RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18119
(263 letters)
>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 = 301 bits (772), Expect = e-104
Identities = 136/243 (55%), Positives = 180/243 (74%), Gaps = 3/243 (1%)
Query: 1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRN- 59
++LL++ G R DGRR ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP +R
Sbjct: 8 LELLSD--QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 65
Query: 60 KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
++ + L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ AAI++++HPRSQI
Sbjct: 66 RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125
Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA T L D+SH+EE G
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 185
Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
GP L +A LP SG++A++E+ +LH DHL RVL+ A + D+H +LD ++QH+ + +
Sbjct: 186 GPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASI 245
Query: 240 ARG 242
G
Sbjct: 246 LLG 248
>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 = 276 bits (708), Expect = 3e-94
Identities = 89/230 (38%), Positives = 141/230 (61%), Gaps = 1/230 (0%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
G R DGR+ +ELR I+ +GV ++GSAYIE G K++AAVYGPR + K ++
Sbjct: 14 NGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRA 73
Query: 69 LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
++ +Y+MA FS ERK +P DR++ EIS ++ A+ A++ E+ PR+ ID+F+EVLQA
Sbjct: 74 ILRVRYNMAPFSVEERK-KPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQA 132
Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
D G A + AA+LAL DAGIPMR+ V AC+A ++D++ E+ G ++ VA +
Sbjct: 133 DAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIM 192
Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
PL + ++++ L D + A+KG ++ A+K+ +K+A
Sbjct: 193 PLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA 242
>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 240
Score = 270 bits (693), Expect = 4e-92
Identities = 91/225 (40%), Positives = 141/225 (62%), Gaps = 1/225 (0%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
+R DGR ELR ++ G+ ++DGS+Y+E G K+L AVYGPR + + ++ +
Sbjct: 15 SVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAV 74
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
I +Y+MA FS ERK RP DR++ EIS +A+ A++ E PRS ID+F+EVL+A+
Sbjct: 75 IRCRYNMAPFSVEERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAE 133
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
GG CA + AA++AL DAGIPMR+ VVAC+A GD ++D+S E+ G ++ VA LP
Sbjct: 134 GGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILP 193
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
+ ++ +++ L + R LD A++GC IH + A+++
Sbjct: 194 RTREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKRY 238
>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 246
Score = 267 bits (685), Expect = 8e-91
Identities = 80/239 (33%), Positives = 129/239 (53%), Gaps = 5/239 (2%)
Query: 1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQS-DGSAYIEQGNTKVLAAVYGPRPVRN 59
+++ + GLR DGRR +ELR+ + + DGS+Y+EQGN K++ V GP+ R
Sbjct: 4 LEIYSP--EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRL 61
Query: 60 KSIKVHGSVLINFQYSMAVFSTGERK-TRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQ 118
KS L+N ++ FS ER + + +R+ EI L + +M ++PR+
Sbjct: 62 KSQMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTV 121
Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETL 178
IDI + VL+ DGG + +N TLALIDAGI M +Y+ S L TPL+D + LEE
Sbjct: 122 IDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN- 180
Query: 179 GGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237
+T+ + S K++++ + K+ LD L VL + G + ++D +++H K
Sbjct: 181 AMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKR 239
>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 = 264 bits (676), Expect = 3e-89
Identities = 82/230 (35%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
G R DGR+ ELR I+ LGV +DGSA E GNTK +AAVYGP+ + + + +
Sbjct: 18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77
Query: 69 LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
++ +Y M FST ERK P R+ E+S +R+A+ +A++ E+ PR+ ID+F E+LQA
Sbjct: 78 VLRVRYHMTPFSTDERK-NPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136
Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
D G+ + AA+LAL DAGIPMR+ + + A ++D++ E G ++ +A +
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMM 196
Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
P +V + +L+ + D + D A+KG I+ + A+K ++
Sbjct: 197 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEFK 246
>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 = 261 bits (670), Expect = 3e-88
Identities = 90/228 (39%), Positives = 139/228 (60%), Gaps = 4/228 (1%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
GLR DGR+ ELR I+ V ++DGS Y+E G KV+AAV+GPR V + ++
Sbjct: 14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKA 73
Query: 69 LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
+I ++Y+MA FS ERK RP DR++ EIS ++A A IM E+ PRS IDIFVEVLQA
Sbjct: 74 IIRYRYNMAPFSVEERK-RPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
D G+ AC+NAA++AL+DAG+PM+ + + + A ++D E+ G ++ A L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192
Query: 189 PLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
+GK +A++++ ++ D + + ++ A KG I+ + AI +
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRR 240
>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 = 246 bits (629), Expect = 6e-82
Identities = 72/247 (29%), Positives = 114/247 (46%), Gaps = 16/247 (6%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK-------- 60
R LR + R G+ SQ+ GSAY+E G TKVL AV GPR
Sbjct: 24 EEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAG 83
Query: 61 ---SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRS 117
+ + A F+ R+ P G + E++L L++A+ A+ +PR+
Sbjct: 84 AGGEAPAALRGRLLCDFRRAPFAGRRRR-APPGGCEERELALALQEALEPAVRLGRYPRA 142
Query: 118 QIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA---GDTPLVDISHL 174
Q+++ +L+ G A + AA LAL DAG+ M + VV C SLA T L+D + L
Sbjct: 143 QLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRL 202
Query: 175 EETLGGPNLTVAALPLSGKVAVMELSQKL-HLDHLPRVLDCALKGCADIHAILDTAIKQH 233
EE LTVA +P+ +VA + S + + + L+GC ++ +L ++ +
Sbjct: 203 EEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLVRA 262
Query: 234 LIKVAGA 240
+ A
Sbjct: 263 ARRRGAA 269
>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 = 240 bits (614), Expect = 4e-80
Identities = 57/230 (24%), Positives = 92/230 (40%), Gaps = 12/230 (5%)
Query: 9 GGLRNDGR-RGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGS 67
G + R G LR C + S+ DGSA QG+T VLA VYGP V+
Sbjct: 17 NGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVS------- 69
Query: 68 VLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
++ A R +R A ++ +HPR+ I + ++V+
Sbjct: 70 ---KEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVS 126
Query: 128 ADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVA 186
G C+NAA +AL+DAG+PMR + +L D T ++D + +E LT A
Sbjct: 127 DAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFA 186
Query: 187 ALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
+ K+ + L + L A + ++++ K
Sbjct: 187 LDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSK 236
>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH.,
transferase; 1.70A {Bacillus anthracis}
Length = 255
Score = 215 bits (549), Expect = 5e-70
Identities = 57/256 (22%), Positives = 109/256 (42%), Gaps = 21/256 (8%)
Query: 1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
M + +R DGR ELR I +GS IE G+TKV+ + V
Sbjct: 1 MGSSHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP-P 59
Query: 61 SIKVHGSVLINFQYSMAVFSTGERKTRPRG----DRKTSEISLQLRQAVSAAIMSEVHPR 116
++ G + +Y+M +T +R R +T EI + +A+ A + E
Sbjct: 60 FMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGE 119
Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALID-----------AGIPMREYVVACSASLAGD 165
+ I +V+QADGG A + A +A++ + IP+++Y+ A S + +
Sbjct: 120 RTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEE 179
Query: 166 TPLV-DISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCAD 221
+V D+++ E++ ++ V + G+ ++ + + L +LD A +G
Sbjct: 180 QGVVLDLNYAEDSKADVDMNV-IMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQ 238
Query: 222 IHAILDTAIKQHLIKV 237
+ I A+ + +
Sbjct: 239 LIDIQKEALGDIVSHI 254
>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 = 213 bits (544), Expect = 9e-70
Identities = 49/218 (22%), Positives = 81/218 (37%), Gaps = 15/218 (6%)
Query: 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
LR++RC L +DGSA QG T + A+ GP V ++ ++ Y
Sbjct: 4 RLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASK-ASDEAMTLDISYRAN-- 60
Query: 80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
GD K + ++ + +S AI E+ P + I + V +Q DG +N
Sbjct: 61 ---------CGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAING 111
Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSG---KVAV 196
A AL+D G+P D ++D + +E + + S +V
Sbjct: 112 ACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVCA 171
Query: 197 MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
M+ L A + I T +K+ L
Sbjct: 172 MDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKL 209
>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 = 209 bits (535), Expect = 3e-68
Identities = 65/238 (27%), Positives = 106/238 (44%), Gaps = 18/238 (7%)
Query: 12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
R GR +LR IR ++GS +E G+TKV+ V V + +K G +
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVP-RFLKGQGQGWLT 61
Query: 72 FQYSMAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
+Y M STGER R K T EI + +++ AA+ + + I +V+Q
Sbjct: 62 AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121
Query: 128 ADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLEE 176
ADGG A + AT+ALIDA G P+++ V A S + P++D+ +LE+
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLED 181
Query: 177 TLGGPNLTVAALPLSGKVAV--MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
+ +L V G + V L +L+ A +G ++ + A+ +
Sbjct: 182 SAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239
>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase;
1.98A {Oryza sativa japonica group}
Length = 246
Score = 208 bits (531), Expect = 2e-67
Identities = 49/244 (20%), Positives = 91/244 (37%), Gaps = 27/244 (11%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
R DGR ++LR C ++ GSA QG+T VLAAVYGP+P + +
Sbjct: 3 ESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGT-RKGENPEKAS 61
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
I + G+++ E + L++ + + + VHP + + ++V+ D
Sbjct: 62 IEVVWKPMTGQIGKQEK---------EYEMTLKRTLQSICLLTVHPNTTTSVILQVVGND 112
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVAAL 188
G +NA AL+ AGIP++ VA + D ++D + EE +
Sbjct: 113 GSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFP 172
Query: 189 P----------------LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
+ + + ++ L + I + T +++
Sbjct: 173 NSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQK 232
Query: 233 HLIK 236
Sbjct: 233 QAPG 236
>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 = 208 bits (530), Expect = 3e-67
Identities = 60/239 (25%), Positives = 105/239 (43%), Gaps = 20/239 (8%)
Query: 11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
+R+DGR+ +LR + + +GS I G TKV+ V +K G I
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP-NWLKGKGQGWI 59
Query: 71 NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL 126
+YSM +T +R R R +T EI + +A+ A+ I + +V+
Sbjct: 60 TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVI 119
Query: 127 QADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHLE 175
QADGG A + A +A+ DA I P++++V A S + D L+D++ E
Sbjct: 120 QADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEE 179
Query: 176 ETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTAIK 231
++ ++ V SG+++ + + D L ++LD A KG ++ +
Sbjct: 180 DSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYV 237
>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU
genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 262
Score = 197 bits (502), Expect = 6e-63
Identities = 64/240 (26%), Positives = 98/240 (40%), Gaps = 21/240 (8%)
Query: 12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
R DGR HELR + G GS IE G+TKVL V + K G +
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP-RWRKATGLGWLT 65
Query: 72 FQYSMAVFSTGERKTR----PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
+Y+M +T R R R +T EIS + +++ A I + I I +VLQ
Sbjct: 66 AEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQ 125
Query: 128 ADGGNFCACVNAATLALIDAGI------------PMREYVVACSASLAGDTPLVDISHLE 175
ADGG A + A +AL DA P+ + A S + VD+ + E
Sbjct: 126 ADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEE 185
Query: 176 ETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
++ ++ V +G + ++ + L ++LD AL C + A A+
Sbjct: 186 DSRAEVDMNV-VATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDALAL 244
>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 = 143 bits (362), Expect = 4e-42
Identities = 60/251 (23%), Positives = 103/251 (41%), Gaps = 31/251 (12%)
Query: 11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
+R+DGR+ ELR I L S +GS I GNTKV+ V ++ G I
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP-PFLRGGGKGWI 59
Query: 71 NFQYSMAVFSTGERKTRPRG----DRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL 126
+YSM +T ++ + +T EI + +A+ A + E I I +V+
Sbjct: 60 TAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVI 119
Query: 127 QADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTP-LVDISHL 174
QADGG A + A LA+ A P+ +++ A S + + L+D+++
Sbjct: 120 QADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYE 179
Query: 175 EETLGGPNLTVA--------ALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAIL 226
E++ ++ V L +G+ A L +L A KG ++
Sbjct: 180 EDSSAEVDMNVIMTGSGRFVELQGTGEEATFSRED------LNGLLGLAEKGIQELIDKQ 233
Query: 227 DTAIKQHLIKV 237
+ L ++
Sbjct: 234 KEVLGDSLPEL 244
>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 = 136 bits (345), Expect = 3e-39
Identities = 51/258 (19%), Positives = 101/258 (39%), Gaps = 41/258 (15%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
G R D R + R I +GV +++GSA ++ G+T+VL + G +
Sbjct: 25 GKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMT 84
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAI------MSEVHPRSQIDI 121
N + ++ + P +R E++ + + + S A+ + + I
Sbjct: 85 TN--VELVPLASPTFEPGPPDER-AIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFI 141
Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP---------------------MREYVVACSA 160
V VL DG A AA AL++A +P + + V +
Sbjct: 142 DVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTF 201
Query: 161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVLDCA 215
+ G+ +VD S EE + +T+ +G ++ + QK L+ + ++ A
Sbjct: 202 AKIGNILVVDPSLDEELVMDGKITITTDE-TGHISAV---QKSEGGAFKLEEVMYAVETA 257
Query: 216 LKGCADIHAILDTAIKQH 233
K +I ++ A+++
Sbjct: 258 FKKAEEIRKLILEAVEKA 275
>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5'
exoribonuclease, hydrolase; 2.65A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 271
Score = 132 bits (333), Expect = 2e-37
Identities = 52/260 (20%), Positives = 99/260 (38%), Gaps = 50/260 (19%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVR-NKSIKV 64
R DGR HE R I GV S+++GS+ ++ GNT+++ V P P +
Sbjct: 23 KERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGV-- 80
Query: 65 HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPR 116
I + ++ + P +R + E+S + + + + M E
Sbjct: 81 -----ILTNSELLPMASPTFEPGPPDER-SVELSRVVDRCIRESRMIDLEKLCIIEGSKV 134
Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALIDAGIP--------------------MREYVV 156
+ + + ++ DG F A V A AL+D IP + +
Sbjct: 135 WMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKAL 194
Query: 157 ACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRV 211
C+ + G+ ++D S EE + +++ G + M QK L D + +
Sbjct: 195 MCTFAKIGNEIVLDPSLEEEDILTARISIGVTE-EGSICAM---QKGGEGPLTRDDVLKA 250
Query: 212 LDCALKGCADIHAILDTAIK 231
+ A++ + LD ++
Sbjct: 251 VSIAVEKVPQLIEYLDKSMT 270
>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 = 122 bits (309), Expect = 5e-34
Identities = 49/249 (19%), Positives = 93/249 (37%), Gaps = 43/249 (17%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV----YGPRPVR-NKSIKV 64
R DGR E RK+ V +++GSA ++ G+T+V+ V P P ++ +
Sbjct: 21 NERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGV-- 78
Query: 65 HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSEV------HPR 116
I + ++ + P + + E++ + + + S A+
Sbjct: 79 -----IIVNAELVPLASPTFEPGPPDEN-SIELARVVDRGIRESEAVDLSKLVIEEGEKV 132
Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------------MREYVVACSASLA 163
+ + + L DG A AA AL++ +P +R+ V+ ++ +
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIV 192
Query: 164 GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVLDCALKG 218
G+ LVD S E ++G LT+ V M QK L +LD ++
Sbjct: 193 GNKYLVDPSREEMSVGDTTLTITTDK-DDNVVAM---QKSGGYLLDEKLFDELLDVSINC 248
Query: 219 CADIHAILD 227
+
Sbjct: 249 ARKLREKFK 257
>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 = 120 bits (302), Expect = 5e-33
Identities = 53/260 (20%), Positives = 88/260 (33%), Gaps = 37/260 (14%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
R DGR E R +G S +DGSA ++ GNT V+ V + G
Sbjct: 23 NCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKG--Y 80
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPRSQIDI 121
+ + + ++ P G+ S + + + + S +
Sbjct: 81 VVPNVDLPPLCSSRFRSGPPGEE-AQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYC 139
Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP----------------------MREYVVACS 159
+ L DG AC A AL + +P +R + VA S
Sbjct: 140 DLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATS 199
Query: 160 ASLAGDTP-LVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPRVLDCAL 216
++ DT +VD + EE L LT+ GK+ + L L + A+
Sbjct: 200 FAVFDDTLLIVDPTGEEEHLATGTLTIVMDE-EGKLCCLHKPGGSGLTGAKLQDCMSRAV 258
Query: 217 KGCADIHAILDTAIKQHLIK 236
++ ++D IK K
Sbjct: 259 TRHKEVKKLMDEVIKSMKPK 278
>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 = 118 bits (297), Expect = 4e-32
Identities = 45/258 (17%), Positives = 94/258 (36%), Gaps = 47/258 (18%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV---YGPRPVRNKSIKVHG 66
G+R DGR+ + R + L ++DGSA ++ G T VLA + G
Sbjct: 28 GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPN---QG 84
Query: 67 SVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAI----MSEVHPRSQID 120
++++N + + + P + E++ + +++ S A+ + +S
Sbjct: 85 NLIVN--VELLPLAYETFEPGPPDEN-AIELARVVDRSLRDSKALDLTKLVIEPGKSVWT 141
Query: 121 IFVE--VLQADGGNFCACVNAATLALIDAGIP---------------------MREYVVA 157
++++ VL G AC A+ AL + + + VV
Sbjct: 142 VWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVT 201
Query: 158 CSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVL 212
S + +VD EE++ ++ + P K+ + QK + L + +
Sbjct: 202 ISVAKVDKYLVVDPDLDEESIMDAKISFSYTP-DLKIVGI---QKSGKGSMSLQDIDQAE 257
Query: 213 DCALKGCADIHAILDTAI 230
+ A + L +
Sbjct: 258 NTARSTAVKLLEELKKHL 275
>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 = 113 bits (284), Expect = 3e-30
Identities = 48/261 (18%), Positives = 83/261 (31%), Gaps = 41/261 (15%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
LR DGR + R + V S + GSA ++ G+T +L V G +
Sbjct: 35 DLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLE 94
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPRSQIDI 121
S + E + GD +EI+ L + + S + +
Sbjct: 95 FFVDCSASATPEFEGR---GGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYV 151
Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP---------------------------MREY 154
V +L+ G F A A AL + IP +
Sbjct: 152 DVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENV 211
Query: 155 VVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLDHLPRVL 212
+ G +VD + EE +L V+ G V M L + + ++
Sbjct: 212 PCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTS-KGVVTCMRKVGKGSLDPESIFEMM 270
Query: 213 DCALKGCADIHAILDTAIKQH 233
+ + +HA L + + +
Sbjct: 271 ETGKRVGKVLHASLQSVVHKE 291
>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 = 100 bits (250), Expect = 7e-25
Identities = 59/292 (20%), Positives = 97/292 (33%), Gaps = 52/292 (17%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
R DGR+ ++ R IR G G +E G T+VL V P+ R
Sbjct: 38 KKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPKLNRAT----E 90
Query: 66 GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSEV------HPRS 117
G + N + S E R +++ + + + S I +E
Sbjct: 91 GILFFNLELSQMAAPAFEPG---RQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVW 147
Query: 118 QIDIFVEVLQADGGNFCACVNAATLALIDAGIP-----------------------MREY 154
QI + + +L DG A AA +AL P +
Sbjct: 148 QIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHM 207
Query: 155 VVACSASL--AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLDHLPR 210
+ S + G LVD + EE + L +A ++ ++ S L D + R
Sbjct: 208 PICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNK-HREICTIQSSGGIMLLKDQVLR 266
Query: 211 VLDCALKGCADIHAILDTAIKQHLI--KVAGARGLGRKFQLGQLTGKKKEEE 260
A A+I ++ A++ K G G ++T K E+
Sbjct: 267 CSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEKA 318
>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 305
Score = 93.6 bits (232), Expect = 1e-22
Identities = 40/274 (14%), Positives = 76/274 (27%), Gaps = 53/274 (19%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
R DGR + R + F + G ++ GNTKV + + G +
Sbjct: 22 NYRLDGRSFDQFRDVEI---TFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFV 78
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRS--------QIDI 121
I+ + S + + + S + ++V + +V +
Sbjct: 79 ISTEISP--MAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRA 136
Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP-----------------------MREYVVAC 158
V L DGG A A L+ P + +
Sbjct: 137 DVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICV 196
Query: 159 S--------------ASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-- 202
+ + ++D + EE L LTV + +V + +
Sbjct: 197 TFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNK-NREVVQVSKAGGLP 255
Query: 203 LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
+ L + A I + +K+ K
Sbjct: 256 MDALTLMKCCHEAYSIIEKITDQILQLLKEDSEK 289
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 44.8 bits (107), Expect = 1e-05
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 17/162 (10%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIK---- 63
R DGR LR + C + +F GSA ++G T+VL V + KS +
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA 375
Query: 64 VHGSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQ 118
++G NF Y ++T E E+ +L + A+ I + P +
Sbjct: 376 INGIKDKNFMLHYEFPPYATNE--IGKVTGLNRRELGHGALAEK-ALYPVIPRDF-PFT- 430
Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV--VAC 158
I + EVL+++G + A +LAL+D+G+P+ V VA
Sbjct: 431 IRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAI 472
Score = 27.5 bits (62), Expect = 5.5
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 33 QSDGSAYIEQGNTKVLAAV 51
+DGSA ++ G+T V+
Sbjct: 27 FADGSAVVQSGDTAVMVTA 45
>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 = 41.3 bits (98), Expect = 2e-04
Identities = 58/195 (29%), Positives = 82/195 (42%), Gaps = 27/195 (13%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGS 67
G R DGR +R + R GV ++ GSA +G T+ L G ++ G
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 371
Query: 68 VLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQIDIF 122
F Y+ +S GE T G K EI L R V A + D F
Sbjct: 372 RTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKR-GVLAVMPDM-------DKF 421
Query: 123 ------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VACSASLAGD--TPLVDI 171
V E+ +++G + A V A+LAL+DAG+P++ V +A GD L DI
Sbjct: 422 PYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDI 481
Query: 172 SHLEETLGGPNLTVA 186
E+ LG + VA
Sbjct: 482 LGDEDHLGDMDFKVA 496
Score = 27.5 bits (62), Expect = 5.2
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 33 QSDGSAYIEQGNTKVLAAV 51
Q+ + + +T V V
Sbjct: 26 QATAAVMVSMDDTAVFVTV 44
>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 = 40.8 bits (95), Expect = 4e-04
Identities = 35/251 (13%), Positives = 76/251 (30%), Gaps = 86/251 (34%)
Query: 13 NDGRRGHELRKIRCRLGVFSQSDG---------------SAYIEQGNTKVL--------A 49
G +G +R+ + + DG ++Y + +L A
Sbjct: 1676 FGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPA 1735
Query: 50 ------AVYGPRPVRNKSIKVHGSVLINF------QYS----MA-VFST----------G 82
A + +++K + + F +Y+ +A V S G
Sbjct: 1736 LTLMEKAAF--EDLKSKGLIPADAT---FAGHSLGEYAALASLADVMSIESLVEVVFYRG 1790
Query: 83 E--RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFC--ACVN 138
+ PR + S + A++ ++ + + VE + G N
Sbjct: 1791 MTMQVAVPRDELGRSNYGMI---AINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN 1847
Query: 139 AATLALIDAGIPMREYVVACSASLAGDTPLVD-ISHLEETLGGPNLTVAALPLSGKVAVM 197
+ ++YV AGD +D ++++ + + + L S + +
Sbjct: 1848 ----------VENQQYVA------AGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEV 1891
Query: 198 ELSQKLHLDHL 208
E HL
Sbjct: 1892 E-------GHL 1895
Score = 35.0 bits (80), Expect = 0.028
Identities = 45/271 (16%), Positives = 79/271 (29%), Gaps = 83/271 (30%)
Query: 15 GRRGHELRKIRCRLGVFSQSDGSA-----YIEQGNTKVLAAVYGPRP---VRNKSIKVHG 66
G R +E + + +E P P + N + +
Sbjct: 307 GVRCYE---------AYPNTSLPPSILEDSLENNEGV-------PSPMLSISNLTQE--- 347
Query: 67 SVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQL----RQAVSAAIMSEVHPRSQIDIF 122
Q V T P G + + + L + V + P+S
Sbjct: 348 ------QVQDYVNKT--NSHLPAGKQ----VEISLVNGAKNLVVSG-----PPQS----- 385
Query: 123 VEVLQADGGNFCACV--NAATLALIDAGIPMREYVVACSAS-LAGDTP-----LVDISH- 173
L + A L + IP E + S L +P LV S
Sbjct: 386 ---LYG----LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL 438
Query: 174 LEETLGGPNLTVAALPLSGKVAV------MELSQKLHLDHLPRVLDCALKGCADIHAILD 227
+ + L N++ A + ++ V +L + L R++DC ++
Sbjct: 439 INKDLVKNNVSFNAKDI--QIPVYDTFDGSDL-RVLSGSISERIVDCIIRLPVKWETTTQ 495
Query: 228 TAIKQHLIKVAGARGLGRKFQLGQLTGKKKE 258
H++ G G LG LT + K+
Sbjct: 496 FKA-THILDF----GPGGASGLGVLTHRNKD 521
Score = 33.1 bits (75), Expect = 0.091
Identities = 22/134 (16%), Positives = 46/134 (34%), Gaps = 31/134 (23%)
Query: 149 IPMREYVVA------CSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGK----VAVME 198
+P + +A + L T E + L GK V+
Sbjct: 22 VPTASFFIASQLQEQFNKILPEPT---------EGFAADDEPTTPAELVGKFLGYVS--S 70
Query: 199 LSQKLHLDHLPRVL--------DCALKGCADIHAILDTAIKQHLIKVAGARGLGRK-FQL 249
L + + +VL +C L+G DIHA+ ++++ + + L +
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCYLEG-NDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Query: 250 GQLTGKKKEEESKS 263
+ + +++S S
Sbjct: 130 RIMAKRPFDKKSNS 143
>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 = 40.3 bits (95), Expect = 4e-04
Identities = 46/200 (23%), Positives = 74/200 (37%), Gaps = 47/200 (23%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPR----------PV 57
R DGR ++R + + + GSA E+G T++L PV
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPV 412
Query: 58 RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
K + Y+ +S GE T G K EI +L R A+ + +
Sbjct: 413 TRKRYMHN--------YNFPPYSVGE--TGRVGSPKRREIGHGALAER-AIVPVLPTR-- 459
Query: 115 PRSQIDIF------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VAC----SAS 161
+ F V E L ++G V A+T++L++AG+P++ V +A
Sbjct: 460 -----EEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEI 514
Query: 162 LAGD--TPLVDISHLEETLG 179
L DI E+ G
Sbjct: 515 NGETHYVALTDILGAEDAFG 534
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 39.8 bits (94), Expect = 6e-04
Identities = 55/196 (28%), Positives = 77/196 (39%), Gaps = 43/196 (21%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-----------GPRPV 57
G R DGR +R + R GV ++ GSA +G T+ L
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 377
Query: 58 RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
R + H Y+ +S GE T G K EI L R V A +
Sbjct: 378 RTDTFLFH--------YNFPPYSVGE--TGMVGSPKRREIGHGRLAKR-GVLAVMPDM-- 424
Query: 115 PRSQIDIF------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VACSASLAGD 165
D F V E+ +++G + A V A+LAL+DAG+P++ V +A GD
Sbjct: 425 -----DKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479
Query: 166 --TPLVDISHLEETLG 179
L DI E+ LG
Sbjct: 480 NYVVLSDILGDEDHLG 495
Score = 27.1 bits (61), Expect = 7.7
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 33 QSDGSAYIEQGNTKVLAAV 51
Q+ + + +T V V
Sbjct: 32 QATAAVMVSMDDTAVFVTV 50
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 39.4 bits (93), Expect = 9e-04
Identities = 41/160 (25%), Positives = 70/160 (43%), Gaps = 23/160 (14%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGS 67
GLR DGR +R I +G+ ++ GSA +G T+ + G + G+
Sbjct: 328 TGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGT 387
Query: 68 VLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQIDIF 122
+F Y+ +S GE T G EI L R A+ + ++ + F
Sbjct: 388 YKESFLLHYNFPPYSVGE--TGRMGSPGRREIGHGKLAWR-ALRPMLPTK-------EDF 437
Query: 123 ------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV 155
V E+ +++G + A V ++LA++DAG+P+ V
Sbjct: 438 PYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPV 477
Score = 27.5 bits (62), Expect = 5.1
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 33 QSDGSAYIEQGNTKVLAAV 51
Q+DG+ G T VLA
Sbjct: 40 QADGAVLATMGETVVLATA 58
>1t57_A Conserved protein MTH1675; structural genomics, FMN; HET: FMN;
2.30A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: c.49.1.2
Length = 206
Score = 29.1 bits (65), Expect = 1.1
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 103 QAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAG-IPMREYVVACSAS 161
V I + + ++I E L+ F CV A +A DAG IP+ E V+A +
Sbjct: 116 SGVGRGISNRFGGVTPVEIMAETLRMVSQGFKVCVEIAIMAA-DAGLIPVDEEVIAIGGT 174
Query: 162 LAG-DTPLV 169
G DT LV
Sbjct: 175 AWGADTALV 183
>3p3v_A PTS system, N-acetylgalactosamine-specific IIB CO; PTS IIB
component, phosphotransferase, sugar transport, STRU
genomics; HET: PGE; 1.65A {Streptococcus pyogenes
serotype M1}
Length = 163
Score = 28.9 bits (65), Expect = 1.1
Identities = 10/117 (8%), Positives = 32/117 (27%), Gaps = 17/117 (14%)
Query: 101 LRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN---FCACVNAAT-LALIDAGIPMREYVV 156
++ + ++I I ++++ F + L++ G+P+ E +
Sbjct: 50 MKTVIPSSIAIRFFS---IQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINI 106
Query: 157 ACSASLAGDTPLV--------DISHLEE--TLGGPNLTVAALPLSGKVAVMELSQKL 203
+ D S + P + +++ +
Sbjct: 107 GNIHKTDDKVAITQFISLGETDKSAIRCLAHDHHVVFNTKTTPAGNSASDVDILDYI 163
>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 = 27.6 bits (60), Expect = 2.5
Identities = 6/20 (30%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 19 HELRKIRCRLGVFSQSDGSA 38
L+K++ L ++ +D SA
Sbjct: 20 QALKKLQASLKLY--ADDSA 37
>1nrz_A PTS system, sorbose-specific IIB component; beta sheet core,
flanking helices, right handed beta-alpha-B crossover,
transferase; 1.75A {Klebsiella pneumoniae} SCOP:
c.38.1.1
Length = 164
Score = 27.8 bits (62), Expect = 2.9
Identities = 20/120 (16%), Positives = 34/120 (28%), Gaps = 17/120 (14%)
Query: 101 LRQAVSAAIMSEVHPRSQIDIFVEVLQ---ADGGN-FCACVNAAT-LALIDAGIPMREYV 155
LRQA + V ++ V V F N L ++ G+ +
Sbjct: 47 LRQAAPPGMKVNVVS---LEKAVAVYHNPQYQDETVFYLFTNPHDVLTMVRQGVQIATLN 103
Query: 156 VACSASLAGDTPLV--------DISHLEETLG-GPNLTVAALPLSGKVAVMELSQKLHLD 206
+ A G L DI E G L + + V +++ +
Sbjct: 104 IGGMAWRPGKKQLTKAVSLDPQDIQAFRELDKLGVKLDLRVVASDPSVNILDKINETAFC 163
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 27.6 bits (61), Expect = 4.9
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 55 RPVRNKSIKVHGSVLINFQY-------SMAVFSTGERKTRPRGDRKTSEISLQLRQAVSA 107
+++ + + + V +T E K + R S+I+L++
Sbjct: 473 EKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALK 532
Query: 108 AIMSEVHPRSQIDI 121
IMS+ ID+
Sbjct: 533 QIMSK---NKVIDV 543
>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 685
Score = 27.3 bits (60), Expect = 6.7
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 55 RPVRNKSIKVHGSVLINFQY-------SMAVFSTGERKTRPRGDRKTSEISLQLRQAVSA 107
+++ + + + V +T E K + R S+I+L++
Sbjct: 473 EKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALK 532
Query: 108 AIMSEVHPRSQIDI 121
IMS+ ID+
Sbjct: 533 QIMSK---NKVIDV 543
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 665
Score = 26.9 bits (59), Expect = 9.1
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 55 RPVRNKSIKVHGSVLINFQY-------SMAVFSTGERKTRPRGDRKTSEISLQLRQAVSA 107
+++ + + + V +T E K + R S+I+L++
Sbjct: 473 EKGKSEGVATGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIALK 532
Query: 108 AIMSEVHPRSQIDI 121
IMS+ ID+
Sbjct: 533 QIMSK---NKVIDV 543
>4fce_A Bifunctional protein GLMU; GLMU. csgid, niaid, structural genomics,
national institute allergy and infectious diseases; HET:
GP1; 1.96A {Yersinia pseudotuberculosis} PDB: 3fww_A
1hv9_A* 2oi5_A* 2oi6_A* 2oi7_A* 1fxj_A* 1fwy_A*
Length = 459
Score = 26.7 bits (60), Expect = 9.2
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 147 AGIPMREYVVACSASLAGDTPLVDISH----LEETLGGPNLTVA 186
AG PM ++V+ + L + H L++TL P+L
Sbjct: 34 AGKPMVQHVIDAAMKLGAQHVHLVYGHGGELLKKTLADPSLNWV 77
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 0.135 0.387
Gapped
Lambda K H
0.267 0.0839 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,934,961
Number of extensions: 236242
Number of successful extensions: 572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 512
Number of HSP's successfully gapped: 54
Length of query: 263
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 171
Effective length of database: 4,133,061
Effective search space: 706753431
Effective search space used: 706753431
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: 56 (25.1 bits)