RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:1-23,A:110-225) Length = 139 Score = 113 bits (284), Expect = 2e-26 Identities = 29/118 (24%), Positives = 51/118 (43%), Gaps = 5/118 (4%) Query: 111 LSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLA 170 S +++ +D +TL + LPG+GR A ILS++ G +D ++ R+ R Sbjct: 6 FSAQVLDWYDKYGRKTLPEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAV 65 Query: 171 PGKT-----PNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCK 223 G NK+ ++ P + ++ G +C KP+C C + N C Sbjct: 66 SGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCI 123 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:23-133) Length = 111 Score = 109 bits (275), Expect = 2e-25 Identities = 55/111 (49%), Positives = 80/111 (72%) Query: 42 ELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIY 101 EL + + F L++AVLLSAQ+TDV+VNKAT L+ +A+TP ML +G + ++ YI+TIG+Y Sbjct: 1 ELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLY 60 Query: 102 RKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 K+ENII IL+ + + ++P+ L LPG+GRK ANV+L+ AFG P Sbjct: 61 NSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWP 111 >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:28-137) Length = 110 Score = 109 bits (273), Expect = 4e-25 Identities = 52/110 (47%), Positives = 79/110 (71%) Query: 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYR 102 L + N F L++AV+LSAQ TD VNK TK LFE TP +A+ ++L+ IR+IG+YR Sbjct: 1 LVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYR 60 Query: 103 KKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 K+ NI L +LI++++ ++P+ + L +LPG+GRK ANV++S+AFG+P Sbjct: 61 NKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGVP 110 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:29-139) Length = 111 Score = 102 bits (255), Expect = 4e-23 Identities = 21/106 (19%), Positives = 56/106 (52%) Query: 45 YVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKK 104 + + +++ +L ++T +V K F + +L + ++ I+ IG+ ++ Sbjct: 4 TRDPYVILITEILLRRTTAGHVKKIYDKFFVKYKCFEDILKTPKSEIAKDIKEIGLSNQR 63 Query: 105 SENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG 150 +E + L+ ++IN++ ++P+ + + LPG+G+ ++ +AFG Sbjct: 64 AEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVMCLAFG 109 >2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:1-49,A:127-233) Length = 156 Score = 102 bits (254), Expect = 5e-23 Identities = 15/107 (14%), Positives = 30/107 (28%), Gaps = 9/107 (8%) Query: 118 EFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPT-IGVDTHIFRISNRIGLAPGKTPN 176 + +E LT + GIG+ A + G + V + + G+ Sbjct: 51 LEGAEATTVIEKLTAIKGIGQWTAEXFXXFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDG 110 Query: 177 --KVEQSLLRIIPPK-----HQYNAHYWLVLHGRYVCKARKPQCQSC 216 + P + + + A R + + Q C Sbjct: 111 KKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHHGNQ-C 156 >2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} (A:1-22,A:134-211) Length = 100 Score = 98.4 bits (245), Expect = 7e-22 Identities = 40/71 (56%), Positives = 54/71 (76%) Query: 153 TIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQ 212 TI VDTHIFR+ NR APGK +VE+ LL+++P + + + H+WL+LHGRY C ARKP+ Sbjct: 23 TIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPR 82 Query: 213 CQSCIISNLCK 223 C SCII +LC+ Sbjct: 83 CGSCIIEDLCE 93 >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* (A:34-143) Length = 110 Score = 98.5 bits (245), Expect = 8e-22 Identities = 18/108 (16%), Positives = 45/108 (41%), Gaps = 1/108 (0%) Query: 45 YVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKK 104 + + + V+ ++ Q+ V + + T + + E ++ +G Y + Sbjct: 3 DRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRV 62 Query: 105 SENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 ++ + + K+P + +RL G+G +LS+A+G+P Sbjct: 63 RNLHAAVKEV-KTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVP 109 >1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} (A:1-28,A:140-221) Length = 110 Score = 96.6 bits (240), Expect = 3e-21 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 4/76 (5%) Query: 152 PTIGVDTHIFRISNRIGLAPGKTPNKVEQSL----LRIIPPKHQYNAHYWLVLHGRYVCK 207 P VD + R+ NR + N ++L ++P + + L+ +C Sbjct: 28 PAAMVDANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCRDFNLGLMDFSAIICA 87 Query: 208 ARKPQCQSCIISNLCK 223 RKP+C+ C +S LC Sbjct: 88 PRKPKCEKCGMSKLCS 103 >1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} (A:1-27,A:138-226) Length = 116 Score = 96.2 bits (239), Expect = 3e-21 Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 1/76 (1%) Query: 153 TIGVDTHIFRISNRIGLAPGK-TPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKP 211 I VDTH+ R+S R+G + +VE++L++IIP + H+ ++ GRY CKA+ P Sbjct: 28 AIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSP 87 Query: 212 QCQSCIISNLCKRIKQ 227 QC SC + +LC+ K+ Sbjct: 88 QCPSCPLLHLCREGKK 103 >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* (A:1-33,A:144-218) Length = 108 Score = 95.4 bits (237), Expect = 5e-21 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%) Query: 151 IPTIGVDTHIFRISNRIG-----LAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYV 205 +P VD ++ R+ +R+ +A T + EQ + I+ ++ + L+ G V Sbjct: 31 LPWPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALV 90 Query: 206 CKARKPQCQSCIISNLCK 223 C R+P C C + C+ Sbjct: 91 CTPRRPSCLLCPVQAYCQ 108 >1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} (A:1-129) Length = 129 Score = 94.7 bits (235), Expect = 9e-21 Identities = 16/116 (13%), Positives = 42/116 (36%), Gaps = 7/116 (6%) Query: 37 PSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIR 96 + E+ + + + L++A + +++ E + + A + + ++ Sbjct: 20 FNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLK 79 Query: 97 TIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 +G+Y +++ II S D + + L GIG+ G + Sbjct: 80 PLGLYDLRAKTIIKFS-------DEYLTKQWRYPIELHGIGKYGNDSYRIFCVNEW 128 >1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} (A:23-145) Length = 123 Score = 93.5 bits (232), Expect = 2e-20 Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 11/115 (9%) Query: 49 FTLIVAVLLSAQSTDVNVNKATKHLFE-------IADTPQKMLAIGEKKLQNYIRTIGIY 101 F ++ +L+ + V K+ ++L +K+ I KL +R G Y Sbjct: 9 FEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFY 68 Query: 102 RKKSENIISLSHILINEFDN----KIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 +K++ +I LS ++ +F + K T E L GIG++ A+ IL A Sbjct: 69 NQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKE 123 >1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} (A:24-109) Length = 86 Score = 87.5 bits (217), Expect = 1e-18 Identities = 10/84 (11%), Positives = 29/84 (34%), Gaps = 1/84 (1%) Query: 45 YVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKK 104 + + ++ ++ Q+ V + T + ++ + +G Y + Sbjct: 4 DKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYA-R 62 Query: 105 SENIISLSHILINEFDNKIPQTLE 128 + N+ + + K P+T E Sbjct: 63 ARNLHKAAQQVATLHGGKFPETFE 86 >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} (A:123-255) Length = 133 Score = 85.9 bits (212), Expect = 4e-18 Identities = 16/131 (12%), Positives = 36/131 (27%), Gaps = 21/131 (16%) Query: 43 LYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGE-----------KKL 91 L + + + + S+ + + + L + L Sbjct: 2 LLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPE 61 Query: 92 QNYIRTIGIYRKKSENIISLSHILINEFDNKIP----------QTLEGLTRLPGIGRKGA 141 ++ + + + ++ E + + L LPG+G K A Sbjct: 62 VEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVA 121 Query: 142 NVILSMAFGIP 152 + I MA P Sbjct: 122 DCICLMALDKP 132 >1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} (A:105-231) Length = 127 Score = 85.4 bits (211), Expect = 5e-18 Identities = 20/120 (16%), Positives = 40/120 (33%), Gaps = 14/120 (11%) Query: 45 YVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKL---------QNYI 95 V+ F V +L + K T + ++ + Sbjct: 6 CVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQAL 65 Query: 96 RTIGIYRKKSENIISLSHILIN-----EFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG 150 + +G+ K++E +I L++ + + Q ++ L PGIGR AN + Sbjct: 66 KALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQ 125 >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} (A:38-150) Length = 113 Score = 80.6 bits (199), Expect = 1e-16 Identities = 19/114 (16%), Positives = 44/114 (38%), Gaps = 14/114 (12%) Query: 45 YVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGI--YR 102 F + +L+A T + K + + L + ++L+ ++ +G YR Sbjct: 4 NEEWFKELCFCILTANFTAEGGIRIQKEIGD------GFLTLPREELEEKLKNLGHRFYR 57 Query: 103 KKSENIISLSHILINEFDNKIPQT-----LEGLTRLPGIGRKGANVIL-SMAFG 150 K++E I+ + + + + + GIG K A+ L ++ + Sbjct: 58 KRAEYIVLARRFKNIKDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYD 111 >2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} (A:50-126) Length = 77 Score = 74.7 bits (184), Expect = 1e-14 Identities = 9/78 (11%), Positives = 28/78 (35%), Gaps = 3/78 (3%) Query: 49 FTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENI 108 F +V+ ++ Q + + + ++ + + +R G+ ++K E I Sbjct: 3 FQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYI 62 Query: 109 ISLSHILINEFDNKIPQT 126 + + ++ T Sbjct: 63 RHVCEHVE---SGRLDFT 77 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} (A:1-326) Length = 326 Score = 33.2 bits (75), Expect = 0.026 Identities = 15/97 (15%), Positives = 25/97 (25%), Gaps = 9/97 (9%) Query: 123 IPQTLEGLTR-LPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQS 181 +P L R + G + G AF + + I LAP + Q Sbjct: 150 LPLLLSNPPRNMIGQSQSGTGKTA--AFALTMLSRVDASVPKPQAICLAP--SRELARQ- 204 Query: 182 LLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCII 218 I+ + + + K I Sbjct: 205 ---IMDVVTEMGKYTEVKTAFGIKDSVPKGAKIDAQI 238 >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 (A:111-127,A:196-236) Length = 58 Score = 33.1 bits (76), Expect = 0.033 Identities = 5/24 (20%), Positives = 12/24 (50%) Query: 130 LTRLPGIGRKGANVILSMAFGIPT 153 L + G+G + A+ I+ + + Sbjct: 35 LKKFMGVGPQVADCIMLFSMQKYS 58 >2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* (A:240-306) Length = 67 Score = 30.0 bits (68), Expect = 0.31 Identities = 6/26 (23%), Positives = 11/26 (42%) Query: 130 LTRLPGIGRKGANVILSMAFGIPTIG 155 L LPG+G + + S ++ Sbjct: 4 LDDLPGVGHSTLSRLESTFDSPHSLN 29 >2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} (A:) Length = 87 Score = 29.3 bits (66), Expect = 0.40 Identities = 7/87 (8%), Positives = 22/87 (25%), Gaps = 18/87 (20%) Query: 58 SAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILIN 117 S + V N + + ++ ++K ++ L Sbjct: 6 SVRPLPVCPNP------LFVRWLTEWRDEAASRGRHTRFV---FQKALRSLQRYPLPL-- 54 Query: 118 EFDNKIPQTLEGLTRLPGIGRKGANVI 144 ++ + L G + ++ Sbjct: 55 -------RSGKEAKILQHFGDRLCRML 74 >1a59_A Citrate synthase; cold-activity; HET: COA CIT; 2.09A {Antarctic bacterium ds2-3r} (A:) Length = 378 Score = 29.1 bits (64), Expect = 0.50 Identities = 18/132 (13%), Positives = 44/132 (33%), Gaps = 8/132 (6%) Query: 63 DVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNK 122 D ++ + + +K++ G + +N + + + ++ + + Sbjct: 244 DEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALD------AMIKHYDRPE 297 Query: 123 IPQTLEGLTRLPGIGRKG-ANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQS 181 + GL ++ N+ +G DT +F G T + +EQ Sbjct: 298 MLGLYNGLEAAMEEAKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTAHIMEQV 357 Query: 182 L-LRIIPPKHQY 192 +I P +Y Sbjct: 358 ADNALIRPLSEY 369 >2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} (A:1-118) Length = 118 Score = 28.6 bits (64), Expect = 0.65 Identities = 8/70 (11%), Positives = 23/70 (32%), Gaps = 8/70 (11%) Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134 + ++ + + ++ YR + ++ L+ E T +P Sbjct: 12 RLVHALERTADLLDILGGEDFKSRA-YRSAARSLEELNE-ETPELL------AREFTGIP 63 Query: 135 GIGRKGANVI 144 +G+ A + Sbjct: 64 KVGKGIAAEL 73 Score = 26.3 bits (58), Expect = 3.4 Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 6/57 (10%) Query: 99 GIYRKKSENIISL----SHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI 151 + + + + + + ++P L L + G+G K + GI Sbjct: 64 KVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLA--GI 118 >2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} (A:1-119) Length = 119 Score = 27.9 bits (62), Expect = 1.2 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 16/84 (19%) Query: 61 STDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFD 120 + +N I D ++ + Q + YRK + I H + Sbjct: 6 APQETLNG------GITDMLTELANFEKNVSQAIHKYNA-YRKAASVIAKYPHKI----- 53 Query: 121 NKIPQTLEGLTRLPGIGRKGANVI 144 ++ +LPG+G K A I Sbjct: 54 ----KSGAEAKKLPGVGTKIAEKI 73 >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} (A:96-122,A:256-317) Length = 89 Score = 27.5 bits (61), Expect = 1.6 Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 5/34 (14%) Query: 156 VDTHIFRISNR-----IGLAPGKTPNKVEQSLLR 184 V+ H++ I+ R + K P+ L Sbjct: 31 VEVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELG 64 >3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} (A:) Length = 457 Score = 26.5 bits (56), Expect = 2.8 Identities = 1/27 (3%), Positives = 5/27 (18%), Gaps = 3/27 (11%) Query: 107 NIISLSHILINEFDNKIPQTLEGLTRL 133 + + + E + Sbjct: 433 YTFTSEN---GAIVGTVTTPFEAPQPI 456 >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 (A:81-110,A:237-290) Length = 84 Score = 26.6 bits (59), Expect = 3.0 Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 4/46 (8%) Query: 156 VDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPP----KHQYNAHYW 197 VDT + + + +AP + K+ QY +Y Sbjct: 34 VDTWVKKAMMSLYVAPDVSLKKIRDFGREKFGSLSGFAQQYLFYYA 79 >1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} (A:1-66) Length = 66 Score = 26.6 bits (59), Expect = 3.2 Identities = 9/23 (39%), Positives = 13/23 (56%) Query: 119 FDNKIPQTLEGLTRLPGIGRKGA 141 + + + L+RLPGIG K A Sbjct: 3 YPPSLVSLIRELSRLPGIGPKSA 25 >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 (A:112-130,A:199-234) Length = 55 Score = 26.3 bits (58), Expect = 3.6 Identities = 11/21 (52%), Positives = 14/21 (66%) Query: 130 LTRLPGIGRKGANVILSMAFG 150 LT GIGR A ++LS+A G Sbjct: 33 LTSFKGIGRWTAELVLSIALG 53 >2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} (A:1-128) Length = 128 Score = 26.3 bits (58), Expect = 4.0 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 >2jk8_A BEPA, putative cell filamentation protein (BEPA protein); T4SS, OB fold, FIC domain, substrate protein, protein translocation; 2.8A {Bartonella henselae} PDB: 2vy3_A 2vza_A* (A:186-302) Length = 117 Score = 26.0 bits (57), Expect = 4.2 Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 17/71 (23%) Query: 58 SAQSTDVNVNKATKHLFEIADTPQKMLAI----------GEKKLQNYIRTI-------GI 100 S + + +HLFE P+K+ + G + G Sbjct: 13 SVAVAENGDLEPMQHLFEDISNPEKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETYTGT 72 Query: 101 YRKKSENIISL 111 YR +L Sbjct: 73 YRGAGLEGFAL 83 >1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} (A:1-95) Length = 95 Score = 25.9 bits (57), Expect = 4.4 Identities = 10/82 (12%), Positives = 23/82 (28%), Gaps = 14/82 (17%) Query: 77 ADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHI--------------LINEFDNK 122 + +++ E + +KK + I S+ + + + Sbjct: 3 GEEVKEIDEFEELGFEPATEETPKKKKKEKIIRSIEDLPGVGPATAEKLREAGYDTLEAI 62 Query: 123 IPQTLEGLTRLPGIGRKGANVI 144 + L + GI A I Sbjct: 63 AVASPIELKEVAGISEGTALKI 84 >1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} (A:) Length = 191 Score = 26.1 bits (57), Expect = 4.7 Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 3/54 (5%) Query: 93 NYIRTIGIYRKKSENIISLSHILINEFDNKIPQ-TLEGLTRLPGIGRKGANVIL 145 + G+ K + + LS + + + LT G+GR+ A I Sbjct: 73 LLLSVSGVGPKVALAL--LSALPPRLLARALLEGDARLLTSASGVGRRLAERIA 124 >1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} (A:66-144) Length = 79 Score = 25.7 bits (57), Expect = 4.8 Identities = 8/16 (50%), Positives = 12/16 (75%) Query: 130 LTRLPGIGRKGANVIL 145 L +LPGIG+K A ++ Sbjct: 45 LVKLPGIGKKTAERLI 60 >2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A (A:80-154) Length = 75 Score = 25.7 bits (57), Expect = 5.0 Identities = 9/16 (56%), Positives = 14/16 (87%) Query: 130 LTRLPGIGRKGANVIL 145 LTR+PGIG++GA ++ Sbjct: 46 LTRVPGIGKRGAERMV 61 >2ysg_A Syntaxin-binding protein 4; synip, STXBP4, WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:) Length = 40 Score = 25.8 bits (57), Expect = 5.1 Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 10/39 (25%) Query: 12 GNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFT 50 G+S L P EE + + G Y++NH T Sbjct: 1 GSSGSSGL--PYGWEEAY--------TADGIKYFINHVT 29 >1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} (A:46-466) Length = 421 Score = 25.6 bits (54), Expect = 5.2 Identities = 5/28 (17%), Positives = 10/28 (35%), Gaps = 3/28 (10%) Query: 106 ENIISLSHILINEFDNKIPQTLEGLTRL 133 + + +L + K +E L L Sbjct: 1 DQVTTLQA---DRLGIKSIDGVEYLNNL 25 >2jxw_A WW domain-binding protein 4; WW domain containing protein, FBP21, WBP4, metal- binding, mRNA processing, mRNA splicing, nucleus, polymorphism; NMR {Homo sapiens} (A:39-75) Length = 37 Score = 25.8 bits (57), Expect = 5.8 Identities = 6/13 (46%), Positives = 6/13 (46%) Query: 38 SPKGELYYVNHFT 50 S G YY N T Sbjct: 15 SEDGFTYYYNTET 27 >1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} (U:48-134) Length = 87 Score = 25.4 bits (56), Expect = 5.8 Identities = 10/82 (12%), Positives = 26/82 (31%), Gaps = 30/82 (36%) Query: 58 SAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILIN 117 +A +++N F + G+Y ++ I+ Sbjct: 2 TAYGEKIDLNNTNIAAFI--------------------QYRGLYPTLAKLIV-------- 33 Query: 118 EFDNKIPQTLEGLTRLPGIGRK 139 N +++E + +PG+ + Sbjct: 34 --KNAPYESVEDVLNIPGLTER 53 >2ysb_A Salvador homolog 1 protein; WW domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:) Length = 49 Score = 25.5 bits (56), Expect = 6.0 Identities = 5/13 (38%), Positives = 9/13 (69%) Query: 38 SPKGELYYVNHFT 50 + +G YY++H T Sbjct: 21 TMRGRKYYIDHNT 33 >1ymz_A CC45; artificial protein, computational design, unknown function; NMR {Synthetic} (A:) Length = 43 Score = 25.5 bits (56), Expect = 6.6 Identities = 5/13 (38%), Positives = 8/13 (61%) Query: 38 SPKGELYYVNHFT 50 +G++YY N T Sbjct: 18 DVEGKVYYFNVRT 30 >1i5h_W Rnedd4, ubiquitin ligase NEDD4; NEDD4, WW domains, ENAC, PY motif, liddle syndrome, proline-rich, ligase; NMR {Rattus norvegicus} (W:) Length = 50 Score = 25.5 bits (56), Expect = 6.7 Identities = 3/13 (23%), Positives = 7/13 (53%) Query: 38 SPKGELYYVNHFT 50 G ++++NH Sbjct: 21 HTDGRVFFINHNI 33 >1ybe_A Naprtase, nicotinate phosphoribosyltransferase; structural genomics, protein structure initiative, NYSGXRC, PSI; 2.50A {Agrobacterium tumefaciens} (A:1-50,A:167-381) Length = 265 Score = 25.3 bits (55), Expect = 7.0 Identities = 6/21 (28%), Positives = 12/21 (57%) Query: 141 ANVILSMAFGIPTIGVDTHIF 161 +NV+L+M + +G + H Sbjct: 115 SNVLLAMDSDLEAVGTNAHEL 135 >1so7_A Sialidase 2; neuraminidase, ganglioside, sugar-induced form, hydrolase; 1.49A {Homo sapiens} (A:1-79,A:271-382) Length = 191 Score = 25.3 bits (55), Expect = 7.3 Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%) Query: 7 SDSYQGNSPLGCLYTPKELEEI-FYLFSLKW 36 G+ GCLY + EEI F +F+LK Sbjct: 152 GTGPDGSPLFGCLYEANDYEEIVFLMFTLKQ 182 >1ywi_A Formin-binding protein 3; WW domain, class II, proline-rich peptides, protein-protein interactions, structural protein; NMR {Homo sapiens} (A:) Length = 41 Score = 25.4 bits (56), Expect = 7.4 Identities = 7/13 (53%), Positives = 7/13 (53%) Query: 38 SPKGELYYVNHFT 50 SP G YY N T Sbjct: 19 SPDGRTYYYNTET 31 >1wr3_A Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {Mus musculus} (A:) Length = 36 Score = 25.4 bits (56), Expect = 7.6 Identities = 6/13 (46%), Positives = 6/13 (46%) Query: 38 SPKGELYYVNHFT 50 G YYVNH Sbjct: 14 DNLGRTYYVNHNN 26 >1jmq_A YAP65, 65 kDa YES-associated protein; polyproline ligand, YAP65 mutant, structural protein; NMR {Homo sapiens} (A:) Length = 46 Score = 25.1 bits (55), Expect = 7.7 Identities = 4/13 (30%), Positives = 7/13 (53%) Query: 38 SPKGELYYVNHFT 50 + G+ Y+ NH Sbjct: 18 TSSGQRYFKNHID 30 >2ysi_A Transcription elongation regulator 1; Ca150, FBP28, WW domain, structural genomics, NPPSFA; NMR {Mus musculus} (A:) Length = 40 Score = 25.0 bits (55), Expect = 8.7 Identities = 6/13 (46%), Positives = 9/13 (69%) Query: 38 SPKGELYYVNHFT 50 +P G++YY N T Sbjct: 17 TPDGKVYYYNART 29 >1wr4_A Ubiquitin-protein ligase NEDD4-2; all-beta; NMR {Mus musculus} (A:) Length = 36 Score = 25.0 bits (55), Expect = 9.0 Identities = 7/13 (53%), Positives = 7/13 (53%) Query: 38 SPKGELYYVNHFT 50 KG YYVNH Sbjct: 14 DAKGRTYYVNHNN 26 >2djy_A SMAD ubiquitination regulatory factor 2; beta sheet, polyproline type II helix, PPII, ligase/signaling protein complex; NMR {Homo sapiens} (A:) Length = 42 Score = 25.1 bits (55), Expect = 9.0 Identities = 4/13 (30%), Positives = 8/13 (61%) Query: 38 SPKGELYYVNHFT 50 + G +Y+V+H Sbjct: 17 TATGRVYFVDHNN 29 >1tk7_A CG4244-PB; WW domain, notch, signaling protein; NMR {Drosophila melanogaster} (A:51-88) Length = 38 Score = 25.0 bits (55), Expect = 9.3 Identities = 5/13 (38%), Positives = 9/13 (69%) Query: 38 SPKGELYYVNHFT 50 + GE ++V+H T Sbjct: 16 TAAGERFFVDHNT 28 >1wr7_A NEDD4-2; all-beta, ligase; NMR {Mus musculus} (A:) Length = 41 Score = 25.0 bits (55), Expect = 9.9 Identities = 4/13 (30%), Positives = 9/13 (69%) Query: 38 SPKGELYYVNHFT 50 +P G ++++H T Sbjct: 18 APNGRPFFIDHNT 30 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.321 0.138 0.411 Gapped Lambda K H 0.267 0.0700 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,669,515 Number of extensions: 73522 Number of successful extensions: 317 Number of sequences better than 10.0: 1 Number of HSP's gapped: 304 Number of HSP's successfully gapped: 67 Length of query: 227 Length of database: 4,956,049 Length adjustment: 85 Effective length of query: 142 Effective length of database: 2,082,624 Effective search space: 295732608 Effective search space used: 295732608 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 (24.3 bits)