RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780952|ref|YP_003065365.1| DNA helicase II [Candidatus Liberibacter asiaticus str. psy62] (685 letters) >gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]. Length = 655 Score = 499 bits (1286), Expect = e-142 Identities = 246/650 (37%), Positives = 363/650 (55%), Gaps = 32/650 (4%) Query: 28 KGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQA 87 LN +Q AV PD PLL+LAGAG+GKT VL R+ +LI + P +ILA+TFTN+A Sbjct: 1 SKLNPEQREAVLHPDG-PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKA 59 Query: 88 IQEMKNRLACYLG---EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQ 144 EM+ RL LG + + TFHSF ILR+HGE +GL +F ILDS + +IK+ Sbjct: 60 AAEMRERLLKLLGLPAAEGLTVGTFHSFALRILRRHGERLGLNANFTILDSDDQLALIKE 119 Query: 145 LLKDLQ-IDDKDYDPHEVIEKIDYWQNRGWNPKDIP----QSSLTEDAEIPKAIYIQYVA 199 LL+ +DDK+ P E + I +N +P + + +E + +Y +Y Sbjct: 120 LLRRELNLDDKELLPREALRYISEAKNALLSPLEASALLLAAIKSEAEKKLAELYEEYQE 179 Query: 200 YLQKTKSCDFGGLIIKTIEVL-HHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQK 258 L+ + DF L++ + +L +P VL+ + YI+VDE+QD N QY LL+LL Sbjct: 180 LLRLNNALDFDDLLLLALRLLEENPEVLEALQARFRYILVDEFQDTNPLQYELLKLLAGN 239 Query: 259 EDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTAN 318 A + VGD++Q IY +RGA +IL+F+KDF A +IKLEQNYRST +IL AN Sbjct: 240 -----AANLFVVGDDDQSIYGFRGADPENILDFEKDFPAAKVIKLEQNYRSTPNILAAAN 294 Query: 319 KLISHNKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIIN-IQNTGMSLNNIA 377 K+I++NK+R K L T+ + KV + ++ + E I EI I+ ++ ++IA Sbjct: 295 KVIANNKKRQAKTLRTEVE-GSGEKVVLLLANDEEDEARWIASEIDALIEIGKVNYSDIA 353 Query: 378 ILVRTSWQTRKFEDAFLEQEIPHKVIGG--SFYDRQEIRDALAYFRLVCQEHRDEDFKRI 435 IL RT+ Q+R E+A IP++++ G SF++R+EI+D LAY RLV D F RI Sbjct: 354 ILYRTNAQSRLIEEALRAAGIPYRIVIGGTSFFERKEIKDLLAYLRLVLNPDDDAAFLRI 413 Query: 436 INCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNN 495 +N PKRGIG +L K+ A + ++SLL+A + L+ + + L +F + I Sbjct: 414 LNLPKRGIGDATLKKLLELARERNLSLLEALKALLSFIRLSERGLALLLDFAELIEELRE 473 Query: 496 CSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSII----EKHETLEGF 551 + +LE GY+ S +++RL+NL ELL ++ E E+L F Sbjct: 474 AILLSTALELIRELLEALGYLEALLEAGSLVAAEDRLENLEELLDVLKRYAEPRESLRAF 533 Query: 552 VLQAPLRENLGSF--IPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGN-- 607 + + L N + + +MT+HAAKGLEF VF+ G E+GL P S++EG+ Sbjct: 534 LSELSLLANDEEEEEPDEDGQVNLMTIHAAKGLEFPYVFLVGLEEGLFPADRSLDEGDEP 593 Query: 608 VEGERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657 +E ERRL YV ITRAKKK +L Y +R+ E S+F+ EL Sbjct: 594 LEEERRLLYVAITRAKKKLYLTYAASRKLWGKEVEEEP-----SRFVSEL 638 >gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family. Length = 494 Score = 392 bits (1008), Expect = e-109 Identities = 195/505 (38%), Positives = 285/505 (56%), Gaps = 30/505 (5%) Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89 LN +Q AVT PLL+LAGAGTGKT VL R+ +LI I P +ILA+TFTN+A + Sbjct: 1 LNPEQRKAVT-HLGGPLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAR 59 Query: 90 EMKNRLACYLGEKIPR---IQTFHSFCASILRKHGEVVG-LPTDFAILDSAESRTIIKQL 145 EMK R+ LG+ I TFHSFC ILRK+ +G L +F+ILD + ++K++ Sbjct: 60 EMKERILKLLGKAEASELNISTFHSFCLRILRKYANRIGDLLPNFSILDELDQLALLKEI 119 Query: 146 LKDLQIDDKDYDPH------EVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKA--IYIQY 197 LK D D D E+ E I +N +P+++ Q+S A Y +Y Sbjct: 120 LKK---DRLDLDSKLLRPLLELKELISKAKNELLSPEELQQASYAATPRDKLAAEFYQEY 176 Query: 198 VAYLQKTKSCDFGGLIIKTIEVLH-HPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLC 256 L++ + DF L++ T+E+L P +L+ Y E+ YI+VDE+QD N QY LL+LL Sbjct: 177 QERLKENNALDFDDLLLLTLELLRSDPELLEAYRERFKYILVDEFQDTNPIQYELLKLLA 236 Query: 257 QKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNT 316 + VGD +Q IY +RGA +IL F+KDF A +I LEQNYRST ILN Sbjct: 237 -----GGHPNLFLVGDPDQSIYGFRGADIENILKFEKDFPAAKVITLEQNYRSTPEILNA 291 Query: 317 ANKLISHNKQRFDK-KLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTG--MSL 373 ANKLIS+N R +K L++Q+ KV+++ ++++ E I EI + +G + Sbjct: 292 ANKLISNNTARKEKRLLWSQKG--SGEKVTVYEAETEQEEAEFIADEIKALHKSGAAIPF 349 Query: 374 NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDF 432 +IA+LVR++ Q+R E+A L+ IP+K++GG SF+DR+EI+D LA RL+ D Sbjct: 350 GDIAVLVRSNSQSRAIEEALLKAGIPYKILGGLSFFDRKEIKDLLALLRLIDNPKDDLAL 409 Query: 433 KRIINCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIR--QSLQNFVKDI 490 RI+N PKRGIG +L K++ A ISL +A +L++ R + L F+ I Sbjct: 410 LRILNTPKRGIGPTTLDKLRNLAKDRQISLFKALNQLLEKLNELLSARAYKKLLLFLALI 469 Query: 491 RRWNNCSKKMDPAPIANMILEQSGY 515 ++ + + +LE GY Sbjct: 470 EELEKLLLEILLEALLDEVLELLGY 494 >gnl|CDD|31272 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]. Length = 1139 Score = 144 bits (365), Expect = 6e-35 Identities = 104/528 (19%), Positives = 174/528 (32%), Gaps = 100/528 (18%) Query: 191 KAIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPH--VLKKYHEKIPYIMVDEYQDINTPQ 248 + + +Y A ++ + DF LI + ++L + + E+ P+I++DE+QD + Q Sbjct: 335 EELIERYDAEKRQRNALDFDDLIHRLAKLLTSEGEELAESLREQYPHILIDEFQDTDPQQ 394 Query: 249 YLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYR 308 + +L L + VGD Q IY +RGA L K I LE NYR Sbjct: 395 WRILSRLFAGFKAGNRTLFL-VGDPKQSIYRFRGADIFTFLEAASSEKAFARITLETNYR 453 Query: 309 STTHILNTANKLISHNKQRFDK---------------------------KLFTQRDCHDD 341 ST +LN N L + F + + Sbjct: 454 STPELLNAVNALFKQAMFAYPGEIDYDPVAELGARNGSPGSVNGEPLPALKFWEEEDDWT 513 Query: 342 AKVSIHVSQSDN-SELSTIIQEIINIQNTG--------MSLNNIAILVRTSWQTRKFEDA 392 A + + E I + + + +IA+LVR+ + E A Sbjct: 514 APENEEDEREIADLEARQIAAWLRELIEGEAVLDGERPIRAGDIAVLVRSRNEAAAIERA 573 Query: 393 FLEQEIPHKVIGG---SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKRGIGKESLH 449 + I V S ++ E +D LA R + D ++ P G+ ++ L Sbjct: 574 LKKAGII-PVYLSNRSSLFETLEAQDLLALLRAILNPEDDLPLAALLRSPLFGLTEDDLA 632 Query: 450 KIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMI 509 L E + + + F + W +K + Sbjct: 633 ------------ALAQDEAEWEFLWENLRQLADIWRFRGVLAMWRALAKITPLHDLIAER 680 Query: 510 LEQSGYMAMWKNNKSSEKSQERLDNLRELLSIIEKHET-----LEGFVLQAPLRENLGSF 564 L + N + L+ELL+ +E LE F+ + Sbjct: 681 LLSTNLGERDLTNGL-----HAQELLQELLTRALSYEHGLLRWLERFI-ALIENNDEEQA 734 Query: 565 I---PDSNCIQIMTLHAAKGLEFDTVFISG-------------------------WEQGL 596 D + ++IMT+H +KGLEF VF+ + Sbjct: 735 RRLESDRDLVRIMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKS 794 Query: 597 LPHQLS------INEGNVEGERRLAYVGITRAKKKCHLFYTINRRTHD 638 P S E + E RL YV +TRAK++ L ++R Sbjct: 795 YPTPESQANKELAEEEALAEELRLLYVALTRAKEQLILIGAPSKREKS 842 Score = 75.9 bits (186), Expect = 3e-14 Identities = 41/163 (25%), Positives = 62/163 (38%), Gaps = 43/163 (26%) Query: 46 LLILAGAGTGKTTVLIARMLHLICHKE-IPPSKILAMTFTNQAIQEMKNRLACYLGEKIP 104 +L+ A AGTGKT VL R+L L+ + +IL +TFT A EMK R+ L E + Sbjct: 19 VLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLKEALQ 78 Query: 105 ----------------------------------------RIQTFHSFCASILRKHGEVV 124 I T H FC ILR+ Sbjct: 79 ENDEKLASDDELLEALAALIQALIQAIRLFALALETNDEAAIFTIHGFCQRILRQFALEA 138 Query: 125 GLPTDFAILDSAESRTIIKQLLKDLQIDDKDYDPHEVIEKIDY 167 G+ DF +L+ + + +L++D P E+ + + Sbjct: 139 GISFDFELLE--DESDLFLELVEDFWRRRFYPLPAELAQLVAQ 179 >gnl|CDD|37319 KOG2108, KOG2108, KOG2108, 3'-5' DNA helicase [Replication, recombination and repair]. Length = 853 Score = 143 bits (363), Expect = 1e-34 Identities = 147/643 (22%), Positives = 229/643 (35%), Gaps = 70/643 (10%) Query: 26 YLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTN 85 LN Q + P ++AG G+GKT VL R+ +LI I P +IL T TN Sbjct: 10 LYSLLNKSQRFSALSPLRR-KRVIAGPGSGKTLVLTERVAYLINFNNIKPDEILINTGTN 68 Query: 86 QAIQEMKNRLACYLG-----EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRT 140 +A +K L L ++I I TFHS + G ++ L + I D ++ Sbjct: 69 KAADSIKLNLIAILRTSKCSKEI--IGTFHSIAVKYSLRDGPLLPLSENCRIQDLPDTYA 126 Query: 141 IIKQLLKDL--QIDD---------KDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEI 189 I+ + L +I + P + N I L E Sbjct: 127 ILGDNIWALLAKIKLPSSSSNRKQRLLFPLRRPDSTVTKPNVTETLYSIAVLLLAMFEEG 186 Query: 190 PK-----AIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDI 244 I Y YLQ + D L + +++VL P V KI +++VDE+QDI Sbjct: 187 INVSNRDDYEIYYYLYLQTLE--DSCTLAMNSLKVLQRPRVCSN---KITHVLVDEFQDI 241 Query: 245 NTPQYLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDAN---II 301 Q L++L + GD +Q IY++ G + I F Sbjct: 242 LKIQLEPLQVL-------KIKAFAGTGDTDQSIYKFAGKW-AEIRILYVTFNKFIATQAE 293 Query: 302 KLEQNYRSTTHILNTANKLISHNKQRFDKK-LFTQRDCHDDAKVSIHVSQSDNSELSTII 360 +L N RS I + A I Q K L + + + + Sbjct: 294 RLFPNNRSCKTIHSLAYGAIGRQYQEKKKLLLRKLTPS--ELNSVLAEFKGGFPKAKLKC 351 Query: 361 QEIINIQNTGMSL---NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDA 416 + N N+ AIL +S Q FE +EQ +K+I SF D E R Sbjct: 352 RTEENFLVAADIEFTINDHAILWCSSSQLSSFESVLVEQREKYKLIAVASFLDSNERRLG 411 Query: 417 LAYFRLVCQEHRDEDFKRIINCPKRGIGKESLHKIQYHASQ------HHISLLQASEKLI 470 L Y +L D K ++ P+R G I +Q ++ L+Q + Sbjct: 412 LNYEKLHANMTPDGYLK-LLQLPERPNGLAKFDYIILDEAQDCTPCIQNLILIQKHNIKV 470 Query: 471 DSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQE 530 G F I R N+ + P + + + K E E Sbjct: 471 FVGDFHQSI--------YSFRGANSALFNLATLPDTLVECLTKSFRFGNEVAKVKETILE 522 Query: 531 RLDNLRELLSIIEKHETLEGFVLQAPLRENLGSFIPDSNC-----IQIMTLHAAKGLEFD 585 + +R+L + H ++ L S + +QI TLH+AKGLE+ Sbjct: 523 KKKRVRKLTLVSNNHFYFLSIPGDVSGQKFLLSRTLSNLTQEEEELQISTLHSAKGLEWP 582 Query: 586 TVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHL 628 V I + ++P + + + V TRA++ HL Sbjct: 583 VVSIGLCRENIIPILFQ---DEEDEDGQNLVVKDTRARRLLHL 622 Score = 31.1 bits (70), Expect = 1.0 Identities = 24/75 (32%), Positives = 30/75 (40%), Gaps = 8/75 (10%) Query: 559 ENLGSFIPDS-NCIQIMTLHAAKGLEFDTVFIS-------GWEQGLLPHQLSINEGNVEG 610 EN D + + T+H AKGLEFD V + G E E Sbjct: 662 ENFHIRDLDKAENVILGTIHQAKGLEFDNVHLQNDFVKVFGSVSNFERLPSFRVETYNED 721 Query: 611 ERRLAYVGITRAKKK 625 E YV +TRAKK+ Sbjct: 722 EWNFLYVAVTRAKKR 736 >gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination and repair]. Length = 649 Score = 42.3 bits (99), Expect = 5e-04 Identities = 29/133 (21%), Positives = 55/133 (41%), Gaps = 7/133 (5%) Query: 25 NYLKGLNAQQTHAVT--IPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT 82 + K LN+ Q AV+ I + L+I GTGKT L+ + L+ K+ ++L Sbjct: 181 FFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK----RVLVCA 236 Query: 83 FTNQAIQEMKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTII 142 +N A+ + RL +L + R+ S+ +++ D + S+ I Sbjct: 237 PSNVAVDNIVERLT-HLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDISKDID 295 Query: 143 KQLLKDLQIDDKD 155 K+ + + Sbjct: 296 ILFQKNTKTKNDK 308 >gnl|CDD|110446 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Length = 226 Score = 37.4 bits (87), Expect = 0.014 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 9/59 (15%) Query: 571 IQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629 ++ T+H +GL FD+V + + + L YV +TR +K H+ Sbjct: 176 VRATTVHEVQGLTFDSVTL---------VLDKDTDLLSISDPELLYVALTRHRKSLHIL 225 >gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]. Length = 696 Score = 36.6 bits (84), Expect = 0.022 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 12/56 (21%) Query: 574 MTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629 MT+H ++G EFD V + LLP + R L Y ITRA+ + L+ Sbjct: 625 MTIHKSQGSEFDRVIV------LLP------SHSPMLSRELLYTAITRARDRLILY 668 >gnl|CDD|33753 COG3972, COG3972, Superfamily I DNA and RNA helicases [General function prediction only]. Length = 660 Score = 35.4 bits (81), Expect = 0.048 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 2/66 (3%) Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89 + QT A I AG+GKT +L + L H + P S+I FT Sbjct: 163 FDTDQTKAAFQSGFGKQRIRGLAGSGKTELLAHKAAEL--HSKNPDSRIAFTFFTKILAS 220 Query: 90 EMKNRL 95 M+ + Sbjct: 221 TMRTLV 226 >gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA processing and modification]. Length = 673 Score = 32.7 bits (74), Expect = 0.39 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 12/106 (11%) Query: 46 LLILAGAGTGKTTVLIARMLHLICH--------KEIPPSKILAMTFTN---QAIQEMKNR 94 + +A G+GKT + +L I I + + T Q I+E N+ Sbjct: 285 PIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNK 344 Query: 95 LACYLGEKIPRIQTFHSFCASILR-KHGEVVGLPTDFAILDSAESR 139 LG + + SF + G + + T ++DS E+R Sbjct: 345 FGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENR 390 >gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]. Length = 654 Score = 32.0 bits (72), Expect = 0.48 Identities = 35/261 (13%), Positives = 64/261 (24%), Gaps = 46/261 (17%) Query: 37 AVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLA 96 A + LLI A GTGKT + L + K++ T T +++ Sbjct: 28 AEALKGGEGLLIEAPTGTGKTLAYLLPALA---YAREEGKKVIISTRTKALQEQLLEED- 83 Query: 97 CYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAE-----SRTIIKQLLKDLQI 151 L H + L FA+L SR L Sbjct: 84 --------------------LPIHKLLKKLGGKFALLKGRSNYLCLSRLERLAQLGGDDD 123 Query: 152 DDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKTKSCDFGG 211 D + + + W + D + + + C + Sbjct: 124 DYLQSLALKALADLLVWLTETKTGDLRELTPKALDDPLWTL--VTDDKDSCLGEDCPY-- 179 Query: 212 LIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGARICCVG 271 + Y + + LL + ++ V Sbjct: 180 ------------YTECFYFPARKEAENADLV-VTNHALLLADVALEESRILLPENDVVVF 226 Query: 272 DENQCIYEWRGAQFSHILNFQ 292 DE + + + S L+ + Sbjct: 227 DEAHNLPDIARSALSIRLSER 247 >gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]. Length = 935 Score = 31.9 bits (72), Expect = 0.66 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 6/85 (7%) Query: 23 VPNYLKGLNAQQTHAVTIPDDTPLLILAGA-GTGKTTVLIARMLHLICHKEIPPSKILAM 81 VPN K LNA Q++AV PL ++ G GTGKT + HL P +L Sbjct: 405 VPNLPK-LNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGP---VLVC 460 Query: 82 TFTNQAIQEMKNRLACYLGEKIPRI 106 +N A+ ++ ++ G K+ R+ Sbjct: 461 APSNIAVDQLAEKIH-KTGLKVVRL 484 >gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General function prediction only]. Length = 747 Score = 31.1 bits (70), Expect = 0.91 Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 1/89 (1%) Query: 30 LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLIC-HKEIPPSKILAMTFTNQAI 88 + +Q + + L++ AG+GKTT+ + R+ +L+ ++ +K + + N+ Sbjct: 213 IQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVF 272 Query: 89 QEMKNRLACYLGEKIPRIQTFHSFCASIL 117 E +R+ LGE+ +TF + +IL Sbjct: 273 LEYISRVLPELGEEGVVQETFEEWALAIL 301 Score = 31.1 bits (70), Expect = 0.95 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 10/59 (16%) Query: 573 IMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLFYT 631 ++ ++ AKGLEFD V + SI E E + R YV +TRA ++F Sbjct: 697 VIPVYDAKGLEFDHVIV---------VDPSIVE-ETEQDLRDLYVAVTRALHSLYIFGE 745 >gnl|CDD|153410 cd07956, Anticodon_Ia_Arg, Anticodon-binding domain of arginyl tRNA synthetases. This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA. Length = 156 Score = 31.0 bits (71), Expect = 1.2 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%) Query: 100 GEKIPRIQTFHSFCASILRKHGEVVGLPTDFAI--LDSAESRTIIKQLLK 147 G+ P +Q H+ SILRK GE + D + L + R +I L K Sbjct: 33 GDTGPYLQYAHARLCSILRKAGETIEAEADADLSLLPEPDERDLILLLAK 82 >gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 577 Score = 30.6 bits (69), Expect = 1.4 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 5/65 (7%) Query: 100 GEKIPRIQTFHSFCASILRKHGE--VVGLPTDFAILDSAESRTIIKQLLK---DLQIDDK 154 G P +Q H+ SILRK GE + A+L E R ++K+LL+ L+ + Sbjct: 453 GNTAPYVQYAHARICSILRKAGEDELDLSTEADALLTELEERELVKKLLEFPEVLEEAAE 512 Query: 155 DYDPH 159 + +PH Sbjct: 513 ELEPH 517 >gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3 [Energy production and conversion, Replication, recombination and repair]. Length = 351 Score = 30.3 bits (68), Expect = 1.9 Identities = 29/132 (21%), Positives = 55/132 (41%), Gaps = 23/132 (17%) Query: 32 AQQTHAVTIPDDTPLLILAG-AGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQE 90 A +++ D P L++ G +G GK T ++ +L + + KI TFT + Sbjct: 22 ANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMC-LLRELYGVGVEKLKIETRTFTTPS--- 77 Query: 91 MKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQLLKDLQ 150 +K+ I T S H E+ P+D D + ++K++ + Q Sbjct: 78 ---------KKKL-EISTVSS------NYHLEIT--PSDAGNYDRVVIQELLKEVAQTQQ 119 Query: 151 IDDKDYDPHEVI 162 I+ + P +V+ Sbjct: 120 IETQGQRPFKVV 131 >gnl|CDD|147737 pfam05746, DALR_1, DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids. Length = 117 Score = 29.9 bits (68), Expect = 2.1 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 110 HSFCASILRKHGE-VVGLPTDFAILDSAESRTIIKQLLK 147 H+ SILRK GE + L D +L E + ++K LL+ Sbjct: 5 HARICSILRKAGELGINLDIDALLLLEEEEKELLKALLQ 43 >gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]. Length = 403 Score = 29.6 bits (66), Expect = 3.3 Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%) Query: 41 PDDTPLLILAGAGTGKTTVLIARMLHLICHK 71 P P+LI+ GTGK L AR++H + + Sbjct: 99 PSGLPVLIIGETGTGKE--LFARLIHALSAR 127 >gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication, recombination and repair]. Length = 1100 Score = 29.2 bits (65), Expect = 3.9 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 10/81 (12%) Query: 20 PSCVPNYLKGLNAQQTHAV--TIPDDTPLLILAGAGTGKTTVL--IARMLHLICHKEIPP 75 P L LN Q A+ + + LIL GTGKTT + + ++L + Sbjct: 660 PKIKKIILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVAL------G 713 Query: 76 SKILAMTFTNQAIQEMKNRLA 96 K+L ++T+ A+ + +L Sbjct: 714 KKVLLTSYTHSAVDNILIKLK 734 >gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.. Length = 144 Score = 28.9 bits (64), Expect = 4.3 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%) Query: 46 LLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT--FTNQAIQEMKNRLACYL 99 +L+ A G+GKT + +L L+ + +LA T NQ + +K + Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGI 58 >gnl|CDD|30845 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme metabolism]. Length = 420 Score = 29.0 bits (65), Expect = 4.3 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 9/58 (15%) Query: 36 HAVTIPDDTPLLILAGAGTGKTTVLIA--RMLHLIC---HKEIPPSKILAMTFTNQAI 88 AV + P + GK +L+A R+++L H PS+++ M+F NQA+ Sbjct: 310 LAVEKREVRPQVDEYELPDGKRIILLAEGRLVNLAAATGH----PSEVMDMSFANQAL 363 >gnl|CDD|33289 COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 436 Score = 28.7 bits (64), Expect = 5.7 Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 18/83 (21%) Query: 608 VEGERRLAYVGITRAKKKC--HLFYTINRRTHD---FTRVERYQPSQVSQFLLELYDPSH 662 + +R + +G ++ + L + + + TR + P S+F LE + P Sbjct: 184 LLQKRSVTVIGSGQSAAEIFLDLLNSQPPQDYQLNWITRSSGFLPMDYSKFGLEYFSPE- 242 Query: 663 TQEIIYDDIYGTFSEHWNQIPEP 685 +++++ +P Sbjct: 243 ------------YTDYFYGLPPE 253 >gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.. Length = 226 Score = 28.7 bits (64), Expect = 5.8 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%) Query: 19 VPSCVPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVL--IARMLH 66 V N+ K ++ + + IL +G+GKTT+L I+ + Sbjct: 9 VGLKAKNWNKYARILNDVSLHVESGQVMAILGSSGSGKTTLLDAISGRVE 58 >gnl|CDD|31309 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]. Length = 767 Score = 28.4 bits (62), Expect = 6.6 Identities = 20/117 (17%), Positives = 41/117 (35%), Gaps = 10/117 (8%) Query: 557 LRENLGSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAY 616 +R L +++ T+ +G E D + +S L+ E G+ R Sbjct: 661 IRRLLNEAGKG---VEVGTVDGFQGREKDVIILS-----LVRSNDDKGEIGFLGDPRRLN 712 Query: 617 VGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLELYDPSHTQEIIYDDIYG 673 V +TRAK+K + + T + + + + + + L + D Sbjct: 713 VALTRAKRKLIVVG--SSSTLESDPLYKRLINDLKRKGLLAELNLLDLRLTDLDDES 767 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 28.6 bits (65), Expect = 6.6 Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%) Query: 46 LLILAGAGTGKTTVL--IAR 63 + I G+GTGKT +L IAR Sbjct: 18 IGIFGGSGTGKTVLLGMIAR 37 >gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like. This group is related to formaldehyde dehydrogenase (FDH), which is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. This family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Another member is identified as a dihydroxyacetone reductase. Like the zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly bound redox cofactor (similar to nicotinamide proteins). The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Length = 345 Score = 28.4 bits (64), Expect = 7.0 Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 1/13 (7%) Query: 12 HILKGDFVPSCVP 24 HILKGD VP+ P Sbjct: 43 HILKGD-VPTVTP 54 >gnl|CDD|147761 pfam05785, CNF1, Rho-activating domain of cytotoxic necrotizing factor. This family consists of several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of rabbit skin and re-organisation of the actin cytoskeleton in cultured cells. Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin which is composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain. Length = 281 Score = 28.1 bits (63), Expect = 7.5 Identities = 14/37 (37%), Positives = 21/37 (56%) Query: 23 VPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTV 59 V N +G N + +P+ PL+I +GA +G TTV Sbjct: 101 VSNGARGTNGIKIALSEVPEGKPLIITSGALSGCTTV 137 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.321 0.136 0.409 Gapped Lambda K H 0.267 0.0706 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,468,239 Number of extensions: 455795 Number of successful extensions: 1334 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1305 Number of HSP's successfully gapped: 39 Length of query: 685 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 585 Effective length of database: 4,102,837 Effective search space: 2400159645 Effective search space used: 2400159645 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 (27.3 bits)