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= 022140
(302 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 174 bits (442), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 92/285 (32%), Positives = 158/285 (55%), Gaps = 16/285 (5%)
Query: 18 AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
F+ + PL Y+ R L E+ RPD R L R TT+++G++++ADGSAL K+G+TT++ +K
Sbjct: 6 GFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVK 65
Query: 78 MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
E PS ++PD+G V + +PP+CS R G P E A V ++ ++D I +S +I ++
Sbjct: 66 AEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKED 125
Query: 138 LSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXX 197
L + GK W++Y D+ C + +AA N+Q+P V++++
Sbjct: 126 LCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINE----------- 174
Query: 198 XXXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSN 255
VN K+K L + P + + + ++ DPT EEE + +T+V+D
Sbjct: 175 --ETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEG 232
Query: 256 QLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
+L L+KPGG+ L + +QDC++ R KE+ ++++E I M+
Sbjct: 233 KLCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 276
>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 = 106 bits (264), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 69/268 (25%), Positives = 124/268 (46%), Gaps = 27/268 (10%)
Query: 27 YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
Y L ++ R D R R I + A+GSAL K+G T ++ +KM+ P+ +
Sbjct: 13 YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPAPD 72
Query: 87 SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
+PD G + ++ + P+ SP PG P E + +A+ + I S ++L +L + G+
Sbjct: 73 TPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKV 132
Query: 147 WMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPV 206
W+V++DI+ +A+AA N ++P D G+ +LP
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLP------------- 179
Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
+ +P S+T ++ N L DP+ EE S+ +T +T+ D + +V++ K GG
Sbjct: 180 --------VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 267 VL------AYTSAVQDCIALTRQRVKEL 288
+L +C R++ KE+
Sbjct: 232 LLDEKLFDELLDVSINCARKLREKFKEI 259
>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 = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 69/268 (25%), Positives = 123/268 (45%), Gaps = 27/268 (10%)
Query: 27 YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
Y L ++ R D R R I + A+GSAL K+G T ++ +KM+ P +
Sbjct: 13 YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPD 72
Query: 87 SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
+PD G + ++ + P+ SP PG P E + +A+ + I S ++L +L + G+
Sbjct: 73 TPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKV 132
Query: 147 WMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPV 206
W+V++DI+ +A+AA N ++P D G+ +LP
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLP------------- 179
Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
+ +P S+T ++ N L DP+ EE S+ +T +T+ D + +V++ K GG
Sbjct: 180 --------VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 267 VL------AYTSAVQDCIALTRQRVKEL 288
+L +C R++ KE+
Sbjct: 232 LLDEKLFDELLDVSINCARKLREKFKEI 259
>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 = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 64/263 (24%), Positives = 133/263 (50%), Gaps = 19/263 (7%)
Query: 37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSID 96
R D RSL R+ +I G ++ A+GS+ K+G+T ++ +K ++ P ++P+ G + +
Sbjct: 25 RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILTN 84
Query: 97 FHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCX 156
+ P+ SP PG P E + +++ + I S MI+L++L ++ G WM++LD++
Sbjct: 85 SELLPMASPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHII 144
Query: 157 XXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVNKEKRKLTLG 216
+ VAA + +IP ++DG++V+ PVN++
Sbjct: 145 DYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVI-----NREKMQPLPVNRK------- 192
Query: 217 GIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAV 274
+L C K N I+ DP+ EEE I+ +++ + + ++ K G L +
Sbjct: 193 ----ALMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKGGEGPLTRDDVL 248
Query: 275 QDCIALTRQRVKELHQILEEAIS 297
+ +++ ++V +L + L+++++
Sbjct: 249 K-AVSIAVEKVPQLIEYLDKSMT 270
>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 = 94.4 bits (233), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 65/239 (27%), Positives = 113/239 (47%), Gaps = 21/239 (8%)
Query: 28 FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
FE+ IR D R L+ R +I++ ADGSAL K+G+T +LA K+E+ P ++
Sbjct: 25 FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 80
Query: 88 PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
P++G + ++ + P+ PG P E A +A+ + ++ S ++L +L + GK+ W
Sbjct: 81 PNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 140
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
V+LD+Y ++VAA N ++ V I VN
Sbjct: 141 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI---------------SVN 185
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
K + KL L +++ Y++ DP +EESIM+ ++ ++V + K G
Sbjct: 186 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 244
>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 = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 65/239 (27%), Positives = 113/239 (47%), Gaps = 21/239 (8%)
Query: 28 FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
FE+ IR D R L+ R +I++ ADGSAL K+G+T +LA K+E+ P ++
Sbjct: 23 FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 78
Query: 88 PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
P++G + ++ + P+ PG P E A +A+ + ++ S ++L +L + GK+ W
Sbjct: 79 PNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 138
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
V+LD+Y ++VAA N ++ V I VN
Sbjct: 139 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI---------------SVN 183
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
K + KL L +++ Y++ DP +EESIM+ ++ ++V + K G
Sbjct: 184 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 242
>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 = 93.2 bits (230), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 64/239 (26%), Positives = 112/239 (46%), Gaps = 25/239 (10%)
Query: 28 FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
FE+ IR D R L+ R +I++ ADGSAL K+G+T +LA K+E+ P ++
Sbjct: 23 FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 78
Query: 88 PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
P++G + ++ + P+ PG P E A +A+ + ++ S ++L +L + GK+ W
Sbjct: 79 PNQGNLIVNVELLPLAYTTFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 138
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
V+LD+Y ++VAA N ++ V VN
Sbjct: 139 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVE-------------------QISVN 179
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
K + KL L +++ Y++ DP +EESIM+ ++ ++V + K G
Sbjct: 180 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 238
>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 = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 68/268 (25%), Positives = 126/268 (47%), Gaps = 18/268 (6%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
L E R D R R I +G + A+GSAL K+GST +L IK + P ++P+ G
Sbjct: 22 LKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMG 81
Query: 92 CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
++ + + P+ SP PG P E A +A+ + I S +NL+++ +V GK +V++
Sbjct: 82 VMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFI 141
Query: 152 DIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDD--GKIVMLPXXXXXXXXXXXPVNKE 209
D++ +A+AA N ++P V ++ G++ L E
Sbjct: 142 DVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETL---------------DE 186
Query: 210 KRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLA 269
L + IP +T N ++ DP+ +EE +M+ +T+ D + + ++ K G
Sbjct: 187 TEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFK 246
Query: 270 YTSAVQDCIALTRQRVKELHQILEEAIS 297
V + ++ +E+ +++ EA+
Sbjct: 247 L-EEVMYAVETAFKKAEEIRKLILEAVE 273
>pdb|2NN6|A Chain A, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 358
Score = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 55/275 (20%), Positives = 121/275 (44%), Gaps = 17/275 (6%)
Query: 26 RYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL 85
R+ R + E R D R RN IS G + G + ++G T +L + E+++P L
Sbjct: 29 RFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL 85
Query: 86 ESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKA 145
EG + + + + +P PGR ++ + + + + +S I+ + L +V G+
Sbjct: 86 NRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEK 145
Query: 146 AWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXP 205
W + +D++ +A+ A + + P VS+ ++ + P
Sbjct: 146 VWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLY-----------TP 194
Query: 206 VNKEKRKLTLGGIPF--SLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKP 263
++ L++ +P S Y+L DP EE +M+ L+ + ++ ++ ++
Sbjct: 195 EERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS 254
Query: 264 GGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298
GG +L ++ C + +V E+ +++ +A+
Sbjct: 255 GGIMLLKDQVLR-CSKIAGVKVAEITELILKALEN 288
>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 = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 40/162 (24%), Positives = 72/162 (44%), Gaps = 8/162 (4%)
Query: 27 YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
Y + E +R D R R + V++ GSA K+G T +L +K E+ TP LE
Sbjct: 27 YIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLE 86
Query: 87 SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTI----SSSGMINLKELSLVG 142
P+EG ++F + CS P + ++++T+ ++ ++LK L +
Sbjct: 87 KPNEG--YLEFFVD--CSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISP 142
Query: 143 GKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSL 184
+ W++Y+D+ + AA N +IP V +
Sbjct: 143 REHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRV 184
>pdb|2WP8|A Chain A, Yeast Rrp44 Nuclease
Length = 305
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 60/305 (19%), Positives = 124/305 (40%), Gaps = 40/305 (13%)
Query: 10 LSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGS 69
++ ++E+ A F L L ++ R D RS + R+ I+ G G K+G+
Sbjct: 1 MAKDIEISASESKFILEA----LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGN 53
Query: 70 TTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGR-PAEAAPVVAKQLSDTIS 128
T + I ++ P + P EG I + P+ G E + ++ + ++
Sbjct: 54 TKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVR 113
Query: 129 SSGMINLKELSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGK 188
SG ++++ L +V G W V D++ + +A + + P +++ +
Sbjct: 114 RSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQ 173
Query: 189 IVMLPXXXXXXXXXXXPVNKEKRKLTLG--GIPFSLTCIL--------------HKNYIL 232
I++ PVN E+ + LG IP +T + +
Sbjct: 174 IIV------------HPVN-EREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISI 220
Query: 233 ADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG---AVLAYTSAVQDCIALTRQRVKELH 289
D T +EE + + ++TV L+ + ++V + K GG L + ++ + ++
Sbjct: 221 IDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQIL 280
Query: 290 QILEE 294
Q+L+E
Sbjct: 281 QLLKE 285
>pdb|4IFD|A Chain A, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 304
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 56/283 (19%), Positives = 115/283 (40%), Gaps = 36/283 (12%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
L ++ R D RS + R+ I+ G G K+G+T + I ++ P + P EG
Sbjct: 18 LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEG 74
Query: 92 CVSIDFHMPPICSPLVRPGR-PAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVY 150
I + P+ G E + ++ + ++ SG ++++ L +V G W V
Sbjct: 75 LFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVR 134
Query: 151 LDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVNKEK 210
D++ + +A + + P +++ +I++ PVN E+
Sbjct: 135 ADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIV------------HPVN-ER 181
Query: 211 RKLTLG--GIPFSLTCIL--------------HKNYILADPTSEEESIMETLVTVVLDSS 254
+ LG IP +T + + D T +EE + + ++TV L+ +
Sbjct: 182 EPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKN 241
Query: 255 NQLVSLYKPGG---AVLAYTSAVQDCIALTRQRVKELHQILEE 294
++V + K GG L + ++ + ++ Q+L+E
Sbjct: 242 REVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE 284
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
L + R D R R+ I +G + +ADGSA+ ++G+T +AA+ E+ L PD
Sbjct: 14 LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 73
Query: 90 EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
+ + +HM P + + P+ ++K + + + S+ ++ L
Sbjct: 74 RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 119
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
L + R D R R+ I +G + +ADGSA+ ++G+T +AA+ E+ L PD
Sbjct: 11 LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 70
Query: 90 EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
+ + +HM P + + P+ ++K + + + S+ ++ L
Sbjct: 71 RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 116
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
L + R D R R+ I +G + +ADGSA+ ++G+T +AA+ E+ L PD
Sbjct: 16 LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 75
Query: 90 EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
+ + +HM P + + P+ ++K + + + S+ ++ L
Sbjct: 76 RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 121
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 35 SIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPDEGC 92
S+R D R+ R I G + ADGS+ + G +L A+ E L+ PD
Sbjct: 15 SVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAV 74
Query: 93 VSIDFHMPPI-CSPLVRPG---RPAEAAPVVAKQL 123
+ ++M P RPG R E + + A+ L
Sbjct: 75 IRCRYNMAPFSVEERKRPGPDRRSVEISKITAEAL 109
>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 = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 29 ERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLE 86
E+ + + +R D R R I + ADGS ++G ++AA+ EV L+
Sbjct: 9 EKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQ 68
Query: 87 SPDEGCVSIDFHMPPI-CSPLVRPG 110
P + + ++M P RPG
Sbjct: 69 DPSKAIIRYRYNMAPFSVEERKRPG 93
>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 = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 29 ERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLE 86
E+ + + +R D R R I + ADGS ++G ++AA+ EV L+
Sbjct: 9 EKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQ 68
Query: 87 SPDEGCVSIDFHMPPI-CSPLVRPG 110
P + + ++M P RPG
Sbjct: 69 DPSKAIIRYRYNMAPFSVEERKRPG 93
>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 = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPDEGCVS 94
R D R R + +G + +A+GSA + G ++AA+ E+ L+ PD +
Sbjct: 17 RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76
Query: 95 IDFHMPPIC 103
+ ++M P
Sbjct: 77 VRYNMAPFS 85
>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 = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 20/43 (46%)
Query: 34 ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI 76
+ R D R R MG A ADGSA + G+T LA +
Sbjct: 14 QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVV 56
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 37/141 (26%), Positives = 56/141 (39%), Gaps = 27/141 (19%)
Query: 18 AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGST-----TM 72
A+R L ER +AE R D R ++ R + A+ GSAL + G T T
Sbjct: 337 AYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTT 396
Query: 73 LAAIKMEVMTPSLESPDEGCVSIDFHMPP--------ICSPLVRP---GRPAEAA----- 116
L ++ME +L +++ PP + SP R G AE A
Sbjct: 397 LNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVL 456
Query: 117 ------PVVAKQLSDTISSSG 131
P +Q+S+ + S+G
Sbjct: 457 PTREEFPYAIRQVSEALGSNG 477
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSI 95
RP R+ + R I+ A+GS L + G T ++ + E P L+ +G ++
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 96 DFHMPP 101
++ M P
Sbjct: 63 EYGMLP 68
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 29/64 (45%)
Query: 18 AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
A+R L ER +AE R D R ++ R + A+ GSAL + G T +L
Sbjct: 337 AYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTT 396
Query: 78 MEVM 81
+ +
Sbjct: 397 LNXL 400
>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 = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 27/56 (48%)
Query: 32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
L E R D R L+ RN + + + GSAL + G T +L + + + ++S
Sbjct: 314 LNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKS 369
>pdb|3KD3|A Chain A, Crystal Structure Of A Phosphoserine Phosphohydrolase-Like
Protein From Francisella Tularensis Subsp. Tularensis
Schu S4
pdb|3KD3|B Chain B, Crystal Structure Of A Phosphoserine Phosphohydrolase-Like
Protein From Francisella Tularensis Subsp. Tularensis
Schu S4
Length = 219
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 4 PNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGS 62
PN D E+ D + F + F L+ESI+P A L+ R ++ + ++DGS
Sbjct: 80 PNLLTDGIKELVQDLKNKGFEIWIFSGGLSESIQPFADYLNIPRENIFAVETIWNSDGS 138
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESPDEGCVS 94
+R D R + R+ I + +GS L ++G T ++ + +E P + +G V+
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVT 70
Query: 95 IDFHMPP 101
++ M P
Sbjct: 71 AEYAMIP 77
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSI 95
RP R+ + R I+ A+GS L + G T ++ + E P L+ +G ++
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 96 DFHMPP 101
++ P
Sbjct: 63 EYGXLP 68
>pdb|2IIU|A Chain A, Crystal Structure Of A Putative Phou-Like Phosphate
Regulatory Protein (Np_719307.1) From Shewanella
Oneidensis Mr-1 At 2.28 A Resolution.
pdb|2IIU|B Chain B, Crystal Structure Of A Putative Phou-Like Phosphate
Regulatory Protein (Np_719307.1) From Shewanella
Oneidensis Mr-1 At 2.28 A Resolution.
pdb|2IIU|C Chain C, Crystal Structure Of A Putative Phou-Like Phosphate
Regulatory Protein (Np_719307.1) From Shewanella
Oneidensis Mr-1 At 2.28 A Resolution.
pdb|2OLT|A Chain A, Crystal Structure Of A Phou-Like Protein (So_3770) From
Shewanella Oneidensis Mr-1 At 2.00 A Resolution
pdb|2OLT|B Chain B, Crystal Structure Of A Phou-Like Protein (So_3770) From
Shewanella Oneidensis Mr-1 At 2.00 A Resolution
pdb|2OLT|C Chain C, Crystal Structure Of A Phou-Like Protein (So_3770) From
Shewanella Oneidensis Mr-1 At 2.00 A Resolution
Length = 227
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 268 LAYTSAVQDCIALTRQRVKELHQILEEAISGMEID 302
+AY D + L +Q + EL +LE G E+D
Sbjct: 123 IAYLQRCIDAVGLAQQVINELDDLLEAGFRGREVD 157
>pdb|2HSD|A Chain A, The Refined Three-Dimensional Structure Of 3alpha,20beta-
Hydroxysteroid Dehydrogenase And Possible Roles Of The
Residues Conserved In Short-Chain Dehydrogenases
pdb|2HSD|B Chain B, The Refined Three-Dimensional Structure Of 3alpha,20beta-
Hydroxysteroid Dehydrogenase And Possible Roles Of The
Residues Conserved In Short-Chain Dehydrogenases
pdb|2HSD|C Chain C, The Refined Three-Dimensional Structure Of 3alpha,20beta-
Hydroxysteroid Dehydrogenase And Possible Roles Of The
Residues Conserved In Short-Chain Dehydrogenases
pdb|2HSD|D Chain D, The Refined Three-Dimensional Structure Of 3alpha,20beta-
Hydroxysteroid Dehydrogenase And Possible Roles Of The
Residues Conserved In Short-Chain Dehydrogenases
Length = 253
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 104 SPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGG 143
+P+ R G P E A V K LSDT S + EL++ GG
Sbjct: 204 TPMGRVGEPGEIAGAVVKLLSDT---SSYVTGAELAVDGG 240
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
0.317 0.132 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,204,275
Number of Sequences: 62578
Number of extensions: 233129
Number of successful extensions: 560
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 518
Number of HSP's gapped (non-prelim): 33
length of query: 302
length of database: 14,973,337
effective HSP length: 98
effective length of query: 204
effective length of database: 8,840,693
effective search space: 1803501372
effective search space used: 1803501372
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: 51 (24.3 bits)