RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780127|ref|YP_003064540.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62] (675 letters) >gnl|CDD|128758 smart00482, POLAc, DNA polymerase A domain. Length = 206 Score = 87.7 bits (218), Expect = 9e-18 Identities = 32/83 (38%), Positives = 49/83 (59%) Query: 364 VRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDK 423 +R +A G LV AD + IE R+LA ++G++ ++AF NG DI+ T A+ F P ++ Sbjct: 4 IRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEEE 63 Query: 424 VSKEQRAIGKVMELALGYQGGAK 446 V+KE R K + + Y GAK Sbjct: 64 VTKELRRAAKAINFGIIYGMGAK 86 Score = 36.8 bits (86), Expect = 0.018 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 7/67 (10%) Query: 579 YLNTATSQLMRERTYGGKLTEN-IVQAISRDILCEGMKNATKNGY------DIVLTVHDE 631 Y+ S+ R + N +Q + DIL M + ++L VHDE Sbjct: 139 YIPDIDSRNPVLRAAAERAAVNAPIQGSAADILKLAMIKMDEALKEKGLRARLLLQVHDE 198 Query: 632 IVSETPD 638 +V E P+ Sbjct: 199 LVFEVPE 205 >gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional. Length = 553 Score = 81.2 bits (201), Expect = 8e-16 Identities = 67/265 (25%), Positives = 103/265 (38%), Gaps = 55/265 (20%) Query: 208 KLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSH 267 +L EL A+ R+ L + LR GI+L + L+ I H Sbjct: 205 RLAELAAEIREALG-------RPRLNPDSPQQVLRALRRA--GIELPSTRKWELREI-DH 254 Query: 268 SNITQLAKDLILNRLASS-GSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQ 326 + L + L++L S+ G A L + DGR G TGRW+ Sbjct: 255 PAVEPLLEYRKLSKLLSANGWAWL------DYWVRDGRFHPEYVPGGVV-TGRWAS--RG 305 Query: 327 P--QNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGI 384 P Q +PR +RS +A G KLVVAD + I Sbjct: 306 PNAQQIPRD------------------------------IRSAFVADPGWKLVVADASQI 335 Query: 385 EARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGG 444 E RVLA +G++ I+AF G D++ T + F P + KE+RA+ K Y Sbjct: 336 ELRVLAAYSGDERMIEAFRTGGDLHRLTASVGFGKPEE--EKEERALAKAANFGAIYGAT 393 Query: 445 AKVFKTMASHCGLDLQQFSQNVKST 469 +K + A + G + + + ++ Sbjct: 394 SKGLQEYAKNYG-EAARLLERLRRA 417 >gnl|CDD|161944 TIGR00593, pola, DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 887 Score = 75.5 bits (186), Expect = 4e-14 Identities = 82/305 (26%), Positives = 127/305 (41%), Gaps = 58/305 (19%) Query: 160 GEYCKRDVEATRELFKRLIPLSDGERDLWLLDQT----------INDRGYRIDLDLVLKL 209 EY R AT+ L + L+ D + L L + + G ++D D + +L Sbjct: 456 TEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQEL 515 Query: 210 QELIAQERKKLDEDIVKL--TDGIIRSSRQTYALRMYLFLITGIDLVD-------MSEGT 260 + +E L+E+I +L + I S +Q L LF G+ + Sbjct: 516 SQEFGEEIADLEEEIYELAGEEFNINSPKQ---LGEVLFEKLGLPVGKKTKTGYSTDADV 572 Query: 261 LKSILSHSNITQLAKDLI---LNRLASSGSAILKLNTLSEAVSSD-GRLRGTLQFYGASR 316 L+ + I +A L L +L S+ ++ L E V+ D GR+ T G + Sbjct: 573 LEKLREKHPI--IALILEYRQLTKLKST-----YVDGLPELVNPDTGRIHTTFNQTGTA- 624 Query: 317 TGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKL 376 TGR S QN+P RSEE G I R +A G L Sbjct: 625 TGRLSSSNPNLQNIPI--RSEE-----------GRKI-----------RKAFVAEKGWLL 660 Query: 377 VVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVME 436 + AD + IE RVLA ++ ++ I+AF NGEDI+ T ++ F I+ V+ R I K + Sbjct: 661 ISADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVEIEDVTPNMRRIAKTIN 720 Query: 437 LALGY 441 + Y Sbjct: 721 FGVVY 725 >gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional. Length = 880 Score = 69.7 bits (172), Expect = 2e-12 Identities = 29/72 (40%), Positives = 47/72 (65%) Query: 364 VRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDK 423 +R +A G KL+ AD + IE R+LA ++G++ I+AFA GEDI+ T ++ F P+++ Sbjct: 641 IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLEE 700 Query: 424 VSKEQRAIGKVM 435 V+ EQR K + Sbjct: 701 VTSEQRRRAKAI 712 >gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated. Length = 309 Score = 31.3 bits (71), Expect = 0.86 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 5/45 (11%) Query: 60 YLRDETVMCVAHNSLFERILFKKTL---GIDIPSKRWICTSVLAR 101 Y + V +AHN+ F+ + +KTL I +PS +ICT LA+ Sbjct: 77 YFNNNLV--IAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAK 119 >gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated. Length = 557 Score = 30.7 bits (70), Expect = 1.3 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%) Query: 48 TEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKK----TLGIDIPSKRWICTSVLART 102 + +P+ L++ R V+ VAHN+ F+ I F + G P +CT LAR Sbjct: 81 PIEEVLPA-FLEFARG-AVL-VAHNAPFD-IGFLRAAAARCGYPWPGPPVLCTVRLARR 135 >gnl|CDD|139997 PRK13938, PRK13938, phosphoheptose isomerase; Provisional. Length = 196 Score = 30.1 bits (67), Expect = 2.2 Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 3/70 (4%) Query: 405 GEDIYVTTYAKAFNTPIDKVSKEQ-RAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFS 463 E+I+V T A D+V E RAIG L GY+ GA+VF D Q F+ Sbjct: 7 AEEIFVETIAVKTRILNDRVLLEAARAIGD--RLIAGYRAGARVFMCGNGGSAADAQHFA 64 Query: 464 QNVKSTSTFE 473 + F+ Sbjct: 65 AELTGHLIFD 74 >gnl|CDD|163170 TIGR03169, Nterm_to_SelD, pyridine nucleotide-disulfide oxidoreductase family protein. Members of this protein family include N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD, or selenide,water dikinase, the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium incorporation, and the function of this protein family is unknown. Length = 364 Score = 29.6 bits (67), Expect = 3.1 Identities = 7/17 (41%), Positives = 9/17 (52%) Query: 7 DIETRSPQPLPKVGVWA 23 D + P PK GV+A Sbjct: 279 DCAVITDAPRPKAGVYA 295 >gnl|CDD|178473 PLN02885, PLN02885, nicotinate phosphoribosyltransferase. Length = 545 Score = 28.9 bits (65), Expect = 4.1 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 7/57 (12%) Query: 203 LDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEG 259 L V KL E+ Q R KL ED+ K+T I ++ Y L+ G LVD+ G Sbjct: 390 LGCVYKLVEINGQPRIKLSEDVEKVT---IPCKKRCYR----LYGKEGYPLVDLMTG 439 >gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional. Length = 219 Score = 28.5 bits (64), Expect = 5.6 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 6/33 (18%) Query: 69 VAHNSLFERILFKKTLGIDIPSKRWICTSVLAR 101 VAHN+ F+R + + G WICT LAR Sbjct: 78 VAHNASFDRRVLPEMPG------EWICTMKLAR 104 >gnl|CDD|178257 PLN02651, PLN02651, cysteine desulfurase. Length = 364 Score = 28.5 bits (64), Expect = 5.7 Identities = 14/51 (27%), Positives = 17/51 (33%), Gaps = 4/51 (7%) Query: 499 IGTACELVKKAWRA--KHQGVLQ--LWKDLTEGFACVVQEGGSISARRVAN 545 +G ACEL K KH L+ L L V G +R Sbjct: 246 LGAACELAMKEMDYDEKHMKALRERLLNGLRAKLGGVRVNGPRDPEKRYPG 296 >gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional. Length = 313 Score = 28.5 bits (64), Expect = 5.7 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 18/73 (24%) Query: 56 DLLQYLRDETVMCVAHNSLF---------ERILFKKTLGIDIPSKRWICTSVLARTNGLP 106 ++ + LR T+ VAHN F ER G ++P + +CT LAR GL Sbjct: 87 EVAELLRGRTL--VAHNVAFDYSFLAAEAERA------GAELPVDQVMCTVELARRLGLG 138 Query: 107 -SSLKNACLALNF 118 +L+ LA ++ Sbjct: 139 LPNLRLETLAAHW 151 >gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. Length = 771 Score = 28.6 bits (64), Expect = 6.0 Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 5/76 (6%) Query: 166 DVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIV 225 D+E L LI L E D + I+D G D + + I + K L+E++V Sbjct: 109 DLEILFHLRLNLITLPPLEND---IIACIDDDGK--VKDGASEELDAIRESLKALEEEVV 163 Query: 226 KLTDGIIRSSRQTYAL 241 K IIRS L Sbjct: 164 KRLHKIIRSKELAKYL 179 >gnl|CDD|184079 PRK13482, PRK13482, DNA integrity scanning protein DisA; Provisional. Length = 352 Score = 27.8 bits (63), Expect = 9.0 Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 14/54 (25%) Query: 162 YCKRDVEATRELFKRLIPLSDGE-RDL-------------WLLDQTINDRGYRI 201 Y + E E+ + L LS E DL LD ++ RGYR+ Sbjct: 235 YSQEKDEDPEEILEELQELSSEELLDLSAIARLLGYPGGSEALDTPVSPRGYRL 288 >gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated. Length = 605 Score = 27.9 bits (62), Expect = 9.4 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 2/57 (3%) Query: 164 KRDVEATRELFKRLIPLSDGE-RD-LWLLDQTINDRGYRIDLDLVLKLQELIAQERK 218 K ++ ++ L+DG RD L +LDQ + ID++ + K L+ +K Sbjct: 193 KEKIKIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSEIDIEDINKTFGLVDNNKK 249 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 0.319 0.134 0.400 Gapped Lambda K H 0.267 0.0745 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,927,258 Number of extensions: 704775 Number of successful extensions: 1357 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1353 Number of HSP's successfully gapped: 25 Length of query: 675 Length of database: 5,994,473 Length adjustment: 100 Effective length of query: 575 Effective length of database: 3,833,673 Effective search space: 2204361975 Effective search space used: 2204361975 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: 60 (26.9 bits)