RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780804|ref|YP_003065217.1| DNA polymerase III subunit delta [Candidatus Liberibacter asiaticus str. psy62] (352 letters) >gnl|CDD|180631 PRK06585, holA, DNA polymerase III subunit delta; Reviewed. Length = 343 Score = 168 bits (427), Expect = 3e-42 Identities = 86/331 (25%), Positives = 161/331 (48%), Gaps = 10/331 (3%) Query: 18 FLSHF-----VFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWN 72 FL+ + YG D+GL+ E + K++ DPF++V L+ ++ + + + Sbjct: 12 FLARPDPKIRAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDDLDADPARLED 71 Query: 73 EINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAE 132 E N+ SLF +++I + + K + L+ ++ + I+I++ ++KK ++LRK+ E Sbjct: 72 EANAISLFGGRRLIWVR--AGSKNLAAALKALLESPPGDAFIVIEAGDLKKGSSLRKLFE 129 Query: 133 KFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLS 192 AI CY D++ L LI++ L I+ +A+ +L+A LGGDR+ASRNE++KL+ Sbjct: 130 TAAYAAAIPCYADDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLA 189 Query: 193 SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLH 252 Y IT V+ ++ D L +++ +A + G + D LA +L Sbjct: 190 LYAHGKGEITLDDVRAVVGDASALSLDDAADAALAGDLAAFERALDRALAEGTAPVLILR 249 Query: 253 GFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKR-NILQESLRIWNKNLVRETLH 311 L+ FQ L + + E + + I + + + KR +++LR W+ + L Sbjct: 250 AALRHFQRLHIVRLKVENGKSAEQAI--ASLRPPVFFKRKPDFEKALRRWSLERLLRALE 307 Query: 312 KIDHRIHLARKKKYLEKNIIFQTILYIAQTA 342 ++ R+ L I + +L IA A Sbjct: 308 RLQAAELDCRRNPALADAIARRVLLSIAVRA 338 >gnl|CDD|162213 TIGR01128, holA, DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp. Length = 302 Score = 70.0 bits (172), Expect = 9e-13 Identities = 46/229 (20%), Positives = 101/229 (44%), Gaps = 21/229 (9%) Query: 57 VLNALEIQKNISTF------WNEI----NSTSLFSKKKIILIENLSTEKKVLDCLEEIII 106 L + N+ WN++ + LFS+++++ + N E K + + Sbjct: 11 ALAQGFDEFNVFRIDGEEFDWNQLLEEAQTLPLFSERRLVELRNP--EGKPGAKGLKALE 68 Query: 107 KNICN----HIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQ 162 + + N +++I++ ++ K L K + + + C + L I+ L Sbjct: 69 EYLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAQIVECKTPKEQELPRWIQARLKKLG 128 Query: 163 KSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEII 222 I +A Q+L + G+ +A EL+KL+ Y D IT + V++ + D+ + ++ Sbjct: 129 LRIDPDAVQLLAELVEGNLLAIAQELEKLALY-APDGKITLEDVEEAVSDSARFNVFDLT 187 Query: 223 NATIQGKIYNAI-MLADFFLASKMPSHALLHGFLQK-FQLLEKIHIIKE 269 +A ++GK A+ +L + P +L LQ+ +LL ++ + + Sbjct: 188 DALLEGKAARALRILKGLLGEGEEP--LILLALLQRQLRLLLQLKRLAQ 234 >gnl|CDD|180139 PRK05574, holA, DNA polymerase III subunit delta; Reviewed. Length = 340 Score = 51.7 bits (125), Expect = 2e-07 Identities = 48/227 (21%), Positives = 98/227 (43%), Gaps = 17/227 (7%) Query: 23 VFIFYGSDKGLIFELINQF-KKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFS 81 +++ YG + L+ E + + + + ++ + E + S LFS Sbjct: 19 LYLLYGDEPLLLQEAKDAIRAAARAQGFDE-RNVFTFDGSET--DWDDVLEACQSLPLFS 75 Query: 82 KKKIILI---ENLSTEK--KVLDCLEEIIIKNICNHIIII----KSNEIKKNNTLRKIAE 132 +K++ + E L+ K K L LE + +++I K ++ KK + K + Sbjct: 76 DRKLVELRLPEFLTGAKGEKALKRLEAYLNPLPHPDLLLIVRLPKLDKAKKKSAWFKALK 135 Query: 133 KFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLS 192 K V + P + L I++ L I A Q+L + G+ +A EL+KL+ Sbjct: 136 KKAVV--VEAQPPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLA 193 Query: 193 SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAI-MLAD 238 + IT + V++ + D+ + ++++A + GKI A+ +L Sbjct: 194 LLYPDGK-ITLEDVEEAVPDSARFDVFDLVDAILAGKIKRALRILDG 239 >gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated. Length = 1437 Score = 37.5 bits (88), Expect = 0.005 Identities = 47/240 (19%), Positives = 90/240 (37%), Gaps = 31/240 (12%) Query: 3 TIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDP------FSLV 56 + E K + + F F L E FK+ + ++ FS+ Sbjct: 27 SAEIEKVVVDKKSKKW--EFHLKF---PNILPIEDFKLFKEKLKQSFSHIADIKVTFSIE 81 Query: 57 VLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIII 116 V N ++ + +WNEI +KK L ++L ++KV +E N +II Sbjct: 82 VENITFTEELLLDYWNEI---IEKAKKNSPLFKSLLKKQKVE--VEG-------NKLIIK 129 Query: 117 KSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHL-----MDLIEESLLIGQKSISKEAKQ 171 +NEI++++ +K K + KI + +E+ ++ K AK+ Sbjct: 130 VNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAKE 189 Query: 172 ILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIY 231 L A A + + K + I ++ K+ I + EE ++G ++ Sbjct: 190 ALEAM--KKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEI-NEEERRVVVEGYVF 246 >gnl|CDD|148006 pfam06144, DNA_pol3_delta, DNA polymerase III, delta subunit. DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction. The delta subunit is also known as HolA. Length = 172 Score = 35.7 bits (83), Expect = 0.016 Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 10/175 (5%) Query: 25 IFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKK 84 + YG D L+ E +Q K + F+ + + E E + FS K+ Sbjct: 2 LLYGEDPFLLEETKDQILKAALDQGFEDFNYIYFDLEE--DWADDVLEECETLPFFSDKR 59 Query: 85 IILIENLSTEKKVLDC-----LEEII-IKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVL 138 I+++ N + ++ L+ LEE + +II ++ + L K+ +K Sbjct: 60 IVILNNPNLKESKLNEKLLKRLEEYLSNPPEDTLLIIEAPGKLDERKKLTKLLKK--KAT 117 Query: 139 AISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSS 193 + C+ + L+ I++ I K+A Q+L + + +A EL+KL+ Sbjct: 118 VVECFTLKEEELIQWIQKRAKELGLKIEKDALQLLAEKVENNLLAIAQELEKLAL 172 >gnl|CDD|181447 PRK08487, PRK08487, DNA polymerase III subunit delta; Validated. Length = 328 Score = 31.8 bits (73), Expect = 0.28 Identities = 51/267 (19%), Positives = 103/267 (38%), Gaps = 11/267 (4%) Query: 77 TSLFSKKKIILIE-NLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFT 135 +SLF K +++I+ + KK L L E+ KN N+ II K + K+ +K Sbjct: 66 SSLFGGKNLLIIKLDKKIPKKELKLLIELCEKNSDNYFIIELYGADSKTKDIEKLFQKKD 125 Query: 136 SVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYC 195 + + + N ++L++E I + A L D + NEL+KL+ Sbjct: 126 EAVFVRFFKPNAREALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAIL- 184 Query: 196 LEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFL 255 + IT + +++++ + E+ + K + L ALL+ Sbjct: 185 --NEPITLKDIQELVFGLGSVSFEDFFEKLLNKKDIKDD--LEKLLEEGFNEIALLNSLE 240 Query: 256 QKFQLLEKIHI-IKECSNISFEKII-QKTEKNIIPMKRNILQESLRIWNKNLVRETLHKI 313 + F L IK ++I+ K K I +++++I + Sbjct: 241 RFFYQLFLFFAYIKINGKPDAKEILGYKPPKQIAENLA---KQAIKIKEAQYKEIFELLL 297 Query: 314 DHRIHLARKKKYLEKNIIFQTILYIAQ 340 + + L +K + + T++ I + Sbjct: 298 EWELELKTGQKIDKNLFLLSTLIKIQK 324 >gnl|CDD|128754 smart00478, ENDO3c, endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases. Length = 149 Score = 29.5 bits (67), Expect = 1.5 Identities = 26/115 (22%), Positives = 44/115 (38%), Gaps = 6/115 (5%) Query: 124 NNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSIS-KEAKQILLANLGGDRI 182 N ++ EKF + ++ + + L +LI +K+ E +IL+ GG+ Sbjct: 11 NKATERLFEKFPTPEDLAAADEEE--LEELIRPLGFYRRKAKYLIELARILVEEYGGEVP 68 Query: 183 ASRNELQKLS---SYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAI 234 R EL KL +L I DTHVL I + + + + Sbjct: 69 DDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEV 123 >gnl|CDD|185647 PTZ00468, PTZ00468, phosphofructokinase family protein; Provisional. Length = 1328 Score = 28.8 bits (64), Expect = 2.3 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%) Query: 78 SLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSV 137 +FS LIENL +K+ D EII+ + + + ++ K N + + FT Sbjct: 1015 LIFSDIDERLIENLINSRKICDVRTEIILSALVQKELKFRRSKNKIKNGMNPVCFSFTDQ 1074 Query: 138 LAISCYP 144 + +C P Sbjct: 1075 VR-ACIP 1080 >gnl|CDD|178674 PLN03128, PLN03128, DNA topoisomerase 2; Provisional. Length = 1135 Score = 27.8 bits (62), Expect = 4.2 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%) Query: 79 LFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEK 133 L+ K+K +L+ENL E K LD + I + I++ N K+ L ++ EK Sbjct: 991 LYVKRKEVLLENLEYELKKLDN-KARFILAVVKGEIVV--NNRKRAELLAELEEK 1042 >gnl|CDD|185606 PTZ00420, PTZ00420, coronin; Provisional. Length = 568 Score = 27.6 bits (61), Expect = 5.3 Identities = 25/109 (22%), Positives = 49/109 (44%), Gaps = 15/109 (13%) Query: 111 NHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHL-----MDLIEESLLIGQKSI 165 N III ++ K+ + +R+ +KFT + H +D +ES+ I KS Sbjct: 409 NSIIIGENYTSKRTSIIRQFTKKFT-------FFKKGEHNDGFSSVDSFKESVFIYPKSF 461 Query: 166 SKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTH 214 ++ LL GG + +S N L++ + + T + ++ + T+ Sbjct: 462 K---EKELLTEKGGAQFSSANSLERGADEDYLIVNGTNEPYEEEVIKTN 507 >gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated. Length = 326 Score = 27.6 bits (62), Expect = 5.3 Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 2/98 (2%) Query: 150 LMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCL-EDILITEQHVKD 208 L L+E + ++ EA ++L +G D NEL+KL+ Y I+ + VK Sbjct: 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKA 194 Query: 209 IICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMP 246 ++ ++ +A +QG A+ L D L + P Sbjct: 195 LV-SNTTQNSLQLADALLQGNTGKALALLDDLLDANEP 231 >gnl|CDD|165167 PHA02817, PHA02817, EEV Host range protein; Provisional. Length = 225 Score = 26.8 bits (59), Expect = 8.3 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 5/84 (5%) Query: 45 ISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEI 104 I + ++ + +N + I N F+N+IN+++ + KI+ I N++ + L + Sbjct: 144 ICSRDNITYNKIYINKVNIDDN---FFNQINNSNTYYFDKILQINNVN--RYTLIFFVVV 198 Query: 105 IIKNICNHIIIIKSNEIKKNNTLR 128 IK + + I S K ++++ Sbjct: 199 SIKILFGFVFIFFSCNKKPLDSIK 222 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.137 0.386 Gapped Lambda K H 0.267 0.0636 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,495,647 Number of extensions: 357829 Number of successful extensions: 720 Number of sequences better than 10.0: 1 Number of HSP's gapped: 710 Number of HSP's successfully gapped: 55 Length of query: 352 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 258 Effective length of database: 3,963,321 Effective search space: 1022536818 Effective search space used: 1022536818 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 58 (26.3 bits)