RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit epsilon [Candidatus Liberibacter asiaticus str. psy62] (245 letters) >2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* Length = 194 Score = 126 bits (316), Expect = 6e-30 Identities = 77/190 (40%), Positives = 115/190 (60%), Gaps = 13/190 (6%) Query: 7 MRKIVFDIETTGLD-----SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALK 61 R+IV D ETTG++ + +IIEIGAVE+++ T F V+L P R PEA Sbjct: 9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKP-DRLVDPEAFG 67 Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP- 120 +HGI DEFL DKP+F+ + EF D+ + AE + HNA FD+GF++ E + +D Sbjct: 68 VHGIADEFLLDKPTFAEVADEFMDYI--RGAELVIHNAAFDIGFMDYEFSLLKRDIPKTN 125 Query: 121 --SRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGG 178 ++ D+L++AR+ P RN L++LC RY I S R+ HGALLD+ +L++VY+ M G Sbjct: 126 TFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMT--G 183 Query: 179 SQINFGFKTN 188 Q + + + Sbjct: 184 GQTSMATRES 193 >2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Length = 224 Score = 108 bits (271), Expect = 1e-24 Identities = 26/181 (14%), Positives = 57/181 (31%), Gaps = 18/181 (9%) Query: 10 IVFDIETTGLDSKND--RIIEIGAVELLDYS-KTNRTFQVFLCP-NGRKNSPEALKLHGI 65 +V D E T + IIE ++L + + TF +++ P + +P +L GI Sbjct: 34 LVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGI 93 Query: 66 TDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF---------INAELQRINKD 116 + +PS + ++ + N K + + Q + Sbjct: 94 IQAMVDGQPSLQQVLERVDEWM--AKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLP 151 Query: 117 -PLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174 + I+ L + K + R H + D ++++ + Sbjct: 152 VADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGR-PHSGIDDCKNIANIMKTL 210 Query: 175 M 175 Sbjct: 211 A 211 >2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase, stable RNA maturation, tRNA END-turnover; 3.10A {Escherichia coli K12} Length = 215 Score = 105 bits (263), Expect = 8e-24 Identities = 38/188 (20%), Positives = 70/188 (37%), Gaps = 16/188 (8%) Query: 4 KNKMRK---IVFDIETTGLDSKNDRIIEIGAVELLDYSKTN-----RTFQVFLCPNGRKN 55 ++ R +V D+ET G ++K D ++EI A+ L + G Sbjct: 11 CDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANL 70 Query: 56 SPEALKLHG-ITDEFLKDKPSFSSIFSEFWDFFNE-------QNAEWIAHNAKFDVGFIN 107 PEAL +G ++ + S E + + A +AHNA FD F+ Sbjct: 71 QPEALAFNGIDPNDPDRGAVSEYEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMM 130 Query: 108 AELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167 A +R + + A + L+ C+ G+ H AL D+ Sbjct: 131 AAAERASLKRNPFHPFATFDTAALAGLALGQTVLSKACQTAGMDFDSTQAHSALYDTERT 190 Query: 168 SDVYIKMM 175 + ++ +++ Sbjct: 191 AVLFCEIV 198 >1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Length = 349 Score = 103 bits (259), Expect = 3e-23 Identities = 35/199 (17%), Positives = 69/199 (34%), Gaps = 20/199 (10%) Query: 10 IVFDIETTGLDSKN----DRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63 + D E T + IIE V L + TFQ ++ P S + L Sbjct: 131 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 190 Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD------- 116 GIT + + +F + + D + E + + ++ + Sbjct: 191 GITQDQVDRADTFPQVLKKVIDLM--KLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRL 248 Query: 117 --PLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 P + I+ K P S+ L + ++ G+ R H L DS ++ + + Sbjct: 249 KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PHCGLDDSKNIARIAV 307 Query: 173 KMMVGGSQINFGFKTNEDR 191 +M+ G ++ K + + Sbjct: 308 RMLQDGCELRINEKMHAGQ 326 >2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI, MCSG, protein structure initiative; 2.09A {Pseudomonas aeruginosa PAO1} SCOP: c.55.3.5 Length = 224 Score = 102 bits (253), Expect = 1e-22 Identities = 44/188 (23%), Positives = 75/188 (39%), Gaps = 17/188 (9%) Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSK----TNRTFQVFLCPN-GRKNSP 57 R +V D+ET G +S D ++EI A + K T+ + P G P Sbjct: 25 RFRGYLPVVVDVETGGFNSATDALLEIAATTVGMDEKGFLFPEHTYFFRIEPFEGANIEP 84 Query: 58 EALKLHGITDEFLKDK-----PSFSSIFSEFWDFFNEQ---NAEWIAHNAKFDVGFINAE 109 AL+ GI + + + IF A + HN+ FD+GF+NA Sbjct: 85 AALEFTGIKLDHPLRMAVQEEAALTEIFRGIRKALKANGCKRAILVGHNSSFDLGFLNAA 144 Query: 110 LQRINKD--PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167 + R P P DT ++A + + L C+ G+ +R H A D+ Sbjct: 145 VARTGIKRNPFHPFSSFDTATLAGLAYG--QTVLAKACQAAGMEFDNREAHSARYDTEKT 202 Query: 168 SDVYIKMM 175 ++++ ++ Sbjct: 203 AELFCGIV 210 >1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Length = 238 Score = 99.7 bits (247), Expect = 5e-22 Identities = 35/195 (17%), Positives = 61/195 (31%), Gaps = 31/195 (15%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN--------------GRKN 55 + D+E TGL S I E+ + S N R Sbjct: 13 VFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPF 72 Query: 56 SPEALKLHGITDEFLKDKPSF---SSIFSEFWDFFNEQNAEWI---AHNAKFDVGFINAE 109 + +A ++ G++ E L ++ F + Q + +D + AE Sbjct: 73 TAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAE 132 Query: 110 LQRINKDPLDPSRIIDTLSIARRKHPSSRNDLN----------SLCKRYGITISHRSKHG 159 L+R+ + +DTL R + + SL RY + H Sbjct: 133 LRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFR-AEPSAAHS 191 Query: 160 ALLDSHLLSDVYIKM 174 A D H L +++ Sbjct: 192 AEGDVHTLLLIFLHR 206 >3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Length = 308 Score = 99.0 bits (246), Expect = 7e-22 Identities = 27/195 (13%), Positives = 66/195 (33%), Gaps = 25/195 (12%) Query: 10 IVFDIETTGLDSKNDR---IIEIGAVELLDYSK---TNRTFQVFLCPN-GRKNSPEALKL 62 ++ D ETT + D +I+ V + + +F ++ P R + + Sbjct: 22 LILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDF 81 Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDV-------GFINAELQRINK 115 GI + +F ++ +F + F +++ N Sbjct: 82 TGIPQRSIDTADTFDVVYEQFQQWL--ITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNI 139 Query: 116 D-PLDPSRIIDT-------LSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLL 167 P + I+ + K S+ ++ + + Y + R H A+ D + Sbjct: 140 QMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGR-AHDAMDDCLNI 198 Query: 168 SDVYIKMMVGGSQIN 182 + + +M+ G+++ Sbjct: 199 ATILQRMINMGAKVT 213 >2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus musculus} SCOP: c.55.3.5 PDB: 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Length = 242 Score = 97.7 bits (242), Expect = 2e-21 Identities = 37/197 (18%), Positives = 66/197 (33%), Gaps = 32/197 (16%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPN-----------------G 52 I D+E TGL S + E+ + + + N + P G Sbjct: 15 IFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPG 74 Query: 53 RKNSPEALKLHGITDEFLKDKP--SFSSIFSEFWDFFN---EQNAEWIAHNAKFDV-GFI 106 + SP A ++ G++ L+ + F + F Q +AHN + Sbjct: 75 KACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLL 134 Query: 107 NAELQRINKD-PLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGIT--------ISHRSK 157 EL R++ PLD + +D+++ + +S N K Y + + Sbjct: 135 QTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDS 194 Query: 158 HGALLDSHLLSDVYIKM 174 H A D L + Sbjct: 195 HTAEGDVLTLLSICQWK 211 >1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} Length = 299 Score = 94.8 bits (235), Expect = 2e-20 Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 16/189 (8%) Query: 10 IVFDIETT----GLDSKNDRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63 + D E T IIE V L + TFQ ++ P S + L Sbjct: 81 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 140 Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQ------NAEWIAHNAKFDVGFINAELQRINKD- 116 GIT + + +F + + D + + + F+N + Q Sbjct: 141 GITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKY 200 Query: 117 PLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKM 174 P + I+ K P S+ L + ++ G+ R + L DS ++ + ++M Sbjct: 201 PPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PNCGLDDSKNIARIAVRM 259 Query: 175 MVGGSQINF 183 + G ++ Sbjct: 260 LQDGCELRI 268 >1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Length = 204 Score = 84.2 bits (207), Expect = 2e-17 Identities = 35/191 (18%), Positives = 66/191 (34%), Gaps = 20/191 (10%) Query: 10 IVFDIETT----GLDSKNDRIIEIGAVEL-LDYSKTNRTFQVFLCPNGRKN-SPEALKLH 63 + D E T IIE V L + TFQ ++ P S + L Sbjct: 13 CIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLT 72 Query: 64 GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRI 123 GIT + + +F + + D+ + E + + ++ + SR+ Sbjct: 73 GITQDQVDRADTFPQVLKKVIDWM--KLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRL 130 Query: 124 -----------IDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 I K P S+ L + ++ G+ R H L DS ++ + + Sbjct: 131 KYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGR-PHCGLDDSKNIARIAV 189 Query: 173 KMMVGGSQINF 183 +M+ G ++ Sbjct: 190 RMLQDGCELRI 200 >2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Length = 186 Score = 81.7 bits (200), Expect = 1e-16 Identities = 49/166 (29%), Positives = 84/166 (50%), Gaps = 7/166 (4%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 +V D ETTGLD + D IIEIGAV++ + L R+ S ++ ++ GIT E Sbjct: 15 VVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDE--YHTLIKPSREISRKSSEITGITQEM 72 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129 L++K S + EF F + +AHNA FD F+ ++++ IDTL++ Sbjct: 73 LENKRSIEEVLPEFLGFLEDS--IIVAHNANFDYRFLRLWIKKVMGLD-WERPYIDTLAL 129 Query: 130 ARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175 A+ L+S+ ++ G+ H AL D+ + + V+++ + Sbjct: 130 AKSLLKLRSYSLDSVVEKLGLGPFRH--HRALDDARVTAQVFLRFV 173 >2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, product bound structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A Length = 482 Score = 78.5 bits (192), Expect = 1e-15 Identities = 24/120 (20%), Positives = 41/120 (34%), Gaps = 4/120 (3%) Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLC--PNGRKNSPEAL 60 K + + D ET G DR + A+ +VF C + P A+ Sbjct: 5 GKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAV 64 Query: 61 KLHGITDEFLKDKP-SFSSIFSEFWDFFNEQNAEWIAHN-AKFDVGFINAELQRINKDPL 118 + GIT + + K + ++ + F + +N +FD R DP Sbjct: 65 LITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPY 124 >1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Length = 189 Score = 66.5 bits (161), Expect = 5e-12 Identities = 24/169 (14%), Positives = 54/169 (31%), Gaps = 13/169 (7%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 + D E GL + + ++ + + F+ P + + ++ G+T + Sbjct: 8 VAMDCEMVGLGPHRESGLARCSLVNVH---GAVLYDKFIRPE-GEITDYRTRVSGVTPQH 63 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129 + F+ E + + H+ K D + ++ D L Sbjct: 64 MVGATPFAVARLEILQLLKGKL--VVGHDLKHDFQALKEDMSGYTIYD----TSTDRLLW 117 Query: 130 ARRK-HPSSRNDLNSLCKRY-GITI-SHRSKHGALLDSHLLSDVYIKMM 175 K R L L +R +I + H ++ D+ ++Y Sbjct: 118 REAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQ 166 >2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Length = 180 Score = 63.5 bits (153), Expect = 4e-11 Identities = 25/169 (14%), Positives = 46/169 (27%), Gaps = 17/169 (10%) Query: 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAV-------ELLDYSKTNRTFQVFLCPNGRKNS 56 N+ I D+E TGLD + DRIIEI + L + + Sbjct: 2 ANENNLIWIDLEMTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWN 61 Query: 57 PEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKD 116 G+ + +F + + +G L + + Sbjct: 62 VRTHTASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPICGNSIGQDRRFLFKYMPE 121 Query: 117 PLDPS--RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163 R +D ++ L+ + + H A+ D Sbjct: 122 LEAYFHYRYLDVSTLKELARRWKPEILDG--------FTKQGTHQAMDD 162 >2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY diffraction, hydrolase; 2.30A {Xanthomonas campestris PV} Length = 194 Score = 57.7 bits (138), Expect = 2e-09 Identities = 28/165 (16%), Positives = 50/165 (30%), Gaps = 17/165 (10%) Query: 8 RKIVFDIETTGLDSKNDRIIEIGAV-------ELLDYSKTNRTFQVFLCPNGRKNSPEAL 60 R I D+E TGLD+ D IIEI + L + + + + + Sbjct: 10 RLIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQH 69 Query: 61 KLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDP 120 + G+ L + + + ++ F E + + L R Sbjct: 70 RRSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERY 129 Query: 121 S--RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLD 163 R +D +I + + + S H AL D Sbjct: 130 FHYRNLDVSTIKELARRWAPAVASG--------FAKSSAHTALSD 166 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 44.5 bits (105), Expect = 2e-05 Identities = 40/234 (17%), Positives = 75/234 (32%), Gaps = 70/234 (29%) Query: 57 PEALKLHG--ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN 114 P A + ++F K P + F+ + AE + KF +G++++ ++ Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAADDEP--TTPAELVG---KF-LGYVSSLVE--- 73 Query: 115 KDPLDPSRIIDTL------------------SIARRKHPSSRNDL---NSLCKRY----- 148 P + L ++A + + L L K Y Sbjct: 74 --PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI 131 Query: 149 ----GITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFGFKTNEDRFFKE--EKKTV-- 200 S AL + + + + GG Q G N D +F+E + Sbjct: 132 MAKRPFDKKSNS---ALFRAVGEGNAQLVAIFGG-Q---G---NTDDYFEELRDLYQTYH 181 Query: 201 PNI-SLLKRDKPLFTRITKEELDEHDKTIQTLGKNAI-W--------DR-YISS 243 + L+K + + + LD + T G N + W D+ Y+ S Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEK--VFTQGLNILEWLENPSNTPDKDYLLS 233 Score = 31.8 bits (72), Expect = 0.15 Identities = 20/88 (22%), Positives = 31/88 (35%), Gaps = 31/88 (35%) Query: 25 RIIEIGAVE-LLDYSKTNRTF----QVFLC-PNGRKN-----SPEAL-----KLHGI--- 65 + V+ ++ KTN QV + NG KN P++L L Sbjct: 342 SNLTQEQVQDYVN--KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399 Query: 66 --TDE----FLKDKPSFSS----IFSEF 83 D+ F + K FS+ + S F Sbjct: 400 SGLDQSRIPFSERKLKFSNRFLPVASPF 427 >1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A* Length = 698 Score = 40.1 bits (92), Expect = 5e-04 Identities = 25/133 (18%), Positives = 41/133 (30%), Gaps = 33/133 (24%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 IV DIE L + + T P+ +AL+ Sbjct: 2 IVSDIEANALLESVTKFHCGVIYDY----STAEYV--SYRPSDFGAYLDALEA------- 48 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFIN--AELQRINKDPLDPSRIIDT 126 + + HN K+DV + A+LQ + L IDT Sbjct: 49 -----------------EVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDT 91 Query: 127 LSIARRKHPSSRN 139 L ++R H + ++ Sbjct: 92 LVLSRLIHSNLKD 104 >2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Length = 605 Score = 39.4 bits (91), Expect = 8e-04 Identities = 24/174 (13%), Positives = 46/174 (26%), Gaps = 29/174 (16%) Query: 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHG 64 K FD ET LD+ + ++ + S P H Sbjct: 24 EKAPVFAFDTETDSLDNISANLVGL--------SFAIEPGVAAYIPVA----------HD 65 Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRII 124 D D+ S ++ A + N K+D G L + Sbjct: 66 YLDA--PDQISRERALELLKPLLEDEKALKVGQNLKYDRGI----LANYGIEL--RGIAF 117 Query: 125 DTLSIARRKHPSSRNDLNSLCKRYGI---TISHRSKHGALLDSHLLSDVYIKMM 175 DT+ + + + + TI+ G + + + ++ Sbjct: 118 DTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEA 171 >2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... Length = 580 Score = 35.4 bits (80), Expect = 0.012 Identities = 17/142 (11%), Positives = 37/142 (26%), Gaps = 39/142 (27%) Query: 9 KIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDE 68 K +E + + I+ I + N + FL P P+ Sbjct: 19 KAALVVEVVEENYHDAPIVGI--------AVVNEHGRFFLRPETALADPQ---------- 60 Query: 69 FLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLS 128 F + ++ + ++K + + + D L Sbjct: 61 --------------FVAWLGDETKKKSMFDSKRAAVALKWKGIELC------GVSFDLLL 100 Query: 129 IARRKHPS-SRNDLNSLCKRYG 149 A P+ +D+ + K Sbjct: 101 AAYLLDPAQGVDDVAAAAKMKQ 122 >3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} Length = 440 Score = 35.4 bits (81), Expect = 0.012 Identities = 24/112 (21%), Positives = 42/112 (37%), Gaps = 25/112 (22%) Query: 81 SEFWDFFNE--QNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSR 138 W+ FN +A WI H++ D+ + ++P R+ DT AR Sbjct: 81 GADWNDFNRAVGDAVWILHDSLQDLPG----FDELG---MEPQRLFDTEIAARLLGLKRF 133 Query: 139 NDLNSLCKRY-GITISHRSKHG--------------ALLDSHLLSDVYIKMM 175 L ++ + + G+T++ A LD LL ++ KM Sbjct: 134 G-LAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMR 184 >3pbh_A Procathepsin B; thiol protease, cysteine protease, proenzyme, papain; 2.50A {Homo sapiens} SCOP: d.3.1.1 PDB: 2pbh_A 1pbh_A 1mir_A Length = 317 Score = 28.0 bits (61), Expect = 1.8 Identities = 9/36 (25%), Positives = 20/36 (55%) Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF 105 ++ +PSF + E ++ N++N W A + ++V Sbjct: 1 MRSRPSFHPLSDELVNYVNKRNTTWQAGHNFYNVDM 36 >2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A* Length = 575 Score = 27.0 bits (59), Expect = 3.5 Identities = 20/137 (14%), Positives = 39/137 (28%), Gaps = 3/137 (2%) Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPS 121 +G + + + EF + + A+ HN KF FI L+R N Sbjct: 26 AYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLER-NGFKWSAD 84 Query: 122 RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDV--YIKMMVGGS 179 + +T + + L + I + + K+ V Sbjct: 85 GLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKG 144 Query: 180 QINFGFKTNEDRFFKEE 196 I++ + E Sbjct: 145 DIDYHKERPVGYKITPE 161 >2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A Length = 293 Score = 26.5 bits (57), Expect = 5.6 Identities = 9/80 (11%), Positives = 27/80 (33%), Gaps = 1/80 (1%) Query: 145 CKRYGITISHRSKHGALLDSHLLSDV-YIKMMVGGSQINFGFKTNEDRFFKEEKKTVPNI 203 + + + G ++ ++ ++ + F + K K T P + Sbjct: 190 LHKTAALLEASAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDDILDVTKSSKLTYPKL 249 Query: 204 SLLKRDKPLFTRITKEELDE 223 L++ + ++ E D+ Sbjct: 250 MGLEKSREFAEKLNTEARDQ 269 >3lji_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.39A {Pseudomonas fluorescens} Length = 304 Score = 26.4 bits (57), Expect = 6.0 Identities = 10/57 (17%), Positives = 16/57 (28%), Gaps = 5/57 (8%) Query: 178 GSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKE---ELDEHDKTIQTL 231 G + D +K T P + L K + + L D + L Sbjct: 230 SDTATLGKRQGAD--IARDKPTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPL 284 >3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* Length = 304 Score = 26.2 bits (57), Expect = 6.4 Identities = 10/57 (17%), Positives = 16/57 (28%), Gaps = 5/57 (8%) Query: 178 GSQINFGFKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKE---ELDEHDKTIQTL 231 G + D +K T P + L K + + L D + L Sbjct: 230 SDTATLGKRQGAD--IARDKPTYPALLGLAAAKEYALELRDQALHALRPFDAAAEPL 284 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Length = 578 Score = 26.4 bits (58), Expect = 6.9 Identities = 7/36 (19%), Positives = 15/36 (41%), Gaps = 1/36 (2%) Query: 96 AHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIAR 131 AH + + + K L P+ ++++L A Sbjct: 517 AHVPG-GLRDARYGVMQARKAGLTPAHVVNSLGRAE 551 >3nae_A DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 DOC DTP; 2.00A {Enterobacteria phage RB69} PDB: 3lzi_A* 3lzj_A* 1ig9_A* 1q9x_A* 2atq_A* 2dy4_A* 2oyq_A* 2ozm_A* 2ozs_A* 2p5g_A* 2p5o_A* 1q9y_A* 3l8b_A* 3lds_A* 3cq8_A* 1ih7_A* 1clq_A* 1waf_A* 1waj_A* 3cfr_A* ... Length = 903 Score = 26.1 bits (56), Expect = 7.8 Identities = 19/111 (17%), Positives = 31/111 (27%), Gaps = 10/111 (9%) Query: 4 KNKMRKIVFDIETTGLD------SKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSP 57 K+R FDIE T D I I F + P G Sbjct: 105 HTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHY--DSIDDRFYVFDLLNSPYGNVEEW 162 Query: 58 EALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQN--AEWIAHNAKFDVGFI 106 + ++ + PS + F NE+ E++ + + Sbjct: 163 SIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVIL 213 >2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Length = 333 Score = 26.0 bits (57), Expect = 8.3 Identities = 24/140 (17%), Positives = 52/140 (37%), Gaps = 27/140 (19%) Query: 55 NSPEALKLHGITDEFLKDKPSFSSIFSEF---WDFFNEQNAEWIAHNAKFDVGFINAELQ 111 S E L GI + ++ + F+E ++ WI ++ +D ++ L+ Sbjct: 122 ESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYL---LK 178 Query: 112 RINKDPLDPS--------------RIIDTLSIARRKHPSSRNDLNSLCKRYGITISHR-- 155 + + PL P+ + D I + ++ L + I HR Sbjct: 179 AMTQIPL-PAEYEEFYKILCIYFPKNYDIKYIMKSVL-NNSKGLQDIADDLQI---HRIG 233 Query: 156 SKHGALLDSHLLSDVYIKMM 175 +H A D+ L + ++ ++ Sbjct: 234 PQHQAGSDALLTARIFFEIR 253 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.319 0.136 0.398 Gapped Lambda K H 0.267 0.0439 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,150,030 Number of extensions: 98733 Number of successful extensions: 388 Number of sequences better than 10.0: 1 Number of HSP's gapped: 361 Number of HSP's successfully gapped: 49 Length of query: 245 Length of database: 5,693,230 Length adjustment: 90 Effective length of query: 155 Effective length of database: 3,511,270 Effective search space: 544246850 Effective search space used: 544246850 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: 55 (25.7 bits)