RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780382|ref|YP_003064795.1| ATP dependent RNA helicase protein [Candidatus Liberibacter asiaticus str. psy62] (465 letters) >gnl|CDD|183308 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional. Length = 460 Score = 344 bits (884), Expect = 4e-95 Identities = 155/385 (40%), Positives = 227/385 (58%), Gaps = 18/385 (4%) Query: 1 MDFADLGLSPKVVCAVLDA-GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPM 59 F+ L L P ++ A L+ GY + TPIQ +++P +L DV A+TG+GKTA+F L + Sbjct: 4 TAFSTLPLPPALL-ANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGL 62 Query: 60 LTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN-YNLTVALLIGGIPFEAQNKK 118 L L+ R RV+ L+L PTRELA QVA + + N+ V L GG+P Q Sbjct: 63 LQKLDVKRFRVQ---ALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDS 119 Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTR 178 LE GA +++ TPGRILDH +G L ++ + LV+DEADRMLDMGF I I P R Sbjct: 120 LEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARR 179 Query: 179 QTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQL 238 QTLLFSAT + + +S+ F ++P ++V + IE F ++ LQ+L Sbjct: 180 QTLLFSATYPEGIAAISQRFQRDPVEVKVESTHD-LPAIEQRFYEV--SPDERLPALQRL 236 Query: 239 L---QSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT 295 L Q + ++FCN KK + +L QGFS A+HG+++QR R ++L F + Sbjct: 237 LLHHQPESC----VVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRS 292 Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355 ++VA+D+AARGLDI + V N+++ E ++HRIGRTGRAG G A +LVA E+++ Sbjct: 293 CSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQ 352 Query: 356 HIDAIEKLIEKKVDWLNGDLSSLNP 380 +AIE + +K++W L SL+P Sbjct: 353 RANAIEDYLGRKLNW--EPLPSLSP 375 >gnl|CDD|182572 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional. Length = 456 Score = 332 bits (854), Expect = 9e-92 Identities = 168/377 (44%), Positives = 234/377 (62%), Gaps = 18/377 (4%) Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 M F LGLSP ++ AV + GY +PTPIQ + IP VL+ D+ AQTGTGKTA F LP+L Sbjct: 1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLL 60 Query: 61 TILE------KGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEA 114 L KGR R R LIL PTRELAAQ+ +N Y K N+ ++ GG+ Sbjct: 61 QHLITRQPHAKGR---RPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINP 117 Query: 115 QNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLV 174 Q KL G DVL+ TPGR+LD ++ + ++ +EILV+DEADRMLDMGFI I+ + + + Sbjct: 118 QMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKL 177 Query: 175 PFTRQTLLFSATMTDELQKVSENFLQNPKRIEV---NTPSSTAETIEHCFVATYAQYSKK 231 P RQ LLFSAT +D+++ ++E L NP IEV NT S H FV +K Sbjct: 178 PAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVH-FV----DKKRK 232 Query: 232 CALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNF 291 LL Q++ + + ++F K +L L K G AIHGN Q +R + L++F Sbjct: 233 RELLSQMI-GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291 Query: 292 KEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAK 351 K G I+++VA+D+AARGLDI ++ HV N+++PN E+Y+HRIGRTGRA G+A +LV Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV 351 Query: 352 EDIKHIDAIEKLIEKKV 368 ++ K + IEKL++K++ Sbjct: 352 DEHKLLRDIEKLLKKEI 368 >gnl|CDD|183029 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional. Length = 434 Score = 314 bits (808), Expect = 2e-86 Identities = 146/381 (38%), Positives = 211/381 (55%), Gaps = 24/381 (6%) Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 F++L L ++ A+ D GY +PT IQ + IP L DV G A TGTGKTA+F+LP L Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60 Query: 61 -TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL 119 +L+ R + PR LIL PTRELA QVAD + K+ +L +A + GG+ + + Sbjct: 61 QHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF 120 Query: 120 ERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179 D+++ TPGR+L + +E L++DEADRMLDMGF I+ I + + +Q Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQ 180 Query: 180 TLLFSATMTDE-LQKVSENFLQNPKRIEVNTPSST----------AETIEHCFVATYAQY 228 TLLFSAT+ + +Q +E L +P +E A+ +EH Sbjct: 181 TLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEH--------- 231 Query: 229 SKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKIL 288 K ALL LL+ Q + I+F ++ V L L K G + C + G + Q R + + Sbjct: 232 --KTALLCHLLK-QPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAI 288 Query: 289 SNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTL 348 +G + ++VA+D+AARG+DI DV HV NFD+P A+ Y+HRIGRTGRAGR G A +L Sbjct: 289 KRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISL 348 Query: 349 VAKEDIKHIDAIEKLIEKKVD 369 V D + IE+ IE+ + Sbjct: 349 VEAHDHLLLGKIERYIEEPLK 369 >gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional. Length = 629 Score = 294 bits (755), Expect = 3e-80 Identities = 142/379 (37%), Positives = 232/379 (61%), Gaps = 10/379 (2%) Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 FADLGL ++ A+ D GY KP+PIQ + IP +L DV G+AQTG+GKTA+F LP+L Sbjct: 6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65 Query: 61 TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN-YNLTVALLIGGIPFEAQNKKL 119 L+ ++ P+ L+L PTRELA QVA+ + K+ + V L GG ++ Q + L Sbjct: 66 HNLD---PELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL 122 Query: 120 ERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179 +G +++ TPGR+LDH RG L ++ + LV+DEAD ML MGFI ++ I + +P Q Sbjct: 123 RQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQ 182 Query: 180 TLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLL 239 T LFSATM + +++++ F++ P+ + + + +T I + + +K L + L Sbjct: 183 TALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGM--RKNEALVRFL 240 Query: 240 QSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLM 299 +++D IIF K + + +LE+ G++ A++G+++Q R + L K+G + ++ Sbjct: 241 EAED-FDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDIL 299 Query: 300 VASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED---IKH 356 +A+D+AARGLD+ + V N+D+P +E+Y+HRIGRTGRAGR G+A V + +++ Sbjct: 300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRN 359 Query: 357 IDAIEKLIEKKVDWLNGDL 375 I+ KL +V+ N +L Sbjct: 360 IERTMKLTIPEVELPNAEL 378 >gnl|CDD|179884 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional. Length = 423 Score = 289 bits (743), Expect = 8e-79 Identities = 149/406 (36%), Positives = 223/406 (54%), Gaps = 15/406 (3%) Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLP---- 58 F+D L P+VV A+ G+ TPIQ +PL L DV G AQTGTGKT +F+ Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69 Query: 59 MLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK 118 +L+ +V PR LI+ PTRELA Q+ + E + L + L GG ++ Q K Sbjct: 70 LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129 Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFT- 177 LE G D+LI T GR++D+ + + + I+++V+DEADRM D+GFI I+ + +P Sbjct: 130 LESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPAN 189 Query: 178 -RQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETI-EHCFVATYAQYSKKCALL 235 R +LFSAT++ +++++ + NP+ +EV T I E F Y +K LL Sbjct: 190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELF---YPSNEEKMRLL 246 Query: 236 QQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT 295 Q L++ ++ IIF N K + L G V + G++ Q+ R++IL F G Sbjct: 247 QTLIE-EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGD 305 Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355 + ++VA+D+AARGL IP V HVFN+D+P+ E+Y+HRIGRTGRAG G + +L +E Sbjct: 306 LDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYAL 365 Query: 356 HIDAIEKLIEKKVDWLNGD----LSSLNPPLEKIDIAQHNHARKNN 397 ++ AIE I + D L+ L PL N R++ Sbjct: 366 NLPAIETYIGHSIPVSKYDSDALLTDLPKPLRLTRPRTGNGPRRSG 411 >gnl|CDD|179276 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional. Length = 475 Score = 283 bits (726), Expect = 6e-77 Identities = 144/375 (38%), Positives = 224/375 (59%), Gaps = 12/375 (3%) Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62 F D L+P+++ A+ D G+ TPIQ + + L HD G AQTGTGKTA+F++ ++ Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148 Query: 63 L-----EKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNK 117 L K R PR LI+ PTREL Q+A + K L V +GG+ F+ Q K Sbjct: 149 LLQTPPPKERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLK 207 Query: 118 KLE-RGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176 +LE R D+L+ TPGR+LD RG++ ++ +E++V+DEADRMLDMGFIP ++ I P Sbjct: 208 QLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPR 267 Query: 177 T--RQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCAL 234 RQTLLFSAT TD++ +++ + +P +E+ + ++T+E A S K L Sbjct: 268 KEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG--SDKYKL 325 Query: 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEG 294 L L+ +Q+ + ++F N+K V + L K G + + G++ Q R+K L F+EG Sbjct: 326 LYNLV-TQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREG 384 Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354 I+++VA+D+A RG+ I + HV NF +P ++Y+HRIGRTGRAG G + + ++D Sbjct: 385 KIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDA 444 Query: 355 KHIDAIEKLIEKKVD 369 + IE+L+ +K+ Sbjct: 445 FQLPEIEELLGRKIS 459 >gnl|CDD|185453 PTZ00110, PTZ00110, helicase; Provisional. Length = 545 Score = 266 bits (682), Expect = 8e-72 Identities = 147/423 (34%), Positives = 230/423 (54%), Gaps = 27/423 (6%) Query: 12 VVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLP-MLTILEKGRARV 70 ++ ++ +AG+ +PTPIQ++ P+ L D+ GIA+TG+GKT +F+LP ++ I + R Sbjct: 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRY 200 Query: 71 -RMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICT 129 P L+L PTRELA Q+ + K+G + + + GG+P Q L RG ++LI Sbjct: 201 GDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIAC 260 Query: 130 PGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTD 189 PGR++D + + LV+DEADRMLDMGF P I+ I S + RQTL++SAT Sbjct: 261 PGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPK 320 Query: 190 ELQKVSENFL-QNPKRIEVNTPSSTA-ETIEHCFVATYAQYSKKCAL---LQQLLQSQDT 244 E+Q ++ + + P + V + TA I+ V ++ K+ L LQ++++ D Sbjct: 321 EVQSLARDLCKEEPVHVNVGSLDLTACHNIKQ-EVFVVEEHEKRGKLKMLLQRIMRDGDK 379 Query: 245 MKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDL 304 + +IF KK L L G+ IHG+ Q R +L+ FK G +M+A+D+ Sbjct: 380 I---LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDV 436 Query: 305 AARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLI 364 A+RGLD+ DV +V NFD PN+ E+Y+HRIGRTGRAG G ++T + + +L Sbjct: 437 ASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKY-------RLA 489 Query: 365 EKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKNYSSQKSHIPLKE 424 V L + P LEK+ ++ R N ++ G+ R N ++ IPL Sbjct: 490 RDLVKVLREAKQPVPPELEKL-----SNERSNGTERRRWGGYGRFSNNVNN----IPLGG 540 Query: 425 SEK 427 S + Sbjct: 541 SNR 543 >gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional. Length = 572 Score = 259 bits (663), Expect = 1e-69 Identities = 138/375 (36%), Positives = 224/375 (59%), Gaps = 10/375 (2%) Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 + F+ L P ++ + AG+ + TPIQ T+P+ L DV G AQTGTGKT +F++ ++ Sbjct: 9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVM 68 Query: 61 TILEKGRARVRM----PRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQN 116 L A PR LIL PTRELA Q+ + K+G + L AL+ GG+ ++ Q Sbjct: 69 NRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQR 128 Query: 117 KKLERGADVLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVP 175 + L++G DV+I TPGR++D+ + K++ ++ EI V+DEADRM D+GFI I+ + +P Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188 Query: 176 --FTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCA 233 TRQTLLFSAT++ + +++ + P+++ V T + TA + + +K Sbjct: 189 ERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIY--FPADEEKQT 246 Query: 234 LLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKE 293 LL LL + + ++F N K V + +LE+ G+ V + G++ Q+ R +L+ F++ Sbjct: 247 LLLGLLSRSEGART-MVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQK 305 Query: 294 GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353 G ++++VA+D+AARGL I V +V+N+D+P AE+Y+HRIGRT R G G A + + Sbjct: 306 GQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERY 365 Query: 354 IKHIDAIEKLIEKKV 368 + IE IE+K+ Sbjct: 366 AMSLPDIEAYIEQKI 380 >gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional. Length = 401 Score = 245 bits (626), Expect = 2e-65 Identities = 125/367 (34%), Positives = 207/367 (56%), Gaps = 5/367 (1%) Query: 3 FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62 F L L+ ++ + G+ KP+ IQ + I +L +D G AQ+GTGKTA+FV+ L + Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89 Query: 63 LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122 ++ + + LIL PTRELA Q+ G + +GG KL+ G Sbjct: 90 ID---YDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAG 146 Query: 123 ADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLL 182 +++ TPGR+ D ++ L ++++++ ++DEAD ML GF I ++ +P Q L Sbjct: 147 VHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVAL 206 Query: 183 FSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ 242 FSATM +E+ +++ F+++PKRI V T E I +VA + K L L ++ Sbjct: 207 FSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKE-EWKFDTLCDLYETL 265 Query: 243 DTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVAS 302 T+ II+CN ++ V L + ++ F+V +HG++DQ+ R I+ F+ G+ ++++ + Sbjct: 266 -TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITT 324 Query: 303 DLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEK 362 DL ARG+D+ V V N+D+P ENYIHRIGR+GR GR G A V +DI+ + IE+ Sbjct: 325 DLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384 Query: 363 LIEKKVD 369 +++ Sbjct: 385 HYNTQIE 391 >gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional. Length = 518 Score = 207 bits (528), Expect = 5e-54 Identities = 112/358 (31%), Positives = 191/358 (53%), Gaps = 7/358 (1%) Query: 1 MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 + F+ GL PK++ + AGY PTPIQ++ IP L + A TG+GKTASF++P++ Sbjct: 121 LSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPII 180 Query: 61 ----TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQN 116 TI + R P ++L PTREL QV D + GK AL++GG Q Sbjct: 181 SRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL 240 Query: 117 KKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176 ++++G ++++ TPGR++D ++ + ++N+ +LV+DE D ML+ GF + I + Sbjct: 241 YRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS- 299 Query: 177 TRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQ 236 Q LLFSAT++ E++K + + ++ I + P+ + ++ + + KK L Sbjct: 300 QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETK-QKKQKLFD 358 Query: 237 QLLQSQDTMKNGIIFCNQKKNVVNLCHSLEK-QGFSVCAIHGNIDQRSRMKILSNFKEGT 295 L Q ++F + + L +++ G +IHG + R +++ +F G Sbjct: 359 ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418 Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353 + ++VA+ + RG+D+ V V FD+PN + YIH+IGR R G G A V +ED Sbjct: 419 VPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEED 476 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 174 bits (444), Expect = 3e-44 Identities = 75/206 (36%), Positives = 115/206 (55%), Gaps = 8/206 (3%) Query: 16 VLDAGYVKPTPIQIKTIPLVLQR-HDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPR 74 + G+ P Q + I +L DV A TG+GKT + +LP L L++G+ R Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG----KR 56 Query: 75 TLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG-ADVLICTPGRI 133 L+L PTRELA Q A+ +K G + L V L GG Q +KLE G D+L+ TPGR+ Sbjct: 57 VLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL 116 Query: 134 LDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQK 193 LD L ++N++++++DEA R+LD GF ++ + L+P Q LL SAT +E++ Sbjct: 117 LDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176 Query: 194 VSENFLQNPKRIEVNTPSSTAETIEH 219 + E FL +P + ++ + E IE Sbjct: 177 LLELFLNDP--VFIDVGPTPLEPIEQ 200 >gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain. Length = 82 Score = 99 bits (250), Expect = 1e-21 Identities = 36/80 (45%), Positives = 50/80 (62%) Query: 261 LCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNF 320 L L++ G V +HG + Q R +IL F G I+++VA+D+A RGLD+P V V + Sbjct: 3 LAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIY 62 Query: 321 DVPNRAENYIHRIGRTGRAG 340 D+P +YI RIGR GRAG Sbjct: 63 DLPWSPASYIQRIGRAGRAG 82 >gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. Length = 591 Score = 85.9 bits (213), Expect = 2e-17 Identities = 88/353 (24%), Positives = 140/353 (39%), Gaps = 47/353 (13%) Query: 20 GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILE 79 GY P Q + I VL DV + TG GK+ + +P L L KG T+++ Sbjct: 10 GYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL--LLKGL-------TVVIS 60 Query: 80 PTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DVLICTPGRIL- 134 P L D G A L + + Q + +L P R+ Sbjct: 61 PLISLMKDQVDQLRAAGVA----AAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQ 116 Query: 135 DHFNRGKLLMNNIEILVIDEADRMLDMG--FIPYIQNITSLV---PFTRQTLLFSATMTD 189 D+F L I ++ +DEA + G F P Q + SL P + +AT Sbjct: 117 DYF-LNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFP-QVPRIALTATADA 174 Query: 190 ELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYA------QYSKKCALLQQLLQ--S 241 E ++ L+ + F+ ++ KK + LL Sbjct: 175 ETRQDIRELLRLAD--------------ANEFITSFDRPNLRFSVVKKNNKQKFLLDYLK 220 Query: 242 QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVA 301 + ++GII+ + +K V L LE QG S A H + + R + +F +++MVA Sbjct: 221 KHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVA 280 Query: 302 SDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354 ++ G+D P+V V ++D+P E+Y GR GR G +A L + DI Sbjct: 281 TNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADI 333 >gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional. Length = 607 Score = 69.4 bits (170), Expect = 2e-12 Identities = 39/112 (34%), Positives = 59/112 (52%), Gaps = 7/112 (6%) Query: 235 LQQL---LQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNF 291 L QL +Q Q K+GII+CN + V + L+ +G S A H +D R + F Sbjct: 224 LDQLMRYVQEQRG-KSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAF 282 Query: 292 KEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHG 343 + +Q++VA+ G++ P+V V +FD+P E+Y TGRAGR G Sbjct: 283 QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQ---ETGRAGRDG 331 >gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 470 Score = 66.3 bits (162), Expect = 1e-11 Identities = 36/134 (26%), Positives = 65/134 (48%), Gaps = 2/134 (1%) Query: 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEG 294 L + ++ + K+GII+C +K + SL+ G + A H ++ +R + F+ Sbjct: 216 LLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRD 275 Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI 354 IQ++VA+ G++ PDV V ++ +P E+Y GR GR G + A DI Sbjct: 276 EIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADI 335 Query: 355 KHIDAIEKLIEKKV 368 + + L+E+ Sbjct: 336 NRLRRL--LMEEPD 347 Score = 27.0 bits (60), Expect = 9.3 Identities = 14/41 (34%), Positives = 20/41 (48%) Query: 20 GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60 G P+Q++ I VL D + TG GK+ + LP L Sbjct: 8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48 >gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed. Length = 1176 Score = 60.7 bits (148), Expect = 7e-10 Identities = 72/346 (20%), Positives = 135/346 (39%), Gaps = 80/346 (23%) Query: 23 KPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPM-LTILEKGRARVRMPRTLILEPT 81 KP +Q +L IA TG GKT +F L M L + +KG+ ++ I+ PT Sbjct: 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKT-TFGLVMSLYLAKKGK------KSYIIFPT 132 Query: 82 RELAAQVADNFEKYGKNYNLTVALLI--GGIPFEAQNKKLER----GADVLICTPGRILD 135 R L QV + EK+G+ V +L + + + + LER D+L+ T + Sbjct: 133 RLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSK 192 Query: 136 HFNRGKLLMNNIEI--LVIDEAD----------RMLDM-GFIP-YIQNITSLVPFTRQTL 181 +F+ + + + +D+ D ++L + GF I+ L+ R+ Sbjct: 193 NFD----ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKY- 247 Query: 182 LFSATMTDELQKVSENFLQ---------------NPK--RI---------EVNTPSSTAE 215 + ++++++ E + P+ R+ EV +P Sbjct: 248 ---EEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLR 304 Query: 216 TIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQ---KKNVVNLCHSLEKQGFSV 272 I ++ K L+++L G+IF K+ L LE G + Sbjct: 305 NIVDSYIVDEDSVEKLVELVKRL------GDGGLIFVPSDKGKEYAEELAEYLEDLGINA 358 Query: 273 CAIHGNIDQRSRMKILSNFKEGTIQLMV--AS--DLAARGLDIPDV 314 +++ F+EG + ++V AS + RG+D+P+ Sbjct: 359 ELAISGFERK-----FEKFEEGEVDVLVGVASYYGVLVRGIDLPER 399 >gnl|CDD|162177 TIGR01054, rgy, reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. Length = 1171 Score = 55.2 bits (133), Expect = 3e-08 Identities = 68/318 (21%), Positives = 116/318 (36%), Gaps = 65/318 (20%) Query: 44 IAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTV 103 IA TG GKT +F L M L K R I+ PT L QVA+ + + Sbjct: 99 IAPTGVGKT-TFGLAMSLFLAKKGKRC-----YIILPTTLLVIQVAEKISSLAEKAGVGT 152 Query: 104 ALLI---GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEAD 156 + +P + + + +ER D+LI T + +++ L + + +D+ D Sbjct: 153 VNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE---LGPKFDFIFVDDVD 209 Query: 157 RMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAET 216 +L + + L+ F+ + + A L+ L KR+E+ + Sbjct: 210 ALLKAS--KNVDKLLKLLGFSEELIE-KAWKLIRLRLKLYRALHAKKRLELLEAIPGKK- 265 Query: 217 IEHCFV---ATYAQYSKKCALLQQLL-----QSQDTMKN--------------------- 247 C + AT K+ L ++LL DT++N Sbjct: 266 -RGCLIVSSATGRPRGKRAKLFRELLGFEVGGGSDTLRNVVDVYVEDEDLKETLLEIVKK 324 Query: 248 ----GIIFCNQ---KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMV 300 GI++ + K+ + LE G A H + F EG I +++ Sbjct: 325 LGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPKE----DYEKFAEGEIDVLI 380 Query: 301 --AS--DLAARGLDIPDV 314 AS RGLD+P+ Sbjct: 381 GVASYYGTLVRGLDLPER 398 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 48.3 bits (116), Expect = 4e-06 Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 24/138 (17%) Query: 231 KCALLQQLLQSQDTMKNG---IIFCNQK---KNVVNLCHSLEKQGFSVCAIHGNID---- 280 K L+++++ Q I+F + + +V+L LEK+G G Sbjct: 348 KLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDL---LEKEGIKAVRFVGQASKDGD 404 Query: 281 ----QRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHV-FNFDVPN--RAENYIHRI 333 Q+ +++IL F+ G ++V++ +A GLDIP V V F VP+ R+ I R Sbjct: 405 KGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS---IQRK 461 Query: 334 GRTGRAGRHGKAFTLVAK 351 GRTGR G+ L+AK Sbjct: 462 GRTGR-QEEGRVVVLIAK 478 Score = 39.9 bits (94), Expect = 0.001 Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 6/111 (5%) Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALL 106 TG GKTA +L + L K +V LIL PT+ L Q A+ F K+ + + Sbjct: 38 TGLGKTAIALLVIAERLHKKGGKV-----LILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92 Query: 107 IGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADR 157 G + + +L A V++ TP I + G++ + ++ +L+ DEA R Sbjct: 93 TGEVS-PEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHR 142 >gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG. Length = 630 Score = 46.6 bits (111), Expect = 1e-05 Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 15/114 (13%) Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLI 107 G+GKT L ML +E G + ++ PT LA Q ++ + VALL Sbjct: 266 GSGKTLVAALAMLAAIEAGY------QVALMAPTEILAEQHYNSLRNLLAPLGIEVALLT 319 Query: 108 GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADR 157 G + + + + LE +++ T I + K+ + +++IDE R Sbjct: 320 GSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHR 368 Score = 33.1 bits (76), Expect = 0.17 Identities = 26/104 (25%), Positives = 47/104 (45%), Gaps = 12/104 (11%) Query: 256 KNVVNLCHSLEK--QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPD 313 K L L+K ++V +HG + + ++ F+EG + ++VA+ + G+D+P+ Sbjct: 467 KAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526 Query: 314 VGHVFNFDVPNRAENY----IHRI-GRTGRAGRHGKAFTLVAKE 352 V AE + +H++ GR GR LV K Sbjct: 527 A----TVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCL-LVYKN 565 >gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional. Length = 1490 Score = 43.0 bits (101), Expect = 2e-04 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 20/131 (15%) Query: 44 IAQTGTGKT-ASFVLPMLTILEKGRARVRMP------RTLILEPTRELAAQVADNF---- 92 IA TG+GKT A+F+ + + +G R R L + P + L V N Sbjct: 2 IAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPL 61 Query: 93 -------EKYGK-NYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRI-LDHFNRGKLL 143 + G+ NL V + G P + ++K D+LI TP + L +R + Sbjct: 62 KGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARET 121 Query: 144 MNNIEILVIDE 154 + +E ++IDE Sbjct: 122 LRGVETVIIDE 132 Score = 37.2 bits (86), Expect = 0.008 Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 15/124 (12%) Query: 276 HGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGR 335 HG++ + R K G ++ +VA+ G+D+ V V P + + RIGR Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367 Query: 336 TGR--AGRHGKAFTLVAKEDIKHIDA---IEKLIEKKVDWLNGDLSSLNPPLEKIDI-AQ 389 G G F + D+ +D+ +E + G L +L PP +D+ AQ Sbjct: 368 AGHQVGGVSKGLFFPRTRRDL--VDSAVIVECM-------FAGRLENLTPPHNPLDVLAQ 418 Query: 390 HNHA 393 A Sbjct: 419 QTVA 422 >gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional. Length = 1195 Score = 42.2 bits (99), Expect = 3e-04 Identities = 25/94 (26%), Positives = 44/94 (46%) Query: 248 GIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAAR 307 GII+C + + + L++ G HG++D R + + + I ++ A+ Sbjct: 683 GIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGM 742 Query: 308 GLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGR 341 G++ PDV V + +P E Y GR GR G+ Sbjct: 743 GINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQ 776 >gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. Length = 926 Score = 41.6 bits (98), Expect = 5e-04 Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 9/98 (9%) Query: 271 SVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENY- 329 + HG + + +++ F +G Q++V + + G+DIP+ N + RA+ + Sbjct: 688 RIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNA----NTIIIERADKFG 743 Query: 330 ---IHRI-GRTGRAGRHGKAFTLVAKEDIKHIDAIEKL 363 ++++ GR GR+ + A+ L + DA ++L Sbjct: 744 LAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRL 781 Score = 31.6 bits (72), Expect = 0.42 Identities = 45/157 (28%), Positives = 67/157 (42%), Gaps = 47/157 (29%) Query: 24 PTPIQIKTI---------PLVLQRHDVCGIAQTGTGKT-----ASFVLPMLTILEKGRAR 69 TP Q+K I P + R VCG G GKT A+F +A Sbjct: 452 ETPDQLKAIEEIKADMESPRPMDRL-VCG--DVGFGKTEVAMRAAF-----------KAV 497 Query: 70 VRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DV 125 + + +L PT LA Q + F++ N+ +T+ LL + QN+ L+ A D+ Sbjct: 498 LDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDI 557 Query: 126 LICTPGRILDHFNRGKLLMNNIE-----ILVIDEADR 157 LI T H KLL +++ +L+IDE R Sbjct: 558 LIGT------H----KLLQKDVKFKDLGLLIIDEEQR 584 >gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 655 Score = 39.2 bits (92), Expect = 0.002 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 6/96 (6%) Query: 255 KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDV 314 KK +L L++ G V +H ID R++I+ + + G ++V +L GLD+P+V Sbjct: 452 KKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEV 511 Query: 315 GHVFNFDVPN----RAE-NYIHRIGRTGRAGRHGKA 345 V D R+E + I IGR R +GK Sbjct: 512 SLVAILDADKEGFLRSERSLIQTIGRAAR-NVNGKV 546 Score = 28.0 bits (63), Expect = 5.0 Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 9/46 (19%) Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNF 92 TG+GKT + M ++ A+V P TL++ + LAAQ+ + F Sbjct: 38 TGSGKTFT----MANVI----AQVNRP-TLVIAHNKTLAAQLYNEF 74 >gnl|CDD|163529 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA. Length = 742 Score = 35.1 bits (81), Expect = 0.040 Identities = 30/80 (37%), Positives = 40/80 (50%), Gaps = 10/80 (12%) Query: 10 PKVVCAVLDAGYVKPTPIQIKTIPLVLQ-RHDVCGIAQTGT--GKTASFVLPMLTILEKG 66 P VV A+ AG +P Q + L RH V +A TGT GK+ ++ LP+L+ L Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVV--VA-TGTASGKSLAYQLPVLSAL--- 76 Query: 67 RARVRMPRTLILEPTRELAA 86 A L L PT+ LAA Sbjct: 77 -ADDPRATALYLAPTKALAA 95 >gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional. Length = 681 Score = 34.0 bits (79), Expect = 0.077 Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 10/86 (11%) Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLI 107 G+GKT L L +E G + ++ PT LA Q +N +K + + VALL Sbjct: 292 GSGKTVVAALAALAAIEAGY------QAALMAPTEILAEQHYENLKKLLEPLGIRVALLT 345 Query: 108 GGIPFEAQNKKLER----GADVLICT 129 G + + + + LE AD++I T Sbjct: 346 GSLKGKERREILEAIASGEADIVIGT 371 Score = 30.1 bits (69), Expect = 1.3 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 14/54 (25%) Query: 256 KNVVNLCHSLEKQ--GFSVCAIHGNIDQRSRMK------ILSNFKEGTIQLMVA 301 ++ L++ V +HG RMK +++ FK G I ++VA Sbjct: 490 QSAEETYEELQEAFPELRVGLLHG------RMKPAEKDAVMAAFKAGEIDILVA 537 >gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional. Length = 876 Score = 32.6 bits (75), Expect = 0.20 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%) Query: 21 YVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKT-ASF--VLPMLTILEK 65 + TP Q IPL+ + +V + TG+GKT A+F ++ L L + Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGR 77 >gnl|CDD|148966 pfam07652, Flavi_DEAD, Flavivirus DEAD domain. Length = 146 Score = 31.2 bits (71), Expect = 0.57 Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 5/43 (11%) Query: 48 GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVAD 90 G GKT VLP L + R+ RTL+L PTR + A++ + Sbjct: 12 GAGKTRK-VLPELV---RECIDRRL-RTLVLAPTRVVLAEMEE 49 >gnl|CDD|171470 PRK12400, PRK12400, D-amino acid aminotransferase; Reviewed. Length = 290 Score = 31.1 bits (70), Expect = 0.67 Identities = 26/92 (28%), Positives = 36/92 (39%), Gaps = 24/92 (26%) Query: 289 SNFKE-GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFT 347 +NF E GTI L V+ + AR H F++DVP YI + R +G Sbjct: 86 NNFHEDGTIYLQVSRGVQART-------HTFSYDVPPTIYAYITKKERPALWIEYG---- 134 Query: 348 LVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLN 379 + + E WL D+ SLN Sbjct: 135 ------------VRAISEPDTRWLRCDIKSLN 154 >gnl|CDD|148463 pfam06862, DUF1253, Protein of unknown function (DUF1253). This family represents the C-terminal portion (approximately 500 residues) of several hypothetical eukaryotic proteins of unknown function. Length = 435 Score = 30.7 bits (70), Expect = 0.80 Identities = 42/239 (17%), Positives = 88/239 (36%), Gaps = 79/239 (33%) Query: 123 ADVLICTP-G--RILDHFNRGKL---LMNNIEILVIDEADRMLDMGFIPYIQN------- 169 +D++I +P G I+++ + K +++IE+L++D+AD +L +QN Sbjct: 126 SDIIIASPLGLRMIIENEDEKKRDYDFLSSIEVLIVDQADVIL-------MQNWEHVLTV 178 Query: 170 -----------------------ITSLVPFTRQTLLFSATMTDEL----QKVSENF---- 198 + + RQT++FS+ +T E+ N+ Sbjct: 179 FKHLNKIPKKSHGADFSRVRMWYLDGQAKYYRQTIIFSSYITPEINSLFNSKCVNYRGKV 238 Query: 199 -LQNP-----------------KRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQ 240 L+ +R + ++ + F + +L QL + Sbjct: 239 KLKPIYKSGVIGQVGLKVRQIFQRFDASSIVDDPDARFKFFTSN---------VLPQLRK 289 Query: 241 SQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLM 299 S +IF + V + + L+K+ S AI Q+ + + F G I+++ Sbjct: 290 S-SYDSGTLIFIPSYFDFVRIRNYLKKENVSFAAISEYTSQKKISRARTLFFSGRIKVL 347 >gnl|CDD|177392 PHA02558, uvsW, UvsW helicase; Provisional. Length = 501 Score = 30.7 bits (70), Expect = 0.83 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 9/52 (17%) Query: 47 TGTGKTASFVLPMLT--ILEKGRARVRMPRTLILEPTRELAAQVADNFEKYG 96 T GK S + +L+ LE +V LI+ PT L Q+ D+F Y Sbjct: 138 TSAGK--SLIQYLLSRYYLENYEGKV-----LIIVPTTSLVTQMIDDFVDYR 182 >gnl|CDD|180000 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional. Length = 652 Score = 30.4 bits (70), Expect = 1.1 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 9/41 (21%) Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQ 87 TG+GKT + M ++ R++ P TL+L + LAAQ Sbjct: 41 TGSGKTFT----MANVIA----RLQRP-TLVLAHNKTLAAQ 72 >gnl|CDD|183477 PRK12367, PRK12367, short chain dehydrogenase; Provisional. Length = 245 Score = 29.6 bits (67), Expect = 1.6 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 19/76 (25%) Query: 332 RIGRTGRAGRHGKAFTLVAK---------------EDIKHIDAIEKLIEKKVDWLNGDLS 376 RIG TG +G GKA T + + ++ + I+ W G Sbjct: 16 RIGITGASGALGKALTKAFRAKGAKVIGLTHSKINNSESNDESPNEWIK----WECGKEE 71 Query: 377 SLNPPLEKIDIAQHNH 392 SL+ L +D+ NH Sbjct: 72 SLDKQLASLDVLILNH 87 >gnl|CDD|152563 pfam12128, DUF3584, Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. There are two conserved sequence motifs: GKT and YLP. Length = 1192 Score = 29.6 bits (67), Expect = 1.9 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 7/93 (7%) Query: 352 EDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQ---KSTGFDR 408 DI+ I A +K I +++ L D L + QH H + + Sbjct: 231 ADIQAIRAFQK-IRPEIEKLQEDFEQLLSLELR---LQHLHGELVADEERLAEEQEERKE 286 Query: 409 RKKNYSSQKSHIPLKESEKISKLQQDIQENDAD 441 K Q + + E +L Q+I +AD Sbjct: 287 AKNELRFQLRTLDDEWKEARDELNQEISAANAD 319 >gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated. Length = 679 Score = 29.4 bits (67), Expect = 1.9 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 27/77 (35%) Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDV---------GHVFNFDVPNRA-ENYIHRIGR 335 ++L+ F G +++ + + A+G D P+V +F+ D RA E R Sbjct: 471 QLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF--RASE-------R 521 Query: 336 T--------GRAGRHGK 344 T GRAGR K Sbjct: 522 TFQLLTQVAGRAGRAEK 538 >gnl|CDD|185024 PRK15064, PRK15064, ABC transporter ATP-binding protein; Provisional. Length = 530 Score = 29.1 bits (66), Expect = 2.8 Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 4/31 (12%) Query: 131 GRILDHFNRGKLLMNNIEILVIDEADRMLDM 161 GR+L F GKL+M +LV+DE +DM Sbjct: 445 GRML--F--GKLMMQKPNVLVMDEPTNHMDM 471 >gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403. Length = 379 Score = 28.7 bits (65), Expect = 3.6 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 15/48 (31%) Query: 248 GIIFCNQKKN-----------VVNLCHSLEKQGFSVCAI----HGNID 280 + +K V++LC LEKQG+ V + G +D Sbjct: 78 SALAAQPEKRHIITTAVEHPAVLSLCQHLEKQGYKVTYLPVDEEGRLD 125 >gnl|CDD|161952 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 732 Score = 28.6 bits (64), Expect = 3.7 Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%) Query: 275 IHGNIDQRSRMKILSNFK-EGTIQLMVASDLAARGLDIPD 313 I+G Q+ RM+IL NF+ + + S + +D+P+ Sbjct: 521 IYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPE 560 >gnl|CDD|162132 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein. Length = 711 Score = 28.5 bits (64), Expect = 4.0 Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 2/42 (4%) Query: 67 RARVRMPRTLIL-EPTRELAAQVADNFEKYGKNYNLTVALLI 107 RA VR PR LIL E T L A+ ++ + TV LLI Sbjct: 630 RALVRKPRVLILDEATSALDAECEQLLQESRSRASRTV-LLI 670 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 28.6 bits (64), Expect = 4.1 Identities = 41/152 (26%), Positives = 62/152 (40%), Gaps = 37/152 (24%) Query: 24 PTPIQIKTI---------PLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPR 74 TP Q + I PL + R VCG G GKT + +E + + Sbjct: 601 TTPDQAQAINAVLSDMCQPLAMDRL-VCG--DVGFGKTEVAMRAAFLAVENHK------Q 651 Query: 75 TLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGA----DVLICTP 130 +L PT LA Q DNF N+ + + +L + Q + L A D+LI T Sbjct: 652 VAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGT- 710 Query: 131 GRILDHFNRGKLLMNNIE-----ILVIDEADR 157 H KLL ++++ +L++DE R Sbjct: 711 -----H----KLLQSDVKWKDLGLLIVDEEHR 733 Score = 27.8 bits (62), Expect = 5.6 Identities = 25/102 (24%), Positives = 51/102 (50%), Gaps = 18/102 (17%) Query: 276 HGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENY----IH 331 HG + +R +++++F ++V + + G+DIP N + RA+++ +H Sbjct: 842 HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA----NTIIIERADHFGLAQLH 897 Query: 332 RI-GRTGRAGR---------HGKAFTLVAKEDIKHIDAIEKL 363 ++ GR GR+ H KA T A++ ++ I ++E L Sbjct: 898 QLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDL 939 >gnl|CDD|180231 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed. Length = 912 Score = 28.1 bits (64), Expect = 5.0 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 7/49 (14%) Query: 80 PTRELAAQVADNFEKYGKN--YNLTVALLIGGIPFEAQNKKLERGADVL 126 PT EL VA FEK G + + L L+ + + E+ D+L Sbjct: 479 PTPELIEHVAKLFEKEGIDAWFELDAKELLP-----DEADEYEKETDIL 522 >gnl|CDD|148831 pfam07451, SpoVAD, Stage V sporulation protein AD (SpoVAD). This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation. Length = 329 Score = 27.9 bits (63), Expect = 5.7 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 9/36 (25%) Query: 289 SNFKEGTIQLMVASDL---------AARGLDIPDVG 315 + K+ I ++A DL AAR L IP +G Sbjct: 66 AGLKKDDIDYLLAGDLLNQIISSSFAARTLGIPFLG 101 >gnl|CDD|161946 TIGR00595, priA, primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 505 Score = 27.7 bits (62), Expect = 5.7 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 13/70 (18%) Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDVG-----------HVFNFDVPNRAENYIHRIG 334 +L+ F G +++ + + A+G P+V H +F R + ++ Sbjct: 303 ALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQV- 361 Query: 335 RTGRAGRHGK 344 GRAGR Sbjct: 362 -AGRAGRAED 370 >gnl|CDD|178197 PLN02585, PLN02585, magnesium protoporphyrin IX methyltransferase. Length = 315 Score = 27.5 bits (61), Expect = 7.5 Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 9/38 (23%) Query: 403 STGFDRRKKNYSSQKSHIPLKESEKISKLQQDIQENDA 440 +TGF+R +K Y E+++++K+Q DI+ A Sbjct: 99 TTGFERWRKIYG---------ETDEVNKVQLDIRLGHA 127 >gnl|CDD|183820 PRK12898, secA, preprotein translocase subunit SecA; Reviewed. Length = 656 Score = 27.3 bits (61), Expect = 8.3 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 12/65 (18%) Query: 299 MVASDLAARGLDI---PDVG-----HVFNFDVPNRAENYIHR--IGRTGRAGRHGKAFTL 348 VA+++A RG DI P V HV + + + I R GR GR G G + Sbjct: 525 TVATNMAGRGTDIKLEPGVAARGGLHVILTE-RHDSAR-IDRQLAGRCGRQGDPGSYEAI 582 Query: 349 VAKED 353 ++ ED Sbjct: 583 LSLED 587 >gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. Length = 850 Score = 27.1 bits (60), Expect = 9.4 Identities = 13/35 (37%), Positives = 18/35 (51%) Query: 45 AQTGTGKTASFVLPMLTILEKGRARVRMPRTLILE 79 A TGTGKT ++LP L + V T +L+ Sbjct: 271 APTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQ 305 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 0.320 0.136 0.394 Gapped Lambda K H 0.267 0.0674 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,617,564 Number of extensions: 496974 Number of successful extensions: 1134 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1083 Number of HSP's successfully gapped: 66 Length of query: 465 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 368 Effective length of database: 3,898,497 Effective search space: 1434646896 Effective search space used: 1434646896 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: 59 (26.6 bits)