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= 026528
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 154 bits (389), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 82/221 (37%), Positives = 131/221 (59%), Gaps = 9/221 (4%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G TD++ VKAE+G P +P++G + FVDCS +A P FEGRGG++L E+++ L
Sbjct: 67 LGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYR- 125
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
+ KS +DL +L + + CW LY+D L++ GNL DA+ A+KAAL NT IP
Sbjct: 126 IFNNKSS----VDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPR 181
Query: 121 VHVAAEAASDEQPEVDISDEEF--LQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSA 178
V V + + ++++SD+ + ++ VP I TL K+G ++VDATL+EE+ ++
Sbjct: 182 VRVLEDEEGSK--DIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLAS 239
Query: 179 VSISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQL 219
+ +S+ +G + M K G LDP I +M+ V + L
Sbjct: 240 LLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVL 280
>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 = 106 bits (264), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 73/223 (32%), Positives = 112/223 (50%), Gaps = 12/223 (5%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G+T +I VK ++G P P+ G + + P A PTFE +E S ELS + C
Sbjct: 55 LGNTQIIVGVKPQIGEPFPDTPEMGVILTNSELLPMASPTFEPGPPDERSVELSRVVDRC 114
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
+ + IDL L ++EG W L++D +I DGNL DA A AAL +T IP+
Sbjct: 115 IRESRM-----IDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPA 169
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSAVS 180
V E EV I+ E+ + ++ T K+G ++D +LEEE +++ +S
Sbjct: 170 AEV-------EDGEVVINREKMQPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARIS 222
Query: 181 ISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQLMDKL 223
I + +G IC M K G L +L +S+A QL++ L
Sbjct: 223 IGVTEEGSICAMQKGGEGPLTRDDVLKAVSIAVEKVPQLIEYL 265
>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 = 94.4 bits (233), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 78/230 (33%), Positives = 112/230 (48%), Gaps = 20/230 (8%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFE-GRGGEELSAELSSALQH 59
+G+T VI VKAE PS PDKG V VD P F G GEE A+++S
Sbjct: 55 LGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEE--AQVASQF-- 110
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIP 119
+ I L + GK+ W LY D + + DGN+LDA A+ AAL N +P
Sbjct: 111 --IADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 168
Query: 120 SVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKH-YIVDATLEEESQMSSA 178
V + E A EV++ + +L T PV T+ IVD T EEE +
Sbjct: 169 EVTINEETA---LAEVNLKKKSYLNIRTH--PVATSFAVFDDTLLIVDPTGEEEHLATGT 223
Query: 179 VSISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSR-----QLMDKL 223
++I ++ +G +C + K GG GL + + D +S A V+R +LMD++
Sbjct: 224 LTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRA--VTRHKEVKKLMDEV 271
>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 = 88.6 bits (218), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 68/198 (34%), Positives = 102/198 (51%), Gaps = 13/198 (6%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+GST V+ +K LG P P+ G + V+ P A PTFE +E + EL+ +
Sbjct: 57 LGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELARVIDRG 116
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
+ K+ ++L +V+V GK+ ++ID V+ DGNL+DA+G A AAL N +P
Sbjct: 117 IRESKA-----LNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPK 171
Query: 121 VHVAAEAASDEQPEVDISDE-EFLQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSAV 179
V E EV+ DE E L + VPV T K+G +VD +L+EE M +
Sbjct: 172 VRYNEETG-----EVETLDETEPLPVEKIPVPV--TFAKIGNILVVDPSLDEELVMDGKI 224
Query: 180 SISINRQGHICGMIKRGG 197
+I+ + GHI + K G
Sbjct: 225 TITTDETGHISAVQKSEG 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 = 88.6 bits (218), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 61/197 (30%), Positives = 99/197 (50%), Gaps = 17/197 (8%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G+T V+A K E+ +P P++G + + V+ P A TFE +E + EL+ +
Sbjct: 58 LGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYTTFEPGPPDENAIELARVVDRS 117
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
L K+ +DL+ LV+ GK W +++D V+ GN+LDA A AAL NT +
Sbjct: 118 LRDSKA-----LDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYK 172
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVIT-TLTKVGKHYIVDATLEEESQMSSAV 179
V ++ ++ E + PV+T ++ KV K+ +VD L+EES M + +
Sbjct: 173 VE-----------QISVNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKI 221
Query: 180 SISINRQGHICGMIKRG 196
S S I G+ K G
Sbjct: 222 SFSYTPDLKIVGIQKSG 238
>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 = 88.2 bits (217), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 62/197 (31%), Positives = 99/197 (50%), Gaps = 13/197 (6%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G+T V+A K E+ +P P++G + + V+ P A TFE +E + EL+ +
Sbjct: 58 LGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRS 117
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
L K+ +DL+ LV+ GK W +++D V+ GN+LDA A AAL NT +
Sbjct: 118 LRDSKA-----LDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYK 172
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVIT-TLTKVGKHYIVDATLEEESQMSSAV 179
V + S ++ E + PV+T ++ KV K+ +VD L+EES M + +
Sbjct: 173 VEQHSNGIS-------VNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKI 225
Query: 180 SISINRQGHICGMIKRG 196
S S I G+ K G
Sbjct: 226 SFSYTPDLKIVGIQKSG 242
>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 = 88.2 bits (217), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 62/197 (31%), Positives = 99/197 (50%), Gaps = 13/197 (6%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G+T V+A K E+ +P P++G + + V+ P A TFE +E + EL+ +
Sbjct: 60 LGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRS 119
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
L K+ +DL+ LV+ GK W +++D V+ GN+LDA A AAL NT +
Sbjct: 120 LRDSKA-----LDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYK 174
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVIT-TLTKVGKHYIVDATLEEESQMSSAV 179
V + S ++ E + PV+T ++ KV K+ +VD L+EES M + +
Sbjct: 175 VEQHSNGIS-------VNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKI 227
Query: 180 SISINRQGHICGMIKRG 196
S S I G+ K G
Sbjct: 228 SFSYTPDLKIVGIQKSG 244
>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 = 87.4 bits (215), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 67/223 (30%), Positives = 112/223 (50%), Gaps = 19/223 (8%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G T V+ VK + G P+ PD+G + + + P A PTFE +E S EL+ +
Sbjct: 53 LGDTQVVVGVKMQPGEPAPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRG 112
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
+ ++ +DLS LV+ EG+ W +++D + DGNLLDA A AAL NT +P+
Sbjct: 113 IRESEA-----VDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPA 167
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSAVS 180
D+ ++ L +PV T VG Y+VD + EE S + ++
Sbjct: 168 ER------------FDLGEDYLLP--VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLT 213
Query: 181 ISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQLMDKL 223
I+ ++ ++ M K GG LD + +++ V+ +R+L +K
Sbjct: 214 ITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKF 256
>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 = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 67/223 (30%), Positives = 109/223 (48%), Gaps = 19/223 (8%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G T V+ VK + G P PD+G + + + P A PTFE +E S EL+ +
Sbjct: 53 LGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRG 112
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
+ +DLS LV+ EG+ W +++D + DGNLLDA A AAL NT +P+
Sbjct: 113 I-----RESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPA 167
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSAVS 180
D+ ++ L +PV T VG Y+VD + EE S + ++
Sbjct: 168 ER------------FDLGEDYLLP--VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLT 213
Query: 181 ISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQLMDKL 223
I+ ++ ++ M K GG LD + +++ V+ +R+L +K
Sbjct: 214 ITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKF 256
>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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 56/214 (26%), Positives = 96/214 (44%), Gaps = 11/214 (5%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFEGRGGEELSAELSSALQHC 60
+G T V+ V EL P + +G + ++ S A P FE +L +L+ ++ C
Sbjct: 67 LGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERC 126
Query: 61 LLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPS 120
L K ID SL VV G+ W + +D +++ DGN++DA A AL + P
Sbjct: 127 LRNSKC-----IDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPD 181
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLT--KVGKHYIVDATLEEESQMSSA 178
V V + + PE + + + +P+ + + G + +VD EE M
Sbjct: 182 VSVQGDEVTLYTPE----ERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGL 237
Query: 179 VSISINRQGHICGMIKRGGVGLDPSVILDMISVA 212
+ I++N+ IC + GG+ L +L +A
Sbjct: 238 LVIAMNKHREICTIQSSGGIMLLKDQVLRCSKIA 271
>pdb|2WP8|A Chain A, Yeast Rrp44 Nuclease
Length = 305
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 54/238 (22%), Positives = 101/238 (42%), Gaps = 24/238 (10%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFE-GRGGEELSAELSSALQH 59
MG+T V + ++ +P +P +G I + SP A FE G E S ++
Sbjct: 51 MGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEK 110
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIP 119
+ +SGA +D+ L +V G CW + D + DG +DA A+ A L + P
Sbjct: 111 SV--RRSGA---LDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKP 165
Query: 120 SVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKH--------------YIV 165
+ V E P +++ E + +P+ T + I+
Sbjct: 166 DITVHGEQII-VHP---VNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISII 221
Query: 166 DATLEEESQMSSAVSISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQLMDKL 223
DATL+EE +++++N+ + + K GG+ +D ++ A + ++ D++
Sbjct: 222 DATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQI 279
>pdb|4IFD|A Chain A, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 304
Score = 57.0 bits (136), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 54/238 (22%), Positives = 101/238 (42%), Gaps = 24/238 (10%)
Query: 1 MGSTDVIASVKAELGRPSAMQPDKGKVAIFVDCSPTAEPTFE-GRGGEELSAELSSALQH 59
MG+T V + ++ +P +P +G I + SP A FE G E S ++
Sbjct: 50 MGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEK 109
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIP 119
+ +SGA +D+ L +V G CW + D + DG +DA A+ A L + P
Sbjct: 110 SV--RRSGA---LDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKP 164
Query: 120 SVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVGKH--------------YIV 165
+ V E P +++ E + +P+ T + I+
Sbjct: 165 DITVHGEQII-VHP---VNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISII 220
Query: 166 DATLEEESQMSSAVSISINRQGHICGMIKRGGVGLDPSVILDMISVANFVSRQLMDKL 223
DATL+EE +++++N+ + + K GG+ +D ++ A + ++ D++
Sbjct: 221 DATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQI 278
>pdb|4IFD|E Chain E, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 267
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 69/136 (50%), Gaps = 6/136 (4%)
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIP 119
LL +G+G+D S L + + K + +++D LVISS + + + AI +AL++T +P
Sbjct: 99 SLLNKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPISLISFAIYSALNSTYLP 157
Query: 120 SVHVAAEAAS-DEQPEVDISDEEFLQFDTSGVPVITTLTKVGKHYIVDATLEEESQMSSA 178
+ A + +E P D + ++ D + P++ L VG + ++D E ++
Sbjct: 158 KLISAFDDLEVEELPT--FHDYDMVKLDINP-PLVFILAVVGNNMLLDPAANESEVANNG 214
Query: 179 VSISINRQGHICGMIK 194
+ IS + G I I+
Sbjct: 215 LIISWS-NGKITSPIR 229
>pdb|4GH4|A Chain A, Crystal Structure Of Foot And Mouth Disease Virus A22
Serotype
Length = 210
Score = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 93 LVISSDGNLLDALGAAIKAALSNTGIPSVHVAA 125
+V+ DGNL A +AALSNTG P+ ++ A
Sbjct: 78 IVVRHDGNLTWVPNGAPEAALSNTGNPTAYLKA 110
>pdb|2Y08|A Chain A, Structure Of The Substrate-Free Fad-Dependent Tirandamycin
Oxidase Taml
pdb|2Y08|B Chain B, Structure Of The Substrate-Free Fad-Dependent Tirandamycin
Oxidase Taml
pdb|2Y3R|A Chain A, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P21 Space Group
pdb|2Y3R|B Chain B, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P21 Space Group
pdb|2Y3R|C Chain C, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P21 Space Group
pdb|2Y3R|D Chain D, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P21 Space Group
pdb|2Y3S|A Chain A, Structure Of The Tirandamycine-Bound Fad-Dependent
Tirandamycin Oxidase Taml In C2 Space Group
pdb|2Y3S|B Chain B, Structure Of The Tirandamycine-Bound Fad-Dependent
Tirandamycin Oxidase Taml In C2 Space Group
pdb|2Y4G|A Chain A, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P212121 Space Group
pdb|2Y4G|B Chain B, Structure Of The Tirandamycin-Bound Fad-Dependent
Tirandamycin Oxidase Taml In P212121 Space Group
Length = 530
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 117 GIPSVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTK--VGKHYIVDATLEEESQ 174
G+P AA+ A P+VD++DEE ++TSGVP K + V A + +
Sbjct: 462 GVPVPGGAADGAYVNYPDVDLADEE---WNTSGVPWSELYYKDAYPRLQAVKARWDPRNV 518
Query: 175 MSSAVSISI 183
A+S+ +
Sbjct: 519 FRHALSVRV 527
>pdb|4GW3|A Chain A, Crystal Structure Of The Lipase From Proteus Mirabilis
pdb|4GXN|A Chain A, Diethylphosphonate Inhibited Structure Of The Proteus
Mirabilis Lipase
Length = 307
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 85 CWDLYIDGLVISSDGNLLDALGAAIK 110
C+ YI GL+ GNLLD AA++
Sbjct: 215 CFGSYIQGLIAGEKGNLLDPTHAAMR 240
>pdb|3AK4|A Chain A, Crystal Structure Of Nadh-Dependent Quinuclidinone
Reductase From Agrobacterium Tumefaciens
pdb|3AK4|B Chain B, Crystal Structure Of Nadh-Dependent Quinuclidinone
Reductase From Agrobacterium Tumefaciens
pdb|3AK4|C Chain C, Crystal Structure Of Nadh-Dependent Quinuclidinone
Reductase From Agrobacterium Tumefaciens
pdb|3AK4|D Chain D, Crystal Structure Of Nadh-Dependent Quinuclidinone
Reductase From Agrobacterium Tumefaciens
Length = 263
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 2/103 (1%)
Query: 68 AGAGIDLSSLVVVEGK-VCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIPSVHVAAE 126
AGA + ++ L V+ + V L G + D ++ AA++ A+ G + A
Sbjct: 35 AGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANA 94
Query: 127 AASDEQPEVDISDEEF-LQFDTSGVPVITTLTKVGKHYIVDAT 168
S +P VDI+DEE+ FD + V +H++ T
Sbjct: 95 GVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNT 137
>pdb|3V4K|A Chain A, First-In-Class Small Molecule Inhibitors Of The
Single-Strand Dna Cytosine Deaminase Apobec3g
pdb|3V4K|B Chain B, First-In-Class Small Molecule Inhibitors Of The
Single-Strand Dna Cytosine Deaminase Apobec3g
Length = 203
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYID 91
C G ++ A AG +S + E K CWD ++D
Sbjct: 144 CQEGLRTLAEAGAKISIMTYSEFKHCWDTFVD 175
>pdb|2KBO|A Chain A, Structure, Interaction, And Real-Time Monitoring Of The
Enzymatic Reaction Of Wild Type Apobec3g
Length = 194
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYID 91
C G ++ A AG +S + E K CWD ++D
Sbjct: 131 CQEGLRTLAEAGAKISIMTYSEFKHCWDTFVD 162
>pdb|3E1U|A Chain A, The Crystal Structure Of The Anti-Viral Apobec3g Catalytic
Domain
pdb|3IQS|A Chain A, Crystal Structure Of The Anti-Viral Apobec3g Catalytic
Domain
Length = 189
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYID 91
C G ++ A AG +S + E K CWD ++D
Sbjct: 130 CQEGLRTLAEAGAKISIMTYSEFKHCWDTFVD 161
>pdb|2H9F|A Chain A, Crystal Structure Of A Prpf Family Methylaconitate
Isomerase (Pa0793) From Pseudomonas Aeruginosa At 1.95 A
Resolution
Length = 396
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 91 DGLVISSDGNLLDALG----AAIKAALSNTGIPSVHVAAE----AASDEQPEVDISDEEF 142
DG I GNL+D L KA N GIP+V V AE ++ + E++ ++
Sbjct: 188 DGGAIFPTGNLVDDLEVPGVGTFKATXINAGIPTVFVNAEEIGYRGTELREEINGDPQQL 247
Query: 143 LQFD 146
+F+
Sbjct: 248 ARFE 251
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
0.314 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: 6,302,015
Number of Sequences: 62578
Number of extensions: 259245
Number of successful extensions: 644
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 587
Number of HSP's gapped (non-prelim): 52
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)