RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA [Candidatus Liberibacter asiaticus str. psy62] (731 letters) >gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated. Length = 665 Score = 762 bits (1971), Expect = 0.0 Identities = 289/712 (40%), Positives = 434/712 (60%), Gaps = 56/712 (7%) Query: 15 EQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGP 74 E+A+K + L +E+++H YY P I D+EYD L R A+ P+L P+ P Sbjct: 3 EEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELIT---PDSP 59 Query: 75 LNKIGGEMNLSLF-KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133 ++GG L F KV H +P LSL+ ++ E+LR F R+ + D + + E K Sbjct: 60 TQRVGGAP-LDGFEKVRHLVPMLSLDNAFSEEELRAFDKRVRKRL---PDPPLTYLCELK 115 Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYI 193 IDG +++ YE G V AA RGDG +GED++A +R I +IP L N PE +EVRGEV++ Sbjct: 116 IDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGNEPERLEVRGEVFM 175 Query: 194 SKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT--RYLNFFVHGLGKTSEIF- 250 K DF ALN+E G KP+ANPRNAA+G LR+L+P IT R L+FF +G+G+ Sbjct: 176 PKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPK-ITAKRPLSFFAYGVGEVEGGEL 234 Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310 Q E L+ ++ GFPVN + + ++++Y E++ R LPYDIDG+V KVD+ + Sbjct: 235 PDSQSEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLA 294 Query: 311 LQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITN 370 LQ++LG A++PRW I++KF ++A+T+LLDI++Q+GRTG +TPVARLEPV + G ++ Sbjct: 295 LQEELGFTAKAPRWAIAYKFPAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSR 354 Query: 371 ATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSF 430 ATLHN D I+ DIR+GD V+V+RAG+VIP+VV +++ +R D + Sbjct: 355 ATLHNADEIERK-----------DIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVM 403 Query: 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ 490 P+ CP+C S +VR G+ A RCT GL+C AQ ERL HFVSR+A +I+GLG++ Sbjct: 404 PTHCPVCGSELVR----VEGE--AVLRCTNGLSCPAQLKERLIHFVSRNAMDIDGLGEKI 457 Query: 491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISL 550 ++ F+ I PAD+F L + + + GFG+ S NL D+I K + SL Sbjct: 458 IEQLFEKGL----IHDPADLFKL------TAEDLLGLEGFGEKSAQNLLDAIEKSKETSL 507 Query: 551 ERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQ 610 RF+++LGIRHVG + A++LA+++ S + L V VG+++AQ Sbjct: 508 ARFLYALGIRHVGEKAAKALARHFGSLEALRA----------ASEEELAAVEGVGEVVAQ 557 Query: 611 AIVEFYQNPRNICAVEALLKEVSPSIGRH--EKNVSSEIENKKLVFTGTLQKIQRHKAQE 668 +IVEF+ N ++ LL G + K ++ K +V TGTL+++ R +A+E Sbjct: 558 SIVEFFAVEENRELIDELL-----EAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKE 612 Query: 669 YVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ 720 + LGA VS +S+KTD+++ G+ GSKL KAQ+LG+++++EE+FL LL + Sbjct: 613 KLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664 >gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed. Length = 652 Score = 646 bits (1668), Expect = 0.0 Identities = 279/699 (39%), Positives = 424/699 (60%), Gaps = 55/699 (7%) Query: 24 LEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMN 83 L + I +HD YY +P I D+EYD L R + P+L P+ P ++G Sbjct: 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELIT---PDSPTQRVGAAPL 57 Query: 84 LSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY 143 KV HS P LSL+ ++ ++L FI RI R K + + +EPKIDG +++ Y Sbjct: 58 SRFPKVRHSTPMLSLDNAFDEDELAAFIKRIRRQLGLK----VEYVVEPKIDGLSVSLTY 113 Query: 144 EKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSL-NIPEIIEVRGEVYISKNDFLALN 202 E G V A RGDG GEDV+A +R I +IP L+ N PE +EVRGEV++ K DF ALN Sbjct: 114 ENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALN 173 Query: 203 DEMIAVGRKPYANPRNAASGILRRLNPTDIT--RYLNFFVHGLGKTSEIFAKGQYEMLQK 260 +E G KP+ANPRNAA+G LR+L+P IT R L FF +GLG+ E+ QYE L Sbjct: 174 EERREQGEKPFANPRNAAAGSLRQLDP-RITAKRKLRFFAYGLGEGLELPDATQYEALAW 232 Query: 261 MRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR 320 ++ GFPV+ +R ++ ++ YY E++ R +LPY+IDG+V KVD+ +LQ +LG ++ Sbjct: 233 LKKWGFPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSK 292 Query: 321 SPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIK 380 +PRW I++KF ++A T+LLD+ +Q+GRTG +TPVA+LEPV + G ++ ATLHNED I+ Sbjct: 293 APRWAIAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIE 352 Query: 381 GLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSR 440 L DIR+GD V+V++AG+VIPKVV +++ +R +P FP+ CP C S Sbjct: 353 EL-----------DIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGSP 401 Query: 441 VVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDP 500 +V+ A RC L C AQ++ER+KHF SR+A +IEGLG + ++ F+ + Sbjct: 402 LVKIEEE------AVIRCP-NLNCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKK-- 452 Query: 501 AFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIR 560 +R AD++ L++ ++E GFG+ S NL ++I K + L R +F+LGIR Sbjct: 453 --LVRSVADLYALKKED---LLELE---GFGEKSAQNLLNAIEKSKEKPLARLLFALGIR 504 Query: 561 HVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR 620 HVG A++LAK++ + ++ + A + ++ L+ V VG +A++IV F+ +P Sbjct: 505 HVGEVTAKNLAKHFGT-------LDKLKAASLEE---LLSVEGVGPKVAESIVNFFHDPN 554 Query: 621 NICAVEALLKEVSPSIGRHEKNVSSEIEN-----KKLVFTGTLQKIQRHKAQEYVTQLGA 675 N ++ L+E+ + + V++E+ K V TGTL ++ R +A+E + LG Sbjct: 555 NRQLIKK-LEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGG 613 Query: 676 VVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQF 714 V++ +S+KTD +I G+ GSKL KAQ+LG+ I+NEE+ Sbjct: 614 KVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEEEL 652 >gnl|CDD|128805 smart00532, LIGANc, Ligase N family. Length = 441 Score = 490 bits (1265), Expect = e-139 Identities = 201/466 (43%), Positives = 288/466 (61%), Gaps = 27/466 (5%) Query: 17 ARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLN 76 A+KE+S L + ++ HD YY PII D+EYD L R + P+L P+ P Sbjct: 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELK---TPDSPTQ 57 Query: 77 KIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDG 136 ++GG+ KV H +P LSL+ ++ ++LR F RI +K + + +EPKIDG Sbjct: 58 RVGGKPLEGFNKVRHPVPMLSLDNAFDEDELRAFDERI----EKALGSPFAYVVEPKIDG 113 Query: 137 TMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN 196 +++ YE GK V AA RGDG GEDV+ ++ I +IP LS ++PE +EVRGEV++ K Sbjct: 114 LSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVPERLEVRGEVFMPKE 173 Query: 197 DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEIF-AKGQ 254 DFLALN+E+ G KP+ANPRNAA+G LR+L+P R L F +GLG E+F K Q Sbjct: 174 DFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQ 233 Query: 255 YEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQ 314 E L+ ++ LGFPV+ R ++ YY E + R+ LPY+IDG+V KVD+ +LQ++ Sbjct: 234 SEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRE 293 Query: 315 LGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLH 374 LG +++PRW I++KF ++A T+LLDI +Q+GRTG +TPVA LEPV + G+ ++ ATLH Sbjct: 294 LGFTSKAPRWAIAYKFPAEEAETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLH 353 Query: 375 NEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFC 434 NED I+ DIR+GD V+V++AG+VIPKVV ++ +R D + P+ C Sbjct: 354 NEDEIEEK-----------DIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHC 402 Query: 435 PICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDA 480 P C S +VR+ + RC L C AQ +ER+ HF SR A Sbjct: 403 PSCGSELVRE------EGEVDIRCPNPL-CPAQLIERIIHFASRKA 441 >gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional. Length = 689 Score = 470 bits (1211), Expect = e-133 Identities = 256/721 (35%), Positives = 388/721 (53%), Gaps = 57/721 (7%) Query: 8 PIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLAR 67 P+E LS ++A ++ L + I HD YY + P+I D YDAL R A+ AF DL Sbjct: 23 PVEELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDT 81 Query: 68 SEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIF 127 N P ++GGE L V H P LS+++ +D+R+F R+ +++ ++ Sbjct: 82 ---ENSPTRRVGGEPLDELETVEHVAPMLSIDQSGEADDVREFDERV-----RREVGAVE 133 Query: 128 FTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEV 187 + EPK DG + + YE G++ AA RGDG G+DV+A +R I ++P+ L + P+ + V Sbjct: 134 YVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRGDYPDFLAV 193 Query: 188 RGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKT 246 RGEVY+ K+ F A N E I G +P+ANPRNAA+G LR+L+P+ + R L+ F + Sbjct: 194 RGEVYMPKDAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDA 253 Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306 SE+F +E L++ G V + + + ++Y + + + R L Y+IDG+V KV Sbjct: 254 SELFDS-HWEELERFPEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKV 312 Query: 307 DEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGA 366 D+ +++LG AR+PRW ++KF + T + DI +Q+GRTG LTPVA L+PV++GG Sbjct: 313 DDRDAREELGATARAPRWAFAYKFPARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGV 372 Query: 367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQ 426 ++ A+LHN I+ L + VGDRV VKRAG+VIP V +++ E+ + Sbjct: 373 TVSRASLHNPAEIEEL-----------GVNVGDRVRVKRAGDVIPYVEEVV--EKDSEGT 419 Query: 427 PFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486 F FP CP+C S V RD G L CTGGLAC AQ ++H+ SRDA +IEGL Sbjct: 420 -FEFPDTCPVCDSAVERD-----GPLAF---CTGGLACPAQLERSIEHYASRDALDIEGL 470 Query: 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR 546 G++++ + + AD++ L ++E G+G+ S NL + R Sbjct: 471 GEERVQQLVDAG----LVESLADLYDLTV---ADLAELE---GWGETSAENLLAELEASR 520 Query: 547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD 606 L F+ +LGI VG AR+L A+E A + D +L V VG Sbjct: 521 EPPLADFLVALGIPEVGPTTARNL----------AREFGTFEAIMDADEEALRAVDDVGP 570 Query: 607 IIAQAIVEFYQNPRNICAVEALLKE-VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHK 665 +A+ I EF+ + RN ++ LL V P E ++ VFTG+L R + Sbjct: 571 TVAEEIREFFDSERNRAVIDDLLDHGVDPQ--PAESEGGDALDGLTFVFTGSLSGYTRSE 628 Query: 666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLLQQYNTT 724 AQE V G + +S TD ++VG+NPG SK + A+ V ++EE+F LL + Sbjct: 629 AQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAERGVA 688 Query: 725 L 725 L Sbjct: 689 L 689 >gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional. Length = 669 Score = 327 bits (840), Expect = 6e-90 Identities = 206/710 (29%), Positives = 358/710 (50%), Gaps = 63/710 (8%) Query: 14 IEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNG 73 + + E+ L++ I D YY S P + D YD R + +P+ + P Sbjct: 2 SKDIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPT- 60 Query: 74 PLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133 K G ++ +V HS P LSL+K+++++ L+ +I ++ ++EPK Sbjct: 61 --LKFGSDLLNDFKEVEHSFPILSLDKVYDLKLLKLWIEKM-DLENSNLGFDFGISVEPK 117 Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEV--RGEV 191 IDG I + Y+ G A RGDG G DV+ +R I +P L I E +E+ RGE+ Sbjct: 118 IDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVP----LFIDEKVELVLRGEI 173 Query: 192 YISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRY-LNFFVHGLGKTSEIF 250 YI+K +FL +N + KPY N RN ASGILRR++ ++ + L+ FV+ + S + Sbjct: 174 YITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDI-LYSSLE 228 Query: 251 AKGQYEMLQKMRCLGFPVNNGVR---QANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVD 307 K ++ K++ GF VN R N+ I++Y +++ R++ Y+IDG+V KV Sbjct: 229 LKTNHDAFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVS 288 Query: 308 EFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGAL 367 +F+L++ LG + P+W +++KF +++ DI +Q+GR+G +TPVA +E V + GA Sbjct: 289 DFALREILGYTSHHPKWSMAYKFESLSGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAF 348 Query: 368 ITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQP 427 ITNA+LHN+DYI + + VGD V + R G+VIP V++++ + Sbjct: 349 ITNASLHNQDYIDSI-----------GLNVGDVVKISRRGDVIP-AVELVIEKLSVGF-- 394 Query: 428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLG 487 F P CP C++ ++++ AH C + +ER+K+F S+ NI GL Sbjct: 395 FKIPDNCPSCKTALIKE---------GAHLFCVNNHCPSVIVERIKYFCSKKCMNIVGLS 445 Query: 488 KQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN 547 + ++F F+ + I D++T + ++ N+ GF D + NL SI + Sbjct: 446 DKTIEFLFEKK----FISSEIDLYTF------NFDRLINLKGFKDKRINNLKRSIEASKK 495 Query: 548 ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDI 607 + + S+GI+ +G L + N +I+ + L+++ +G+ Sbjct: 496 RPFSKLLLSMGIKDLGENTILLL---INNNLNSFDKISTLCQDREFALSKLLKIKGIGEK 552 Query: 608 IAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIEN-----KKLVFTGTLQKIQ 662 IA I+E + N + I K + + E +++ ++EN KK TG+ Sbjct: 553 IALNIIEAF-NDKIILDKFNFFKNLGFKM--EEDSINIDVENSFLFGKKFCITGSFNGYS 609 Query: 663 RHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEE 712 R + +T+ GA+ + +++ D ++VG+ G KL+KA LG+KIM+ Sbjct: 610 RSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANNLGIKIMSLF 659 >gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed. Length = 562 Score = 148 bits (377), Expect = 4e-36 Identities = 144/642 (22%), Positives = 245/642 (38%), Gaps = 157/642 (24%) Query: 13 SIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPN 72 S +A++E+++L+Q+++ DD Y++ K + D YD L+ R F + Sbjct: 26 SPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPE---PRD 82 Query: 73 GPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEP 132 PL + G KV H + ++K+ + + L +++ W ++P Sbjct: 83 VPLPPLNG-------KVLHPVAHTGVKKLADKQALARWMAGRSDLW-----------VQP 124 Query: 133 KIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVY 192 K+DG +T+ Y GK V A RG+G GED +A R IP IP+ L + ++ ++GE++ Sbjct: 125 KVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLPGALANLV-LQGELF 183 Query: 193 ISKNDFLALNDEMIAV--GRKPYANPRNAASGILRRLNPTDITRYLNFFV----HGLGKT 246 L + G N R +G++ R +P+ + FV G Sbjct: 184 ------LRREGHIQQQMGG----INARAKVAGLMMRKDPSPTLNQIGVFVWAWPDG---- 229 Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVS----------YYNEMKSIRSTLP 296 E L ++ GFP+ Q T H + + +Y R+ LP Sbjct: 230 ----PASMPERLAQLATAGFPLT----QRYT-HPVKNAEEVARWRERWY------RAPLP 274 Query: 297 YDIDGLVYKVDEFSLQKQLGE--RARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTP 354 + DG+V + ++ G + W ++ K+ Q + + +GRTG +T Sbjct: 275 FVTDGVVVR----QAKEPPGRYWQPGQGEWAVAWKYPPVQQVAEVRAVQFAVGRTGKITV 330 Query: 355 VARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGR-DIRVGDRVLVKRAGEVIPKV 413 V LEPV + ++ + G V R + DI GD+VLV AG+ IP++ Sbjct: 331 VLELEPVMLDDKRVSRVNI------------GSVRRWQQWDIAPGDQVLVSLAGQGIPRL 378 Query: 414 VDII--VNERH----PDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ 467 ++ ER PDA F S C A+ C Q Sbjct: 379 DKVVWRGAERTKPTPPDADRFHSLS-C-----------------FRASP------GCQEQ 414 Query: 468 QLERLKHFVSRDAFNIEGLGK---QQL---DFFFKSEDPAFSIRIPADIF---TLQRRQQ 518 L RL + ++G+G+ + L F +F L Q Sbjct: 415 FLARLVWLSGKQGLGLDGIGEGTWRALHQTGLF-------------EHLFSWLALTPEQ- 460 Query: 519 TSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQ 578 + N G G L+ N R R++ +LGI A + + S+Q Sbjct: 461 -----LANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNALDDR---SWQ 512 Query: 579 NFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR 620 + W L P +G+ A+ ++ F Q+P Sbjct: 513 QLLS-------RSEQQWQQL---PGIGEGRARQLIAFLQHPE 544 >gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated. Length = 309 Score = 61.0 bits (148), Expect = 1e-09 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 14/86 (16%) Query: 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--------- 694 + + + +VFTG L + R +A V +LG V + +++KT ++ Sbjct: 218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEM 277 Query: 695 GSKLEKAQQL-----GVKIMNEEQFL 715 +KL+KA L +K +NEE+FL Sbjct: 278 SNKLKKAIDLKKKGQNIKFLNEEEFL 303 >gnl|CDD|128588 smart00292, BRCT, breast cancer carboxy-terminal domain. Length = 80 Score = 55.1 bits (133), Expect = 7e-08 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 3/75 (4%) Query: 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKT-DIIIVGDNPGSKLE--KAQQL 704 + K V TG K +R + +E + LG V++ LS KT +IVG G KLE A L Sbjct: 4 KGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIAL 63 Query: 705 GVKIMNEEQFLFLLQ 719 G+ I+ E+ L L+ Sbjct: 64 GIPIVTEDWLLDCLK 78 >gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional. Length = 313 Score = 35.4 bits (82), Expect = 0.051 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%) Query: 668 EYVTQLGAVVSAILSRKTDIIIVGD-NPG-SKLEKAQQLGVKIMNEEQFLFLLQ 719 E + G S + R T +++ D P K A+QLGV +++E FL LL+ Sbjct: 253 ERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLR 306 >gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. Length = 654 Score = 30.8 bits (70), Expect = 1.3 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 6/51 (11%) Query: 357 RLEPVNIGGALITNATLHNEDYIKGLDASGKVMRG---GRDIRVGDRVLVK 404 RL+ I G LI +TLHN+ Y+ D + G G+ R+GDRV VK Sbjct: 591 RLDDNGIDG-LIHISTLHNDYYV--FDQEKMALIGKGTGKVYRIGDRVTVK 638 >gnl|CDD|179229 PRK01122, PRK01122, potassium-transporting ATPase subunit B; Provisional. Length = 679 Score = 30.5 bits (70), Expect = 1.8 Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 6/32 (18%) Query: 394 DIRVGDRVLVKRAGEVIPKVVDII-----VNE 420 ++R GD VLV+ AGE+IP ++I V+E Sbjct: 122 ELRKGDIVLVE-AGEIIPADGEVIEGVASVDE 152 >gnl|CDD|162397 TIGR01512, ATPase-IB2_Cd, heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase. . Length = 536 Score = 30.0 bits (68), Expect = 2.1 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 6/35 (17%) Query: 393 RDIRVGDRVLVKRAGEVIP---KVVD--IIVNERH 422 +++VGD V+V + GE +P V+ V+E Sbjct: 71 EELKVGDVVVV-KPGERVPVDGVVLSGTSTVDESA 104 >gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase. This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512. Length = 556 Score = 29.5 bits (67), Expect = 2.9 Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 3/26 (11%) Query: 393 RDIRVGDRVLVKRAGEVIPKVVDIIV 418 +++VGD V+V R GE IP VD +V Sbjct: 72 EELQVGDIVIV-RPGERIP--VDGVV 94 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 29.1 bits (66), Expect = 4.0 Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 11/64 (17%) Query: 552 RFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQA 611 +I + VG +AR+L +++ S + ++ + ++ L+ V +G+ A+ Sbjct: 714 EYIVE-SLPDVGPVLARNLLEHFGS-------VEAVMTASEEE---LMEVEGIGEKTAKR 762 Query: 612 IVEF 615 I E Sbjct: 763 IREV 766 >gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions. Length = 864 Score = 29.0 bits (65), Expect = 4.9 Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 15/93 (16%) Query: 340 LDIDIQIGRTGILTPVA-------RLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGG 392 L + I++ R GI T A R N+GGA + HN I+ + A+ + Sbjct: 698 LGVPIELIRAGIRTFDADAAQAPGRFNLFNLGGAHVLVDYGHNPAAIEAVGAAIRNWPAR 757 Query: 393 RDIRV----GDRV---LVKRAGEVIPKVVDIIV 418 R I V GDR LV++ GE++ D I+ Sbjct: 758 RRIGVIGGPGDRRDEDLVEQ-GELLGGAFDQII 789 >gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc. Length = 708 Score = 28.9 bits (65), Expect = 5.2 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%) Query: 570 LAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN 618 YYL + I+ I H L +I + L+ I Q I+ + Q Sbjct: 174 AGSYYLQ-----KIIDTYIPHKMMGTLGIISIGLIIAYIIQQILSYIQI 217 >gnl|CDD|184554 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional. Length = 284 Score = 28.6 bits (64), Expect = 7.0 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 14/56 (25%) Query: 687 IIIVGDNPGS------KLEKAQQLGVK--------IMNEEQFLFLLQQYNTTLRIH 728 +I+VGDNP S K A G K +++E+ L L+++YN H Sbjct: 37 VILVGDNPASQVYVRNKERSALAAGFKSEVVRLPETISQEELLDLIERYNQDPTWH 92 >gnl|CDD|162406 TIGR01536, asn_synth_AEB, asparagine synthase (glutamine-hydrolyzing). This model describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the phylogenetic tree (which typically were also second or third candidate members from their genomes) were removed from the seed alignment and score below trusted cutoff. Length = 467 Score = 28.1 bits (63), Expect = 7.6 Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 13/99 (13%) Query: 44 LDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEK--- 100 E +A+ R D IAH PD + E +G N I G L++ ++ +S E Sbjct: 11 AVEEDEAILRMSDTIAHRGPDASGIEYKDG--NAILGHRRLAIIDLSGGAQPMSNEGKTY 68 Query: 101 -------IWNIEDLRK-FITRIYRFWQKKDDNSIFFTLE 131 I+N E+LR+ + Y F D I E Sbjct: 69 VIVFNGEIYNHEELREELEAKGYTFQTDSDTEVILHLYE 107 >gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional. Length = 876 Score = 28.3 bits (64), Expect = 7.9 Identities = 7/28 (25%), Positives = 16/28 (57%) Query: 96 LSLEKIWNIEDLRKFITRIYRFWQKKDD 123 +++E+ W+IE+ + R Y + D+ Sbjct: 436 MAIERPWDIEEAYNIVRRAYPYRDLSDE 463 >gnl|CDD|148092 pfam06277, EutA, Ethanolamine utilisation protein EutA. This family consists of several bacterial EutA ethanolamine utilisation proteins. The EutA protein is thought to protect the lyase (EutBC) from inhibition by CNB12. Length = 473 Score = 28.0 bits (63), Expect = 9.8 Identities = 30/121 (24%), Positives = 46/121 (38%), Gaps = 22/121 (18%) Query: 333 KQASTRLLDIDIQIGRTGI-LTPVARLEP---VNIGGALITNATLHNEDYIKGLDASGKV 388 K+ T +L+IDI G T + L + ++IGG LI YI S K Sbjct: 139 KEHHTTVLNIDIGGGTTNLALFENGEVIDTACLDIGGRLIKIDPTGRITYI-----SPKG 193 Query: 389 MR----GGRDIRVGDRVLVKRAGEVIPKVVDIIVN-----ERHPDAQPF----SFPSFCP 435 R G ++ VGDR ++ +V ++ ++ P AQ P Sbjct: 194 RRLIAELGLELEVGDRATPEQLDQVCREMAQLLEEVLGGQPESPLAQLLMTTKPLPGLDR 253 Query: 436 I 436 I Sbjct: 254 I 254 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 0.321 0.138 0.400 Gapped Lambda K H 0.267 0.0799 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 12,288,064 Number of extensions: 835934 Number of successful extensions: 1833 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1780 Number of HSP's successfully gapped: 38 Length of query: 731 Length of database: 5,994,473 Length adjustment: 100 Effective length of query: 631 Effective length of database: 3,833,673 Effective search space: 2419047663 Effective search space used: 2419047663 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: 61 (27.1 bits)