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= 037553
(151 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/119 (35%), Positives = 68/119 (57%), Gaps = 4/119 (3%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIGRL 95
+R D R F + RP G + A GS+Y EFG K++V+V+GPRE++ + + + +
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75
Query: 96 NCNVSYTTFATPIRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151
C + F+ R + G D + + S + +AL A+ILE FP++ +DVF VLE+ G
Sbjct: 76 RCRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEG 134
>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 = 75.1 bits (183), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 43/121 (35%), Positives = 67/121 (55%), Gaps = 4/121 (3%)
Query: 33 DVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE-SKKAMMYSN 91
D + R D R ++ RP G + +A+GSAY E+G K+I +V+GPRE K + +
Sbjct: 12 DENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPD 71
Query: 92 IGRLNCNVSYTTFATPIRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVLE 148
L + F+ R + G D + + S ++ ALE A+ILE FP+T +DVF VL+
Sbjct: 72 RAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQ 131
Query: 149 S 149
+
Sbjct: 132 A 132
>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 = 72.0 bits (175), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 45/144 (31%), Positives = 72/144 (50%), Gaps = 16/144 (11%)
Query: 23 KTRPPIFSGSDVDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRE 82
+++PP +D + P +R + RP + R G ++ A GSAY E G TKV+ +V GPR+
Sbjct: 13 ESQPPQLYAADEEEA-PGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQ 71
Query: 83 SKKAMMYSNI------------GRLNCNVSYTTFATPIRGQ---GSDHKDFSSMLHKALE 127
++ GRL C+ FA R G + ++ + L +ALE
Sbjct: 72 AEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALE 131
Query: 128 GAIILETFPKTTVDVFALVLESGG 151
A+ L +P+ ++V AL+LE GG
Sbjct: 132 PAVRLGRYPRAQLEVSALLLEDGG 155
>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 = 67.0 bits (162), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 42/122 (34%), Positives = 61/122 (50%), Gaps = 8/122 (6%)
Query: 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMY---S 90
VD LR D R F + RP + A GS Y E G KVI +VFGPRE +
Sbjct: 13 VDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSK 72
Query: 91 NIGRLNCNVSYTTFATPIRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVL 147
I R N++ F+ R + G D + + S + +A E I+ E FP++ +D+F VL
Sbjct: 73 AIIRYRYNMA--PFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVL 130
Query: 148 ES 149
++
Sbjct: 131 QA 132
>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 = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 39/120 (32%), Positives = 60/120 (50%), Gaps = 4/120 (3%)
Query: 34 VDWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNI 92
VD LR D R F + RP + A GS Y E G KVI +VFGPRE + + +
Sbjct: 13 VDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSK 72
Query: 93 GRLNCNVSYTTFATPIRGQ-GSDHK--DFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
+ + F+ R + G D + + S + +A E I+ E FP++ +D+F VL++
Sbjct: 73 AIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
>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 = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 38/119 (31%), Positives = 62/119 (52%), Gaps = 4/119 (3%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 16 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 75
Query: 94 RLNCNVSYTTFATPIRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 76 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 134
>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 = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 38/119 (31%), Positives = 62/119 (52%), Gaps = 4/119 (3%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77
Query: 94 RLNCNVSYTTFATPIRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 78 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136
>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 = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 38/119 (31%), Positives = 62/119 (52%), Gaps = 4/119 (3%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSNIG 93
D R D R + R G + +A GSA E GNTK I +V+GP+E + + +
Sbjct: 13 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 72
Query: 94 RLNCNVSYTTFATPIRGQGSDHK---DFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
L T F+T R + + + S ++ +ALE A+++E FP+T +DVF +L++
Sbjct: 73 VLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 131
>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 = 62.8 bits (151), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 59/121 (48%), Gaps = 8/121 (6%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESK--KAMMYSNIGRL 95
R D R + R R G A GSAY E GNTK + V+GP E + +A + +
Sbjct: 17 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76
Query: 96 NCNVSYTTFATPIRGQGSDHKDFSS-----MLHKALEGAIILETFPKTTVDVFALVLESG 150
NC S TF+T R + H D S L + E AI+ + P++ +D++ VL++
Sbjct: 77 NCQYSSATFSTGERKR-RPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQAD 135
Query: 151 G 151
G
Sbjct: 136 G 136
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 56.2 bits (134), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 41/126 (32%), Positives = 68/126 (53%), Gaps = 15/126 (11%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNS----ASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSN 91
LR D R +++ R F + ++N+ A GS+Y E GN K+I V GP+E + K+ M ++
Sbjct: 14 LRLDGRRWNELRR--FES-SINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTS 70
Query: 92 IGRLNCNVSYTTFATPIRGQGSDHK------DFSSMLHKALEGAIILETFPKTTVDVFAL 145
LN +V+ T F+ R + S HK + + L + E ++L +P+T +D+
Sbjct: 71 KALLNVSVNITKFSKFERSKSS-HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIH 129
Query: 146 VLESGG 151
VLE G
Sbjct: 130 VLEQDG 135
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/126 (31%), Positives = 67/126 (53%), Gaps = 15/126 (11%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNS----ASGSAYAEFGNTKVIVSVFGPRESK-KAMMYSN 91
LR D R +++ R F + ++N+ A GS+Y E GN K+I V GP+E + K+ M ++
Sbjct: 12 LRLDGRRWNELRR--FES-SINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTS 68
Query: 92 IGRLNCNVSYTTFATPIRGQGSDHK------DFSSMLHKALEGAIILETFPKTTVDVFAL 145
LN +V+ F+ R + S HK + + L + E ++L +P+T +D+
Sbjct: 69 KALLNVSVNINKFSKFERSKSS-HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIH 127
Query: 146 VLESGG 151
VLE G
Sbjct: 128 VLEQDG 133
>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 = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 32/115 (27%), Positives = 49/115 (42%), Gaps = 7/115 (6%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNC 97
R D R +Q RP ++ A GSA G+T V+ +V+GP+ + G
Sbjct: 5 RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK------GENPE 58
Query: 98 NVSYTTFATPIRGQ-GSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLESGG 151
S P+ GQ G K++ L + L+ +L P TT V V+ + G
Sbjct: 59 KASIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDG 113
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 11/75 (14%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMY-----SNI 92
R D RGF RP G + A GSA + G+T+V+V + K ++ N+
Sbjct: 27 RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGI------KTSLGEPFPDTPNM 80
Query: 93 GRLNCNVSYTTFATP 107
G + NV A+P
Sbjct: 81 GVMTTNVELVPLASP 95
>pdb|3B4T|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|E Chain E, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|F Chain F, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
Length = 262
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 53/122 (43%), Gaps = 8/122 (6%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNC 97
R D R H+ RP G + +GS EFG+TKV+ + + + +G L
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66
Query: 98 NVSYTTFAT-------PIRGQGSDH-KDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
+ AT +RG+ S ++ S ++ ++L I L + T+ + VL++
Sbjct: 67 EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126
Query: 150 GG 151
G
Sbjct: 127 DG 128
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
R D R H+ R TG ++ A GS+ + GNT++IV V
Sbjct: 25 RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGV 64
>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 = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLN 96
LR D RG R T V++ SGSA + G+T ++V V + K + N G L
Sbjct: 36 LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPK-LEKPNEGYLE 94
Query: 97 CNVSYTTFATP-IRGQGSD 114
V + ATP G+G D
Sbjct: 95 FFVDCSASATPEFEGRGGD 113
>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 = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
RPD R + R G++++A GSA + GNT VI V
Sbjct: 25 RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGV 64
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 8/122 (6%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFG----PRESK---KAMMYS 90
RP R Q RP A GS EFG+TKVI +V PR K + + +
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 91 NIGRLNCNVSYTTFATPIRG-QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
G L + RG QG + ++ ++L A+ L + T+ + V+++
Sbjct: 63 EYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122
Query: 150 GG 151
G
Sbjct: 123 DG 124
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 8/122 (6%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFG----PRESK---KAMMYS 90
RP R Q RP A GS EFG+TKVI +V PR K + + +
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62
Query: 91 NIGRLNCNVSYTTFATPIRG-QGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALVLES 149
G L + RG QG + ++ ++L A+ L + T+ + V+++
Sbjct: 63 EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122
Query: 150 GG 151
G
Sbjct: 123 DG 124
>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 = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 35 DWLRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
D R D RGF + R + A GSA + G+T+V+V V
Sbjct: 20 DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 62
>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 = 34.3 bits (77), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 38 RPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVSV 77
R D RGF + R + A GSA + G+T+V+V V
Sbjct: 23 RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV 62
>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 = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 28/105 (26%)
Query: 46 QCRPAFFRTGAVNSASGSAYAEFGNTKVIVSVFGP------RESKKAMMYSNIGRLNCNV 99
+C +F + +A GSA G T + S GP + S +AM ++
Sbjct: 9 RCELSFLK-----NADGSACFSQGATCIWASCSGPGDVHASKASDEAMTL--------DI 55
Query: 100 SYTTFATPIRGQGSDHK--DFSSMLHKALEGAIILETFPKTTVDV 142
SY R D+K ++++H L AI LE FP TT+ V
Sbjct: 56 SY-------RANCGDNKFNVLNNIIHSTLSNAINLELFPHTTISV 93
>pdb|4IFD|F Chain F, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 250
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 23/99 (23%), Positives = 48/99 (48%), Gaps = 9/99 (9%)
Query: 52 FRTGAVNSASGSAYAE---FGN-TKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATP 107
TG + + +GSA E G+ T +I +V+GPR + + +++ G ++ +
Sbjct: 48 LHTGFIENCNGSALVEARSLGHQTSLISAVYGPRSIRGS--FTSQGTISIQLKNGLLE-- 103
Query: 108 IRGQGSDHKDFSSMLHKALEGAIILETFPKTTVDVFALV 146
+ ++ K+ SS L + L +PK+ +D+F +
Sbjct: 104 -KYNTNELKEVSSFLMGIFNSVVNLSRYPKSGIDIFVYL 141
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 30.0 bits (66), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 37/97 (38%), Gaps = 7/97 (7%)
Query: 55 GAVNSASGSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIRGQGSD 114
G ++ GS+ +TKVI SV GP E K L ++ P +G +
Sbjct: 30 GILDHVDGSSEFVSQDTKVICSVTGPIEPKARQ------ELPTQLALEIIVRPAKGVATT 83
Query: 115 -HKDFSSMLHKALEGAIILETFPKTTVDVFALVLESG 150
K L L I +P+ + +LESG
Sbjct: 84 REKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESG 120
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 30/127 (23%), Positives = 51/127 (40%), Gaps = 16/127 (12%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS----------VFGPRESKKA 86
+R D R Q RP + + GS FG TKVI + + G +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60
Query: 87 MMYSNIGRLNCNVSYTTFATPIRGQ--GSDHKDFSSMLHKALEGAIILETFPKTTVDVFA 144
YS + R T ++G+ G+ H + M+ +A+ A+ L + T+ V
Sbjct: 61 AEYSMLPRAT---QQRTIRESVQGRIGGATH-EIQRMIGRAMRTAVELTKIGERTIWVDC 116
Query: 145 LVLESGG 151
V+++ G
Sbjct: 117 DVIQADG 123
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS 76
+R D R Q RP + + GS FG TKVI +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICT 40
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS 76
+R D R Q RP + + GS FG TKVI +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICT 40
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS 76
+R D R Q RP + + GS FG TKVI +
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICT 40
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVI 74
+R D R + RP F ++ GS GNTKVI
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVI 38
>pdb|1OYP|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVI 74
+R D R + RP F ++ GS GNTKVI
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVI 38
>pdb|1YJD|C Chain C, Crystal Structure Of Human Cd28 In Complex With The Fab
Fragment Of A Mitogenic Antibody (5.11a1)
Length = 140
Score = 27.3 bits (59), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 10/50 (20%)
Query: 81 RESKKAMMYSNIGRLNCNVSYTTFATPIRGQGSDHKDFSSMLHKALEGAI 130
++S + Y N L+C SY F+ ++F + LHK L+ A+
Sbjct: 8 KQSPMLVAYDNAVNLSCKYSYNLFS----------REFRASLHKGLDSAV 47
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From
Bacillus Anthracis At 1.7 A Resolution
Length = 255
Score = 26.9 bits (58), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 37 LRPDSRGFHQCRPAFFRTGAVNSASGSAYAEFGNTKVIVS 76
+R D R + R T + GS E G+TKVI S
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICS 50
>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 = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 5/90 (5%)
Query: 62 GSAYAEFGNTKVIVSVFGPRESKKAMMYSNIGRLNCNVSYTTFATPIRGQGSDHKDFSSM 121
GSA G+T V+ V+GP E K + N L I G K +
Sbjct: 45 GSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLE-----VILRPKIGLPGVAEKSRERL 99
Query: 122 LHKALEGAIILETFPKTTVDVFALVLESGG 151
+ E ++ P+T++ V V+ G
Sbjct: 100 IRNTCEAVVLGTLHPRTSITVVLQVVSDAG 129
>pdb|2ID5|A Chain A, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|B Chain B, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|C Chain C, Crystal Structure Of The Lingo-1 Ectodomain
pdb|2ID5|D Chain D, Crystal Structure Of The Lingo-1 Ectodomain
Length = 477
Score = 26.9 bits (58), Expect = 5.0, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 94 RLNCNVSYTTFATPIRGQGSDHKDFSSML 122
RLN N T ATP QG + KDF +L
Sbjct: 347 RLNFNRQQPTCATPEFVQGKEFKDFPDVL 375
>pdb|3FCY|A Chain A, Crystal Structure Of Acetyl Xylan Esterase 1 From
Thermoanaerobacterium Sp. JwSL YS485
pdb|3FCY|B Chain B, Crystal Structure Of Acetyl Xylan Esterase 1 From
Thermoanaerobacterium Sp. JwSL YS485
pdb|3FCY|C Chain C, Crystal Structure Of Acetyl Xylan Esterase 1 From
Thermoanaerobacterium Sp. JwSL YS485
Length = 346
Score = 26.2 bits (56), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 90 SNIGRLNCNVSY-----TTFATPIRGQGSDHKDFSSMLHKALEGAII 131
SN G N ++Y T A +RGQG +D + L G II
Sbjct: 119 SNSGDWNDKLNYVAAGFTVVAMDVRGQGGQSQDVGGVTGNTLNGHII 165
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
0.320 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,993,527
Number of Sequences: 62578
Number of extensions: 148664
Number of successful extensions: 320
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 281
Number of HSP's gapped (non-prelim): 36
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)