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= 030980
(168 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 = 121 bits (304), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 63/167 (37%), Positives = 100/167 (59%), Gaps = 9/167 (5%)
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--LQFDTSGVPVITTLTKVPFPLIV 165
V V + + ++++SD+ + ++ VP I TL K+ + +V
Sbjct: 182 VRVLEDEEGSK--DIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVV 226
>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 = 72.8 bits (177), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 53/159 (33%), Positives = 77/159 (48%), Gaps = 12/159 (7%)
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-----IDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIP- 168
Query: 121 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKV 159
AA E EV I+ E+ + ++ T K+
Sbjct: 169 ------AAEVEDGEVVINREKMQPLPVNRKALMCTFAKI 201
>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 = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 55/157 (35%), Positives = 74/157 (47%), Gaps = 12/157 (7%)
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 SVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTL 156
V + E A EV++ + +L T PV T+
Sbjct: 169 EVTINEETA---LAEVNLKKKSYLNIRTH--PVATSF 200
>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 = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 44/135 (32%), Positives = 70/135 (51%), Gaps = 5/135 (3%)
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 VHVAAEAASDEQPEV 135
V + S + EV
Sbjct: 173 VEQHSNGISVNKNEV 187
>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 = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 44/135 (32%), Positives = 70/135 (51%), Gaps = 5/135 (3%)
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 VHVAAEAASDEQPEV 135
V + S + EV
Sbjct: 175 VEQHSNGISVNKNEV 189
>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 = 67.0 bits (162), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 41/122 (33%), Positives = 65/122 (53%), Gaps = 5/122 (4%)
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 VH 122
V
Sbjct: 173 VE 174
>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 = 63.9 bits (154), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 54/163 (33%), Positives = 81/163 (49%), Gaps = 20/163 (12%)
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 VHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVPFPL 163
V E EV+ DE T +PV K+P P+
Sbjct: 172 VRYNEETG-----EVETLDE------TEPLPV----EKIPVPV 199
>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 = 61.2 bits (147), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 43/120 (35%), Positives = 66/120 (55%), Gaps = 5/120 (4%)
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
>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 = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 43/120 (35%), Positives = 63/120 (52%), Gaps = 5/120 (4%)
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
>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 = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/134 (29%), Positives = 63/134 (47%), Gaps = 5/134 (3%)
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 VHVAAEAASDEQPE 134
V V + + PE
Sbjct: 182 VSVQGDEVTLYTPE 195
>pdb|4IFD|A Chain A, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 304
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 36/127 (28%), Positives = 57/127 (44%), Gaps = 6/127 (4%)
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 SVHVAAE 126
+ V E
Sbjct: 165 DITVHGE 171
>pdb|2WP8|A Chain A, Yeast Rrp44 Nuclease
Length = 305
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 36/127 (28%), Positives = 57/127 (44%), Gaps = 6/127 (4%)
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 SVHVAAE 126
+ V E
Sbjct: 166 DITVHGE 172
>pdb|4IFD|E Chain E, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 267
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 60 CLLGGKSGAGAGIDLSSLVVVEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALSNTGIP 119
LL +G+G+D S L + + K + +++D LVISS + + + AI +AL++T +P
Sbjct: 99 SLLNKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPISLISFAIYSALNSTYLP 157
Query: 120 SV 121
+
Sbjct: 158 KL 159
>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 = 30.8 bits (68), Expect = 0.36, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 117 GIPSVHVAAEAASDEQPEVDISDEEFLQFDTSGVPVITTLTKVPFP 162
G+P AA+ A P+VD++DEE ++TSGVP K +P
Sbjct: 462 GVPVPGGAADGAYVNYPDVDLADEE---WNTSGVPWSELYYKDAYP 504
>pdb|4GH4|A Chain A, Crystal Structure Of Foot And Mouth Disease Virus A22
Serotype
Length = 210
Score = 30.4 bits (67), Expect = 0.46, 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|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 = 1.2, 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|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 = 1.4, 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 = 1.5, 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 = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 49 LSAELSSALQHCLLGGKSGAGAGIDLSSLVVVEGKVCWDLYID 91
+A + C G ++ A AG +S + E K CWD ++D
Sbjct: 119 FTARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVD 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 = 27.3 bits (59), Expect = 4.2, 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
>pdb|1QDL|A Chain A, The Crystal Structure Of Anthranilate Synthase From
Sulfolobus Solfataricus
Length = 422
Score = 26.6 bits (57), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 95 ISSDGNLLDALGAAIKAALSNTGIPSVHVAAEAASDEQPEVDISDEE 141
IS+DGN A+ AI+ A N + +H A D PE + + E
Sbjct: 365 ISADGNAEFAI--AIRTAFLNKELLRIHAGAGIVYDSNPESEYFETE 409
>pdb|1ZBA|1 Chain 1, Foot-And-Mouth Disease Virus Serotype A1061 Complexed With
Oligosaccharide Receptor.
pdb|1ZBE|1 Chain 1, Foot-And Mouth Disease Virus Serotype A1061
Length = 212
Score = 26.6 bits (57), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 93 LVISSDGNLLDALGAAIKAALSNTGIPSVHVAA 125
+V+ DGNL A +AALSNT P+ + A
Sbjct: 78 IVVRHDGNLTWVPNGAPEAALSNTSNPTAYNKA 110
>pdb|3LQY|A Chain A, Crystal Structure Of Putative Isochorismatase Hydrolase
From Oleispira Antarctica
Length = 190
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 106 GAAIKAALSNTGIPSVHVAAEAASDEQP 133
GA + A G+P VHV E +DE P
Sbjct: 40 GAKLLAKFRQQGLPVVHVRHEFPTDEAP 67
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 0.133 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,040,195
Number of Sequences: 62578
Number of extensions: 207904
Number of successful extensions: 468
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 420
Number of HSP's gapped (non-prelim): 51
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
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: 48 (23.1 bits)