RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781193|ref|YP_003065606.1| 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 = 95.4 bits (238), Expect = 5e-20 Identities = 60/281 (21%), Positives = 101/281 (35%), Gaps = 85/281 (30%) Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423 +R +A G LV AD + IE R+LA ++G++ L+AF G D++ T A+ F V + Sbjct: 4 IRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVPEEE 63 Query: 424 VTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCR 483 VTK+ R K + + Y G A +A G++ L+K Sbjct: 64 VTKELRRAAKAINFGIIY--GMGAK-GLAEQLGISEAEAKELIKA--------------- 105 Query: 484 WMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKR 543 P VK+ ++ + + T+ +R Sbjct: 106 -YFARFPG--------------VKRYIKRTLEEARR------KGYVTTLFG-------RR 137 Query: 544 RDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQ 603 R +P + +N P R+ R+ +N +Q Sbjct: 138 RYIPDI---DSRN------PVLRAA------AERAAVNA------------------PIQ 164 Query: 604 AVSRDILAEGMMNATKAGY------DIVLTVHDEIVCETPD 638 + DIL M+ +A ++L VHDE+V E P+ Sbjct: 165 GSAADILKLAMIKMDEALKEKGLRARLLLQVHDELVFEVPE 205 >gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional. Length = 553 Score = 86.2 bits (214), Expect = 3e-17 Identities = 46/163 (28%), Positives = 65/163 (39%), Gaps = 38/163 (23%) Query: 296 EAMNSDGRLRGTLQFLGASRTGRWSGCVFPP--QNLPRPSRSHEELDQIITHLPTSITSD 353 + DGR G TGRW+ P Q +PR Sbjct: 279 DYWVRDGRFHPEYVPGGVV-TGRWAS--RGPNAQQIPRD--------------------- 314 Query: 354 PDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTY 413 +RS +A G KLVVAD + IE RVLA +G++ ++AF TG DL+ T Sbjct: 315 ----------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAFRTGGDLHRLTA 364 Query: 414 ARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTG 456 + F + K++RA+ K Y +K Q+ A G Sbjct: 365 SVGFGKPEEE--KEERALAKAANFGAIYGATSKGLQEYAKNYG 405 Score = 28.8 bits (65), Expect = 4.1 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 6/50 (12%) Query: 595 GKLTEN-IVQAVSRDILAEGMM-----NATKAGYDIVLTVHDEIVCETPD 638 G+ T N VQ + D + A ++V VHDE+V E P+ Sbjct: 463 GRFTRNFPVQGTAADWAKLALALLRRRLAEGLDAELVFFVHDEVVVECPE 512 >gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional. Length = 880 Score = 64.7 bits (159), Expect = 7e-11 Identities = 27/72 (37%), Positives = 44/72 (61%) Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423 +R +A EG KL+ AD + IE R+LA ++G++ ++AF GED++ T + F V + Sbjct: 641 IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLEE 700 Query: 424 VTKDQRAIGKVM 435 VT +QR K + Sbjct: 701 VTSEQRRRAKAI 712 Score = 32.8 bits (76), Expect = 0.29 Identities = 32/139 (23%), Positives = 48/139 (34%), Gaps = 29/139 (20%) Query: 57 LKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLA-------RSNGLPSAL 109 LK LE+ + V N ++ VL I + +LA R +GL S Sbjct: 362 LKPLLEDPAIKKVGQNLKYDLHVLA---RYGIELRGIAFDTMLASYLLDPGRRHGLDSL- 417 Query: 110 KAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTR 169 A + K +E+ K T + + EA EY D VT Sbjct: 418 -----AERYLGHKTISFEEVAG---KQLT------FAQVDLEEA----AEYAAEDADVTL 459 Query: 170 EIFKRLEPLSSKEQELWYL 188 + + L+P +E L L Sbjct: 460 RLHEVLKPKLLEEPGLLEL 478 >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 = 61.2 bits (149), Expect = 9e-10 Identities = 39/124 (31%), Positives = 59/124 (47%), Gaps = 9/124 (7%) Query: 325 PPQNLPRPSRSHEELDQIITHLPTSITSDPDP-LQII------SDCVRSCVIASEGKKLV 377 P P R H +Q T T S +P LQ I +R +A +G L+ Sbjct: 604 PELVNPDTGRIHTTFNQTGT--ATGRLSSSNPNLQNIPIRSEEGRKIRKAFVAEKGWLLI 661 Query: 378 VADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMEL 437 AD + IE RVLA ++ ++ ++AF+ GED++ T +R F V VT + R I K + Sbjct: 662 SADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVEIEDVTPNMRRIAKTINF 721 Query: 438 ALGY 441 + Y Sbjct: 722 GVVY 725 >gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated. Length = 309 Score = 38.6 bits (90), Expect = 0.005 Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 6/55 (10%) Query: 68 IVAHNSYFERTVLKAC---FNLDIPIHRWICTLVLARS--NGLPSA-LKAVGEAL 116 ++AHN+ F+ +VL+ +N+ +P +ICT+ LA++ + + +A L V L Sbjct: 83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFL 137 >gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes. Length = 172 Score = 37.3 bits (87), Expect = 0.012 Identities = 37/180 (20%), Positives = 63/180 (35%), Gaps = 38/180 (21%) Query: 4 LFIDFETRSPIDLTKCGICKYAEDVCVILFAFG----FDDHPVELWDCVHDPVMPQVLKE 59 + +D ET T Y+ + +I + F P+ L D + +LK+ Sbjct: 24 VALDTET------TGLNS--YSGKLVLIQISVTGEGAFIIDPLALGDDLE------ILKD 69 Query: 60 ALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLS 119 LE+ +T V HN+ F+ VL I + T++ A L L+ Sbjct: 70 LLEDETITKVGHNAKFDLHVLA---RFGIELENIFDTMLAAY------LLLGGPSKHGLA 120 Query: 120 SQ-KMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178 + K G EL K + +P E +Y D ++++LE Sbjct: 121 TLLKEYLGVELDKEEQKSDW------GARPLSEEQL----QYAAEDADALLRLYEKLEKE 170 >gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated. Length = 557 Score = 37.2 bits (87), Expect = 0.014 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%) Query: 51 PVMPQVLKEALE-NTDVTIVAHNSYFERTVLKA-CFNLDI--PIHRWICTLVLAR 101 P + +VL LE +VAHN+ F+ L+A P +CT+ LAR Sbjct: 80 PPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLAR 134 >gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional. Length = 219 Score = 33.9 bits (78), Expect = 0.14 Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 18/78 (23%) Query: 69 VAHNSYFERTVLKACFNLDIPIHRWICTLVLARS--NGLPSALKAVGEALKLSSQKMEEG 126 VAHN+ F+R VL ++P WICT+ LAR G+ + A+ ++ KL+ Q Sbjct: 78 VAHNASFDRRVLP-----EMP-GEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPP-- 129 Query: 127 KELIARFCKGETHECLYD 144 L H LYD Sbjct: 130 -GLHH-------HRALYD 139 >gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional. Length = 313 Score = 32.4 bits (74), Expect = 0.37 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 9/57 (15%) Query: 67 TIVAHNSYFERTVLKACFNL---DIPIHRWICTLVLARSNGLPSALKAVGEALKLSS 120 T+VAHN F+ + L A ++P+ + +CT+ LAR GL L+L + Sbjct: 96 TLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGL------PNLRLET 146 >gnl|CDD|151519 pfam11074, DUF2779, Domain of unknown function(DUF2779). This domain is conserved in bacteria. The function is not known. Length = 127 Score = 31.8 bits (73), Expect = 0.60 Identities = 11/25 (44%), Positives = 16/25 (64%) Query: 57 LKEALENTDVTIVAHNSYFERTVLK 81 LK+A+ +IV +N FE+T LK Sbjct: 61 LKKAIGKDYGSIVVYNKSFEKTRLK 85 >gnl|CDD|162272 TIGR01255, pyr_form_ly_1, formate acetyltransferase 1. This model describes formate acetyltransferase 1. More distantly related putative formate acetyltransferases have also been identified, including formate acetyltransferase 2 from E. coli, which is excluded from this model. Length = 744 Score = 31.0 bits (70), Expect = 1.1 Identities = 9/37 (24%), Positives = 18/37 (48%) Query: 474 EWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAW 510 W + N ++Q+N+ + ++ F+ ER K W Sbjct: 9 NWRNKVNVRDFIQKNYKPYDGDESFLAGPTERTLKVW 45 >gnl|CDD|129770 TIGR00687, pyridox_kin, pyridoxal kinase. ThiD and related proteins form an outgroup. Length = 286 Score = 29.4 bits (66), Expect = 2.8 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 18/69 (26%) Query: 285 RSAVLKLNTL---VEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQ 341 R+A L L V A+N T+QF + G+W+G V PP L E +D Sbjct: 19 RAATFPLQRLGFEVWAVN-------TVQFSNHTGYGKWTGQVLPPDEL------TELVDG 65 Query: 342 I--ITHLPT 348 + I L Sbjct: 66 LAAINKLNQ 74 >gnl|CDD|180238 PRK05756, PRK05756, pyridoxamine kinase; Validated. Length = 286 Score = 29.1 bits (66), Expect = 3.5 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 10/49 (20%) Query: 285 RSAVLKLNTL---VEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLP 330 +AV + L V +N T+QF + G+W+GCV PP +L Sbjct: 19 SAAVFPMQRLGVNVWPLN-------TVQFSNHTGYGKWTGCVMPPSHLT 60 >gnl|CDD|173399 PTZ00107, PTZ00107, hexokinase; Provisional. Length = 464 Score = 28.9 bits (65), Expect = 4.0 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%) Query: 71 HNSYFERTVLKACFNLDIPIH-----RWICTLVLARSNGLPSALKA 111 + F R V+K +++D+ R IC LV R+ L +A A Sbjct: 348 PDLQFSRQVIKEAWDVDLTDEDLYTIRKICELVRGRAAQLAAAFIA 393 >gnl|CDD|128862 smart00595, MADF, subfamily of SANT domain. Length = 89 Score = 28.9 bits (65), Expect = 5.0 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 6/45 (13%) Query: 137 ETHECLYDRNKPNHR------EAWRLFGEYCKGDVTVTREIFKRL 175 CL+DR P++R +AW E V ++ +K L Sbjct: 7 RERPCLWDRRHPDYRNKEEKRKAWEEIAEELGLSVEECKKRWKNL 51 >gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit beta; Validated. Length = 356 Score = 28.4 bits (63), Expect = 5.6 Identities = 15/35 (42%), Positives = 18/35 (51%) Query: 6 IDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDH 40 I E RSP ++ CG C+ A DV V AF H Sbjct: 294 IPIEERSPEEVLTCGGCRIAPDVDVYNPAFDVTPH 328 >gnl|CDD|151247 pfam10797, YhfT, Protein of unknown function. This family is conserved in Firmicutes and Proteobacteria. The function is not known but several members are annotated as being homologues of E coli YhfT, a protein thought to be involved in fatty acid oxidation. Length = 421 Score = 28.4 bits (64), Expect = 6.4 Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%) Query: 430 AIGKVMELALGYQGGAKAFQKMASTTG 456 A+ +++E+AL GGA A KMA TG Sbjct: 352 AMTRLLEVAL-LIGGANAANKMAPGTG 377 >gnl|CDD|184639 PRK14346, PRK14346, lipoate-protein ligase B; Provisional. Length = 230 Score = 28.2 bits (63), Expect = 6.4 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 4/39 (10%) Query: 38 DDHPVELWDCVHDPVMPQVLKEALENT----DVTIVAHN 72 + P ELW C H PV Q L ++ D+ +VA N Sbjct: 29 PETPDELWICEHPPVYTQGLAGKADHVLNPGDIPVVATN 67 >gnl|CDD|182034 PRK09698, PRK09698, D-allose kinase; Provisional. Length = 302 Score = 28.0 bits (63), Expect = 8.2 Identities = 5/17 (29%), Positives = 11/17 (64%) Query: 483 RWMQENHPEHAIEDLFI 499 RW ++ ++ + DLF+ Sbjct: 193 RWYEQQPRDYPLSDLFV 209 >gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated. Length = 1437 Score = 27.9 bits (63), Expect = 8.2 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%) Query: 55 QVLKEALENTDVTI-VAHNSYFERTVLKACF---NLDIPIHRWICTLVLAR 101 +VL + E +I VAHN+ F+ + + L+ + I TL L+R Sbjct: 488 EVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSR 538 >gnl|CDD|182592 PRK10619, PRK10619, histidine/lysine/arginine/ornithine transporter subunit; Provisional. Length = 257 Score = 28.0 bits (62), Expect = 8.6 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 5/39 (12%) Query: 112 VGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNH 150 VGE L++ Q EEGK ++ THE + R+ +H Sbjct: 188 VGEVLRIMQQLAEEGKTMVV-----VTHEMGFARHVSSH 221 >gnl|CDD|151090 pfam10545, MADF_DNA_bdg, Alcohol dehydrogenase transcription factor Myb/SANT-like. The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Length = 84 Score = 28.1 bits (63), Expect = 8.7 Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 10/52 (19%) Query: 129 LIARFCKGETHECLYDRNKPNHR------EAWRLFGEYCKGDVTVTREIFKR 174 LI K H CL+DR+ P++R AW E DV V E KR Sbjct: 1 LIELVRK---HPCLWDRSHPDYRNKELRERAWEEIAEELGEDVDVE-ECKKR 48 >gnl|CDD|163533 TIGR03821, AblA_like_1, lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in E. coli, Buchnera, Yersinia, etc. Length = 321 Score = 27.7 bits (62), Expect = 9.2 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%) Query: 143 YDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTIND 194 Y N+PN + W+ EY + I +PL +K+ L +L + Sbjct: 120 YQENQPNKAQ-WKEALEYIAQHPEINEVILSGGDPLMAKDHRLDWLLNLLEQ 170 >gnl|CDD|179363 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit HisF; Provisional. Length = 253 Score = 27.7 bits (63), Expect = 9.7 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 12/48 (25%) Query: 591 YTYGGK------LTENIVQAVSR---DILAEGMMNA--TKAGYDIVLT 627 YT+GG+ E + +IL M+ TK GYD+ LT Sbjct: 143 YTHGGRKPTGLDAVEWAKEVEELGAGEILLT-SMDRDGTKNGYDLELT 189 >gnl|CDD|177948 PLN02314, PLN02314, pectinesterase. Length = 586 Score = 27.9 bits (62), Expect = 9.8 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 3/52 (5%) Query: 57 LKEALENTDVTIVAHNSY-FERTVLKACFNLDIPIHRWICTLVLARSNGLPS 107 +K A+ N+ T NS +L +L IPIHR + + S+G PS Sbjct: 212 VKTAMSNS--TEFTSNSLAIVSKILGILSDLGIPIHRRLLSFHHDLSSGFPS 261 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 0.133 0.403 Gapped Lambda K H 0.267 0.0728 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,920,933 Number of extensions: 701189 Number of successful extensions: 1391 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1383 Number of HSP's successfully gapped: 35 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)