + ++
Sbjct: 107 EAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGK 166
Query: 176 AESGYCILDPTKLEEQKMKG---FAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG 232
A+ G +LDP K E+ + FA+L+ I S+ +L+Q G
Sbjct: 167 AD-GQLVLDPMKEEDNFGEADMPFAFLIRNGKIESI-----ALLQ------------MDG 208
Query: 233 AMSVDDYFHCLERGRAASAKLSDFLRRSL 261
M+ D+ +E + + ++ + R ++
Sbjct: 209 RMTRDEVKQAIELAKKGALQIYEMQREAI 237
>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 = 77.4 bits (189), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 65/269 (24%), Positives = 114/269 (42%), Gaps = 60/269 (22%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR ++LRP+ S+L RA GS CY
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGS--------------------------CYLEM--- 47
Query: 65 SGDTKVLAAVYGPKAGTKKN-ENPEKASIEVIWK------PRTGQIGKPEKEYEI--ILK 115
G KV+AAV+GP+ ++ ++P KA I + + G + EI + K
Sbjct: 48 -GKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSK 106
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+++ + + P + + ++V+ D +NAA ALVDAG+PMK + ++
Sbjct: 107 EAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGK 166
Query: 176 AESGYCILDPTKLEEQKMKG---FAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG 232
A+ G +LDP K E+ + FA+L+ I S+ +L+Q G
Sbjct: 167 AD-GQLVLDPMKEEDNFGEADMPFAFLIRNGKIESI-----ALLQ------------MDG 208
Query: 233 AMSVDDYFHCLERGRAASAKLSDFLRRSL 261
M+ D+ +E + + ++ + R ++
Sbjct: 209 RMTRDEVKQAIELAKKGALQIYEMQREAI 237
>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 = 75.5 bits (184), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 67/269 (24%), Positives = 108/269 (40%), Gaps = 57/269 (21%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR +LRP+ +L A+GSA + W
Sbjct: 17 RIDGRKKYELRPIKMEVGVLKNANGSA---------------------------YIEW-- 47
Query: 65 SGDTKVLAAVYGPKAGTKKN-ENPEKASIEVIWK------PRTGQIGKPEKEYEI--ILK 115
G K++AAVYGP+ K+ + P++A + V + + G + EI ++K
Sbjct: 48 -GKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIK 106
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
L+ IL + P T V I+V+ D I AA AL DAGIPM+ L VA C
Sbjct: 107 GALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDL-VAACAAG 165
Query: 176 AESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMS 235
G +LD K E+ + P +I+ P+++ I G ++
Sbjct: 166 KIEGEIVLDLNKEEDN----YGEADVPVAIM-------------PLKNDITLLQMDGYLT 208
Query: 236 VDDYFHCLERGRAASAKLSDFLRRSLQSK 264
D++ ++ + + R +L+ K
Sbjct: 209 KDEFIEAVKLAIKGAKAVYQKQREALKEK 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 = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 50/199 (25%), Positives = 86/199 (43%), Gaps = 46/199 (23%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR +LR + + +A GSA ++
Sbjct: 17 RVDGRRAGELRKIQARMGVFAQADGSA------------------------------YIE 46
Query: 65 SGDTKVLAAVYGPKA--GTKKNENPEKASIEVIWKPRTGQIGKPEK---------EYEII 113
G+TK LA VYGP G++ P++A + + T G+ ++ E +
Sbjct: 47 QGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQ 106
Query: 114 LKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICC 173
L++T ++ + ++P + + +QV+ DG +NAA A++DAGIPM+ +C
Sbjct: 107 LRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDF---VCA 163
Query: 174 CSAE--SGYCILDPTKLEE 190
CSA G + D + +EE
Sbjct: 164 CSAGFVDGTALADLSHVEE 182
>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 = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 50/195 (25%), Positives = 84/195 (43%), Gaps = 40/195 (20%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR P++LR + +L A GSA + G
Sbjct: 19 RTDGRKPDELRSIKIELGVLKNADGSAIFEMG---------------------------- 50
Query: 65 SGDTKVLAAVYGPKAGTKKNEN-PEKASIEVIW--------KPRTGQIGKPEKEYEIILK 115
+TK +AAVYGPK ++ + P++A + V + + + + E E +++
Sbjct: 51 --NTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIR 108
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
L+S ++ + P T V +++ D ++ AA AL DAGIPM+ L +
Sbjct: 109 EALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK 168
Query: 176 AESGYCILDPTKLEE 190
A+ G ILD + E+
Sbjct: 169 AD-GVIILDLNETED 182
>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 = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 59/202 (29%), Positives = 85/202 (42%), Gaps = 50/202 (24%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR ++LRPL IL RA GS+ + F
Sbjct: 17 REDGRAFDELRPLKIEAGILERADGSS-------------YLEF---------------- 47
Query: 65 SGDTKVLAAVYGPK-AGTKKNENPEKA-----------SIEVIWKPRTGQIGKPEKEYEI 112
G K+L AVYGP+ A +K + P++A S+E +P G + EI
Sbjct: 48 -GGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFSVEERKRP-----GPDRRSVEI 101
Query: 113 --ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVA 170
I L+ IL P + V I+V+ +G I AA AL DAGIPM+ + VA
Sbjct: 102 SKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVA 161
Query: 171 ICCCSAESGYCILDPTKLEEQK 192
C +LD ++ E+++
Sbjct: 162 -CAAGKVGDQVVLDLSEEEDKE 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 = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 50/195 (25%), Positives = 84/195 (43%), Gaps = 40/195 (20%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR P++LR + +L A GSA + G
Sbjct: 16 RTDGRKPDELRSIKIELGVLKNADGSAIFEMG---------------------------- 47
Query: 65 SGDTKVLAAVYGPKAGTKKNEN-PEKASIEVIW--------KPRTGQIGKPEKEYEIILK 115
+TK +AAVYGPK ++ + P++A + V + + + + E E +++
Sbjct: 48 --NTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIR 105
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
L+S ++ + P T V +++ D ++ AA AL DAGIPM+ L +
Sbjct: 106 EALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK 165
Query: 176 AESGYCILDPTKLEE 190
A+ G ILD + E+
Sbjct: 166 AD-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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 50/194 (25%), Positives = 83/194 (42%), Gaps = 40/194 (20%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR P++LR + +L A GSA + G
Sbjct: 21 RTDGRKPDELRSIKIELGVLKNADGSAIFEMG---------------------------- 52
Query: 65 SGDTKVLAAVYGPKAGTKKNEN-PEKASIEVIW--------KPRTGQIGKPEKEYEIILK 115
+TK +AAVYGPK ++ + P++A + V + + + + E E +++
Sbjct: 53 --NTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIR 110
Query: 116 RTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
L+S ++ + P T V +++ D ++ AA AL DAGIPM+ L +
Sbjct: 111 EALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGK 170
Query: 176 AESGYCILDPTKLE 189
A+ G ILD + E
Sbjct: 171 AD-GVIILDLNETE 183
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 60.8 bits (146), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 57/209 (27%), Positives = 89/209 (42%), Gaps = 20/209 (9%)
Query: 65 SGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICIL 124
S DTKV+ +V GP + E P + ++E+I +P G EK E L+ L +
Sbjct: 43 SQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITR 102
Query: 125 TINPNTTTSVIIQVV---HDDGAL----LPCAINAACAALVDAGIPMKHLAVAI-CCCSA 176
P + Q++ D+ L C INAA ALVDAGI + + +I
Sbjct: 103 HCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIK 162
Query: 177 ESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSV 236
++ I+DPT E+ K+ LSV V G + ++ ++G +
Sbjct: 163 DTSDIIVDPTA-EQLKIS-----------LSVHTLALEFVNGGKVVKNVLLLDSNGDFNE 210
Query: 237 DDYFHCLERGRAASAKLSDFLRRSLQSKL 265
D F LE G +L +RR +Q +
Sbjct: 211 DQLFSLLELGEQKCQELVTNIRRIIQDNI 239
>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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 49/186 (26%), Positives = 82/186 (44%), Gaps = 39/186 (20%)
Query: 13 QLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDTKVLA 72
+LR + C S L A GSA +SQG + C + G GD
Sbjct: 4 RLREMRCELSFLKNADGSACFSQG------------------ATCIWASCSGPGD----- 40
Query: 73 AVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEI---ILKRTLQSICILTINPN 129
V+ KA + E ++++ ++ G + ++ + I+ TL + L + P+
Sbjct: 41 -VHASKA------SDEAMTLDISYRANCG-----DNKFNVLNNIIHSTLSNAINLELFPH 88
Query: 130 TTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLE 189
TT SV + + DDG++ AIN AC AL+D G+P + + + + I+DPT +
Sbjct: 89 TTISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETVFCGVLIVRVKDEL-IIDPTAKQ 147
Query: 190 EQKMKG 195
E G
Sbjct: 148 EAASTG 153
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 55/201 (27%), Positives = 78/201 (38%), Gaps = 43/201 (21%)
Query: 5 RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWV 63
R DGR N+LR S + H A GS+ QG
Sbjct: 15 RLDGRRWNELRRFESSINTHPHAADGSSYMEQG--------------------------- 47
Query: 64 GSGDTKVLAAVYGPKAGTKKNE-NPEKASIEV---IWK----PRTGQIGKPEK---EYEI 112
+ K++ V GPK K++ + KA + V I K R+ K E+ E +
Sbjct: 48 ---NNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQT 104
Query: 113 ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAIC 172
L R + +L I P T + I V+ DG ++ IN AL+DAGI M I
Sbjct: 105 SLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGIS 164
Query: 173 CCSAESGYCILDPTKLEEQKM 193
++ +LD LEE M
Sbjct: 165 VGLYDT-TPLLDTNSLEENAM 184
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 55/201 (27%), Positives = 78/201 (38%), Gaps = 43/201 (21%)
Query: 5 RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWV 63
R DGR N+LR S + H A GS+ QG
Sbjct: 13 RLDGRRWNELRRFESSINTHPHAADGSSYMEQG--------------------------- 45
Query: 64 GSGDTKVLAAVYGPKAGTKKNE-NPEKASIEV---IWK----PRTGQIGKPEK---EYEI 112
+ K++ V GPK K++ + KA + V I K R+ K E+ E +
Sbjct: 46 ---NNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQT 102
Query: 113 ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAIC 172
L R + +L I P T + I V+ DG ++ IN AL+DAGI M I
Sbjct: 103 SLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGIS 162
Query: 173 CCSAESGYCILDPTKLEEQKM 193
++ +LD LEE M
Sbjct: 163 VGLYDT-TPLLDTNSLEENAM 182
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 76/190 (40%), Gaps = 37/190 (19%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR + +R L +L R HGSA +++G ++ +G
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRG-----------------ETQALVTATLG 363
Query: 65 SG-DTKVLAAVYGPKAGT---KKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+ D +VL + G + T N P TG +G P K EI R L
Sbjct: 364 TARDAQVLDELMGERTDTFLFHYNFPPYSVG-------ETGMVGSP-KRREIGHGR-LAK 414
Query: 121 ICILTINPNT-----TTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+L + P+ T V+ ++ +G+ ++ A AL+DAG+P+K I
Sbjct: 415 RGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGL 474
Query: 176 AESG--YCIL 183
+ G Y +L
Sbjct: 475 VKEGDNYVVL 484
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 76/190 (40%), Gaps = 37/190 (19%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR + +R L +L R HGSA +++G ++ +G
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRG-----------------ETQALVTATLG 357
Query: 65 SG-DTKVLAAVYGPKAGT---KKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+ D +VL + G + T N P TG +G P K EI R L
Sbjct: 358 TARDAQVLDELMGERTDTFLFHYNFPPYSVG-------ETGMVGSP-KRREIGHGR-LAK 408
Query: 121 ICILTINPNT-----TTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+L + P+ T V+ ++ +G+ ++ A AL+DAG+P+K I
Sbjct: 409 RGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGL 468
Query: 176 AESG--YCIL 183
+ G Y +L
Sbjct: 469 VKEGDNYVVL 478
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 76/190 (40%), Gaps = 37/190 (19%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR + +R L +L R HGSA +++G ++ +G
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRG-----------------ETQALVTATLG 357
Query: 65 SG-DTKVLAAVYGPKAGT---KKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+ D +VL + G + T N P TG +G P K EI R L
Sbjct: 358 TARDAQVLDELMGERTDTFLFHYNFPPYSVG-------ETGMVGSP-KRREIGHGR-LAK 408
Query: 121 ICILTINPNT-----TTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+L + P+ T V+ ++ +G+ ++ A AL+DAG+P+K I
Sbjct: 409 RGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGL 468
Query: 176 AESG--YCIL 183
+ G Y +L
Sbjct: 469 VKEGDNYVVL 478
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 47/190 (24%), Positives = 76/190 (40%), Gaps = 37/190 (19%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR + +R L +L R HGSA +++G ++ +G
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRG-----------------ETQALVTATLG 363
Query: 65 SG-DTKVLAAVYGPKAGT---KKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+ D +VL + G + T N P TG +G P K EI R L
Sbjct: 364 TARDAQVLDELMGERTDTFLFHYNFPPYSVG-------ETGMVGSP-KRREIGHGR-LAK 414
Query: 121 ICILTINPNT-----TTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCS 175
+L + P+ T V+ ++ +G+ ++ A AL+DAG+P+K I
Sbjct: 415 RGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGL 474
Query: 176 AESG--YCIL 183
+ G Y +L
Sbjct: 475 VKEGDNYVVL 484
>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 = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/185 (20%), Positives = 72/185 (38%), Gaps = 27/185 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR+ +RP+ IL R HGSA +++G ++ +G
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRG-----------------ETQAIVVATLG 373
Query: 65 SGDTK----VLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+GD + L Y N P V R G G+ E + + R L+
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPP----YSVGETGRMGSPGRREIGHGKLAWRALRP 429
Query: 121 ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAES 178
+ + T ++ ++ +G+ + + A++DAG+P+ +A+ +
Sbjct: 430 MLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD 489
Query: 179 GYCIL 183
G+ +L
Sbjct: 490 GFAVL 494
>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 = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/185 (20%), Positives = 72/185 (38%), Gaps = 27/185 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR+ +RP+ IL R HGSA +++G ++ +G
Sbjct: 322 RIDGRDVKTVRPILGEVGILPRTHGSALFTRG-----------------ETQAIVVATLG 364
Query: 65 SGDTK----VLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+GD + L Y N P V R G G+ E + + R L+
Sbjct: 365 TGDDEQFIDALEGTYKESFLLHYNFPP----YSVGETGRMGSPGRREIGHGKLAWRALRP 420
Query: 121 ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAES 178
+ + T ++ ++ +G+ + + A++DAG+P+ +A+ +
Sbjct: 421 MLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD 480
Query: 179 GYCIL 183
G+ +L
Sbjct: 481 GFAVL 485
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/185 (20%), Positives = 72/185 (38%), Gaps = 27/185 (14%)
Query: 5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVG 64
R DGR+ +RP+ IL R HGSA +++G ++ +G
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRG-----------------ETQAIVVATLG 373
Query: 65 SGDTK----VLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS 120
+GD + L Y N P V R G G+ E + + R L+
Sbjct: 374 TGDDEQFIDALEGTYKESFLLHYNFPP----YSVGETGRMGSPGRREIGHGKLAWRALRP 429
Query: 121 ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAES 178
+ + T ++ ++ +G+ + + A++DAG+P+ +A+ +
Sbjct: 430 MLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD 489
Query: 179 GYCIL 183
G+ +L
Sbjct: 490 GFAVL 494
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 33.9 bits (76), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 47/199 (23%), Positives = 73/199 (36%), Gaps = 29/199 (14%)
Query: 3 VDRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYW 62
++R GR +QLRP+ + A GS G + + + F K W
Sbjct: 1 MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFL-KGQGQGW 59
Query: 63 VGSGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSIC 122
L A YG + N +AS G+ G E + ++ R+L++
Sbjct: 60 --------LTAEYGMLPRSTGERNQREAS--------RGKQGGRTLEIQRLIGRSLRAAL 103
Query: 123 ILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAVAI 171
L+ T + V+ DG +I A AL+DA G P+K + VA
Sbjct: 104 DLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQM-VAA 162
Query: 172 CCCSAESGYCILDPTKLEE 190
G +LD LE+
Sbjct: 163 VSVGIYQGVPVLDLDYLED 181
>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 = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 140 HDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI-LDPTKLEE----QKMK 194
+DDG P + + + + +P+ V I + + + + P ++E + +K
Sbjct: 54 YDDGKQRPVKVTSEQISGFSSSVPVDKQEVTITIEGKQKSFSVHISPVRVENGVLTEILK 113
Query: 195 GFAYLVFPNSILSV 208
G+ ++ PNS+ S+
Sbjct: 114 GYNEIILPNSVKSI 127
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 71/198 (35%), Gaps = 29/198 (14%)
Query: 4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWV 63
+R GR +QLRP+ + A GS G + + + F K W
Sbjct: 2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFL-KGQGQGW- 59
Query: 64 GSGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICI 123
L A YG + N +AS G+ G E + ++ R+L++
Sbjct: 60 -------LTAEYGXLPRSTGERNQREAS--------RGKQGGRTLEIQRLIGRSLRAALD 104
Query: 124 LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAVAIC 172
L+ T + V+ DG +I A AL+DA G P+K VA
Sbjct: 105 LSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQ-XVAAV 163
Query: 173 CCSAESGYCILDPTKLEE 190
G +LD LE+
Sbjct: 164 SVGIYQGVPVLDLDYLED 181
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 53/207 (25%), Positives = 76/207 (36%), Gaps = 54/207 (26%)
Query: 9 RNPNQLRPLACSCSILHRAHGSASWSQGFRFIQTSHFYHFNLFVFTSKCYFCYWVGSGDT 68
R+P +LRP+ +L +A GSA ++ +G T
Sbjct: 31 RDPTRLRPVYARAGLLSQAKGSA------------------------------YLEAGGT 60
Query: 69 KVLAAVYGPKAGTKKNENPEKASIEVIW--------------------KPRTGQIGKPEK 108
KVL AV GP+ A + R G E+
Sbjct: 61 KVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEER 120
Query: 109 EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLA 168
E + L+ L+ L P V ++ D G+ L A+ AA AL DAG+ M L
Sbjct: 121 ELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLV 180
Query: 169 VAICCCSAESGYC---ILDPTKLEEQK 192
V C S G +LDPT+LEE++
Sbjct: 181 VG-CGLSLAPGPAPTWLLDPTRLEEER 206
>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 = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 27/104 (25%), Positives = 44/104 (42%), Gaps = 31/104 (29%)
Query: 193 MKGFAYLVFPNSILSV------------LPEGSSLV------QGEPME------------ 222
++G AYL FP + L++ LPEG +LV QG E
Sbjct: 108 LRGVAYLAFPTTTLAIVDASVGGKTGINLPEGKNLVGAFHFPQGVYAELRALKTLPLPTF 167
Query: 223 -HGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 265
G++ + HG ++ D+ +E S +L FL R++ K+
Sbjct: 168 KEGLVEAFKHGLIAGDEALLKVEDLTPQSPRLEAFLARAVAVKV 211
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQG 36
E R DGR +R LA + R HGSA + +G
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERG 387
>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 = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQG 36
E R DGR+ LR ++C + HGSA + +G
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRG 350
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 31.6 bits (70), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQG 36
E R DGR +R LA + R HGSA + +G
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERG 387
>pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synthetase Complexed
With Its Cognate Trna
Length = 642
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 46 YHFNLFVFTSKCYFCYWVGSGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGK 105
+HF L K YW G + K+L +YG KK N +E K +IGK
Sbjct: 194 HHFKLM----KTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLEEAAKRDHRKIGK 249
>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 = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 13/98 (13%)
Query: 77 PKAGTKKNENPEKASI--EVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSV 134
P+ K NP KA + V+ P TG +P+KE E ++ R +L I+ + V
Sbjct: 11 PQINLFKKSNPYKAKVISNVLLTPETGTGKRPKKEGEALVHR-----IVLAIDHSAYPYV 65
Query: 135 IIQVVHDDGALLPCAINAACAA--LVDAGIPMKHLAVA 170
I Q G ++P + A L D G ++ ++A
Sbjct: 66 IGQ----SGGVIPPGEDPEKKAKGLADVGYTVRLYSIA 99
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
0.321 0.135 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,322,881
Number of Sequences: 62578
Number of extensions: 330663
Number of successful extensions: 638
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 574
Number of HSP's gapped (non-prelim): 59
length of query: 273
length of database: 14,973,337
effective HSP length: 97
effective length of query: 176
effective length of database: 8,903,271
effective search space: 1566975696
effective search space used: 1566975696
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)