RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Length = 226 Score = 181 bits (460), Expect = 1e-46 Identities = 84/204 (41%), Positives = 133/204 (65%), Gaps = 1/204 (0%) Query: 21 TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80 T +++ + +P EL + N F L++AV+LSAQ TD VNK TK LFE TP Sbjct: 6 TKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTP 65 Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140 +A+ ++L+ IR+IG+YR K+ NI L +LI++++ ++P+ + L +LPG+GRK Sbjct: 66 HDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKT 125 Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPG-KTPNKVEQSLLRIIPPKHQYNAHYWLV 199 ANV++S+AFG+P I VDTH+ R+S R+G + +VE++L++IIP + H+ ++ Sbjct: 126 ANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMI 185 Query: 200 LHGRYVCKARKPQCQSCIISNLCK 223 GRY CKA+ PQC SC + +LC+ Sbjct: 186 FFGRYHCKAQSPQCPSCPLLHLCR 209 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Length = 221 Score = 164 bits (417), Expect = 1e-41 Identities = 41/211 (19%), Positives = 98/211 (46%), Gaps = 8/211 (3%) Query: 21 TPKELEEIFYLFSLKW-PSPKGELYYVNH---FTLIVAVLLSAQSTDVNVNKATKHLFEI 76 + ++F L + + + + + + + +++ +L ++T +V K F Sbjct: 4 ATNKKRKVFVSTILTFWNTDRRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVK 63 Query: 77 ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGI 136 + +L + ++ I+ IG+ +++E + L+ ++IN++ ++P+ + + LPG+ Sbjct: 64 YKCFEDILKTPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGV 123 Query: 137 GRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLR----IIPPKHQY 192 G+ ++ +AFG VD + R+ NR + N ++L ++P Sbjct: 124 GKYTCAAVMCLAFGKKAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCR 183 Query: 193 NAHYWLVLHGRYVCKARKPQCQSCIISNLCK 223 + + L+ +C RKP+C+ C +S LC Sbjct: 184 DFNLGLMDFSAIICAPRKPKCEKCGMSKLCS 214 >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Length = 225 Score = 153 bits (387), Expect = 4e-38 Identities = 35/182 (19%), Positives = 70/182 (38%), Gaps = 6/182 (3%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSE 106 + + ++ ++ Q+ V + T + ++ + +G Y + Sbjct: 29 TPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARAR- 87 Query: 107 NIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR 166 N+ + + K P+T E + LPG+GR A ILS++ G +D ++ R+ R Sbjct: 88 NLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLAR 147 Query: 167 IGLAPGKTPNKVEQSLLR-----IIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNL 221 G K ++ L + P + ++ G +C KP+C C + N Sbjct: 148 CYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNG 207 Query: 222 CK 223 C Sbjct: 208 CI 209 >3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Length = 369 Score = 149 bits (377), Expect = 4e-37 Identities = 37/182 (20%), Positives = 79/182 (43%), Gaps = 6/182 (3%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSE 106 + + + V+ ++ Q+ V + + T + + E ++ +G Y + Sbjct: 38 DPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVR- 96 Query: 107 NIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR 166 N+ + + + K+P + +RL G+G +LS+A+G+P VD ++ R+ +R Sbjct: 97 NLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSR 156 Query: 167 IGLAPGK-----TPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNL 221 + L T + EQ + I+ ++ + L+ G VC R+P C C + Sbjct: 157 LFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAY 216 Query: 222 CK 223 C+ Sbjct: 217 CQ 218 >1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Length = 218 Score = 142 bits (359), Expect = 6e-35 Identities = 33/190 (17%), Positives = 72/190 (37%), Gaps = 28/190 (14%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEI-------ADTPQKMLAIGEKKLQNYIRTIG 99 F ++ +L+ + V K+ ++L +K+ I KL +R G Sbjct: 29 LKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSG 88 Query: 100 IYRKKSENIISLSHILINEFDN----KIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIG 155 Y +K++ +I LS ++ +F + K T E L GIG++ A+ IL A + Sbjct: 89 FYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMV 148 Query: 156 VDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNA----------------HYWLV 199 VD + + ++G+ + ++++ + + H +V Sbjct: 149 VDKYSYLFLKKLGIEI-EDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIV 207 Query: 200 LHGRYVCKAR 209 + + + Sbjct: 208 EFSKQKLELK 217 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Length = 211 Score = 133 bits (334), Expect = 4e-32 Identities = 99/203 (48%), Positives = 139/203 (68%) Query: 21 TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80 + EI P P EL + + F L++AVLLSAQ+TDV+VNKAT L+ +A+TP Sbjct: 2 NKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTP 61 Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140 ML +G + ++ YI+TIG+Y K+ENII IL+ + + ++P+ L LPG+GRK Sbjct: 62 AAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKT 121 Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVL 200 ANV+L+ AFG PTI VDTHIFR+ NR APGK +VE+ LL+++P + + + H+WL+L Sbjct: 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLIL 181 Query: 201 HGRYVCKARKPQCQSCIISNLCK 223 HGRY C ARKP+C SCII +LC+ Sbjct: 182 HGRYTCIARKPRCGSCIIEDLCE 204 >3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Length = 287 Score = 132 bits (333), Expect = 7e-32 Identities = 34/198 (17%), Positives = 71/198 (35%), Gaps = 7/198 (3%) Query: 33 SLKW--PSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKK 90 L W + + + V+ ++ Q+ V + T Q + + ++ Sbjct: 32 DLPWRRRAEDEMDLDRRAYAVWVSEVMLQQTQVATVINYYTGWMQKWPTLQDLASASLEE 91 Query: 91 LQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG 150 + +G Y + ++ + LPG+GR A I S+AFG Sbjct: 92 VNQLWAGLGYYSRGRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIAFG 151 Query: 151 IPTIGVDTHIFRISNRIGLAPGKTPNKVEQS-----LLRIIPPKHQYNAHYWLVLHGRYV 205 T VD ++ R+ R+ + + +++ P + + + G V Sbjct: 152 QATGVVDGNVARVLCRVRAIGADPSSTLVSQQLWGLAQQLVDPARPGDFNQAAMELGATV 211 Query: 206 CKARKPQCQSCIISNLCK 223 C ++P C C + +LC+ Sbjct: 212 CTPQRPLCSQCPVESLCR 229 >3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} Length = 214 Score = 112 bits (280), Expect = 9e-26 Identities = 27/159 (16%), Positives = 53/159 (33%), Gaps = 13/159 (8%) Query: 34 LKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQN 93 ++ F + +L+A T + K + + L + ++L+ Sbjct: 30 IQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQKEIGD------GFLTLPREELEE 83 Query: 94 YIRTIGI--YRKKSENIISLSHIL-----INEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 ++ +G YRK++E I+ + F+N+ + + GIG K A+ L Sbjct: 84 KLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLR 143 Query: 147 MAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRI 185 +D HI R + L I Sbjct: 144 NVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEI 182 >3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Length = 207 Score = 93.2 bits (231), Expect = 4e-20 Identities = 30/150 (20%), Positives = 56/150 (37%), Gaps = 16/150 (10%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGI--YRKK 104 F + LL+A S+ ++ +A L + K+ E++++N +++ Y K Sbjct: 32 VWFRELTLCLLTANSSFISAYQALNCLGQ------KIYYANEEEIRNILKSCKYRFYNLK 85 Query: 105 SENIISLSHILINEFDNKI--------PQTLEGLTRLPGIGRKGANVILSMAFGIPTIGV 156 ++ II + +I E L + GIG + A+ L + Sbjct: 86 AKYIIMAREKVYGRLKEEIKPLADEDQQLARERLLNIKGIGMQEASHFLRNVGYFDLAII 145 Query: 157 DTHIFRISNRIGLAPGKTPNKVEQSLLRII 186 D HI RIG ++ +SL Sbjct: 146 DRHIIDFMRRIGAIGETNVKQLSKSLYISF 175 >1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2 PDB: 3iho_A Length = 155 Score = 92.3 bits (229), Expect = 9e-20 Identities = 19/141 (13%), Positives = 49/141 (34%), Gaps = 15/141 (10%) Query: 35 KWPSPKG------ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGE 88 KW P+ E+ + + + L++A + +++ E + + A Sbjct: 12 KWTPPRSPFNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADW 71 Query: 89 KKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 + + ++ +G+Y +++ II S + + L GIG+ G + Sbjct: 72 RDVSELLKPLGLYDLRAKTIIKFSDEYLTKQ-------WRYPIELHGIGKYGNDSYRIFC 124 Query: 149 FG--IPTIGVDTHIFRISNRI 167 D + + + + Sbjct: 125 VNEWKQVHPEDHKLNKYHDWL 145 >1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A* ... Length = 317 Score = 74.0 bits (181), Expect = 3e-14 Identities = 27/192 (14%), Positives = 62/192 (32%), Gaps = 35/192 (18%) Query: 39 PKGELYYVNHFTLIVAVLLSAQSTDVNVNKATK---------------HLFEIADTPQKM 83 L + + + + S+ + + + + + Q + Sbjct: 120 QGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQAL 179 Query: 84 LAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKI----------PQTLEGLTRL 133 + +R +G+ + + + + ++ E + + L L Sbjct: 180 AGPEVEAH---LRKLGLGYRA-RYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCIL 235 Query: 134 PGIGRKGANVILSMAFGIP-TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQY 192 PG+G K A+ I MA P + V+ H++ I+ R T S P ++ Sbjct: 236 PGVGTKVADCICLMALDKPQAVPVEVHMWHIAQRDYSWHPTTSQAKGPS-----PQTNKE 290 Query: 193 NAHYWLVLHGRY 204 +++ L G Y Sbjct: 291 LGNFFRSLWGPY 302 >3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Length = 290 Score = 69.7 bits (170), Expect = 4e-13 Identities = 25/179 (13%), Positives = 59/179 (32%), Gaps = 28/179 (15%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHL--------------FEIADTPQKMLAIGEKKLQ 92 + F ++++ ++SA + + K ++ + T K+ EK Sbjct: 114 DPFEILLSFIISANNRIPMIKKCINNISEKAGKKLEYKGKIYYAFPTVDKLHEFTEK--- 170 Query: 93 NYIRTIGIYRKKSENIISLS-HILINEFD------NKIPQTLEGLTRLPGIGRKGANVIL 145 +++ + I E + + E L + G+G + A+ I+ Sbjct: 171 --DFEECTAGFRAKYLKDTVDRIYNGELNLEYIKSLNDNECHEELKKFMGVGPQVADCIM 228 Query: 146 SMAFGIP-TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGR 203 + VDT + + + +AP + K+ + A +L + R Sbjct: 229 LFSMQKYSAFPVDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGSLSGF-AQQYLFYYAR 286 >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 = 65.0 bits (158), Expect = 1e-11 Identities = 55/275 (20%), Positives = 91/275 (33%), Gaps = 112/275 (40%) Query: 16 LGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFT-LIVAVLLSAQST----DVNVNKAT 70 LG TP EL LK + G H L+ AV ++ + V+V KA Sbjct: 256 LGF--TPGELRS-----YLKGAT--G------HSQGLVTAVAIAETDSWESFFVSVRKAI 300 Query: 71 KHLFEI------------------AD-------TPQKMLAI---GEKKLQNYIRTIGIYR 102 LF I D P ML+I ++++Q+Y+ + Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL 360 Query: 103 KKSENIISLSHILINEFDNKI----PQTLEGL-TRLPGIGRKGANVILSMAFGIPTIGVD 157 + + +S L+N N + PQ+L GL L RK P+ G+D Sbjct: 361 PAGKQ-VEIS--LVNGAKNLVVSGPPQSLYGLNLTL----RK---------AKAPS-GLD 403 Query: 158 -THI-F-----RISNR---IGLAPGKTP------NKVEQSL-----------LRIIPPKH 190 + I F + SNR + +P + + + + L ++ IP Sbjct: 404 QSRIPFSERKLKFSNRFLPVA-SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ-IPVYD 461 Query: 191 QYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRI 225 ++ G + R I + I Sbjct: 462 TFD--------GSDL---R--VLSGSISERIVDCI 483 >2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Length = 295 Score = 60.5 bits (146), Expect = 3e-10 Identities = 37/185 (20%), Positives = 70/185 (37%), Gaps = 21/185 (11%) Query: 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIA--------------DTPQKMLAIGE 88 L ++ F I ++ Q + V K + T + +L G Sbjct: 113 LMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGV 172 Query: 89 KKLQNYIRTIGIYRKKSENIISLSHILINEFDNKI--PQTLEGLTRLPGIGRKGANVILS 146 + L R G+ R+K+E I+ ++ E + + E LT GIGR A ++LS Sbjct: 173 EGL----RECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLS 228 Query: 147 MAFGIPTIGV-DTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYV 205 +A G D + R +R+ + + + R + + ++L L+ R+ Sbjct: 229 IALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFF 288 Query: 206 CKARK 210 K + Sbjct: 289 SKKTE 293 >1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* Length = 282 Score = 36.1 bits (83), Expect = 0.006 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 9/81 (11%) Query: 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISL-----SHILINEFDNKIPQTLEGLTRL 133 TPQ++ A + L + +G+ K++E +I L L + Q ++ L Sbjct: 157 TPQRLAAADPQAL----KALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTF 212 Query: 134 PGIGRKGANVILSMAFGIPTI 154 PGIGR AN + + Sbjct: 213 PGIGRWTANYFALRGWQAKDV 233 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Length = 578 Score = 32.5 bits (74), Expect = 0.071 Identities = 10/79 (12%), Positives = 30/79 (37%), Gaps = 12/79 (15%) Query: 67 NKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQT 126 + ++H + ++ + + ++ YR + ++ L+ + P+ Sbjct: 6 DAPSRH--RLVHALERTADLLDILGGEDFKSRA-YRSAARSLEELNE--------ETPEL 54 Query: 127 L-EGLTRLPGIGRKGANVI 144 L T +P +G+ A + Sbjct: 55 LAREFTGIPKVGKGIAAEL 73 >2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Length = 335 Score = 32.4 bits (73), Expect = 0.087 Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 10/70 (14%) Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134 I D ++ + Q + YRK + I H + ++ +LP Sbjct: 14 GITDMLTELANFEKNVSQAIHKYNA-YRKAASVIAKYPHKI---------KSGAEAKKLP 63 Query: 135 GIGRKGANVI 144 G+G K A I Sbjct: 64 GVGTKIAEKI 73 >2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 1nzp_A* Length = 335 Score = 32.1 bits (72), Expect = 0.10 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 13/78 (16%) Query: 68 KATKHLFEIADTPQKMLAIGEKKLQNY-IRTIGIYRKKSENIISLSHILINEFDNKIPQT 126 KAT H I + + + + + Y K + S + + Sbjct: 8 KATNHNLHITEKLEVLAKAYSVQGDKWRALG---YAKAINALKSFHKPV---------TS 55 Query: 127 LEGLTRLPGIGRKGANVI 144 + +PGIG++ A I Sbjct: 56 YQEACSIPGIGKRMAEKI 73 >3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571 Score = 29.2 bits (65), Expect = 0.79 Identities = 20/105 (19%), Positives = 33/105 (31%), Gaps = 8/105 (7%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQ-NYIRTI--GIYRK 103 N T + + S ++ DV+ N + + N I I I Sbjct: 170 NQLTFLPELPESLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENRITHIPENILSL 229 Query: 104 KSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMA 148 I L N ++I ++L T P G + SM+ Sbjct: 230 DPTCTIILED---NPLSSRIRESLSQQTAQP--DYHGPRIYFSMS 269 >1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Length = 381 Score = 28.5 bits (63), Expect = 1.4 Identities = 13/84 (15%), Positives = 30/84 (35%), Gaps = 17/84 (20%) Query: 61 STDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFD 120 +T N N+ D + E + +N + + + S + SL + Sbjct: 30 TTLNNYNQ------LFTDALDILAENDELR-ENEGSCLA-FMRASSVLKSLPFPI----- 76 Query: 121 NKIPQTLEGLTRLPGIGRKGANVI 144 +++ +P +G K ++I Sbjct: 77 ----TSMKDTEGIPCLGDKVKSII 96 >1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Length = 228 Score = 27.5 bits (61), Expect = 2.3 Identities = 9/24 (37%), Positives = 14/24 (58%) Query: 118 EFDNKIPQTLEGLTRLPGIGRKGA 141 ++ + + L+RLPGIG K A Sbjct: 2 KYPPSLVSLIRELSRLPGIGPKSA 25 >2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Length = 360 Score = 27.4 bits (60), Expect = 2.5 Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 11/70 (15%) Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134 +++ + + + N R + + + + + SL + +L L LP Sbjct: 19 LLSEALETLAEAAGFE-ANEGRLLS-FSRAASVLKSLPCPV---------ASLSQLHGLP 67 Query: 135 GIGRKGANVI 144 G VI Sbjct: 68 YFGEHSTRVI 77 >3klk_A Glucansucrase; native form, open conformation, multidomain protein, glycosyltransferase, transferase; 1.65A {Lactobacillus reuteri} PDB: 3kll_A* 3hz3_A* Length = 1039 Score = 27.3 bits (60), Expect = 2.6 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 11/82 (13%) Query: 36 WPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKML--AIGEKK--- 90 WP+ + YY+N+ LL A + + + L ++ Q+ + I E Sbjct: 113 WPNTVTQAYYLNYMKQ-YGNLLPASLPSFSTDADSAELNHYSELVQQNIEKRISETGSTD 171 Query: 91 -----LQNYIRTIGIYRKKSEN 107 + ++ ++ K SEN Sbjct: 172 WLRTLMHEFVTKNSMWNKDSEN 193 >2qh9_A UPF0215 protein AF_1433; structural genomics, PSI-2, MCSG, protein structure initiative, midwest center for structural genomics; 1.80A {Archaeoglobus fulgidus} Length = 184 Score = 27.1 bits (60), Expect = 3.2 Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 4/28 (14%) Query: 133 LPGIGRKGANVI----LSMAFGIPTIGV 156 LPGI G N++ + IP + V Sbjct: 70 LPGITLGGFNLVDIQRVYRETKIPVVVV 97 >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 = 27.3 bits (59), Expect = 3.4 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 18/48 (37%) Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLE 128 +K A+ KKLQ ++ +Y S +L+ I T+E Sbjct: 18 EKQ-AL--KKLQASLK---LYADDSAP--ALA----------IKATME 47 >3g5c_A ADAM 22; alpha/beta fold, cross-linked domain, alternative splicing, cell adhesion, cleavage on PAIR of basic residues, EGF-like domain; HET: NAG; 2.36A {Homo sapiens} Length = 510 Score = 26.5 bits (57), Expect = 4.7 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 8/77 (10%) Query: 65 NVNKATKH--LFEIAD-TPQKMLAIGEKKLQNYIRTI-----GIYRKKSENIISLSHILI 116 NV + TK+ L + D K + Y +++ IY+ + + I L + Sbjct: 1 NVEEETKYIELMIVNDHLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMET 60 Query: 117 NEFDNKIPQTLEGLTRL 133 DNK + L L Sbjct: 61 WATDNKFAISENPLITL 77 >1ybe_A Naprtase, nicotinate phosphoribosyltransferase; structural genomics, protein structure initiative, NYSGXRC, PSI; 2.50A {Agrobacterium tumefaciens} SCOP: c.1.17.2 d.41.2.2 Length = 449 Score = 26.5 bits (58), Expect = 4.8 Identities = 6/21 (28%), Positives = 12/21 (57%) Query: 141 ANVILSMAFGIPTIGVDTHIF 161 +NV+L+M + +G + H Sbjct: 231 SNVLLAMDSDLEAVGTNAHEL 251 >2c36_A Glycoprotein D HSV-1; viral protein, immunoglobulin-like, transmembrane; HET: NAG MAN BMA NDG; 2.11A {Human herpesvirus 1} PDB: 2c3a_A* 1l2g_A* 1jma_A* Length = 285 Score = 26.5 bits (58), Expect = 5.9 Identities = 9/25 (36%), Positives = 12/25 (48%) Query: 184 RIIPPKHQYNAHYWLVLHGRYVCKA 208 R IP + A Y L + G + KA Sbjct: 200 RFIPENQRTVAVYSLKIAGWHGPKA 224 >1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Length = 203 Score = 25.9 bits (57), Expect = 7.1 Identities = 8/12 (66%), Positives = 10/12 (83%) Query: 130 LTRLPGIGRKGA 141 L +LPGIG+K A Sbjct: 110 LVKLPGIGKKTA 121 >2l4j_A YES-associated protein 2 (YAP2); WW domain, medaka, transcription; NMR {Oryzias latipes} Length = 46 Score = 25.7 bits (57), Expect = 8.6 Identities = 7/13 (53%), Positives = 11/13 (84%) Query: 38 SPKGELYYVNHFT 50 +P+GE+YY+NH Sbjct: 21 TPEGEIYYINHKN 33 >2kpz_A E3 ubiquitin-protein ligase NEDD4; WW domain, HTLV1, NEDD4, human modular domain, complex, HOST interaction, ligase; NMR {Homo sapiens} PDB: 2kq0_A Length = 49 Score = 25.8 bits (57), Expect = 9.6 Identities = 4/13 (30%), Positives = 9/13 (69%) Query: 38 SPKGELYYVNHFT 50 +P G ++++H T Sbjct: 22 APNGRPFFIDHNT 34 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 0.321 0.138 0.411 Gapped Lambda K H 0.267 0.0690 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,908,043 Number of extensions: 85674 Number of successful extensions: 345 Number of sequences better than 10.0: 1 Number of HSP's gapped: 328 Number of HSP's successfully gapped: 37 Length of query: 227 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 138 Effective length of database: 3,535,514 Effective search space: 487900932 Effective search space used: 487900932 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 (25.0 bits)