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= psy15057
(151 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 154 bits (389), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 68/147 (46%), Positives = 101/147 (68%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
SLR + N+LSR DGS F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct: 29 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 88
Query: 63 SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
V ++ +E +I++TCE+ +L LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct: 89 PGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 148
Query: 123 SMRYILAAVSCIINDKNEVILDANQIQ 149
MR + V+C ++ ++LD Q
Sbjct: 149 PMRALFCGVACALDSDGTLVLDPTSKQ 175
>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 = 110 bits (275), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 53/148 (35%), Positives = 89/148 (60%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
+ LR N L R+ GS ++QG T+V+A++YGP + +KAS+EV+++P +G
Sbjct: 12 NQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTG 71
Query: 62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
Q++ E +K T +S L +HP T+ + +Q + + GSLL C INA C AL+ +G
Sbjct: 72 QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAG 131
Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
I ++++ A+ C + + EVILD N+ +
Sbjct: 132 IPLKHLAVAIGCGVLEDGEVILDTNKAE 159
>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 = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 46/146 (31%), Positives = 82/146 (56%), Gaps = 3/146 (2%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
LRE++ +L+ L +DGS FSQG T + AS GP + K + ++++ +R G +
Sbjct: 5 LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGDN 64
Query: 64 FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
+ + ++I ST +A+ L P T++ +T+ +QD GS+ + IN AC AL+++G+
Sbjct: 65 --KFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMP 122
Query: 124 MRYILAAVSCIINDKNEVILDANQIQ 149
+ V I+ K+E+I+D Q
Sbjct: 123 FETVFCGV-LIVRVKDELIIDPTAKQ 147
>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 = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 45/145 (31%), Positives = 77/145 (53%), Gaps = 11/145 (7%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVE--AKIQKTIIDKASVEVIFRPKSG 61
LR++++++ + +++DGS QG T +A +YGP E + + D+A V + +
Sbjct: 26 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 85
Query: 62 LSFVQDRLKESVIKS---------TCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
+ + R KS T E+A+LT LHPR+ + + +Q LQ G + C+NA
Sbjct: 86 STGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNA 145
Query: 113 ACLALINSGISMRYILAAVSCIIND 137
A LA++++GI MR + A S D
Sbjct: 146 ATLAVLDAGIPMRDFVCACSAGFVD 170
>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 = 77.0 bits (188), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 56/162 (34%), Positives = 85/162 (52%), Gaps = 18/162 (11%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
D LR +K +L +L +DGS IF G T +A++YGP E + ++ D+A + V +
Sbjct: 28 DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 84
Query: 61 GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
F D K VI+ ESA+L L PRT++ + + LQ D GS L
Sbjct: 85 MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 143
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS 150
+ AA LAL ++GI MR ++A V+ D +ILD N+ ++
Sbjct: 144 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETEA 184
>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 = 76.6 bits (187), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 18/161 (11%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
D LR +K +L +L +DGS IF G T +A++YGP E + ++ D+A + V +
Sbjct: 26 DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 82
Query: 61 GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
F D K VI+ ESA+L L PRT++ + + LQ D GS L
Sbjct: 83 MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 141
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ 149
+ AA LAL ++GI MR ++A V+ D +ILD N+ +
Sbjct: 142 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 181
>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 = 76.6 bits (187), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 18/161 (11%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
D LR +K +L +L +DGS IF G T +A++YGP E + ++ D+A + V +
Sbjct: 23 DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 79
Query: 61 GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
F D K VI+ ESA+L L PRT++ + + LQ D GS L
Sbjct: 80 MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 138
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ 149
+ AA LAL ++GI MR ++A V+ D +ILD N+ +
Sbjct: 139 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 178
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 76.6 bits (187), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 45/151 (29%), Positives = 86/151 (56%), Gaps = 8/151 (5%)
Query: 7 LKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQ 66
+++++ IL DGS F T V+ S+ GP+E K ++ + + ++E+I RP G++ +
Sbjct: 25 VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTR 84
Query: 67 DRLKESVIKSTCESALLTMLHPRTSVILTIQEL---QDQGSL----LSCCINAACLALIN 119
+++ E +++ + +PR +T Q L +D+ LSCCINAA LAL++
Sbjct: 85 EKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVD 144
Query: 120 SGISMRYILAAVS-CIINDKNEVILDANQIQ 149
+GI++ + A++ II D +++I+D Q
Sbjct: 145 AGIALNSMCASIPIAIIKDTSDIIVDPTAEQ 175
>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 = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 84/165 (50%), Gaps = 24/165 (14%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVE---AKIQKTIIDKASVEVIFR-- 57
LR +K ++ +L ++GS G+ ++A++YGP E +Q+ D+A + V +
Sbjct: 25 ELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRP--DRAILRVRYNMA 82
Query: 58 PKSGLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
P S V++R K VIK E AL+ + PRT++ + I+ LQ
Sbjct: 83 PFS----VEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRV 138
Query: 108 CCINAACLALINSGISMRYILAAVSCIIND-KNEVILDANQIQSN 151
I AA LAL ++GI MR ++AA C + E++LD N+ + N
Sbjct: 139 AGITAASLALADAGIPMRDLVAA--CAAGKIEGEIVLDLNKEEDN 181
>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 = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 84/161 (52%), Gaps = 12/161 (7%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKS 60
D LR +K + ++L R+DGS G+ V+A+++GP E + + D + + +R
Sbjct: 23 FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVH-PRHLQDPSKAIIRYRYNM 81
Query: 61 GLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
V++R + V K E+ ++ L PR+++ + ++ LQ + C+
Sbjct: 82 APFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACL 141
Query: 111 NAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
NAA +AL+++G+ M+ ++ +V+ D +++LD + + N
Sbjct: 142 NAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDN 181
>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 = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 84/161 (52%), Gaps = 12/161 (7%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKS 60
D LR +K + ++L R+DGS G+ V+A+++GP E + + D + + +R
Sbjct: 23 FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEH-LQDPSKAIIRYRYNM 81
Query: 61 GLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
V++R + V K E+ ++ L PR+++ + ++ LQ + C+
Sbjct: 82 APFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACL 141
Query: 111 NAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
NAA +AL+++G+ M+ ++ +V+ D +++LD + + N
Sbjct: 142 NAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDN 181
>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 = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 52/163 (31%), Positives = 81/163 (49%), Gaps = 24/163 (14%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKA--------- 50
D LR LK + IL R+DGS G ++ ++YGP EA+I+K D+A
Sbjct: 23 FDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMA 82
Query: 51 --SVEVIFRPKSGLSFVQDRLKESVIKSTCES---ALLTMLHPRTSVILTIQELQDQGSL 105
SVE RP DR + K T E+ AL+ PR+ + + I+ L+ +G
Sbjct: 83 PFSVEERKRPGP------DRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGT 136
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIIND-KNEVILDANQ 147
I AA +AL ++GI MR ++ V+C ++V+LD ++
Sbjct: 137 RCAGITAASVALADAGIPMRDMV--VACAAGKVGDQVVLDLSE 177
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 81/166 (48%), Gaps = 19/166 (11%)
Query: 1 MDSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDKASVEV---- 54
+ LR +S +N + DGS QG ++ + GP E +++ + KA + V
Sbjct: 21 WNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNI 80
Query: 55 -----IFRPKSGLSFVQDR----LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
R KS S +R ++ S+++ ++ +L ++PRT + + I L+ G +
Sbjct: 81 TKFSKFERSKS--SHKNERRVLEIQTSLVRMFEKNVMLN-IYPRTVIDIEIHVLEQDGGI 137
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
+ IN LALI++GISM ++ +S + D +LD N ++ N
Sbjct: 138 MGSLINGITLALIDAGISMFDYISGISVGLYDTTP-LLDTNSLEEN 182
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 81/166 (48%), Gaps = 19/166 (11%)
Query: 1 MDSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDKASVEV---- 54
+ LR +S +N + DGS QG ++ + GP E +++ + KA + V
Sbjct: 19 WNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNI 78
Query: 55 -----IFRPKSGLSFVQDR----LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
R KS S +R ++ S+++ ++ +L ++PRT + + I L+ G +
Sbjct: 79 NKFSKFERSKS--SHKNERRVLEIQTSLVRMFEKNVMLN-IYPRTVIDIEIHVLEQDGGI 135
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
+ IN LALI++GISM ++ +S + D +LD N ++ N
Sbjct: 136 MGSLINGITLALIDAGISMFDYISGISVGLYDTTP-LLDTNSLEEN 180
>pdb|3OIS|A Chain A, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|B Chain B, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|C Chain C, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|D Chain D, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
Length = 291
Score = 32.7 bits (73), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 57 RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLA 116
R KSG ++ D T E +++ L P+ + Q + DQG + SC NA A
Sbjct: 28 RKKSGYGYIPDIADIRDFSYTPEKSVIAALPPKVDLTPPFQ-VYDQGRIGSCTANALAAA 86
Query: 117 L 117
+
Sbjct: 87 I 87
>pdb|1OE9|B Chain B, Crystal Structure Of Myosin V Motor With Essential Light
Chain - Nucleotide-Free
pdb|1W7I|B Chain B, Crystal Structure Of Myosin V Motor Without Nucleotide
Soaked In 10 Mm Mgadp
pdb|1W7J|B Chain B, Crystal Structure Of Myosin V Motor With Essential Light
Chain + Adp-Befx - Near Rigor
Length = 151
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 2 DSLRELKSQLNILSR-SDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEV 54
D L E K + R DG +++SQ V+ A P A++ K + + S E+
Sbjct: 7 DQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEL 60
>pdb|1LXJ|A Chain A, X-Ray Structure Of Ybl001c Northeast Structural Genomics
(Nesg) Consortium Target Ytyst72
Length = 104
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQG 103
++ ++ +++ES +KST SA T+ P V I E+ + G
Sbjct: 26 VALIEKKIRESPLKSTLHSAGTTIEGPWDDVXGLIGEIHEYG 67
>pdb|3GWB|A Chain A, Crystal Structure Of Peptidase M16 Inactive Domain From
Pseudomonas Fluorescens. Northeast Structural Genomics
Target Plr293l
pdb|3GWB|B Chain B, Crystal Structure Of Peptidase M16 Inactive Domain From
Pseudomonas Fluorescens. Northeast Structural Genomics
Target Plr293l
Length = 434
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 14 LSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKS 60
LSRSD I +Q V A GP AKI++ KAS+ I P S
Sbjct: 205 LSRSDAEAIAAQ---VSAALPKGPALAKIEQPAEPKASIGHIEFPSS 248
>pdb|2OB9|A Chain A, Structure Of Bacteriophage Hk97 Tail Assembly Chaperone
pdb|2OB9|B Chain B, Structure Of Bacteriophage Hk97 Tail Assembly Chaperone
Length = 130
Score = 26.9 bits (58), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 11 LNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIID 48
+++L +D +FS + V +YGPV +++ K +D
Sbjct: 77 IDVLCDTDKQPVFSVDEEEQVREIYGPVHSRLLKQALD 114
>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 = 26.2 bits (56), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 73/173 (42%), Gaps = 32/173 (18%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS----------MYGPVEAKI--QKTIIDK 49
D LR + L+ +S +GSV+ + G T V+ + + G + I + +++ +
Sbjct: 9 DELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPR 68
Query: 50 ASVEVIFRPK-----SGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS 104
A+ + R SG + RL +++ + L L RT + + +Q G
Sbjct: 69 ATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVD---LEKLGERT-IWIDCDVIQADGG 124
Query: 105 LLSCCINAACLA-------LINSGI----SMRYILAAVSCIINDKNEVILDAN 146
+ I A LA LI +G + LAA+S I+ + ++LD N
Sbjct: 125 TRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLN 177
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVV 31
D LR + L+ +S +GSV+ + G T V+
Sbjct: 9 DELRPITFDLDFISHPEGSVLITAGNTKVI 38
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 25.8 bits (55), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 41/172 (23%), Positives = 68/172 (39%), Gaps = 32/172 (18%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVAS----------MYGPVEAKI--QKTIIDKA 50
LR + N L +GSV+ G T V+ S M G + + + +I +A
Sbjct: 20 ELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRA 79
Query: 51 SVEVIFRPKS-----GLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
+ + R S G + RL +++ + L L RT V + +Q G
Sbjct: 80 TEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVD---LEALGERT-VWIDCDVIQADGGT 135
Query: 106 LSCCINAACLALI-----------NSGISMRYILAAVSCIINDKNEVILDAN 146
+ I A +A++ S I ++ LAA S I ++ V+LD N
Sbjct: 136 RTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLN 187
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
0.319 0.131 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,423,934
Number of Sequences: 62578
Number of extensions: 106982
Number of successful extensions: 312
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 278
Number of HSP's gapped (non-prelim): 26
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)