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)