RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780724|ref|YP_003065137.1| component of type IV pilus [Candidatus Liberibacter asiaticus str. psy62] (483 letters) >gnl|CDD|163531 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer. Length = 340 Score = 328 bits (843), Expect = 2e-90 Identities = 135/306 (44%), Positives = 192/306 (62%), Gaps = 2/306 (0%) Query: 109 EQLDLFEDLCNDILGYGPLQPLIARDDIADIMVNGSNKVFIEVNGKTVETGINFRDNEQL 168 E L L +++G GPL+PL+A + D++VNG ++V+++ T + F D + Sbjct: 37 EVLAAARALRRELVGAGPLEPLLADPGVTDVLVNGPDEVWVDRGEGLERTDVRFPDEAAV 96 Query: 169 LSVCQRIVNQVGRRVDESSPICDARLLDGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDH 228 + QR+ GRR+D++ P D RL DG+R++ ++PP+A DG L++R + TLD Sbjct: 97 RRLAQRLAAAAGRRLDDAQPWVDGRLPDGTRLHAVLPPVATDGTCLSLRVPRPRTFTLDE 156 Query: 229 LVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAE 288 LV+ G ARLL+ I R LISGGTGSGKTTLL+ L + DERIV ED AE Sbjct: 157 LVASGTFPPGVARLLRAIVAARLAFLISGGTGSGKTTLLSALLALVAPDERIVLVEDAAE 216 Query: 289 LQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNT 348 L+ PHVVRLE RP N+EG G +T+ DLV+ LRMRP+RI++GEVRG EV+DLL A+NT Sbjct: 217 LRPDHPHVVRLEARPANVEGAGAVTLTDLVRQALRMRPDRIVVGEVRGAEVVDLLAALNT 276 Query: 349 GHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRR 408 GHDG GT+HAN+ + R+EA+ A+GG L + + + ++L V++ R G RR Sbjct: 277 GHDGGAGTLHANSPADVPARLEALGALGG--LDREALHSQLAAALQVVLHVVRTPRGRRR 334 Query: 409 ITNICE 414 + I Sbjct: 335 VAEIGV 340 >gnl|CDD|163021 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA. Length = 308 Score = 217 bits (556), Expect = 4e-57 Identities = 105/307 (34%), Positives = 163/307 (53%), Gaps = 27/307 (8%) Query: 131 IARDDIADIMVNGSNKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDESSPIC 190 + +D+ +I +N +V++E G + L+ + + I + + + E +PI Sbjct: 2 LDDEDVTEICINRPGEVWVEGPGGWQRFDVPDLTFSHLMRLARAIASFSKQSISEENPIL 61 Query: 191 DARLLDGSRVNVIIPPLAL-DGPTLTIRKFKKDKLTLDHLV---SFGAVTAEGARL---- 242 A L G RV ++IPP D ++TIRK +LD F V A+ L Sbjct: 62 SATLPGGERVQIVIPPACENDTVSITIRKPSLVDFSLDDYEEKGFFDTVRAQSGTLSDND 121 Query: 243 ---------------LQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTA 287 L++ R N++ISGGTGSGKTT L L I KDERI+T EDT Sbjct: 122 EQLLELLDAGDIKEFLRLAIASRKNIIISGGTGSGKTTFLKSLVDEIPKDERIITIEDTR 181 Query: 288 ELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMN 347 E+ L P+ V L +G ++T +DL+++CLRMRP+RIILGE+RG E D ++A+N Sbjct: 182 EIFLPHPNYVHL-FYSKGGQGLAKVTPKDLLQSCLRMRPDRIILGELRGDEAFDFIRAVN 240 Query: 348 TGHDGSMGTIHANNARESFGRMEAMI--AMGGFTLPSQMVREIITSSLDVIVQTQRLRDG 405 TGH GS+ T+HA + E+F ++ M+ + G L + +++ +D++VQ R R G Sbjct: 241 TGHPGSITTLHAGSPEEAFEQLALMVKSSQAGLGLDFAYIVKLVREVIDIVVQINR-RGG 299 Query: 406 SRRITNI 412 R+IT + Sbjct: 300 GRKITEV 306 >gnl|CDD|163017 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA. Length = 299 Score = 200 bits (510), Expect = 6e-52 Identities = 113/308 (36%), Positives = 160/308 (51%), Gaps = 23/308 (7%) Query: 127 LQPLIAR----DDIADIMVNGSNKVFIEVNGKTVE-TGINFRDNEQLLSVCQRIVNQVGR 181 L P IA + +IM+N ++++E G + G + + + +G Sbjct: 6 LGPEIAAALDDPGVVEIMLNPDGRLWVERLGSGMSPLGE--MSPADAQRIIGLVADYLGT 63 Query: 182 RVDESSPICDARL-LDGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGA 240 VD PI + L LDGSR +IPP+ + P+ IRK TLD V G +TA Sbjct: 64 EVDRDKPIVEGELPLDGSRFEGLIPPV-VAAPSFAIRKKAVAVFTLDDYVEAGIMTAAQR 122 Query: 241 RLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYI---DKDERIVTCEDTAELQLQQPHVV 297 +L+ R N+L+ GGTGSGKTTL N L I D +R+V EDT ELQ P+VV Sbjct: 123 DVLREAVLARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVV 182 Query: 298 RLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTI 357 +L T I+M L+K LR+RP+RII+GEVRG E LDLL+A NTGH G + TI Sbjct: 183 QLRTSD------DAISMTRLLKATLRLRPDRIIVGEVRGGEALDLLKAWNTGHPGGIATI 236 Query: 358 HANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVG 417 HANNA+ + R+E +I T ++ E + D+++ R RR+ I ++ G Sbjct: 237 HANNAKAALDRLEQLIQEVSVTPMQTLIAEAV----DLVIFIAR-TPAGRRVQEIAKVKG 291 Query: 418 MEGNVIIT 425 + IT Sbjct: 292 FDDGNYIT 299 >gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional. Length = 319 Score = 175 bits (445), Expect = 3e-44 Identities = 109/296 (36%), Positives = 153/296 (51%), Gaps = 16/296 (5%) Query: 137 ADIMVNGSNKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDESSPICDARL-L 195 +IM+N K++ E G+ + R Q ++ + I G+ V S PI + L L Sbjct: 36 VEIMLNADGKLWQERLGEPMRCIGTLRV-AQAQAIIETIAGYHGKEVTRSKPILEGELPL 94 Query: 196 DGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLI 255 DGSR +PP+ PT IRK TLD V G +TA + R N+L+ Sbjct: 95 DGSRFAGQLPPVV-PAPTFAIRKKAVAIFTLDQYVERGIMTAAQREAIIAAVRAHRNILV 153 Query: 256 SGGTGSGKTTLLNCLTR---YIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEI 312 GGTGSGKTTL+N + D ER+ EDT E+Q + V+ T ++ Sbjct: 154 IGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSI-------DV 206 Query: 313 TMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRMEAM 372 M L+K LRMRP+RI++GEVRGPE LDLL A NTGH+G T+HANNA+ R++++ Sbjct: 207 NMTALLKTTLRMRPDRILVGEVRGPEALDLLMAWNTGHEGGAATLHANNAKAGLDRLKSL 266 Query: 373 IAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVGMEGNVIITQDL 428 I+M P + +I ++ V+V R G RRI I E+ G IT+ L Sbjct: 267 ISMHP-DAPKP-IEPLIGEAVHVVVHIAR-TPGGRRIQEILEVSGYANGQYITKTL 319 >gnl|CDD|184381 PRK13900, PRK13900, type IV secretion system ATPase VirB11; Provisional. Length = 332 Score = 167 bits (424), Expect = 6e-42 Identities = 93/310 (30%), Positives = 159/310 (51%), Gaps = 24/310 (7%) Query: 126 PLQPLIARDDIADIMVNGSNKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDE 185 PL+ + A D + +I +N +V++E G I D L ++ + + +++ E Sbjct: 14 PLKNIFAEDGVNEISINKPGEVWVEKKGDIRCEQIPELDLSHLKALGRLVAQATEQKISE 73 Query: 186 SSPICDARLLDGSRVNVIIPPLA-LDGPTLTIRKFKKDKLTLDHLVSFGAV--TAEGARL 242 P+ A L +G R+ ++ PP + +IRK +LTLD GA TA + + Sbjct: 74 EKPLLSATLPNGYRIQIVFPPACEIGQIVYSIRKPSGMQLTLDDYEKMGAFDETATESLV 133 Query: 243 LQIIGRIRC-------------------NVLISGGTGSGKTTLLNCLTRYIDKDERIVTC 283 + + N++ISGGT +GKTT N R I ER++T Sbjct: 134 DEDDVILNELLAEKKIKEFLEHAVISKKNIIISGGTSTGKTTFTNAALREIPAIERLITV 193 Query: 284 EDTAELQL-QQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDL 342 ED E+ L P+ V L +G ++T +DL++ CLR+RP+RII+GE+RG E Sbjct: 194 EDAREIVLSNHPNRVHLLASKGG-QGRAKVTTQDLIEACLRLRPDRIIVGELRGAEAFSF 252 Query: 343 LQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRL 402 L+A+NTGH GS+ T+HA++ + +++ M+ G +P +++ I + +D++VQ +R Sbjct: 253 LRAINTGHPGSISTLHADSPAMAIEQLKLMVMQAGLGMPPDQIKKYILNVVDIVVQLKRG 312 Query: 403 RDGSRRITNI 412 G R ++ I Sbjct: 313 SGGKRYVSEI 322 >gnl|CDD|172360 PRK13833, PRK13833, conjugal transfer protein TrbB; Provisional. Length = 323 Score = 148 bits (375), Expect = 3e-36 Identities = 101/301 (33%), Positives = 154/301 (51%), Gaps = 24/301 (7%) Query: 128 QPLIARDD--IADIMVNGSNKVFIEVNGKTVETG--INFRDNEQLLSVCQRIVNQVGRRV 183 Q +A DD + +IM+N K+FIE G V ++ E V + + + Sbjct: 21 QLCVALDDATVVEIMLNPDGKLFIERLGHGVAPAGEMSAAAAE---VVIGSVAHALQSEA 77 Query: 184 DESSPICDARL-LDGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARL 242 D+ PI L + G R ++PP+ GP TIR+ + LD V+ +T A + Sbjct: 78 DDERPIISGELPIGGHRFEGLLPPVV-SGPAFTIRRRASRLIPLDDYVTSKIMTEAQASV 136 Query: 243 LQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDK---DERIVTCEDTAELQLQQPHVVRL 299 ++ R N++ISGGTGSGKTTL N + I ++R+V EDTAE+Q + V L Sbjct: 137 IRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCAAENAVAL 196 Query: 300 ETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHA 359 T + M L+K+ +R+RP+RII+GEVR L LL+A NTGH G + TIH+ Sbjct: 197 HT-------SDTVDMARLLKSTMRLRPDRIIVGEVRDGAALTLLKAWNTGHPGGVTTIHS 249 Query: 360 NNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVGME 419 N A + R+E + A Q ++E+I ++D+IV +R G RR+ + + G Sbjct: 250 NTAMSALRRLEQLTA----EASQQPMQEVIGEAVDLIVSIERTGKG-RRVREVIHVEGFA 304 Query: 420 G 420 Sbjct: 305 N 305 >gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11; Provisional. Length = 344 Score = 105 bits (263), Expect = 3e-23 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 33/245 (13%) Query: 183 VDESSPICDARLLDGSRVNVIIPPLALDGP-TLTIR------------------------ 217 V +P+C L G R+ + +PP G +LTIR Sbjct: 69 VGPRNPLCATELPGGERLQICLPPTVPSGTVSLTIRRPSSRVSELKEVSSRYDASRWNQW 128 Query: 218 ---KFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYI 274 + ++D+L L + E ++GR+ +L+ G TGSGKTT+ L I Sbjct: 129 QERRKRRDQLDEAILRHYDNGDLEAFLHACVVGRL--TMLLCGPTGSGKTTMSKTLISAI 186 Query: 275 DKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEV 334 ER++T EDT EL + + VRL N G G +T L++ LRMRP+RI+LGE+ Sbjct: 187 PPQERLITIEDTLELVIPHENHVRL-LYSKNGAGLGAVTAEHLLQASLRMRPDRILLGEM 245 Query: 335 RGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRMEAMI--AMGGFTLPSQMVREIITSS 392 R L + +GH GS+ TIH N + F ++ +++ + G +L + + +++ ++ Sbjct: 246 RDDAAWAYLSEVVSGHPGSISTIHGANPVQGFKKLFSLVKSSAQGASLEDRTLIDMLATA 305 Query: 393 LDVIV 397 +DVIV Sbjct: 306 IDVIV 310 >gnl|CDD|162351 TIGR01420, pilT_fam, pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation. Length = 343 Score = 64.6 bits (158), Expect = 6e-11 Identities = 50/167 (29%), Positives = 86/167 (51%), Gaps = 19/167 (11%) Query: 242 LLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDK--DERIVTCEDTAEL--QLQQPHVV 297 L ++ R R +L++G TGSGK+T L + YI+K I+T ED E + ++ + Sbjct: 114 LRELAERPRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLIN 173 Query: 298 RLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDL-LQAMNTGHDGSMGT 356 + E G ++ + ++ LR P+ I++GE+R E ++L L A TGH GT Sbjct: 174 QREV------GLDTLSFANALRAALREDPDVILIGEMRDLETVELALTAAETGHL-VFGT 226 Query: 357 IHANNARESFGRMEAMIAMGGFTLPSQ-MVREIITSSLDVIVQTQRL 402 +H N+A ++ R+ + F Q +R + SL ++ +QRL Sbjct: 227 LHTNSAAQTIERI-----IDVFPAEEQDQIRTQLAESLVAVI-SQRL 267 >gnl|CDD|131577 TIGR02525, plasmid_TraJ, plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524). Length = 372 Score = 59.0 bits (143), Expect = 2e-09 Identities = 57/207 (27%), Positives = 81/207 (39%), Gaps = 41/207 (19%) Query: 254 LISGGTGSGKTTLLNCLTRYI---DKDERIVTCEDTAELQLQQPHVVRLETRPPNIE-GE 309 LI G TGSGK+TL + ++ D +IVT ED E L P P + G Sbjct: 153 LICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGSP---DDLLPPAQSQIGR 209 Query: 310 GEITMRDLVKNCLRMRPERIILGEVRGPEVLD-LLQAMNTGHDGSMGTIHANNARESFGR 368 + + ++ LR P+ I +GE+R E + A +GH +GT+H + E+ R Sbjct: 210 DVDSFANGIRLALRRAPKIIGVGEIRDLETFQAAVLAGQSGH-FCLGTLHVKSPGEAISR 268 Query: 369 MEAMIAMGGFTLPSQMVREIITSSLDVIVQ---TQRL---RDGSRRITNICEIVGMEGNV 422 M P +M RE L I+Q QRL DG R Sbjct: 269 CLQMY-------PPEM-REAAAFDLLSILQYIIVQRLLRTTDGKR--------------- 305 Query: 423 IITQDLLKYEVMGEDETGKLIGQHIST 449 Q + +Y V + KL S Sbjct: 306 ---QAVREYIVFDDSLRRKLYDVDYSK 329 >gnl|CDD|162908 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems. Length = 564 Score = 58.1 bits (141), Expect = 6e-09 Identities = 50/166 (30%), Positives = 86/166 (51%), Gaps = 24/166 (14%) Query: 253 VLISGGTGSGKT-TLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGE 311 VL++G TGSGKT +L L ++ I T ED E+ L + V N+ + Sbjct: 319 VLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINLPGINQV-------NVNPKIG 371 Query: 312 ITMRDLVKNCLRMRPERIILGEVRGPEVLDL-LQAMNTGHDGSMGTIHANNARESFGRME 370 +T +++ LR P+ I++GE+R E ++ ++A TGH + T+H N+A E+ R Sbjct: 372 LTFAAALRSFLRQDPDIIMVGEIRDLETAEIAIKAAQTGH-LVLSTLHTNDAPETLAR-- 428 Query: 371 AMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIV 416 ++ MG + I SS+++I+ QRL +RR+ + C+ Sbjct: 429 -LVNMG---IAPFN----IASSVNLIM-AQRL---ARRLCSHCKAP 462 >gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis. Length = 486 Score = 52.4 bits (126), Expect = 3e-07 Identities = 45/143 (31%), Positives = 69/143 (48%), Gaps = 26/143 (18%) Query: 240 ARLLQIIGRIRCNVLISGGTGSGK-TTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVR 298 +R ++I R +L++G TGSGK TTL L+R + I+T ED E Q Sbjct: 232 SRFERLIRRPHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEYQ-------- 283 Query: 299 LETRPPNIEGEGEITMRDLV--------KNCLRMRPERIILGEVRGPEVLDL-LQAMNTG 349 IEG G+I + + + LR P+ I++GE+R E + +QA TG Sbjct: 284 -------IEGIGQIQVNPKIGLTFAAGLRAILRQDPDIIMVGEIRDLETAQIAIQASLTG 336 Query: 350 HDGSMGTIHANNARESFGRMEAM 372 H + T+H N+A + R+ M Sbjct: 337 HL-VLSTLHTNDAAGAVTRLIDM 358 >gnl|CDD|131576 TIGR02524, dot_icm_DotB, Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems. Length = 358 Score = 48.1 bits (114), Expect = 5e-06 Identities = 39/127 (30%), Positives = 57/127 (44%), Gaps = 17/127 (13%) Query: 253 VLISGGTGSGKTTLLNCLTRYI----DKDERIVTCEDTAELQLQQPHVVRLETRPPNIEG 308 V I+G TGSGK+TLL + R + D +I+T E E V Sbjct: 137 VFITGATGSGKSTLLAAIIRELAEAPDSHRKILTYEAPIE------FVYDEIETISASVC 190 Query: 309 EGEI-----TMRDLVKNCLRMRPERIILGEVRGPEVLD-LLQAMNTGHDGSMGTIHANNA 362 + EI V+N LR +P I++GE R E + L+A TGH T+H++ Sbjct: 191 QSEIPRHLNNFAAGVRNALRRKPHAILVGEARDAETISAALEAALTGHP-VYTTLHSSGV 249 Query: 363 RESFGRM 369 E+ R+ Sbjct: 250 AETIRRL 256 >gnl|CDD|182459 PRK10436, PRK10436, hypothetical protein; Provisional. Length = 462 Score = 45.7 bits (109), Expect = 3e-05 Identities = 54/187 (28%), Positives = 88/187 (47%), Gaps = 36/187 (19%) Query: 224 LTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKT-TLLNCLTRYIDKDERIVT 282 L L+ L G A+ A+ Q + + + +L++G TGSGKT TL + L I + Sbjct: 195 LDLETL---GMTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTLYSALQTLNTAQINICS 251 Query: 283 CEDTAELQLQ-----QPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGP 337 ED E+ L Q H P + +R L LR P+ I++GE+R Sbjct: 252 VEDPVEIPLAGINQTQIH--------PKAGLTFQRVLRAL----LRQDPDVIMVGEIRDG 299 Query: 338 EVLDL-LQAMNTGHDGSMGTIHANNARESFGRMEAM-IAMGGFTLPSQMVREIITSSLDV 395 E ++ ++A TGH + T+H N+ E+ R++ M IA R ++ S+L + Sbjct: 300 ETAEIAIKAAQTGHL-VLSTLHTNSTSETLVRLQQMGIA-----------RWMLASALKL 347 Query: 396 IVQTQRL 402 ++ QRL Sbjct: 348 VI-AQRL 353 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 43.9 bits (103), Expect = 8e-05 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 5/86 (5%) Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDER---IVTCEDTAELQLQQPHVVRLETRPPNIEG 308 +LI G GSGKTTL L R + + ED E L Q ++ + + + G Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63 Query: 309 EGEITMRDLVKNCLRMRPERIILGEV 334 E + R + +++P+ +IL E+ Sbjct: 64 ELRL--RLALALARKLKPDVLILDEI 87 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 36.2 bits (84), Expect = 0.021 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 5/30 (16%) Query: 257 GGTGSGKTTLLNCL-----TRYIDKDERIV 281 G +G+GKTTLLN L T I +R+V Sbjct: 796 GASGAGKTTLLNVLAERVTTGVITGGDRLV 825 >gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation). Length = 785 Score = 35.4 bits (82), Expect = 0.037 Identities = 18/38 (47%), Positives = 20/38 (52%), Gaps = 11/38 (28%) Query: 252 NVLISGGTGSGKTTLLNCL----TRY-------IDKDE 278 + LI G TGSGKTTLLN L +Y DKD Sbjct: 436 HTLIFGPTGSGKTTLLNFLLAQMQKYGGMTIFAFDKDR 473 >gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Length = 529 Score = 34.7 bits (80), Expect = 0.059 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 12/56 (21%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQL------------QQPHV 296 V I G +GSGK+TLL LT +D + VT + + L Q H+ Sbjct: 364 VAILGPSGSGKSTLLMLLTGLLDPLQGEVTLDGVSVSSLQDELRRRISVFAQDAHL 419 >gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD. Length = 529 Score = 34.2 bits (79), Expect = 0.071 Identities = 12/26 (46%), Positives = 18/26 (69%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278 V + G +G+GK+TLLN L ++D E Sbjct: 351 VALVGPSGAGKSTLLNLLLGFVDPTE 376 >gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related. Length = 585 Score = 33.7 bits (77), Expect = 0.10 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%) Query: 228 HLVSFG-AVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKD 277 ++F A +++G + + V I G TG+GKTTL+N L R D Sbjct: 338 RHITFEFANSSQGVFDVSFEAKAGQTVAIVGPTGAGKTTLINLLQRVYDPT 388 >gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 574 Score = 33.3 bits (77), Expect = 0.16 Identities = 13/23 (56%), Positives = 15/23 (65%) Query: 253 VLISGGTGSGKTTLLNCLTRYID 275 V + G TG GK+TLL LTR D Sbjct: 369 VALLGRTGCGKSTLLQLLTRAWD 391 >gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export. Length = 386 Score = 32.9 bits (76), Expect = 0.20 Identities = 11/23 (47%), Positives = 14/23 (60%) Query: 252 NVLISGGTGSGKTTLLNCLTRYI 274 ++LI G TG+GKT L L I Sbjct: 17 HILIVGTTGTGKTQALRELLDQI 39 >gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168 Score = 32.9 bits (76), Expect = 0.21 Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 6/81 (7%) Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVV-RLETRPPNIEGEG 310 + L G TG GKT L L + DER + D +E + H V RL PP G Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSE--YMEEHSVSRLIGAPPGYVGYE 62 Query: 311 EITMRDLVKNCLRMRPERIIL 331 E + +R +P I+L Sbjct: 63 E---GGQLTEAVRRKPYSIVL 80 >gnl|CDD|180114 PRK05480, PRK05480, uridine/cytidine kinase; Provisional. Length = 209 Score = 32.8 bits (76), Expect = 0.21 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 7/41 (17%) Query: 245 IIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285 IIG I+GG+GSGKTT+ + + + + V +D Sbjct: 8 IIG-------IAGGSGSGKTTVASTIYEELGDESIAVIPQD 41 >gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM). Length = 566 Score = 32.8 bits (75), Expect = 0.22 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 8/68 (11%) Query: 209 LDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLN 268 L P I+K KK + D + G L G ++LI G TGSGK+ + Sbjct: 143 LSSPKELIKKLKKSRRASDIKI--------GGLPLIKFGSETQHILIHGTTGSGKSVAIR 194 Query: 269 CLTRYIDK 276 L R+I + Sbjct: 195 KLLRWIRQ 202 >gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein. Length = 617 Score = 31.9 bits (73), Expect = 0.36 Identities = 10/23 (43%), Positives = 14/23 (60%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKD 277 + G +G+GKTTL+N L K Sbjct: 56 VMGSSGAGKTTLMNALAFRSPKG 78 >gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated. Length = 223 Score = 31.9 bits (73), Expect = 0.37 Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 2/41 (4%) Query: 243 LQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTC 283 L + +R V I G T SGKTT + L I K R V Sbjct: 17 LNLTRPLR--VAIDGITASGKTTFADELAEEIKKRGRPVIR 55 >gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter; Provisional. Length = 588 Score = 31.5 bits (72), Expect = 0.49 Identities = 13/23 (56%), Positives = 16/23 (69%) Query: 253 VLISGGTGSGKTTLLNCLTRYID 275 V I G TG+GK+TL+N L R D Sbjct: 364 VAIVGPTGAGKSTLINLLQRVFD 386 >gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK; Provisional. Length = 258 Score = 31.0 bits (71), Expect = 0.68 Identities = 12/16 (75%), Positives = 13/16 (81%) Query: 255 ISGGTGSGKTTLLNCL 270 I G +GSGKTTLLN L Sbjct: 37 IVGESGSGKTTLLNAL 52 >gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding protein. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates. Length = 243 Score = 30.7 bits (70), Expect = 0.77 Identities = 13/34 (38%), Positives = 20/34 (58%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDT 286 V I G +G+GK+TLL C+ R ++ + E T Sbjct: 31 VAIIGPSGAGKSTLLRCINRLVEPSSGSILLEGT 64 >gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes. Length = 571 Score = 30.8 bits (70), Expect = 0.80 Identities = 11/26 (42%), Positives = 18/26 (69%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278 V + G +GSGK+TL+N + R+ + D Sbjct: 361 VALVGRSGSGKSTLVNLIPRFYEPDS 386 >gnl|CDD|182732 PRK10789, PRK10789, putative multidrug transporter membrane\ATP-binding components; Provisional. Length = 569 Score = 30.8 bits (70), Expect = 0.84 Identities = 13/24 (54%), Positives = 17/24 (70%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDE 278 I G TGSGK+TLL+ + R+ D E Sbjct: 346 ICGPTGSGKSTLLSLIQRHFDVSE 369 >gnl|CDD|148992 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side. Length = 301 Score = 30.8 bits (70), Expect = 0.90 Identities = 9/27 (33%), Positives = 14/27 (51%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDER 279 + + G GSGKT+ LN L + + Sbjct: 23 IGLYGAWGSGKTSFLNLLEDELKEFPE 49 >gnl|CDD|185088 PRK15134, PRK15134, microcin C ABC transporter ATP-binding protein YejF; Provisional. Length = 529 Score = 30.4 bits (69), Expect = 1.00 Identities = 15/35 (42%), Positives = 20/35 (57%) Query: 368 RMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRL 402 R MIAM T P ++ + T++LDV VQ Q L Sbjct: 162 RQRVMIAMALLTRPELLIADEPTTALDVSVQAQIL 196 >gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional. Length = 345 Score = 30.2 bits (69), Expect = 1.1 Identities = 10/16 (62%), Positives = 12/16 (75%) Query: 253 VLISGGTGSGKTTLLN 268 V++ G TGSGKT LL Sbjct: 144 VVLGGNTGSGKTELLQ 159 >gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional. Length = 172 Score = 30.1 bits (68), Expect = 1.2 Identities = 12/20 (60%), Positives = 13/20 (65%) Query: 253 VLISGGTGSGKTTLLNCLTR 272 VLI G +GSGKTTL L Sbjct: 18 VLIDGRSGSGKTTLAGALAA 37 >gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein; Provisional. Length = 582 Score = 30.0 bits (68), Expect = 1.3 Identities = 14/28 (50%), Positives = 19/28 (67%) Query: 251 CNVLISGGTGSGKTTLLNCLTRYIDKDE 278 V + G +GSGK+T+ N LTR+ D DE Sbjct: 370 KTVALVGRSGSGKSTIANLLTRFYDIDE 397 >gnl|CDD|163352 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins. Length = 206 Score = 29.9 bits (68), Expect = 1.4 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDER---IVTCEDTAELQLQQPHVVRLET 301 I G +GSGK+TLLN + ++K + + ++T L ++ R E Sbjct: 27 YAIIGESGSGKSTLLNIIGL-LEKFDSGQVYLNGKETPPLNSKKASKFRREK 77 >gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. Length = 586 Score = 30.1 bits (68), Expect = 1.4 Identities = 23/91 (25%), Positives = 35/91 (38%), Gaps = 19/91 (20%) Query: 205 PPLALDGPTLTIRKFKKDKLTLDH----LVSFGAVTAEGARLLQIIGR------------ 248 PPL L L +R++ +++ L L+ TA A L + Sbjct: 96 PPLVLCDGRLYLRRYWREEEKLAAKLRTLLEARKRTAPSAILENLFPLLNEQNWQKVAVA 155 Query: 249 ---IRCNVLISGGTGSGKTTLLNCLTRYIDK 276 LI+GG G+GKTT + L + K Sbjct: 156 LALKSNFSLITGGPGTGKTTTVARLLLALVK 186 >gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se. Length = 253 Score = 29.8 bits (67), Expect = 1.4 Identities = 13/31 (41%), Positives = 16/31 (51%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285 I G +GSGK+TLL CL + D T Sbjct: 34 IVGESGSGKSTLLGCLAGRLAPDHGTATYIM 64 >gnl|CDD|182996 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed. Length = 635 Score = 29.9 bits (68), Expect = 1.5 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 10/58 (17%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVV-RLETRPP-NIEG 308 V + G G+GK+TL+ L + D+ + +Q +V RL+ PP N+EG Sbjct: 32 VCLVGRNGAGKSTLMKILNGEVLLDD--------GRIIYEQDLIVARLQQDPPRNVEG 81 >gnl|CDD|161782 TIGR00235, udk, uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below. Length = 207 Score = 30.0 bits (68), Expect = 1.5 Identities = 12/31 (38%), Positives = 19/31 (61%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285 I GG+GSGKTT+ + + K E ++ +D Sbjct: 11 IGGGSGSGKTTVARKIYEQLGKLEIVIISQD 41 >gnl|CDD|184314 PRK13767, PRK13767, ATP-dependent helicase; Provisional. Length = 876 Score = 29.9 bits (68), Expect = 1.5 Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 5/32 (15%) Query: 252 NVLISGGTGSGKT-----TLLNCLTRYIDKDE 278 NVLIS TGSGKT +++ L R + E Sbjct: 49 NVLISSPTGSGKTLAAFLAIIDELFRLGREGE 80 >gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional. Length = 1047 Score = 29.8 bits (67), Expect = 1.6 Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 2/21 (9%) Query: 255 ISGGTGSGKTTLLN--CLTRY 273 I+G TG+GKTTLL+ CL Y Sbjct: 35 ITGPTGAGKTTLLDAICLALY 55 >gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional. Length = 288 Score = 29.7 bits (68), Expect = 1.8 Identities = 7/18 (38%), Positives = 13/18 (72%) Query: 253 VLISGGTGSGKTTLLNCL 270 V+++G +G+GK+ L L Sbjct: 9 VIVTGLSGAGKSVALRAL 26 >gnl|CDD|163076 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. Length = 365 Score = 29.5 bits (67), Expect = 2.0 Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 5/38 (13%) Query: 252 NVLISGGTGSGKTTLLNCLTRYI-----DKDERIVTCE 284 NV I G TG+GKT + + + + D+D R+VT Sbjct: 42 NVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVY 79 >gnl|CDD|167016 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional. Length = 1809 Score = 29.4 bits (66), Expect = 2.0 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 5/62 (8%) Query: 206 PLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTT 265 L P L + ++ TL +S + L + + V ISG +GSGKT+ Sbjct: 1477 ALKQSQPDLHNTRSSEETPTLSVSLSIHTIQ-----NLNVSAPLHSLVAISGVSGSGKTS 1531 Query: 266 LL 267 LL Sbjct: 1532 LL 1533 >gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated. Length = 329 Score = 29.5 bits (67), Expect = 2.0 Identities = 11/23 (47%), Positives = 16/23 (69%) Query: 252 NVLISGGTGSGKTTLLNCLTRYI 274 N+L G TG+GKT L NC+ + + Sbjct: 185 NLLFYGNTGTGKTFLSNCIAKEL 207 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 29.4 bits (67), Expect = 2.0 Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIV-TCEDTAELQL 291 +LI+G G+GK+T L + +IV T E +LQ+ Sbjct: 260 ILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQV 299 >gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Length = 348 Score = 29.1 bits (66), Expect = 2.3 Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 1/30 (3%) Query: 250 RCNVLISGGTGSGKT-TLLNCLTRYIDKDE 278 + L++GG G+GKT LN D D Sbjct: 1 KAVFLVTGGPGTGKTVVALNLFAELSDSDL 30 >gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter ATP-binding protein YecC; Provisional. Length = 250 Score = 28.9 bits (65), Expect = 2.6 Identities = 12/18 (66%), Positives = 14/18 (77%) Query: 253 VLISGGTGSGKTTLLNCL 270 V I G +GSGKTTLL C+ Sbjct: 32 VAIIGPSGSGKTTLLRCI 49 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 29.0 bits (65), Expect = 2.7 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 3/57 (5%) Query: 240 ARLLQIIGRIRCNVLISGGTGSGKTT-LLNCLTRYIDKDERIVT--CEDTAELQLQQ 293 ++ + +V+++ TGSGKT L + + + T EL Q Sbjct: 14 KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQW 70 >gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel. Length = 199 Score = 29.1 bits (65), Expect = 2.8 Identities = 14/51 (27%), Positives = 24/51 (47%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPN 305 ++G GSGKT L+ LTR + + ++ + Q +V+ PP Sbjct: 6 VAGPVGSGKTALIEALTRALRQKYQLAVITNDIYTQEDAEFLVKNSALPPE 56 >gnl|CDD|177536 PHA03132, PHA03132, thymidine kinase; Provisional. Length = 580 Score = 28.6 bits (64), Expect = 3.4 Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%) Query: 251 CNVLISGGTGSGKTTLLNCLTRYIDKDERIV 281 C + + G G GKTTLLN + I D +V Sbjct: 258 CFLFLEGVMGVGKTTLLNHMRG-ILGDNVLV 287 >gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein; Reviewed. Length = 240 Score = 28.5 bits (64), Expect = 3.6 Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 4/28 (14%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERI 280 V+I G +GSGK+TLL C I+K E I Sbjct: 30 VVIIGPSGSGKSTLLRC----INKLEEI 53 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 28.6 bits (65), Expect = 3.7 Identities = 13/24 (54%), Positives = 16/24 (66%) Query: 252 NVLISGGTGSGKTTLLNCLTRYID 275 N+L+ G TGSGKT L L R +D Sbjct: 110 NILLIGPTGSGKTLLAQTLARILD 133 >gnl|CDD|173501 PTZ00265, PTZ00265, multidrug resistance protein (mdr1); Provisional. Length = 1466 Score = 28.5 bits (63), Expect = 3.9 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 6/45 (13%) Query: 255 ISGGTGSGKTTLLNCLTRYID--KDERIV----TCEDTAELQLQQ 293 I G TGSGK+T+++ L R+ D D IV D Q Q Sbjct: 1199 IVGETGSGKSTVMSLLMRFYDLKNDHHIVFKNEHTNDMTNEQDYQ 1243 >gnl|CDD|184125 PRK13538, PRK13538, cytochrome c biogenesis protein CcmA; Provisional. Length = 204 Score = 28.6 bits (65), Expect = 4.1 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 253 VLISGGTGSGKTTLLNCLT 271 V I G G+GKT+LL L Sbjct: 30 VQIEGPNGAGKTSLLRILA 48 >gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit, DevA family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts. Length = 220 Score = 28.4 bits (64), Expect = 4.3 Identities = 10/16 (62%), Positives = 14/16 (87%) Query: 253 VLISGGTGSGKTTLLN 268 V+++G +GSGKTTLL Sbjct: 34 VILTGPSGSGKTTLLT 49 >gnl|CDD|180976 PRK07431, PRK07431, aspartate kinase; Provisional. Length = 587 Score = 28.3 bits (64), Expect = 4.9 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 392 SLDVIVQTQRLRDGSRR 408 S+D+IVQ+QR R R Sbjct: 467 SVDMIVQSQRCRSDGTR 483 >gnl|CDD|148381 pfam06745, KaiC, KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria. Length = 231 Score = 28.0 bits (63), Expect = 5.1 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 253 VLISGGTGSGKTTL 266 VLI+GG G+GKT Sbjct: 22 VLITGGPGTGKTIF 35 >gnl|CDD|181771 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed. Length = 509 Score = 27.9 bits (63), Expect = 5.3 Identities = 9/15 (60%), Positives = 12/15 (80%) Query: 253 VLISGGTGSGKTTLL 267 +L+SG TG+GKT L Sbjct: 276 ILVSGATGTGKTLLA 290 >gnl|CDD|185024 PRK15064, PRK15064, ABC transporter ATP-binding protein; Provisional. Length = 530 Score = 27.9 bits (63), Expect = 5.4 Identities = 10/18 (55%), Positives = 11/18 (61%) Query: 253 VLISGGTGSGKTTLLNCL 270 + I G G GKTTLL L Sbjct: 348 LAIIGENGVGKTTLLRTL 365 >gnl|CDD|183080 PRK11300, livG, leucine/isoleucine/valine transporter ATP-binding subunit; Provisional. Length = 255 Score = 28.0 bits (63), Expect = 5.6 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 253 VLISGGTGSGKTTLLNCLT 271 V + G G+GKTT+ NCLT Sbjct: 34 VSLIGPNGAGKTTVFNCLT 52 >gnl|CDD|184583 PRK14237, PRK14237, phosphate transporter ATP-binding protein; Provisional. Length = 267 Score = 27.8 bits (62), Expect = 5.9 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 5/64 (7%) Query: 216 IRKFKKDKLTL---DHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTR 272 I F ++++ L D V +G A +Q + + LI G +GSGK+T L L R Sbjct: 11 IITFPEEEIALSTKDLHVYYGKKEAIKGIDMQF-EKNKITALI-GPSGSGKSTYLRSLNR 68 Query: 273 YIDK 276 D Sbjct: 69 MNDT 72 >gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. Length = 413 Score = 27.8 bits (62), Expect = 6.0 Identities = 12/24 (50%), Positives = 16/24 (66%) Query: 252 NVLISGGTGSGKTTLLNCLTRYID 275 N+L+ G TGSGKT L L R ++ Sbjct: 118 NILLIGPTGSGKTLLAQTLARILN 141 >gnl|CDD|164820 PHA00520, PHA00520, packaging NTPase P4. Length = 330 Score = 27.9 bits (62), Expect = 6.4 Identities = 12/30 (40%), Positives = 17/30 (56%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVT 282 ++ GGTGSGKT LLN L + ++ Sbjct: 127 EVVVGGTGSGKTPLLNALAPDVGGGDKYAV 156 >gnl|CDD|163168 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene. Length = 311 Score = 27.9 bits (63), Expect = 6.5 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 253 VLISGGTGSGKTTLLNCLTR 272 +++ G TGSGKT LL+ L Sbjct: 130 IVLGGMTGSGKTELLHALAN 149 >gnl|CDD|140270 PTZ00243, PTZ00243, ABC transporter; Provisional. Length = 1560 Score = 27.8 bits (62), Expect = 6.6 Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 12/60 (20%) Query: 228 HLVSFGAVTAEGARL-------LQIIG---RI--RCNVLISGGTGSGKTTLLNCLTRYID 275 H V G++ EG ++ L + G RI R V I G TGSGK+TLL R ++ Sbjct: 1302 HPVQAGSLVFEGVQMRYREGLPLVLRGVSFRIAPREKVGIVGRTGSGKSTLLLTFMRMVE 1361 >gnl|CDD|130045 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding protein. This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters. Length = 247 Score = 27.6 bits (62), Expect = 6.7 Identities = 10/22 (45%), Positives = 13/22 (59%) Query: 255 ISGGTGSGKTTLLNCLTRYIDK 276 + G +G GK+TLL L R D Sbjct: 32 LIGPSGCGKSTLLRSLNRMNDL 53 >gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein PhnL. Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se. Length = 224 Score = 27.7 bits (62), Expect = 6.8 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 253 VLISGGTGSGKTTLLNCLTR 272 V +SG +G+GK+TLL L Sbjct: 37 VALSGPSGAGKSTLLKSLYA 56 >gnl|CDD|184123 PRK13536, PRK13536, nodulation factor exporter subunit NodI; Provisional. Length = 340 Score = 27.9 bits (62), Expect = 6.9 Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 5/80 (6%) Query: 233 GAVTAEGARLLQIIGRIRCNVL-ISGGTGSGKTTLLNCLTRYIDKDERIVTC----EDTA 287 G AEG I I C V+ I GG ++L+ R I+ + C + Sbjct: 248 GRKIAEGRPHALIDEHIGCQVIEIYGGDPHELSSLVKPYARRIEVSGETLFCYAPDPEQV 307 Query: 288 ELQLQQPHVVRLETRPPNIE 307 +QL+ +RL RPPN+E Sbjct: 308 RVQLRGRAGLRLLQRPPNLE 327 >gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional. Length = 327 Score = 27.7 bits (62), Expect = 6.9 Identities = 11/31 (35%), Positives = 17/31 (54%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285 ++G +G GKTT L L + ++ V C D Sbjct: 13 VAGDSGCGKTTFLRGLADLLGEELVTVICTD 43 >gnl|CDD|150482 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members of this family include various bacterial predicted ABC class ATPases. Length = 447 Score = 27.6 bits (62), Expect = 7.1 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 6/40 (15%) Query: 254 LISGGTGSGKTTLLNCLTRYI------DKDERIVTCEDTA 287 LI GG GK+TLL L R + D E +VT D Sbjct: 247 LIVGGGYHGKSTLLEALERGVYDHIPGDGREFVVTDPDAV 286 >gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease protein; Provisional. Length = 648 Score = 27.8 bits (62), Expect = 7.2 Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDK 276 V I G +GSGK+TL+N L +DK Sbjct: 37 VAIVGASGSGKSTLMNILG-CLDK 59 >gnl|CDD|178984 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed. Length = 943 Score = 27.7 bits (63), Expect = 7.3 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 6/33 (18%) Query: 152 NGKTV----E--TGINFRDNEQLLSVCQRIVNQ 178 GKT+ E TG++F D +LL V R+V++ Sbjct: 850 TGKTLYILDEPTTGLHFEDIRKLLEVLHRLVDK 882 >gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed. Length = 394 Score = 27.5 bits (62), Expect = 7.3 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 252 NVLISGGTGSGKTT 265 NVLI G G+GKTT Sbjct: 57 NVLIYGPPGTGKTT 70 >gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional. Length = 1470 Score = 27.5 bits (61), Expect = 7.6 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 7/46 (15%) Query: 242 LLQIIGRIRCNVLIS--GGTGSGKTTLLNCLT-----RYIDKDERI 280 L ++ G R VL + G +G+GKTTL++ L YI+ D RI Sbjct: 896 LREVTGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGDIRI 941 >gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein; Provisional. Length = 623 Score = 27.5 bits (61), Expect = 7.7 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 13/80 (16%) Query: 324 MRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQ 383 M + +L +VR PE +L G M R MIAM P+ Sbjct: 143 MVEAKRMLDQVRIPEAQTILSRYPHQLSGGM-------------RQRVMIAMALSCRPAV 189 Query: 384 MVREIITSSLDVIVQTQRLR 403 ++ + T++LDV +Q Q L+ Sbjct: 190 LIADEPTTALDVTIQAQILQ 209 >gnl|CDD|161968 TIGR00630, uvra, excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 924 Score = 27.7 bits (62), Expect = 7.8 Identities = 28/98 (28%), Positives = 44/98 (44%), Gaps = 31/98 (31%) Query: 105 MSLDEQLDLFED----------LCNDILGYGPL-QPL-------IARDDIADIMVNGSNK 146 M+++E + FE LC+ LGY L QP R +A + S + Sbjct: 790 MTVEEAYEFFEAVPSISRKLQTLCDVGLGYIKLGQPATTLSGGEAQRIKLAKEL---SKR 846 Query: 147 VFIEVNGKTV------ETGINFRDNEQLLSVCQRIVNQ 178 G+T+ TG++F D ++LL V QR+V+Q Sbjct: 847 S----TGRTLYILDEPTTGLHFDDIKKLLEVLQRLVDQ 880 >gnl|CDD|182592 PRK10619, PRK10619, histidine/lysine/arginine/ornithine transporter subunit; Provisional. Length = 257 Score = 27.6 bits (61), Expect = 8.0 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 16/77 (20%) Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITM 314 I G +GSGK+T L C+ +++K E + + Q ++VR + +G++ + Sbjct: 36 IIGSSGSGKSTFLRCIN-FLEK-----PSEGSIVVNGQTINLVR--------DKDGQLKV 81 Query: 315 RDLVKNCLRMRPERIIL 331 D KN LR+ R+ + Sbjct: 82 AD--KNQLRLLRTRLTM 96 >gnl|CDD|181888 PRK09473, oppD, oligopeptide transporter ATP-binding component; Provisional. Length = 330 Score = 27.4 bits (61), Expect = 8.1 Identities = 13/33 (39%), Positives = 18/33 (54%) Query: 368 RMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQ 400 R MIAM P ++ + T++LDV VQ Q Sbjct: 167 RQRVMIAMALLCRPKLLIADEPTTALDVTVQAQ 199 >gnl|CDD|162629 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. Length = 1283 Score = 27.4 bits (61), Expect = 8.1 Identities = 11/15 (73%), Positives = 13/15 (86%) Query: 253 VLISGGTGSGKTTLL 267 V+I+G TGSGKTT L Sbjct: 85 VIIAGETGSGKTTQL 99 >gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. Length = 650 Score = 27.3 bits (61), Expect = 8.2 Identities = 10/18 (55%), Positives = 14/18 (77%) Query: 253 VLISGGTGSGKTTLLNCL 270 +LI G G+GKTTLL+ + Sbjct: 31 ILIGGLNGAGKTTLLDAI 48 >gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional. Length = 316 Score = 27.3 bits (61), Expect = 8.3 Identities = 11/31 (35%), Positives = 16/31 (51%) Query: 247 GRIRCNVLISGGTGSGKTTLLNCLTRYIDKD 277 GRI +L S G+GKTT+ L + + Sbjct: 40 GRIPNMLLHSPSPGTGKTTVAKALCNEVGAE 70 >gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se. Length = 1490 Score = 27.6 bits (61), Expect = 8.5 Identities = 12/24 (50%), Positives = 16/24 (66%) Query: 257 GGTGSGKTTLLNCLTRYIDKDERI 280 G TGSGK+TLL+ L R + + I Sbjct: 1252 GRTGSGKSTLLSALLRLLSTEGEI 1275 >gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional. Length = 1294 Score = 27.3 bits (61), Expect = 9.2 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 253 VLISGGTGSGKTTLL 267 V+++G TGSGKTT L Sbjct: 92 VIVAGETGSGKTTQL 106 >gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid. Length = 191 Score = 27.2 bits (61), Expect = 9.6 Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 2/52 (3%) Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPP 304 VL+ G G+GKT L L + + D EL+ P L+ P Sbjct: 15 VLLGGQPGAGKTELARALLEELGGGNVVRIDPD--ELRTYHPDYDELQKADP 64 >gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional. Length = 675 Score = 27.2 bits (61), Expect = 9.8 Identities = 9/16 (56%), Positives = 13/16 (81%) Query: 250 RCNVLISGGTGSGKTT 265 R V+++GGTG GKT+ Sbjct: 179 RKPVVLTGGTGVGKTS 194 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 0.318 0.136 0.380 Gapped Lambda K H 0.267 0.0738 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,807,823 Number of extensions: 520154 Number of successful extensions: 1564 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1537 Number of HSP's successfully gapped: 138 Length of query: 483 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 386 Effective length of database: 3,898,497 Effective search space: 1504819842 Effective search space used: 1504819842 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (26.5 bits)