RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15057
(151 letters)
>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 237
Score = 150 bits (380), Expect = 2e-46
Identities = 68/150 (45%), Positives = 101/150 (67%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
SLR + N+LSR DGS F QG T V+A +YGP E K+ K I +KA++EVI RPK G
Sbjct: 28 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIG 87
Query: 62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
L V ++ +E +I++TCE+ +L LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G
Sbjct: 88 LPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAG 147
Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQSN 151
+ MR + V+C ++ ++LD Q
Sbjct: 148 VPMRALFCGVACALDSDGTLVLDPTSKQEK 177
>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase;
1.98A {Oryza sativa japonica group}
Length = 246
Score = 150 bits (380), Expect = 2e-46
Identities = 53/150 (35%), Positives = 89/150 (59%)
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 ISMRYILAAVSCIINDKNEVILDANQIQSN 151
I ++++ A+ C + + EVILD N+ +
Sbjct: 132 IPLKHLAVAIGCGVLEDGEVILDTNKAEEQ 161
>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain,
homodimer, exosome, cell-death-related DNAS hydrolase;
3.92A {Caenorhabditis elegans}
Length = 222
Score = 140 bits (355), Expect = 5e-43
Identities = 44/148 (29%), Positives = 80/148 (54%), Gaps = 3/148 (2%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
LRE++ +L+ L +DGS FSQG T + AS GP + K + ++++ +R G
Sbjct: 3 GRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG 62
Query: 62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
+ + + ++I ST +A+ L P T++ +T+ +QD GS+ + IN AC AL+++G
Sbjct: 63 DN--KFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNG 120
Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
+ + V + +E+I+D Q
Sbjct: 121 MPFETVFCGVLIVRVK-DELIIDPTAKQ 147
>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic,
hydrolase/transferase complex; 3.35A {Homo sapiens}
SCOP: d.14.1.4 d.101.1.1
Length = 272
Score = 102 bits (255), Expect = 2e-27
Identities = 33/167 (19%), Positives = 67/167 (40%), Gaps = 22/167 (13%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK------------TIIDK 49
LR + ++ +LS++ GS G T V+ ++ GP +A+ + +
Sbjct: 34 TRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALR 93
Query: 50 ASVEVIF--------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQD 101
+ F R ++ ++R ++ E A+ +PR + ++ L+D
Sbjct: 94 GRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLED 153
Query: 102 QGSLLSCCINAACLALINSGISMRYILAAVSC--IINDKNEVILDAN 146
GS L+ + AA LAL ++G+ M ++ +LD
Sbjct: 154 GGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPT 200
>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 249
Score = 88.9 bits (221), Expect = 1e-22
Identities = 46/164 (28%), Positives = 83/164 (50%), Gaps = 24/164 (14%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK--TIIDKASV------- 52
LR++++++ + +++DGS QG T +A +YGP E + + + D+A V
Sbjct: 24 GELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSA 83
Query: 53 -----EVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
E RP + E ++ T E+A+LT LHPR+ + + +Q LQ G
Sbjct: 84 TFSTGERKRRPHGD-----RKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGT 138
Query: 106 LSCCINAACLALINSGISMRYILAAVSC-IINDKNEVILDANQI 148
+ C+NAA LA++++GI MR + A S ++ + D + +
Sbjct: 139 YAACVNAATLAVLDAGIPMRDFVCACSAGFVDG--TALADLSHV 180
>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 246
Score = 88.1 bits (219), Expect = 2e-22
Identities = 38/159 (23%), Positives = 69/159 (43%), Gaps = 15/159 (9%)
Query: 2 DSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASV--EVIFR 57
+ LR +S +N + DGS QG ++ + GP E +++ + KA + V
Sbjct: 20 NELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNIN 79
Query: 58 PKSGLSFVQDRLKES--------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCC 109
S + K + E ++ ++PRT + + I L+ G ++
Sbjct: 80 KFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSL 139
Query: 110 INAACLALINSGISMRYILAAVSC-IINDKNEVILDANQ 147
IN LALI++GISM ++ +S + + +LD N
Sbjct: 140 INGITLALIDAGISMFDYISGISVGLYDT--TPLLDTNS 176
>2po1_A Probable exosome complex exonuclease 1; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*
Length = 249
Score = 78.1 bits (193), Expect = 1e-18
Identities = 49/160 (30%), Positives = 76/160 (47%), Gaps = 22/160 (13%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
LR +K ++ +L ++GS G+ ++A++YGP E + D+A
Sbjct: 24 YELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAP 83
Query: 51 -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
SVE +P R E VIK E AL+ + PRT++ + I+ LQ
Sbjct: 84 FSVEERKKPGPD-----RRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRV 138
Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILDAN 146
I AA LAL ++GI MR ++AA + I E++LD N
Sbjct: 139 AGITAASLALADAGIPMRDLVAACAAGKIEG--EIVLDLN 176
>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 240
Score = 78.0 bits (193), Expect = 1e-18
Identities = 48/158 (30%), Positives = 74/158 (46%), Gaps = 22/158 (13%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
D LR LK + IL R+DGS G ++ ++YGP EA+I+ D+A
Sbjct: 24 DELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAP 83
Query: 51 -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
SVE RP R E + AL+ PR+ + + I+ L+ +G
Sbjct: 84 FSVEERKRPGPD-----RRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRC 138
Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILD 144
I AA +AL ++GI MR ++ A + + D +V+LD
Sbjct: 139 AGITAASVALADAGIPMRDMVVACAAGKVGD--QVVLD 174
>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU
genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 262
Score = 74.9 bits (184), Expect = 3e-17
Identities = 25/170 (14%), Positives = 48/170 (28%), Gaps = 26/170 (15%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA--SVEVIFRPK 59
LR + GSV+ G T V+ + + + E P
Sbjct: 14 HELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPS 73
Query: 60 SGLSFV--------QDRL---KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
+ S +I + + + ++ + LQ G +
Sbjct: 74 ATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTA 133
Query: 109 CINAACLALINSGISM------------RYILAAVSCIINDKNEVILDAN 146
I A +AL ++ + +AAVS + D + +D
Sbjct: 134 AITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVD-GRIRVDLP 182
>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B
2c37_B* 2c38_B* 2c39_B* 3l7z_B
Length = 250
Score = 69.2 bits (170), Expect = 3e-15
Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 19/145 (13%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
D LR +K +L +L +DGS IF G T +A++YGP E + ++ D+A
Sbjct: 28 DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTP 87
Query: 51 -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
S + P R E VI+ ESA+L L PRT++ + + LQ
Sbjct: 88 FSTDERKNPAPS-----RREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL 142
Query: 108 CCINAACLALINSGISMRYILAAVS 132
+ AA LAL ++GI MR ++A V+
Sbjct: 143 VSLMAASLALADAGIPMRDLIAGVA 167
>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease,
hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E
Length = 258
Score = 69.2 bits (170), Expect = 4e-15
Identities = 44/159 (27%), Positives = 77/159 (48%), Gaps = 24/159 (15%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
D LR +K + ++L R+DGS G+ V+A+++GP E + KA
Sbjct: 24 DELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAP 83
Query: 51 -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
SVE RP R E V K E+ ++ L PR+++ + ++ LQ +
Sbjct: 84 FSVEERKRPGPD-----RRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRT 138
Query: 108 CCINAACLALINSGISMRYILA--AVSCIINDKNEVILD 144
C+NAA +AL+++G+ M+ ++ AV +++LD
Sbjct: 139 ACLNAASVALVDAGVPMKGMITSVAVGKA---DGQLVLD 174
>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate
bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa}
SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A
Length = 239
Score = 65.1 bits (159), Expect = 9e-14
Identities = 30/170 (17%), Positives = 59/170 (34%), Gaps = 27/170 (15%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
D LR ++ + ++GSV+ G T V+ ++ +
Sbjct: 10 DQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPR 69
Query: 51 SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
S + ++ R E +I + +AL ++ + +Q G +
Sbjct: 70 STGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTA 129
Query: 109 CINAACLALIN-----------SGISMRYILAAVSC-IINDKNEVILDAN 146
I A +ALI+ G ++ ++AAVS I +LD +
Sbjct: 130 SITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQG--VPVLDLD 177
>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural
genomics/proteomics initiative structural genomics;
2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB:
1udq_A 1uds_A 1udo_A
Length = 255
Score = 64.4 bits (157), Expect = 2e-13
Identities = 31/168 (18%), Positives = 61/168 (36%), Gaps = 27/168 (16%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
D LR + Q + L +GS + S G+T V+ + +
Sbjct: 9 DQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPR 68
Query: 51 SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
+ + +S + R E +I +A+ ++ + +Q G +
Sbjct: 69 ATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTA 128
Query: 109 CINAACLALINSGIS-----------MRYILAAVSC-IINDKNEVILD 144
I A +A+ ++ I ++ +AAVS I+ND ++LD
Sbjct: 129 AITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--RILLD 174
>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH.,
transferase; 1.70A {Bacillus anthracis}
Length = 255
Score = 63.5 bits (155), Expect = 4e-13
Identities = 35/169 (20%), Positives = 56/169 (33%), Gaps = 24/169 (14%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
LR + N L +GSV+ G T V+ S K
Sbjct: 19 TELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPR 78
Query: 51 SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
+ E +S V R E +I + + +V + +Q G +
Sbjct: 79 ATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTA 138
Query: 109 CINAACLALIN-----------SGISMRYILAAVSCIINDKNEVILDAN 146
I A +A++ S I ++ LAA S I ++ V+LD N
Sbjct: 139 SITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLN 187
>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus
subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A
Length = 245
Score = 46.9 bits (112), Expect = 3e-07
Identities = 30/169 (17%), Positives = 59/169 (34%), Gaps = 28/169 (16%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDK------------ 49
D LR + L+ +S +GSV+ + G T V+ + VE ++ +
Sbjct: 9 DELRPITFDLDFISHPEGSVLITAGNTKVICNAS--VEDRVPPFLRGGGKGWITAEYSML 66
Query: 50 -ASVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
+ +S + R E +I + + ++ + +Q G
Sbjct: 67 PQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTR 126
Query: 107 SCCINAACLAL-----------INSGISMRYILAAVSCIINDKNEVILD 144
+ I A LA+ + LAA+S I+ + ++LD
Sbjct: 127 TASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLD 175
>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 278
Score = 43.0 bits (101), Expect = 8e-06
Identities = 28/182 (15%), Positives = 49/182 (26%), Gaps = 37/182 (20%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEA-----------KIQKTIIDKA 50
R + +S +DGS + G T V+ + A +
Sbjct: 32 GEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLC 91
Query: 51 SVEVIFRPKSG----LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
S P S + E+ E ++ + + L G++L
Sbjct: 92 SSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNIL 151
Query: 107 SCCINAACLALINSGI----------------------SMRYILAAVSCIINDKNEVILD 144
C A AL N + ++R A S + D +I+D
Sbjct: 152 DACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVD 211
Query: 145 AN 146
Sbjct: 212 PT 213
>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease,
hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus
fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G
Length = 259
Score = 42.7 bits (101), Expect = 1e-05
Identities = 34/173 (19%), Positives = 65/173 (37%), Gaps = 29/173 (16%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVA---------SMYGPVEAKIQKT--IIDKA 50
D R+++ N++ +++GS + G T VV P I ++ A
Sbjct: 30 DEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLA 89
Query: 51 SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
S P S R+ + I+ + ++ V + I L D G+LL
Sbjct: 90 SPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLL 149
Query: 107 SCCINAACLALINSGI-------------SMRYILAAVSCIINDKNEVILDAN 146
AA AL+N+ + +R + +V+ +I N+ ++D +
Sbjct: 150 DASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVG-NKYLVDPS 201
>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 271
Score = 40.4 bits (95), Expect = 7e-05
Identities = 26/180 (14%), Positives = 55/180 (30%), Gaps = 36/180 (20%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKTI--IDKA 50
R++ + ++S+++GS G T ++ P I + A
Sbjct: 32 HEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILTNSELLPMA 91
Query: 51 SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
S P S R+ + I+ + E + + L + + G+L
Sbjct: 92 SPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLF 151
Query: 107 SCCINAACLALINSGI--------------------SMRYILAAVSCIINDKNEVILDAN 146
+ A AL+++ I + + NE++LD +
Sbjct: 152 DAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCTFAKIG-NEIVLDPS 210
>2po1_B Probable exosome complex exonuclease 2; RNAse PH,
hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus
abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*
Length = 277
Score = 40.5 bits (95), Expect = 7e-05
Identities = 26/181 (14%), Positives = 61/181 (33%), Gaps = 37/181 (20%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKTI--IDKA 50
+ R ++ ++ ++ +++GS + G T V+ P + + + A
Sbjct: 34 EDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLA 93
Query: 51 SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
S P + R+ + I+ + E ++ V + + L G+L+
Sbjct: 94 SPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLM 153
Query: 107 SCCINAACLALINSGI---------------------SMRYILAAVSCIINDKNEVILDA 145
AA AL+N+ + + I V+ N +++D
Sbjct: 154 DAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIG-NILVVDP 212
Query: 146 N 146
+
Sbjct: 213 S 213
>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A
2c37_A* 2c38_A* 2c39_A* 3l7z_A
Length = 277
Score = 38.5 bits (90), Expect = 4e-04
Identities = 29/183 (15%), Positives = 62/183 (33%), Gaps = 41/183 (22%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKT--IIDKA 50
R L L+ ++DGS + G T+V+A P + + ++ A
Sbjct: 37 TDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLA 96
Query: 51 SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRT--SVILTIQELQDQGS 104
P + R+ + ++ + L + ++ +V L + L G+
Sbjct: 97 YETFEPGPPDENAIELARVVDRSLRDSKALDLTK--LVIEPGKSVWTVWLDVYVLDYGGN 154
Query: 105 LLSCCINAACLALINSGI---------------------SMRYILAAVSCIINDKNEVIL 143
+L C A+ AL N+ + + Y + +S D +++
Sbjct: 155 VLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAKVD-KYLVV 213
Query: 144 DAN 146
D +
Sbjct: 214 DPD 216
>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 305
Score = 37.7 bits (87), Expect = 6e-04
Identities = 18/136 (13%), Positives = 44/136 (32%), Gaps = 15/136 (11%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT-----------IIDKA 50
+ R ++ + +++S + GS G T ++ + + + A
Sbjct: 44 EDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASA 103
Query: 51 SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
+ E R L + + ++ ++ + + + L+ G+L
Sbjct: 104 TPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLF 163
Query: 107 SCCINAACLALINSGI 122
A AL N+ I
Sbjct: 164 DAISIAVKAALFNTRI 179
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 35.8 bits (82), Expect = 0.004
Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 32/87 (36%)
Query: 1 MDSLRELKSQLNILSRSDGSVI----F-SQGQTVVVASMYGPVEA-----------KIQK 44
++L+ + ++ + G ++ + + Q V A G + A K+QK
Sbjct: 1823 QEALQYVVERV---GKRTGWLVEIVNYNVENQQYVAA---GDLRALDTVTNVLNFIKLQK 1876
Query: 45 TIIDKASVEVIFRPKSGLSFVQDRLKE 71
ID ++ S + ++
Sbjct: 1877 --IDIIELQK--------SLSLEEVEG 1893
Score = 27.7 bits (61), Expect = 1.7
Identities = 17/112 (15%), Positives = 33/112 (29%), Gaps = 25/112 (22%)
Query: 46 IIDKASVEVIFR-PKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS 104
+ S+E + P + F+ +L+E K L T E
Sbjct: 10 TLSHGSLEHVLLVPTA-SFFIASQLQEQFNKI---------LPEPTEGFAADDEPTTPAE 59
Query: 105 LLSCCINAACLALINSGI------SMRYILAAVSCIINDKNEVILDANQIQS 150
L+ L ++S + +L + + L+ N I +
Sbjct: 60 LV-----GKFLGYVSSLVEPSKVGQFDQVLNLC---LTEFENCYLEGNDIHA 103
>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: d.14.1.4 d.101.1.1
Length = 358
Score = 33.8 bits (77), Expect = 0.013
Identities = 21/188 (11%), Positives = 54/188 (28%), Gaps = 50/188 (26%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS-----VEVIF 56
R ++ G I G+T V+ V ++ +++A+ +
Sbjct: 47 YDYRNIRISFG---TDYGCCIVELGKTRVLGQ----VSCELVSPKLNRATEGILFFNLEL 99
Query: 57 RPKSGLSFVQDRLKE------SVIKSTCESALLTML--------HPRTSVILTIQELQDQ 102
+ +F R + +++ ++ + + + L
Sbjct: 100 SQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHD 159
Query: 103 GSLLSCCINAACLALINSGI-----------------------SMRYILAAVS-CIINDK 138
G+++ AA +AL + S+ ++ VS
Sbjct: 160 GNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQG 219
Query: 139 NEVILDAN 146
+++D N
Sbjct: 220 TYLLVDPN 227
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.1 bits (69), Expect = 0.086
Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 30/54 (55%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEA---KIQKTIIDKASVE 53
+L++L++ L +Y A I KA++E
Sbjct: 21 ALKKLQASLK---------------------LYADDSAPALAI------KATME 47
>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 305
Score = 30.1 bits (67), Expect = 0.22
Identities = 19/134 (14%), Positives = 34/134 (25%), Gaps = 19/134 (14%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYG---------PVEAKIQKTIIDKASV 52
D R+++ + G V G T V + P E +
Sbjct: 31 DQFRDVEITF---GKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMA 87
Query: 53 EVIFRPKSGLSFVQDRLKESVIKSTCESALLTM-------LHPRTSVILTIQELQDQGSL 105
F + + + KS S L + +V + L G
Sbjct: 88 GSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGF 147
Query: 106 LSCCINAACLALIN 119
+ A L++
Sbjct: 148 IDASCIAVMAGLMH 161
>2ob9_A Tail assembly chaperone; bacteriophage HK97, morphogenesis; 2.30A
{Enterobacteria phage HK97}
Length = 130
Score = 28.7 bits (63), Expect = 0.53
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 13 ILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIID 48
+L +D +FS + V +YGPV +++ K +D
Sbjct: 79 VLCDTDKQPVFSVDEEEQVREIYGPVHSRLLKQALD 114
>1h0h_A Formate dehydrogenase (large subunit); tungsten selenium formate
dehydrogenase, selenocysteine, molybdopterin, MGD,
iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A
{Desulfovibrio gigas} SCOP: b.52.2.2 c.81.1.1
Length = 977
Score = 27.6 bits (61), Expect = 2.1
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 26 GQTVVVASMYGPVEAK------IQKTIIDKASVEVIFRP 58
G V++ S+ G + AK I+ I V ++ P
Sbjct: 897 GDKVILESVRGKLWAKAIITKRIKPFAIQGQQVHMVGIP 935
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 27.1 bits (61), Expect = 2.3
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQT 28
+ SLR + ++++ GS +F +GQT
Sbjct: 325 LTSLRNVSCEVDMFKTLHGSALFQRGQT 352
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 27.2 bits (61), Expect = 2.6
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQT 28
+ +R L +++ + R GS +F +G+T
Sbjct: 362 VTDIRTLAAEVEAIPRVHGSALFERGET 389
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 26.7 bits (60), Expect = 3.3
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQT 28
D +R L + +L R+ GS +F++G+T
Sbjct: 327 KDMIRGLDVRTGVLPRTHGSALFTRGET 354
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 26.7 bits (60), Expect = 3.3
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQT 28
+ ++R + ++ IL R+ GS +F++G+T
Sbjct: 337 VKTVRPILGEVGILPRTHGSALFTRGET 364
>1ujt_A KIAA1568 protein; fibronectin type III domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, unknown function; NMR {Homo sapiens}
SCOP: b.1.2.1
Length = 120
Score = 26.0 bits (57), Expect = 3.4
Identities = 10/44 (22%), Positives = 17/44 (38%)
Query: 54 VIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQ 97
V++R SGL T SA+L L + + ++
Sbjct: 50 VMYRQTSGLQATSSWQNLDAKVPTERSAVLVNLKKGVTYEIKVR 93
>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex,
cytoplasm, nucleotidyltransferase, RNA- binding,
transferase, hydrolase; 2.40A {Escherichia coli E24377A}
PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A
Length = 549
Score = 26.7 bits (60), Expect = 3.8
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 1 MDSLRELKSQLNILSRSDGSVIFSQGQT 28
D +R L + +L R+ GS +F++G+T
Sbjct: 321 KDMIRGLDVRTGVLPRTHGSALFTRGET 348
>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET:
GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP:
b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*
Length = 594
Score = 25.7 bits (57), Expect = 6.8
Identities = 2/18 (11%), Positives = 8/18 (44%)
Query: 25 QGQTVVVASMYGPVEAKI 42
+ T+ + + + +I
Sbjct: 260 KDDTIAMMTSKDVISTRI 277
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
DNA mismatch, methylation; 2.00A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: a.96.1.2
Length = 221
Score = 25.6 bits (57), Expect = 7.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 125 RYILAAVSCIINDKNEVILDAN 146
+Y AAV C+ K ++DAN
Sbjct: 125 KYTCAAVMCLAFGKKAAMVDAN 146
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.131 0.353
Gapped
Lambda K H
0.267 0.0490 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,994,446
Number of extensions: 104161
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 39
Length of query: 151
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 66
Effective length of database: 4,328,508
Effective search space: 285681528
Effective search space used: 285681528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.8 bits)