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= 047153
(100 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HKM|A Chain A, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|B Chain B, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|C Chain C, Crystal Structure Of Rice(Oryza Sativa) Rrp46
Length = 246
Score = 155 bits (393), Expect = 4e-39, Method: Compositional matrix adjust.
Identities = 77/108 (71%), Positives = 85/108 (78%), Gaps = 9/108 (8%)
Query: 1 MEIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA---------KNENPEKV 51
ME RADGRNPNQLRP +C + L RAHGSA W+QGDT VLAA K ENPEK
Sbjct: 1 MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60
Query: 52 SIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQV 99
SIEV+WK TGQIGKQEKEYEM LKRTLQSIC+LT++PNTTTSVI+QV
Sbjct: 61 SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQV 108
>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 = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 37/101 (36%), Positives = 56/101 (55%), Gaps = 10/101 (9%)
Query: 9 RNPN-QLRPLACYCSILHRAHGSASWSQGDTKVLAA---------KNENPEKVSIEVIWK 58
R P LR AC ++L R GSAS+ QGDT VLA E K ++EVI +
Sbjct: 24 RGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 83
Query: 59 SKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQV 99
K G G EK E +++ T +++ + T++P T+ +V++QV
Sbjct: 84 PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQV 124
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----KNENPEKVS------IE 54
R DGR P++LR + +L A GSA + G+TK +AA K +P +S +
Sbjct: 19 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 78
Query: 55 VIW--------KSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100
V + + K ++E E +++ L+S ++ + P T V ++
Sbjct: 79 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEIL 132
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----KNENPEKVS------IE 54
R DGR P++LR + +L A GSA + G+TK +AA K +P +S +
Sbjct: 16 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 75
Query: 55 VIW--------KSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100
V + + K ++E E +++ L+S ++ + P T V ++
Sbjct: 76 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEIL 129
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 18/114 (15%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----KNENPEKVS------IE 54
R DGR P++LR + +L A GSA + G+TK +AA K +P +S +
Sbjct: 21 RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 80
Query: 55 VIW--------KSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQVW 100
V + + K ++E E +++ L+S ++ + P T V ++
Sbjct: 81 VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEIL 134
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/116 (22%), Positives = 50/116 (43%), Gaps = 20/116 (17%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA-----------KNENPEKVSI 53
R DGR +LR + + +A GSA QG+TK LA P++ +
Sbjct: 17 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76
Query: 54 EVIWKSKTGQIGKQEK---------EYEMILKRTLQSICILTINPNTTTSVIIQVW 100
+ S T G++++ E + L++T ++ + ++P + + +QV
Sbjct: 77 NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVL 132
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 49/114 (42%), Gaps = 18/114 (15%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----------KNENPEKVSIE 54
R DGR +LRP+ +L A+GSA G K++AA + P++ +
Sbjct: 17 RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76
Query: 55 VIWKSKTGQIGKQEK--------EYEMILKRTLQSICILTINPNTTTSVIIQVW 100
V + + +++K E ++K L+ IL + P T V I+V
Sbjct: 77 VRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVL 130
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 23/39 (58%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R DGR ++LRP+ S+L RA GS G KV+AA
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAA 55
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 23/39 (58%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R DGR ++LRP+ S+L RA GS G KV+AA
Sbjct: 17 RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAA 55
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 46/114 (40%), Gaps = 18/114 (15%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA----------KNENPEKVSIE 54
R DGR ++LRPL IL RA GS+ G K+L A K + P++ I
Sbjct: 17 REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIR 76
Query: 55 VIWKSKTGQIGKQEK--------EYEMILKRTLQSICILTINPNTTTSVIIQVW 100
+ + ++++ E I L+ IL P + V I+V
Sbjct: 77 CRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVL 130
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 11/96 (11%)
Query: 12 NQLRPLACYCSILHRAHGSASWSQGDTKVLA---------AKNENPEKVSIEVIWKSKTG 62
+LR + C S L A GSA +SQG T + A A + E +++++ +++ G
Sbjct: 3 GRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG 62
Query: 63 QIGKQEKEYEMILKRTLQSICILTINPNTTTSVIIQ 98
+ I+ TL + L + P+TT SV +
Sbjct: 63 D--NKFNVLNNIIHSTLSNAINLELFPHTTISVTVH 96
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAAKNEN 47
E R DGR +R LA + R HGSA + +G+T++L N
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLN 398
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAAKNEN 47
E R DGR +R LA + R HGSA + +G+T++L N
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLN 398
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR+ +RP+ IL R HGSA +++G+T+ +
Sbjct: 322 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAI 358
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR+ +RP+ IL R HGSA +++G+T+ +
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAI 367
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR+ +RP+ IL R HGSA +++G+T+ +
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAI 367
>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 = 35.4 bits (80), Expect = 0.007, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 2 EIDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
E R DGR+ LR ++C + HGSA + +G T+VL
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVL 355
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 22/104 (21%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL--AAKNEN--------------- 47
R+DGR +QLRP++ L GS S G TKV+ A+ EN
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 48 -----PEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILT 86
P I +S G+IG + E + ++ R +++ LT
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELT 105
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 22/104 (21%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL--AAKNEN--------------- 47
R+DGR +QLRP++ L GS S G TKV+ A+ EN
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 48 -----PEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILT 86
P I +S G+IG + E + ++ R +++ LT
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELT 105
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 22/104 (21%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL--AAKNEN--------------- 47
R+DGR +QLRP++ L GS S G TKV+ A+ EN
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 48 -----PEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILT 86
P I +S G+IG + E + ++ R +++ LT
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELT 105
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 34.7 bits (78), Expect = 0.013, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR + +R L +L R HGSA +++G+T+ L
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQAL 351
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 34.7 bits (78), Expect = 0.013, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR + +R L +L R HGSA +++G+T+ L
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQAL 351
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 34.7 bits (78), Expect = 0.013, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR + +R L +L R HGSA +++G+T+ L
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQAL 357
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 34.3 bits (77), Expect = 0.016, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR + +R L +L R HGSA +++G+T+ L
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQAL 357
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 43/104 (41%), Gaps = 22/104 (21%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL--AAKNEN--------------- 47
R+DGR +QLRP++ L GS S G TKV+ A+ EN
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 48 -----PEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICILT 86
P I +S G+IG E + ++ R +++ LT
Sbjct: 62 EYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELT 105
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 21/35 (60%)
Query: 9 RNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R+P +LRP+ +L +A GSA G TKVL A
Sbjct: 31 RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCA 65
>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 = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 4 DRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAAKNENP 48
+R DGR ++ R + +++ +A GSA GDT+V+ P
Sbjct: 22 ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQP 66
>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 = 32.7 bits (73), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 4 DRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAAKNENP 48
+R DGR ++ R + +++ +A GSA GDT+V+ P
Sbjct: 22 ERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQP 66
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 32.3 bits (72), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/103 (22%), Positives = 43/103 (41%), Gaps = 22/103 (21%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL----------------------A 42
R DGR ++LRP+ + GS + G+TKV+ A
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61
Query: 43 AKNENPEKVSIEVIWKSKTGQIGKQEKEYEMILKRTLQSICIL 85
+ P+ + + I +S G+I + E + ++ R L+++ L
Sbjct: 62 EYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDL 104
>pdb|4IFD|E Chain E, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 267
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSA 31
R DGR P+Q RP+ + L ++GS+
Sbjct: 24 RPDGRLPHQFRPIEIFTDFLPSSNGSS 50
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R DGR RPL+ +A GSA G T VLA
Sbjct: 28 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAG 66
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R DGR RPL+ +A GSA G T VLA
Sbjct: 28 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAG 66
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R DGR RPL+ +A GSA G T VLA
Sbjct: 30 RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAG 68
>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 = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR ++LRP+ + GS + G+TKV+
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVI 38
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From
Bacillus Anthracis At 1.7 A Resolution
Length = 255
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
R DGR +LR + + + L GS GDTKV+
Sbjct: 12 RVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVI 48
>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 = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
R D R RP+ ++ +A GSA G T+VL
Sbjct: 27 RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVG 65
>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 = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 10/40 (25%), Positives = 24/40 (60%)
Query: 4 DRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVLAA 43
+R DGR+ ++ R ++ ++ +A GS+ G+T+++
Sbjct: 24 ERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVG 63
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 3 IDRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
++R GR +QLRP+ A GS GDTKV+
Sbjct: 1 MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVI 39
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 23 ILHRAHGSASWSQGDTKVLA---------AKNENPEKVSIEVIWKSKTGQIGKQEKEYEM 73
IL GS+ + DTKV+ A+ E P ++++E+I + G +EK E
Sbjct: 31 ILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLED 90
Query: 74 ILKRTL 79
L+ L
Sbjct: 91 KLRAVL 96
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 4 DRADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL 41
+R GR +QLRP+ A GS GDTKV+
Sbjct: 2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVI 39
>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 = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 5 RADGRNPNQLRPLACYCSILHRAHGSASWSQGDTKVL--AAKNENPEKVSIEVIWKSKTG 62
R DGR ++LRP+ GS G TKVL A+ E + W+ TG
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPR------WRKATG 60
Query: 63 QIGKQEKEYEMI 74
+G EY M+
Sbjct: 61 -LGWLTAEYAML 71
>pdb|3N4G|A Chain A, Crystal Structure Of Native Cg10062
pdb|3N4G|B Chain B, Crystal Structure Of Native Cg10062
pdb|3N4G|C Chain C, Crystal Structure Of Native Cg10062
Length = 148
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 56 IWKSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVII 97
IW T + G+ EK+ E +L R Q I ++ PN V I
Sbjct: 63 IWVQATIRSGRTEKQKEELLLRLTQEIALILGIPNEEVWVYI 104
>pdb|3N4D|A Chain A, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|B Chain B, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|C Chain C, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|D Chain D, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|E Chain E, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|F Chain F, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|G Chain G, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|H Chain H, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4D|I Chain I, Crystal Structure Of Cg10062 Inactivated
By(R)-Oxirane-2-Carboxylate
pdb|3N4H|A Chain A, Crystal Structure Of Cg10062 Inactivated By
(S)-Oxirane-2-Carboxylate
Length = 148
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 56 IWKSKTGQIGKQEKEYEMILKRTLQSICILTINPNTTTSVII 97
IW T + G+ EK+ E +L R Q I ++ PN V I
Sbjct: 63 IWVQATIRSGRTEKQKEELLLRLTQEIALILGIPNEEVWVYI 104
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
0.315 0.129 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,021,798
Number of Sequences: 62578
Number of extensions: 103066
Number of successful extensions: 252
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 209
Number of HSP's gapped (non-prelim): 44
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)