RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 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|34569 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
           [Intracellular trafficking and secretion].
          Length = 355

 Score =  455 bits (1171), Expect = e-128
 Identities = 207/360 (57%), Positives = 254/360 (70%), Gaps = 5/360 (1%)

Query: 78  LSQYDSQSARDEIATLMNEIVSVKKITMSLDEQLDLFEDLCNDILGYGPLQPLIARDDIA 137
           L   D +  +  +   + E V    I +S  E   L  D+ +++ GYGPL+PL+A DDI 
Sbjct: 1   LEILDLERGKRSLKDEVREYVRENNIAISEAELDSLARDIQDELTGYGPLEPLLADDDIE 60

Query: 138 DIMVNGSNKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDESSPICDARLLDG 197
           DIMVNG  +VF+E  G    T I F D   LL + QRI   VGRR+DES PI DARL DG
Sbjct: 61  DIMVNGPGRVFVERKGGLEPTDIRFLDEAALLRIIQRIAAAVGRRIDESQPIVDARLPDG 120

Query: 198 SRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISG 257
           SR+N   PP+A+DGPTL+IRKF K KLTL  L+ FG +    A+ L+    IRCN+LISG
Sbjct: 121 SRLNANSPPVAIDGPTLSIRKFPKIKLTLLDLIIFGTMIRRAAKFLRRAVGIRCNILISG 180

Query: 258 GTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRDL 317
           GTGSGKTTLLN L+ +ID DER++T EDTAELQL  PHVVRLETRPPN+EG GE+TMRDL
Sbjct: 181 GTGSGKTTLLNALSGFIDSDERVITIEDTAELQLAHPHVVRLETRPPNVEGTGEVTMRDL 240

Query: 318 VKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGG 377
           VKN LRMRP+RII+GEVRG E LDLLQAMNTGHDG MGT+HAN+ RE+  R+E +IA GG
Sbjct: 241 VKNALRMRPDRIIVGEVRGVEALDLLQAMNTGHDGGMGTLHANSPREALTRLEQLIAEGG 300

Query: 378 FTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVGMEGNVIITQDLLKYEVMGED 437
                Q +R  I S++DVIVQ  RL DG RRIT I E+ GMEG V +TQD+ +++  G+D
Sbjct: 301 ----VQTIRRQIASAVDVIVQIARLGDG-RRITEIAEVTGMEGGVYVTQDIFEFDPGGKD 355


>gnl|CDD|109493 pfam00437, GSPII_E, Type II/IV secretion system protein.  This
           family contains both type II and type IV pathway
           secretion proteins from bacteria. VirB11 ATPase is a
           subunit of the Agrobacterium tumefaciens transfer DNA
           (T-DNA) transfer system, a type IV secretion pathway
           required for delivery of T-DNA and effector proteins to
           plant cells during infection.
          Length = 283

 Score =  251 bits (644), Expect = 2e-67
 Identities = 107/282 (37%), Positives = 149/282 (52%), Gaps = 16/282 (5%)

Query: 125 GPLQPLIARDDIADIMVNGSNKVFIE--VNGKTVETGINFRDNEQLLSVCQRIVNQVGRR 182
            PL+ L+     +DI VN   +V++   V G  +   I        + +  RI    G  
Sbjct: 13  IPLEALLDDPGASDIHVNPPGRVWVRFRVGGIVLRE-IPDPSPAAAMRLISRIAVMAGLD 71

Query: 183 VDESSPICDARL-LDGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGAR 241
           + E  P  DARL L G R  V  PP+   G    IRK     LTLD L   GA  A+ A 
Sbjct: 72  ISERRPPQDARLPLGGERFRVSTPPVVA-GEAFVIRKPSSRSLTLDDLGMTGAFDADIAE 130

Query: 242 LLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDK-DERIVTCEDTAELQLQQPHVVRLE 300
            L+   + R N+L+SGGTGSGKTTLL  L   I+  DERIVT ED  E+QL+ P+ V+L 
Sbjct: 131 FLRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTIEDPVEIQLEGPNQVQLN 190

Query: 301 TRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHAN 360
           TR         +T  DL++  LR RP+RI++GE+R  E  D+L+A NTGH GS+ T+HAN
Sbjct: 191 TR------LAGVTFADLLRAALRQRPDRIMVGEIRDGETADILRAANTGHPGSLSTLHAN 244

Query: 361 NARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRL 402
           +A  +  R+E +       L    +R  I + +D++ +  R 
Sbjct: 245 SAAGALTRLEQLGME----LEPFEIRSSILAVVDIVQRLVRR 282


>gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
           VirB11, and related ATPases. The homohexamer, VirB11 is
           one of eleven Vir proteins, which are required for
           T-pilus biogenesis and virulence in the transfer of
           T-DNA from the Ti (tumor-inducing) plasmid of bacterial
           to plant cells. The pilus is a fibrous cell surface
           organelle, which mediates adhesion between bacteria
           during conjugative transfer or between bacteria and host
           eukaryotic cells during infection. VirB11- related
           ATPases include the archaeal flagella biosynthesis
           protein and the pilus assembly proteins CpaF/TadA and
           TrbB.  This alignment contains the C-terminal domain,
           which is the ATPase..
          Length = 186

 Score =  248 bits (635), Expect = 2e-66
 Identities = 105/187 (56%), Positives = 130/187 (69%), Gaps = 4/187 (2%)

Query: 226 LDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285
           LD L++ G  +   A  L +    R N+LISGGTGSGKTTLLN L  +I  DERI+T ED
Sbjct: 1   LDDLIAQGTFSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLAFIPPDERIITIED 60

Query: 286 TAELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQA 345
           TAELQL  P+ VRL TRP N+EG GE+TM DL+++ LRMRP+RII+GEVRG E LDLLQA
Sbjct: 61  TAELQLPHPNWVRLVTRPGNVEGSGEVTMADLLRSALRMRPDRIIVGEVRGGEALDLLQA 120

Query: 346 MNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRL--R 403
           MNTGH G M TIHAN+A E+  R+E + +      P  ++RE I  ++DVIV   RL  R
Sbjct: 121 MNTGHPGGMTTIHANSAEEALTRLELLPSNVPLGRP--LLREQIKEAIDVIVHIARLKGR 178

Query: 404 DGSRRIT 410
            G RR+T
Sbjct: 179 RGIRRVT 185


>gnl|CDD|30975 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
           related ATPases involved in archaeal flagella
           biosynthesis [Cell motility and secretion /
           Intracellular trafficking and secretion].
          Length = 312

 Score =  218 bits (556), Expect = 3e-57
 Identities = 117/300 (39%), Positives = 176/300 (58%), Gaps = 12/300 (4%)

Query: 120 DILGYGPLQPLIARDDIADIMVNGSNKVFIE-VNGKTVETGINFRDNEQLLSVCQRIVNQ 178
           +I+G G L+PL+    I DI+VNG   V++E   G +  T I F   E+L S+  R+  +
Sbjct: 11  EIIGLGKLEPLLRDPRIEDIVVNGPGPVYVEHKGGGSYVTNIPFLTEEELDSLAIRLAQR 70

Query: 179 VGRRVDESSPICDARLLDGSRVNVIIPPL-ALDGPTLTIRKFKKDKLTLDHLVSFGAVTA 237
            G+ + E++PI DA L DGSR+ +++ P  + +G + TIRKF  + +T + L+ +G ++ 
Sbjct: 71  SGKPISEANPILDATLPDGSRIQIVLGPEVSPNGSSFTIRKFSDEPITPEDLIEYGTISP 130

Query: 238 EGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVV 297
           E A  L +    R +++I GGT SGKTTLLN L  +I  +ERIVT EDT EL+L   + V
Sbjct: 131 EQAAYLWLAIEARKSIIICGGTASGKTTLLNALLDFIPPEERIVTIEDTPELKLPHENWV 190

Query: 298 RLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTI 357
           +L TR     G  E+++ DL++  LR RP+ II+GE+RG E   L QAM TGH G++ TI
Sbjct: 191 QLVTREGE-SGSSEVSLEDLLRAALRQRPDYIIVGELRGREAFVLFQAMQTGH-GTISTI 248

Query: 358 HANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVG 417
           HA++      R+          LP  + +E++     +I Q     D  RR++ I EIVG
Sbjct: 249 HADSPELVLDRLTE--------LPLNVPKEMLLKLDVIIEQYADRVDVLRRVSRIAEIVG 300


>gnl|CDD|32635 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
           assembly pathway, ATPase PilB [Cell motility and
           secretion / Intracellular trafficking and secretion].
          Length = 500

 Score = 76.2 bits (187), Expect = 2e-14
 Identities = 62/200 (31%), Positives = 101/200 (50%), Gaps = 25/200 (12%)

Query: 216 IRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYID 275
           +R   KD++ LD L   G    + ARLL+++ R +  +L++G TGSGKTT L      ++
Sbjct: 225 LRILDKDQVILD-LEKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELN 283

Query: 276 KDER-IVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEV 334
             ER I+T ED  E QL  P + +++  P     +  +T    ++  LR  P+ I++GE+
Sbjct: 284 TPERNIITIEDPVEYQL--PGINQVQVNP-----KIGLTFARALRAILRQDPDVIMVGEI 336

Query: 335 RGPEVLD-LLQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREIITSSL 393
           R  E  +  +QA  TGH   + T+H N+A  +  R+  M           +   ++ SSL
Sbjct: 337 RDLETAEIAVQAALTGHL-VLSTLHTNDAPGAITRLLEM----------GVEPYLLASSL 385

Query: 394 DVIVQTQRLRDGSRRITNIC 413
             ++  QRL    RR+   C
Sbjct: 386 LGVI-AQRL---VRRLCPHC 401


>gnl|CDD|29995 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
           main terminal branch of the general secretory pathway
           (GSP).  It is responsible for the export the majority of
           Gram-negative bacterial exoenzymes and toxins. PulE is a
           cytoplasmic protein of the GSP, which contains an ATP
           binding site and a tetracysteine motif. This subgroup
           also includes PillB and HofB..
          Length = 264

 Score = 70.3 bits (172), Expect = 1e-12
 Identities = 52/206 (25%), Positives = 97/206 (47%), Gaps = 25/206 (12%)

Query: 211 GPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCL 270
           G ++ +R   K    LD L   G          +++ +    +L++G TGSGKTT L   
Sbjct: 42  GESVVLRILDKKNQILD-LEKLGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSA 100

Query: 271 TRYIDKDER-IVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERI 329
              ++  E+ I+T ED  E Q+  P + +++        +  +T    ++  LR  P+ I
Sbjct: 101 LSELNTPEKNIITVEDPVEYQI--PGINQVQVNE-----KAGLTFARGLRAILRQDPDII 153

Query: 330 ILGEVRGPEVLDL-LQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREI 388
           ++GE+R  E  ++ +QA  TGH   + T+H N+A  +  R+  M           +   +
Sbjct: 154 MVGEIRDAETAEIAVQAALTGH-LVLSTLHTNDAPGAITRLLDM----------GIESYL 202

Query: 389 ITSSLDVIVQTQRLRDGSRRITNICE 414
           ++S+L  ++  QRL    R++   C+
Sbjct: 203 LSSALIGVI-AQRL---VRKLCPHCK 224


>gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
           PilT [Cell motility and secretion / Intracellular
           trafficking and secretion].
          Length = 353

 Score = 64.5 bits (157), Expect = 6e-11
 Identities = 72/292 (24%), Positives = 127/292 (43%), Gaps = 46/292 (15%)

Query: 136 IADIMVNGSNKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDESSPICDARLL 195
            +D+ ++      I ++G+           E + S+ + I+N   R++ E     +   L
Sbjct: 17  ASDLHLSAGLPPRIRIDGELRPINYPPLTAEDVQSLLREILNDDQRKILE-----ENGEL 71

Query: 196 DGS---------RVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQII 246
           D S         RVN         G  L +R       TL+ L            + ++ 
Sbjct: 72  DFSYTLPGVARFRVNAF---KQRGGYALVLRLIPSKIPTLEEL-------GLPPIVRELA 121

Query: 247 GRIRCNVLISGGTGSGKTTLLNCLTRYIDK--DERIVTCEDTAEL--QLQQPHVVRLETR 302
              R  +L++G TGSGK+T L  +  YI+K   + I+T ED  E   + ++  + + E  
Sbjct: 122 ESPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDPIEYVHESKKSLINQREV- 180

Query: 303 PPNIEGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDL-LQAMNTGHDGSMGTIHANN 361
                G   ++  + ++  LR  P+ I++GE+R  E + L L A  TGH    GT+H N+
Sbjct: 181 -----GRDTLSFANALRAALREDPDVILVGEMRDLETIRLALTAAETGHL-VFGTLHTNS 234

Query: 362 ARESFGRMEAMIAMGGFTLPSQ-MVREIITSSLDVIVQTQRL---RDGSRRI 409
           A ++  R+  +     F    +  VR  +  SL  ++ +QRL   +DG  R+
Sbjct: 235 AAKTIDRIIDV-----FPAEEKDQVRSQLAESLRAVI-SQRLLPKKDGGGRV 280


>gnl|CDD|29997 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
           binding protein responsible for the retraction of type
           IV pili, likely by pili disassembly. This retraction
           provides the force required for travel of bacteria in
           low water environments by a mechanism known as twitching
           motility..
          Length = 198

 Score = 62.2 bits (151), Expect = 3e-10
 Identities = 47/158 (29%), Positives = 78/158 (49%), Gaps = 18/158 (11%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDK--DERIVTCEDTAEL--QLQQPHVVRLETRPPNIEG 308
           VL++G TGSGK+T L  +  YI+K     I+T ED  E   + ++  + + E       G
Sbjct: 4   VLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVHESKRSLINQREV------G 57

Query: 309 EGEITMRDLVKNCLRMRPERIILGEVRGPEVLDL-LQAMNTGHDGSMGTIHANNARESFG 367
              ++  + +K  LR  P+ I++GE+R  E + L L A  TGH   M T+H N+A ++  
Sbjct: 58  LDTLSFENALKAALRQDPDVILVGEMRDLETIRLALTAAETGHL-VMSTLHTNSAAKTID 116

Query: 368 RMEAMIAMGGFTLPSQ-MVREIITSSLDVIVQTQRLRD 404
           R+  +     F    +  +R  +  SL  ++  Q L  
Sbjct: 117 RIIDV-----FPAEERDQIRTQLAESLKAVISQQLLPK 149


>gnl|CDD|34613 COG5008, PilU, Tfp pilus assembly protein, ATPase PilU [Cell
           motility and secretion / Intracellular trafficking and
           secretion].
          Length = 375

 Score = 58.8 bits (142), Expect = 3e-09
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 8/120 (6%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE--RIVTCEDTAELQLQQPHVVRLETRPPNIEGEG 310
           V+I G TGSGK+T +  +  Y +K+    I+T ED  E  + +     +  R   ++ E 
Sbjct: 130 VIIVGATGSGKSTTMAAMIGYRNKNSTGHIITIEDPIEF-IHKHKRCIVTQREVGVDTE- 187

Query: 311 EITMRDLVKNCLRMRPERIILGEVRGPEVLD-LLQAMNTGHDGSMGTIHANNARESFGRM 369
             +    +KN LR  P+ I++GEVR  E ++  +Q   TGH   M T+HANNA ++  R+
Sbjct: 188 --SWEVALKNTLRQAPDVILIGEVRSRETMEYAIQFAETGHL-CMATLHANNANQALERI 244


>gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 952

 Score = 38.1 bits (88), Expect = 0.005
 Identities = 39/188 (20%), Positives = 66/188 (35%), Gaps = 29/188 (15%)

Query: 251 CNVLISGGTGSGKTTLLNCLTRYIDKDE----RIVTCEDTAELQLQQPHVVRLETRPPNI 306
            N+L++G  GSGKT L+  L  Y  KD      IV+C       L++             
Sbjct: 432 GNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQK---------- 481

Query: 307 EGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHA---NNAR 363
                  + ++    L   P  I+L ++   + L    +   G DG +    A   N   
Sbjct: 482 ------FLNNVFSEALWYAPSIIVLDDL---DCLASASSNENGQDGVVSERLAAFLNQVI 532

Query: 364 ESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLR--DGSRRITNICEIVGMEGN 421
           + + +    IA+       Q +  ++ S L +      L     +RR   +  I     +
Sbjct: 533 KIYLKRNRKIAVIATGQELQTLNPLLVSPL-LFQIVIALPAPAVTRRKEILTTIFSKNLS 591

Query: 422 VIITQDLL 429
            I   DL 
Sbjct: 592 DITMDDLD 599


>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
           only].
          Length = 604

 Score = 37.9 bits (88), Expect = 0.006
 Identities = 31/127 (24%), Positives = 50/127 (39%), Gaps = 14/127 (11%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIV-TCEDTAELQLQQPHVVRLETRPPNIE--GE 309
           +LI+G  G+GK+T    L  +     +IV T E   +LQ+            P I     
Sbjct: 266 ILIAGAPGAGKSTFAQALAEFYASQGKIVKTMESPRDLQV-----------SPEITQYSP 314

Query: 310 GEITMRDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRM 369
            E  M       L +RP+  I  E+R  E   +   +     G +G +HA    ++  R 
Sbjct: 315 LEGDMEKTADILLLVRPDYTIYDEMRKTEDFQVYADLRLAGVGMVGVVHATRPIDAIQRF 374

Query: 370 EAMIAMG 376
              + +G
Sbjct: 375 IGRVELG 381


>gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport
           systems, contain duplicated ATPase [General function
           prediction only].
          Length = 539

 Score = 37.9 bits (88), Expect = 0.007
 Identities = 43/199 (21%), Positives = 68/199 (34%), Gaps = 48/199 (24%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITM 314
           I G +GSGK+TL   L   + +  RI + E            V L+ R  ++ G  E  M
Sbjct: 40  IVGESGSGKSTLALALMGLLPEGGRITSGE------------VILDGR--DLLGLSEREM 85

Query: 315 RDLVKNCLRMRPER-----------------------IILGEVRGPEVLDLLQAMNTGHD 351
           R L    + M  +                                   ++LL+ +     
Sbjct: 86  RKLRGKRIAMIFQDPMTSLNPVMTIGDQIREALRLHGKGSRAEARKRAVELLEQVGLPDP 145

Query: 352 GSMGTIHANNARESFG--RMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRI 409
                       +  G  R   MIAM     P  ++ +  T++LDV  Q Q L      +
Sbjct: 146 ER----RDRYPHQLSGGMRQRVMIAMALALKPKLLIADEPTTALDVTTQAQILDL----L 197

Query: 410 TNICEIVGMEGNVIITQDL 428
            ++   +GM   + IT DL
Sbjct: 198 KDLQRELGM-AVLFITHDL 215



 Score = 28.2 bits (63), Expect = 4.7
 Identities = 8/28 (28%), Positives = 13/28 (46%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVT 282
           + G +GSGK+TL   L   +      + 
Sbjct: 322 LVGESGSGKSTLARILAGLLPPSSGSII 349


>gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 786

 Score = 37.6 bits (87), Expect = 0.008
 Identities = 36/118 (30%), Positives = 51/118 (43%), Gaps = 12/118 (10%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVV-RLETRPPNIEGEG 310
           + L  G TG GKT L   L   +  DE+ +   D +E    + H V RL   PP   G  
Sbjct: 523 SFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSE--YMEKHSVSRLIGAPPGYVGYE 580

Query: 311 EITMRDLVKNCLRMRPERIILG---EVRGPEVLD-LLQAMNTGH--DGSMGTIHANNA 362
           E      +   +R +P  +IL    E   P+V + LLQ ++ G   DG   T+   N 
Sbjct: 581 E---GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNT 635


>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance Protein)-like
           transporters are involved in drug, peptide, and lipid
           export.  They belong to the subfamily C of the
           ATP-binding cassette (ABC) superfamily of transport
           proteins.  The ABCC subfamily contains transporters with
           a diverse functional spectrum that includes ion
           transport, cell surface receptor, and toxin secretion
           activities.  The MRP-like family, simlar to all ABC
           proteins, have a common four-domain core structure
           constituted by two membrane-spanning domains, each
           composed of six transmembrane (TM) helices, and two
           nucleotide-binding domains (NBD).  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 171

 Score = 33.5 bits (77), Expect = 0.15
 Identities = 13/26 (50%), Positives = 15/26 (57%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V I G +GSGK+TLL  L R  D   
Sbjct: 31  VAIVGPSGSGKSTLLKLLLRLYDPTS 56


>gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
          Length = 218

 Score = 33.3 bits (76), Expect = 0.17
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDT 286
           + I+GG+GSGKTT+   L+  +  ++ +V   D 
Sbjct: 11  IGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDD 44


>gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 591

 Score = 32.9 bits (75), Expect = 0.18
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERI 280
            V I G  GSGK+T+L  L R+ D    I
Sbjct: 380 KVAIVGSNGSGKSTILRLLLRFFDYSGSI 408


>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
           cellular Activities) superfamily represents an ancient
           group of ATPases belonging to the ASCE (for additional
           strand, catalytic E) division of the P-loop NTPase fold.
           The ASCE division also includes ABC, RecA-like,
           VirD4-like, PilT-like, and SF1/2 helicases. Members of
           the AAA+ ATPases function as molecular chaperons, ATPase
           subunits of proteases, helicases, or nucleic-acid
           stimulated ATPases. The AAA+ proteins contain several
           distinct features in addition to the conserved
           alpha-beta-alpha core domain structure and the Walker A
           and B motifs of the P-loop NTPases..
          Length = 151

 Score = 32.9 bits (75), Expect = 0.19
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGE 311
           N+L+ G  G+GKTTL   +   + +        + ++  L +  VV        +    E
Sbjct: 21  NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASD--LLEGLVVAELFGHFLVRLLFE 78

Query: 312 I 312
           +
Sbjct: 79  L 79


>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
           a cobalt transport family found in bacteria, archaea,
           and eukaryota.  The transition metal cobalt is an
           essential component of many enzymes and must be
           transported into cells in appropriate amounts when
           needed.  This ABC transport system of the CbiMNQO family
           is involved in cobalt transport in association with the
           cobalamin (vitamin B12) biosynthetic pathways.  Most of
           cobalt (Cbi) transport systems possess a separate CbiN
           component, the cobalt-binding periplasmic protein, and
           they are encoded by the conserved gene cluster cbiMNQO. 
           Both the CbiM and CbiQ proteins are integral cytoplasmic
           membrane proteins, and the CbiO protein has the linker
           peptide and the Walker A and B motifs commonly found in
           the ATPase components of the ABC-type transport
           systems..
          Length = 211

 Score = 32.4 bits (74), Expect = 0.28
 Identities = 13/34 (38%), Positives = 16/34 (47%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDT 286
           VLI G  GSGK+TLL  L   +      V  +  
Sbjct: 30  VLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVDGK 63


>gnl|CDD|73013 cd03254, ABCC_Glucan_exporter_like, Glucan exporter ATP-binding
           protein.  In A. tumefaciens cyclic beta-1, 2-glucan must
           be transported into the periplasmic space to exert its
           action as a virluence factor.  This subfamily belongs to
           the MRP-like family and is involved in drug, peptide,
           and lipid export.  The MRP-like family, similar to all
           ABC proteins, have a common four-domain core structure
           constituted by two membrane-spanning domains each
           composed of six transmembrane (TM) helices and two
           nucleotide-binding domains (NBD).  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 229

 Score = 32.1 bits (73), Expect = 0.31
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V I G TG+GKTTL+N L R+ D  +
Sbjct: 32  VAIVGPTGAGKTTLINLLMRFYDPQK 57


>gnl|CDD|34592 COG4987, CydC, ABC-type transport system involved in cytochrome bd
           biosynthesis, fused ATPase and permease components
           [Energy production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 573

 Score = 32.1 bits (73), Expect = 0.34
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDT 286
           V I G +GSGK+TLL  L    D  +  +T    
Sbjct: 367 VAILGRSGSGKSTLLQLLAGAWDPQQGSITLNGV 400


>gnl|CDD|30793 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
           system, ATPase component [Amino acid transport and
           metabolism / Inorganic ion transport and metabolism].
          Length = 316

 Score = 32.1 bits (73), Expect = 0.35
 Identities = 44/191 (23%), Positives = 73/191 (38%), Gaps = 29/191 (15%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRL-ETRPPNIEGEGEIT 313
           I G +GSGK+ L   +   + K    +      E+      ++ L E     I G+ EI 
Sbjct: 36  IVGESGSGKSVLAKAIMGLLPKPNARIV---GGEILFDGKDLLSLSEKELRKIRGK-EIA 91

Query: 314 M---------------RDLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIH 358
           M                D +   LR+  + +   E +    ++LL+ +  G       + 
Sbjct: 92  MIFQDPMTSLNPVMTIGDQIAEVLRLHGKGLSKKEAKE-RAIELLELV--GIPDPERRLK 148

Query: 359 ANNARESFG-RMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVG 417
           +     S G R   MIAM     P  ++ +  T++LDV VQ Q L      +  +    G
Sbjct: 149 SYPHELSGGMRQRVMIAMALALNPKLLIADEPTTALDVTVQAQIL----DLLKELQREKG 204

Query: 418 MEGNVIITQDL 428
               ++IT DL
Sbjct: 205 T-ALILITHDL 214


>gnl|CDD|31323 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
           component [Amino acid transport and metabolism].
          Length = 240

 Score = 32.0 bits (73), Expect = 0.37
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLET 301
           V+I G +GSGK+TLL CL    + D   +T +       +    +R + 
Sbjct: 31  VVIIGPSGSGKSTLLRCLNGLEEPDSGSITVDGEDVGDKKDILKLRRKV 79


>gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/phosphonate
           transport system.  Phosphonates are a class of
           organophosphorus compounds characterized by a chemically
           stable carbon-to-phosphorus (C-P) bond.  Phosphonates
           are widespread among naturally occurring compounds in
           all kingdoms of wildlife, but only procaryotic
           microorganisms are able to cleave this bond.  Certain
           bacteria such as E. coli can use alkylphosphonates as a
           phosphorus source.  ABC transporters are a subset of
           nucleotide hydrolases that contain a signature motif,
           Q-loop, and H-loop/switch region, in addition to, the
           Walker A motif/P-loop and Walker B motif commonly found
           in a number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 241

 Score = 31.7 bits (72), Expect = 0.48
 Identities = 13/40 (32%), Positives = 22/40 (55%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQ 292
           V + G +G+GK+TLL CL   ++     V  + T   +L+
Sbjct: 30  VALIGPSGAGKSTLLRCLNGLVEPTSGSVLIDGTDINKLK 69


>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
           ATPase component [Defense mechanisms].
          Length = 226

 Score = 31.7 bits (72), Expect = 0.50
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 253 VLISGGTGSGKTTLLNCL 270
           V I G +GSGK+TLLN L
Sbjct: 34  VAIVGPSGSGKSTLLNLL 51


>gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of MJ0796
           ATP-binding cassette, macrolide-specific ABC-type efflux
           carrier (MacAB), and proteins involved in cell division
           (FtsE), and release of liporoteins from the cytoplasmic
           membrane (LolCDE).  They are clustered together
           phylogenetically.  MacAB is an exporter that confers
           resistance to macrolides, while the LolCDE system is not
           a transporter at all.  An FtsE null mutants showed
           filamentous growth and appeared viable on high salt
           medium only, indicating a role for FtsE in cell division
           and/or salt transport.  The LolCDE complex catalyses the
           release of lipoproteins from the cytoplasmic membrane
           prior to their targeting to the outer membrane..
          Length = 218

 Score = 31.6 bits (72), Expect = 0.54
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 253 VLISGGTGSGKTTLLNCL 270
           V I G +GSGK+TLLN L
Sbjct: 33  VAIVGPSGSGKSTLLNIL 50


>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
           (PDR1-15), ABC superfamily [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 1391

 Score = 31.4 bits (71), Expect = 0.56
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 11/62 (17%)

Query: 219 FKKDKLTLDHLVSF----GAVTAEGARLLQII----GRIRCNVL--ISGGTGSGKTTLLN 268
           F    LT   +  +      +  +G    Q++    G  +  VL  + G +G+GKTTLL+
Sbjct: 777 FTPLSLTFKDVFYWVDLPYEMPIQGGTR-QLLNNVSGAFKPGVLTALMGESGAGKTTLLD 835

Query: 269 CL 270
            L
Sbjct: 836 VL 837


>gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction
           only].
          Length = 183

 Score = 31.1 bits (70), Expect = 0.62
 Identities = 11/20 (55%), Positives = 15/20 (75%)

Query: 253 VLISGGTGSGKTTLLNCLTR 272
            +++GG G+GKTTLL  L R
Sbjct: 12  FILTGGPGAGKTTLLAALAR 31


>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
           recombination, and repair].
          Length = 908

 Score = 31.2 bits (70), Expect = 0.63
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 7/52 (13%)

Query: 220 KKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLT 271
           K  +L L +  SF  +  E      I        LI G  G+GK+++L+ +T
Sbjct: 2   KILRLRLKNFRSFKDIDIEKLFDSGIF-------LIVGPNGAGKSSILDAIT 46


>gnl|CDD|73010 cd03251, ABCC_MsbA, MsbA is an essential ABC transporter, closely
           related to eukaryotic MDR proteins.  ABC transporters
           are a large family of proteins involved in the transport
           of a wide variety of different compounds, like sugars,
           ions, peptides, and more complex organic molecules.  The
           nucleotide binding domain shows the highest similarity
           between all members of the family.  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 234

 Score = 31.3 bits (71), Expect = 0.68
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCE--DTAELQLQQ 293
           V + G +GSGK+TL+N + R+ D D   +  +  D  +  L  
Sbjct: 31  VALVGPSGSGKSTLVNLIPRFYDVDSGRILIDGHDVRDYTLAS 73


>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
           transduction [Signal transduction mechanisms].
          Length = 260

 Score = 31.2 bits (70), Expect = 0.71
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 7/95 (7%)

Query: 250 RCNVLISGGTGSGKTTL-LNCLTRYIDKDER--IVTCEDTAELQLQQPHVVRLETRPPNI 306
              VLI+G  G+GKT   L  L     + E    V+ E++ E  L+              
Sbjct: 23  GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEELLEN--ARSFGWDLEVY 80

Query: 307 EGEGEITMRDLVKNCLRMRPERIILGEVRGPEVLD 341
             +G++ + D   +        I++G+    E L 
Sbjct: 81  IEKGKLAILDAFLS--EKGLVSIVVGDPLDLEELL 113


>gnl|CDD|145920 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein. 
           Members of this family are found in a range of archaea
           and eukaryotes and have hypothesized ATP binding
           activity.
          Length = 234

 Score = 31.2 bits (71), Expect = 0.74
 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 13/65 (20%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITM 314
           + GG GSGKTT +  L+                 L+ +  +VV L+    N+  E +I +
Sbjct: 1   VVGGAGSGKTTFVGALSEI-------------LPLRGRSVYVVNLDPAAENLPYEADIDI 47

Query: 315 RDLVK 319
           R+L+ 
Sbjct: 48  RELIT 52


>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
           cancer resistance protein) [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 613

 Score = 30.7 bits (69), Expect = 0.81
 Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 13/65 (20%)

Query: 213 TLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTR 272
           TL+ ++  K   T+   VS    TA+   LL I+G           +GSGKTTLLN L  
Sbjct: 32  TLSSKEKSKKTKTILKGVSG---TAKPGELLAIMG----------PSGSGKTTLLNALAG 78

Query: 273 YIDKD 277
            ++  
Sbjct: 79  RLNGG 83


>gnl|CDD|35194 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
           transduction mechanisms].
          Length = 824

 Score = 30.8 bits (69), Expect = 0.81
 Identities = 44/292 (15%), Positives = 88/292 (30%), Gaps = 39/292 (13%)

Query: 28  SSSNIQKQNLQSSSPSAEGEIGNFVNRTPHYYEVKSTIFTTLIEMIDITQLSQYDSQSAR 87
               +  ++LQ+S      +    +       E          E    T+  +  +    
Sbjct: 24  IPDLMALRSLQASDLGT-RKGKPALEFKAEEAEKL------APEEGLKTRQPKIRTFLLA 76

Query: 88  DEIATLMNEIVSVKKITMSLDEQLDLFEDLCNDILGYGPLQPLIA---RDDIADIMVNGS 144
           D   +   EI  V  + ++L+E L   +      LG   L+ L A   R D   +++   
Sbjct: 77  DARRSTFGEICQV--LLLNLNEILLHAKVFKELWLGETWLRLLGAQTTRIDDDPLLLQQL 134

Query: 145 NKVFIEVNGKTVETGINFRDNEQLLSVCQRIVNQVGRRVDESSPICDARLLDGSRVNVII 204
              + E         +      + +    +++              D  +L+   +    
Sbjct: 135 RCEWQESKILAQAGTLLELLIARGVQSQDKLI--------------DVNILEEVPLASQR 180

Query: 205 PPLALDGPTLTIRKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKT 264
                D  T   ++F ++ L      +       G   L+   ++    LI G  GSGKT
Sbjct: 181 SKRIFDLNTKGEKRFDEEFLLELTQSADDQDALPGLEALEKYAKL----LILGAPGSGKT 236

Query: 265 TLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRD 316
           T L  L          +            P  + L       + E ++++ D
Sbjct: 237 TFLQRLA---------LWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLID 279


>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
           nucleotide-binding domain; ABC transporters are a large
           family of proteins involved in the transport of a wide
           variety of different compounds, like sugars, ions,
           peptides, and more complex organic molecules.  The
           nucleotide-binding domain shows the highest similarity
           between all members of the family.  ABC transporters are
           a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 157

 Score = 30.7 bits (69), Expect = 0.88
 Identities = 9/30 (30%), Positives = 14/30 (46%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVT 282
           V + G  GSGK+TLL  +   +      + 
Sbjct: 28  VALVGPNGSGKSTLLRAIAGLLKPTSGEIL 57


>gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family.  FtsK has extensive
           sequence similarity to wide variety of proteins from
           prokaryotes and plasmids, termed the FtsK/SpoIIIE
           family. This domain contains a putative ATP binding
           P-loop motif.  It is found in the FtsK cell division
           protein from E. coli and the stage III sporulation
           protein E SpoIIIE which has roles in regulation of
           prespore specific gene expression in B. subtilis. A
           mutation in FtsK causes a temperature sensitive block in
           cell division and it is involved in peptidoglycan
           synthesis or modification. The SpoIIIE protein is
           implicated in intercellular chromosomal DNA transfer.
          Length = 202

 Score = 30.8 bits (70), Expect = 0.88
 Identities = 12/19 (63%), Positives = 16/19 (84%)

Query: 252 NVLISGGTGSGKTTLLNCL 270
           ++LI+G TGSGK+T LN L
Sbjct: 40  HLLIAGATGSGKSTFLNTL 58


>gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment
           (EP) precursor transport, regulation of
           lipid-trafficking mechanisms, and pleiotropic drug
           resistance (DR).  DR is a well-described phenomenon
           occurring in fungi and shares several similarities with
           processes in bacteria and higher eukaryotes.  Compared
           to other members of the ABC transporter subfamilies, the
           ABCG transporter family is composed of proteins that
           have an ATP-binding cassette domain at the N-terminus
           and a TM (transmembrane) domain at the C-terminus..
          Length = 194

 Score = 30.5 bits (69), Expect = 0.93
 Identities = 10/19 (52%), Positives = 13/19 (68%)

Query: 253 VLISGGTGSGKTTLLNCLT 271
             I G +G+GK+TLLN L 
Sbjct: 38  TAIMGPSGAGKSTLLNALA 56


>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
           only].
          Length = 296

 Score = 30.7 bits (69), Expect = 0.93
 Identities = 14/30 (46%), Positives = 22/30 (73%)

Query: 241 RLLQIIGRIRCNVLISGGTGSGKTTLLNCL 270
           R+LQ+  +   NVL+ G TG+GK++L+N L
Sbjct: 30  RMLQLTEKEPVNVLLMGATGAGKSSLINAL 59


>gnl|CDD|30196 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
           also known as uridine kinase or uridine-cytidine kinase
           (UCK), catalyzes the reversible phosphoryl transfer from
           ATP to uridine or cytidine to yield UMP or CMP. In the
           primidine nucleotide-salvage pathway, this enzyme
           combined with nucleoside diphosphate kinases further
           phosphorylates UMP and CMP to form UTP and CTP. This
           kinase also catalyzes the phosphorylation of several
           cytotoxic ribonucleoside analogs such as 5-flurrouridine
           and cyclopentenyl-cytidine..
          Length = 198

 Score = 30.5 bits (69), Expect = 0.98
 Identities = 10/33 (30%), Positives = 20/33 (60%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285
           + I+GG+GSGKTT+   +   +   + ++  +D
Sbjct: 2   IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQD 34


>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
           the NTP binding domain of F1 and V1 H+ATPases, DnaB and
           related helicases as well as bacterial RecA and related
           eukaryotic and archaeal recombinases. This group also
           includes bacterial conjugation proteins and related DNA
           transfer proteins involved in type II and type IV
           secretion..
          Length = 165

 Score = 30.5 bits (68), Expect = 0.99
 Identities = 27/131 (20%), Positives = 43/131 (32%), Gaps = 3/131 (2%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGEGE 311
            +L+ G TGSGKTTL   L   I      V   D  E   +    +  E+    ++    
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60

Query: 312 ITMR--DLVKNCLRMRPERIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNARESFGRM 369
           +     D     L  + ER+         +LD L  +       +   +     E    +
Sbjct: 61  VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRA-LREIREGYPGELDEELREL 119

Query: 370 EAMIAMGGFTL 380
                 GG T+
Sbjct: 120 LERARKGGVTV 130


>gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta
           subunit (SR-beta).  SR-beta and SR-alpha form the
           heterodimeric signal recognition particle (SRP or SR)
           receptor that binds SRP to regulate protein
           translocation across the ER membrane.  Nascent
           polypeptide chains are synthesized with an N-terminal
           hydrophobic signal sequence that binds SRP54, a
           component of the SRP.  SRP directs targeting of the
           ribosome-nascent chain complex (RNC) to the ER membrane
           via interaction with the SR, which is localized to the
           ER membrane.  The RNC is then transferred to the
           protein-conducting channel, or translocon, which
           facilitates polypeptide translation across the ER
           membrane or integration into the ER membrane.  SR-beta
           is found only in eukaryotes; it is believed to control
           the release of the signal sequence from SRP54 upon
           binding of the ribosome to the translocon.  High
           expression of SR-beta has been observed in human colon
           cancer, suggesting it may play a role in the development
           of this type of cancer.
          Length = 203

 Score = 30.4 bits (69), Expect = 1.0
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 252 NVLISGGTGSGKTTLLNCLT 271
            VL+ G + SGKT L   LT
Sbjct: 2   TVLLLGPSDSGKTALFTKLT 21


>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
           systems, ATPase components [Inorganic ion transport and
           metabolism / Coenzyme metabolism].
          Length = 258

 Score = 30.1 bits (68), Expect = 1.2
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 255 ISGGTGSGKTTLLNCLTRYI 274
           I G  GSGK+TLL CL   +
Sbjct: 33  ILGPNGSGKSTLLKCLAGLL 52


>gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC
           superfamily [Secondary metabolites biosynthesis,
           transport and catabolism].
          Length = 1228

 Score = 30.2 bits (68), Expect = 1.2
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V + G +GSGK+TL+  L R+ D   
Sbjct: 382 VALVGPSGSGKSTLIQLLARFYDPTS 407


>gnl|CDD|31327 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
           permease components [Defense mechanisms].
          Length = 567

 Score = 30.0 bits (67), Expect = 1.3
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 4/64 (6%)

Query: 217 RKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCN--VLISGGTGSGKTTLLNCLTRYI 274
            K     +  ++ VSF     +   L  I   I     V I G +GSGK+TL+  L R  
Sbjct: 322 LKDTIGSIEFEN-VSFSY-PGKKPVLKDISFSIEPGEKVAIVGPSGSGKSTLIKLLLRLY 379

Query: 275 DKDE 278
           D   
Sbjct: 380 DPTS 383


>gnl|CDD|33254 COG3451, VirB4, Type IV secretory pathway, VirB4 components
           [Intracellular trafficking and secretion].
          Length = 796

 Score = 30.3 bits (68), Expect = 1.3
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 252 NVLISGGTGSGKTTLLNCL 270
           + LI G TG+GKT LL+ L
Sbjct: 438 HTLIIGPTGAGKTVLLSFL 456


>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
           recombination, and repair].
          Length = 254

 Score = 30.0 bits (67), Expect = 1.5
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAEL 289
           N+++ G  G GKT L   +   + K    V      +L
Sbjct: 107 NLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL 144


>gnl|CDD|33864 COG4107, PhnK, ABC-type phosphonate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 258

 Score = 29.9 bits (67), Expect = 1.5
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVT 282
           I G +GSGKTTLL C++  +  D   VT
Sbjct: 37  IVGESGSGKTTLLKCISGRLTPDAGTVT 64


>gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA
           processing and modification].
          Length = 924

 Score = 29.9 bits (67), Expect = 1.7
 Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 2/24 (8%)

Query: 244 QIIGRIRCN--VLISGGTGSGKTT 265
            I+  I  N  V+ISG TG GKTT
Sbjct: 180 TILDAIEENQVVVISGETGCGKTT 203


>gnl|CDD|32933 COG3119, AslA, Arylsulfatase A and related enzymes [Inorganic ion
           transport and metabolism].
          Length = 475

 Score = 29.7 bits (66), Expect = 1.7
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 341 DLLQAMNTGHDGSMGTIHANNARESFGRMEAMIAMGGFTLPSQMVREIITSSLDV 395
             L A  T   G  GT++     E   R+  +I   G   P   V + + S +D+
Sbjct: 299 AWLGAHGTPFRGYKGTLY-----EGGTRVPLIIRWPGGIKPGGRVVDALVSLIDL 348


>gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin.  Septins are a conserved family of
           GTP-binding proteins associated with diverse processes
           in dividing and non-dividing cells.  They were first
           discovered in the budding yeast S. cerevisiae as a set
           of genes (CDC3, CDC10, CDC11 and CDC12) required for
           normal bud morphology. Septins are also present in
           metazoan cells, where they are required for cytokinesis
           in some systems, and implicated in a variety of other
           processes involving organization of the cell cortex and
           exocytosis.  In humans, 12 septin genes generate dozens
           of polypeptides, many of which comprise heterooligomeric
           complexes. Since septin mutants are commonly defective
           in cytokinesis and formation of the neck formation of
           the neck filaments/septin rings, septins have been
           considered to be the primary constituents of the neck
           filaments.  Septins belong to the GTPase superfamily for
           their conserved GTPase motifs and enzymatic activities.
          Length = 276

 Score = 29.8 bits (68), Expect = 1.8
 Identities = 8/19 (42%), Positives = 14/19 (73%)

Query: 252 NVLISGGTGSGKTTLLNCL 270
           N+++ G +G GK+T +N L
Sbjct: 6   NIMVVGESGLGKSTFINTL 24


>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
           transporters homologous to the Drosophila white gene,
           which acts as a dimeric importer for eye pigment
           precursors.  The eye pigmentation of Drosophila is
           developed from the synthesis and deposition in the cells
           of red pigments, which are synthesized from guanine, and
           brown pigments, which are synthesized from tryptophan.
           The pigment precursors are encoded by the white, brown,
           and scarlet genes, respectively.  Evidence from genetic
           and biochemical studies suggest that the White and Brown
           proteins function as heterodimers to import guanine,
           while the White and Scarlet proteins function to import
           tryptophan.  However, a recent study also suggests that
           White may be involved in the transport of a metabolite,
           such as 3-hydroxykynurenine, across intracellular
           membranes.  Mammalian ABC transporters belonging to the
           White subfamily (ABCG1, ABCG5, and ABCG8) have been
           shown to be involved in the regulation of
           lipid-trafficking mechanisms in macrophages,
           hepatocytes, and intestinal mucosa cells.  ABCG1 (ABC8),
           the human homolog of the Drosophila white gene is
           induced in monocyte-derived macrophages during
           cholesterol influx mediated by acetylated low-density
           lipoprotein.  It is possible that human ABCG1 forms
           heterodimers with several heterologous partners..
          Length = 226

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERI 280
           I G +GSGKTTLL+ ++  ++     
Sbjct: 38  ILGSSGSGKTTLLDAISGRVEGGGTT 63


>gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated
            protein/mitoxantrone resistance protein, ABC superfamily
            [Secondary metabolites biosynthesis, transport and
            catabolism].
          Length = 1381

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 255  ISGGTGSGKTTLLNCLTRYIDKDERIVTCE--DTAELQLQQ 293
            I G TG+GK++L+  L R ++  E  +  +  D +++ L  
Sbjct: 1171 IVGRTGAGKSSLILALFRLVEPAEGEILIDGVDISKIGLHD 1211



 Score = 27.5 bits (61), Expect = 8.3
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 253 VLISGGTGSGKTTLLNCL 270
           V + G  GSGK++LL+ +
Sbjct: 550 VAVVGPVGSGKSSLLSAI 567


>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 308

 Score = 29.6 bits (66), Expect = 2.0
 Identities = 30/122 (24%), Positives = 53/122 (43%), Gaps = 20/122 (16%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKD------ERIVTCEDTAELQL------QQPHVVRL 299
           N LI G    GKTTLL  + R +         +++   ++ +E+        Q     R+
Sbjct: 139 NTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRM 198

Query: 300 ETRPPNIEGEGEITMRDLVKNCLRMRPERIILGEV-RGPEVLDLLQAMNTGHDGSMGTIH 358
           +   P  + EG +     +++   M PE II+ E+    + L +L A++ G    + T H
Sbjct: 199 DVLDPCPKAEGMMMA---IRS---MSPEVIIVDEIGTEEDALAILTALHAGVK-LITTAH 251

Query: 359 AN 360
            N
Sbjct: 252 GN 253


>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
           nucleotide-binding domain.  This family includes the ATP
           synthase alpha and beta subunits, the ATP synthase
           associated with flagella and the termination factor Rho.
          Length = 213

 Score = 29.3 bits (67), Expect = 2.1
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKD 277
           + I GG+G+GKT LL  + R    D
Sbjct: 18  IGIFGGSGTGKTVLLGMIARNAKAD 42


>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
           an N-terminal double-glycine peptidase domain [Defense
           mechanisms].
          Length = 709

 Score = 29.4 bits (66), Expect = 2.2
 Identities = 11/26 (42%), Positives = 14/26 (53%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V I G +GSGK+TLL  L       +
Sbjct: 502 VAIVGRSGSGKSTLLKLLLGLYKPQQ 527


>gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
           ATPase component [Inorganic ion transport and
           metabolism].
          Length = 258

 Score = 29.4 bits (66), Expect = 2.3
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V I G +G+GK+TLL  L   +D   
Sbjct: 33  VAIIGPSGAGKSTLLRSLNGLVDPTS 58


>gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding
           Protein Dependent) systems that are largely represented
           in archaea and eubacteria and are primarily involved in
           scavenging solutes from the environment.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules.  The nucleotide binding domain shows the
           highest similarity between all members of the family.
           ABC transporters are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 178

 Score = 29.4 bits (66), Expect = 2.4
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDT 286
           V + G +GSGK+TLL C+    + D   +  +  
Sbjct: 29  VALLGPSGSGKSTLLRCIAGLEEPDSGSILIDGE 62


>gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C.  This
           family is also known as MRP (mulrtidrug
           resisitance-associated protein).  Some of the MRP
           members have five additional transmembrane segments in
           their N-terminas, but the function of these additional
           membrane-spanning domains is not clear.  The MRP was
           found in the multidrug-resisting lung cancer cell in
           which p-glycoprotein was not overexpressed. MRP exports
           glutathione by drug stimulation, as well as, certain
           substrates in conjugated forms with anions, such as
           glutathione, glucuronate, and sulfate..
          Length = 204

 Score = 29.3 bits (66), Expect = 2.4
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQP 294
           V I G  GSGK++LL+ L   ++K    V+   +     Q+P
Sbjct: 34  VAIVGPVGSGKSSLLSALLGELEKLSGSVSVPGSIAYVSQEP 75


>gnl|CDD|31314 COG1117, PstB, ABC-type phosphate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 253

 Score = 29.3 bits (66), Expect = 2.5
 Identities = 11/22 (50%), Positives = 13/22 (59%)

Query: 257 GGTGSGKTTLLNCLTRYIDKDE 278
           G +G GK+TLL CL R  D   
Sbjct: 40  GPSGCGKSTLLRCLNRMNDLIP 61


>gnl|CDD|72992 cd03233, ABC_PDR_domain1, The pleiotropic drug resistance (PDR)
           family of ATP-binding cassette (ABC) transporters.  PDR
           is a well-described phenomenon occurring in fungi and
           shares several similarities with processes in bacteria
           and higher eukaryotes.  This PDR subfamily represents
           domain I of its (ABC-IM)2 organization.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds
           including sugars, ions, peptides, and more complex
           organic molecules.  The nucleotide-binding domain shows
           the highest similarity between all members of the
           family.  ABC transporters are a subset of nucleotide
           hydrolases that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 202

 Score = 29.4 bits (66), Expect = 2.5
 Identities = 10/28 (35%), Positives = 15/28 (53%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERI 280
           VL+ G  GSG +TLL  L    + +  +
Sbjct: 36  VLVLGRPGSGCSTLLKALANRTEGNVSV 63


>gnl|CDD|111395 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain.  This
           domain is found in HypB, a hydrogenase expression /
           formation protein, and UreG a urease accessory protein.
           Both these proteins contain a P-loop nucleotide binding
           motif. HypB has GTPase activity and is a guanine
           nucleotide binding protein. It is not known whether UreG
           binds GTP or some other nucleotide. Both enzymes are
           involved in nickel binding. HypB can store nickel and is
           required for nickel dependent hydrogenase expression.
           UreG is required for functional incorporation of the
           urease nickel metallocenter. GTP hydrolysis may required
           by these proteins for nickel incorporation into other
           nickel proteins. This family of domains also contains
           P47K, a Pseudomonas chlororaphis protein needed for
           nitrile hydratase expression, and the cobW gene product,
           which may be involved in cobalamin biosynthesis in
           Pseudomonas denitrificans.
          Length = 174

 Score = 29.1 bits (66), Expect = 2.7
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERI 280
            +++G  GSGKTTLL  L R   +  +I
Sbjct: 3   TVLTGFLGSGKTTLLEHLLRDNREGLKI 30


>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3  Elongation factor 3 (EF-3) is a
           cytosolic protein required by fungal ribosomes for in
           vitro protein synthesis and for in vivo growth.  EF-3
           stimulates the binding of the EF-1: GTP: aa-tRNA ternary
           complex to the ribosomal A site by facilitated release
           of the deacylated tRNA from the E site.  The reaction
           requires ATP hydrolysis.  EF-3 contains two ATP
           nucleotide binding sequence (NBS) motifs.  NBSI is
           sufficient for the intrinsic ATPase activity. NBSII is
           essential for the ribosome-stimulated functions..
          Length = 144

 Score = 29.3 bits (66), Expect = 2.8
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAEL 289
           + G  G+GK+TLL  +   ++ DE IVT   T ++
Sbjct: 31  LVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKI 65


>gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, Phosphate uptake is of
           fundamental importance in the cell physiology of
           bacteria because phosphate is required as a nutrient.
           The Pst system of E. coli comprises four distinct
           subunits encoded by the pstS, pstA, pstB, and pstC
           genes.  The PstS protein is a phosphate-binding protein
           located in the periplasmic space. P stA and PstC are
           hydrophobic and they form the transmembrane portion of
           the Pst system.  PstB is the catalytic subunit, which
           couples the energy of ATP hydrolysis to the import of
           phosphate across cellular membranes through the Pst
           system, often referred as ABC-protein.  PstB belongs to
           one of the largest superfamilies of proteins
           characterized by a highly conserved adenosine
           triphosphate (ATP) binding cassette (ABC), which is also
           a nucleotide binding domain (NBD)..
          Length = 227

 Score = 29.0 bits (65), Expect = 2.9
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
             + G +G GK+TLL  L R  D   
Sbjct: 29  TALIGPSGCGKSTLLRLLNRLNDLIP 54


>gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC transporter
           subfamily is involved in the transport of the
           hydrophobic amino acids leucine, isoleucine and valine. 
           MJ1267 is a branched-chain amino acid transporter with
           29% similarity to both the LivF and LivG components of
           the E. coli  branched-chain amino acid transporter.
           MJ1267 contains an insertion from residues 114 to 123
           characteristic of LivG (Leucine-Isoleucine-Valine)
           homologs.  The branched-chain amino acid transporter
           from E. coli comprises a heterodimer of ABCs (LivF and
           LivG), a heterodimer of six-helix TM domains (LivM and
           LivH), and one of two alternative soluble periplasmic
           substrate binding proteins (LivK or LivJ)..
          Length = 236

 Score = 28.9 bits (65), Expect = 2.9
 Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 224 LTLDHL-VSFGAVTA-EGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYI 274
           L +  L   FG + A +        G I    LI G  G+GKTTL N ++ ++
Sbjct: 1   LEVRGLTKRFGGLVALDDVSFSVRPGEIHG--LI-GPNGAGKTTLFNLISGFL 50


>gnl|CDD|37960 KOG2749, KOG2749, KOG2749, mRNA cleavage and polyadenylation factor
           IA/II complex, subunit CLP1 [RNA processing and
           modification].
          Length = 415

 Score = 29.1 bits (65), Expect = 2.9
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHV 296
           V++ G T  GK+TL   L  Y  K  R        EL + Q  +
Sbjct: 106 VMVVGPTDVGKSTLCRILLNYAVKQGRRPLF---VELDVGQGSI 146


>gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase
           component [Defense mechanisms].
          Length = 293

 Score = 29.2 bits (65), Expect = 3.0
 Identities = 29/130 (22%), Positives = 50/130 (38%), Gaps = 20/130 (15%)

Query: 217 RKFKKDKLTLDHLVSFGAVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDK 276
           +K+  DK  LD  VSF     E   +  ++G            G+GKTTLL  L   +  
Sbjct: 12  KKYGGDKTALDG-VSF---EVEPGEIFGLLGP----------NGAGKTTLLKILAGLLKP 57

Query: 277 DE---RIVTCEDTAELQLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERIILGE 333
                 ++  +   E    +  +  +   P       E+T+R+ ++   R+        E
Sbjct: 58  TSGEILVLGYDVVKEPAKVRRRIGYV---PQEPSLYPELTVRENLEFFARLYGLSKEEAE 114

Query: 334 VRGPEVLDLL 343
            R  E+L+L 
Sbjct: 115 ERIEELLELF 124


>gnl|CDD|36745 KOG1532, KOG1532, KOG1532, GTPase XAB1, interacts with DNA repair
           protein XPA [Replication, recombination and repair].
          Length = 366

 Score = 28.8 bits (64), Expect = 3.1
 Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 13/70 (18%)

Query: 250 RCNVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRPPNIEGE 309
              +L+ G  GSGKTT +  L  ++   +               P+V+ L+    N+   
Sbjct: 19  PVIILVVGMAGSGKTTFMQRLNSHLHAKK-------------TPPYVINLDPAVRNVPYP 65

Query: 310 GEITMRDLVK 319
             I +RD VK
Sbjct: 66  ANIDIRDTVK 75


>gnl|CDD|28990 cd01175, IPT_COE, IPT domain of the COE family (Col/Olf-1/EBF) of
           non-basic, helix-loop-helix (HLH)-containing
           transcription factors. COE family proteins are all
           transcription factors and play an important role in
           variety of developmental processes. Mouse EBF is
           involved in the regulation of the early stages of B-cell
           differentiation, Drosophila collier is a regulator of
           the head patterning, and a related protein in Xenopus is
           involved in primary neurogenesis. All COE family members
           have a well conserved DNA binding domain that contains
           an atypical Zn finger motif. The function of the IPT
           domain is unknown..
          Length = 85

 Score = 28.9 bits (64), Expect = 3.2
 Identities = 13/41 (31%), Positives = 22/41 (53%)

Query: 290 QLQQPHVVRLETRPPNIEGEGEITMRDLVKNCLRMRPERII 330
           +L  PH +R++T P +I G  E+T+    K   +  P R +
Sbjct: 42  ELITPHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGTPGRFV 82


>gnl|CDD|30869 COG0523, COG0523, Putative GTPases (G3E family) [General function
           prediction only].
          Length = 323

 Score = 28.7 bits (64), Expect = 3.3
 Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)

Query: 254 LISGGTGSGKTTLLNCLTRYIDKDERIV 281
           +I+G  GSGKTTLLN L    D  ++I 
Sbjct: 5   VITGFLGSGKTTLLNHLLANRD-GKKIA 31


>gnl|CDD|113806 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
           Interferon-inducible GTPase (IIGP) is thought to play a
           role in in intracellular defence. IIGP is predominantly
           associated with the Golgi apparatus and also localizes
           to the endoplasmic reticulum and exerts a distinct role
           in IFN-induced intracellular membrane trafficking or
           processing.
          Length = 375

 Score = 28.6 bits (64), Expect = 3.4
 Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 243 LQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDE 278
           +Q I      + ++G +G+GK++ +N L R I  +E
Sbjct: 28  IQEISSAPLKIAVTGDSGNGKSSFINAL-RGIGHEE 62


>gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like
           (PDR) family of ATP-binding cassette (ABC) transporters.
           PDR is a well-described phenomenon occurring in fungi
           and shares several similarities with processes in
           bacteria and higher eukaryotes.  This PDR subfamily
           represents domain I of its (ABC-IM)2 organization.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds
           including sugars, ions, peptides, and more complex
           organic molecules.  The nucleotide binding domain shows
           the highest similarity between all members of the
           family.  ABC transporters are a subset of nucleotide
           hydrolases that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 192

 Score = 28.6 bits (64), Expect = 3.6
 Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 3/33 (9%)

Query: 241 RLLQ-IIGRIRCNVLIS--GGTGSGKTTLLNCL 270
           +LL  I G ++   L +  G +G+GKTTLL+ L
Sbjct: 21  QLLNNISGYVKPGTLTALMGESGAGKTTLLDVL 53


>gnl|CDD|133260 cd01851, GBP, Guanylate-binding protein (GBP), N-terminal domain.
           Guanylate-binding proteins (GBPs) define a group of
           proteins that are synthesized after activation of the
           cell by interferons.  The biochemical properties of GBPs
           are clearly different from those of Ras-like and
           heterotrimeric GTP-binding proteins.  They bind guanine
           nucleotides with low affinity (micromolar range), are
           stable in their absence and have a high turnover GTPase.
            In addition to binding GDP/GTP, they have the unique
           ability to bind GMP with equal affinity and hydrolyze
           GTP not only to GDP, but also to GMP. Furthermore, two
           unique regions around the base and the phosphate-binding
           areas, the guanine and the phosphate caps, respectively,
           give the nucleotide-binding site a unique appearance not
           found in the canonical GTP-binding proteins.  The
           phosphate cap, which constitutes the region analogous to
           switch I, completely shields the phosphate-binding site
           from solvent such that a potential GTPase-activating
           protein (GAP) cannot approach.
          Length = 224

 Score = 28.8 bits (65), Expect = 3.7
 Identities = 8/19 (42%), Positives = 10/19 (52%)

Query: 255 ISGGTGSGKTTLLNCLTRY 273
           + G   SGK+ LLN L   
Sbjct: 12  VFGPQSSGKSFLLNHLFGT 30


>gnl|CDD|30938 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
           replication, recombination, and repair].
          Length = 408

 Score = 28.7 bits (64), Expect = 3.7
 Identities = 15/62 (24%), Positives = 19/62 (30%), Gaps = 11/62 (17%)

Query: 222 DKLTLDHLVSFGAVTAEGARLLQIIGRIRCN-------VLISGGTGSGKTTLLNCLTRYI 274
            K T D+ V    V             +  N       + I GG G GKT LL  +    
Sbjct: 82  PKYTFDNFV----VGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEA 137

Query: 275 DK 276
             
Sbjct: 138 LA 139


>gnl|CDD|30760 COG0411, LivG, ABC-type branched-chain amino acid transport
           systems, ATPase component [Amino acid transport and
           metabolism].
          Length = 250

 Score = 28.6 bits (64), Expect = 3.8
 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 224 LTLDHLV-SFGAVTA-EGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDE 278
           L +  L   FG +TA     L    G I   V + G  G+GKTTL N +T +     
Sbjct: 5   LEVRGLSKRFGGLTAVNDVSLEVRPGEI---VGLIGPNGAGKTTLFNLITGFYKPSS 58


>gnl|CDD|30586 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
          Length = 201

 Score = 28.7 bits (64), Expect = 4.0
 Identities = 28/160 (17%), Positives = 55/160 (34%), Gaps = 31/160 (19%)

Query: 253 VLISGGTGSGKTTLLNCLTRY----IDKDERIVTCEDTAELQLQQPHVVRL----ETRPP 304
           + ++GG GSGK+T+   L       ID D+           ++ +P    L    E    
Sbjct: 5   IGLTGGIGSGKSTVAKILAELGFPVIDADDVA--------REVVEPGGEALQEIAERFGL 56

Query: 305 NIEGEGEITMRDLVKNCLRMRPE-RIILGEVRGPEVLDLLQAMNTGHDGSMGTIHANNAR 363
            I  E     R  ++  +   PE R+ L ++  P +   ++ +  G       +      
Sbjct: 57  EILDEDGGLDRRKLREKVFNDPEARLKLEKILHPLIRAEIKVVIDGARSPYVVLEIPLLF 116

Query: 364 ESFGRMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLR 403
           E+ G               +   ++I       ++ +RL 
Sbjct: 117 EAGGE--------------KYFDKVIVVYAPPEIRLERLM 142


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
           nucleotide-binding domain (P-loop) near the N-terminus,
           participates in the maturation of the nickel center of
           carbon monoxide dehydrogenase (CODH). CODH from
           Rhodospirillum rubrum catalyzes the reversible oxidation
           of CO to CO2. CODH contains a nickel-iron-sulfur cluster
           (C-center) and an iron-sulfur cluster (B-center). CO
           oxidation occurs at the C-center. Three accessory
           proteins encoded by cooCTJ genes are involved in nickel
           incorporation into a nickel site. CooC functions as a
           nickel insertase that mobilizes nickel to apoCODH using
           energy released from ATP hydrolysis. CooC is a homodimer
           and has NTPase activities. Mutation at the P-loop
           abolishs its function..
          Length = 116

 Score = 28.6 bits (64), Expect = 4.0
 Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETRP-----PNI 306
            + I+G  G GKTT+   L RY+ +  + V   D     L +   V +            
Sbjct: 1   KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPDDLPERLSVEVGEIKLLLVMGMG 60

Query: 307 EGEGE---ITMRDLVKNCLR 323
              GE        L+   LR
Sbjct: 61  RPGGEGCYCPENALLNALLR 80


>gnl|CDD|147025 pfam04665, Pox_A32, Poxvirus A32 protein.  The A32 protein is
           thought to be involved in viral DNA packaging.
          Length = 241

 Score = 28.5 bits (64), Expect = 4.1
 Identities = 12/21 (57%), Positives = 14/21 (66%)

Query: 252 NVLISGGTGSGKTTLLNCLTR 272
            + I GG+GSGKTT L  L R
Sbjct: 15  RMAIVGGSGSGKTTYLLSLLR 35


>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
           involved in the uptake of siderophores, heme, and
           vitamin B12, are widely conserved in bacteria and
           archaea.  Only very few species lack representatives of
           the siderophore family transporters.  The E. coli BtuCD
           protein is an ABC transporter mediating vitamin B12
           uptake.  The two ATP-binding cassettes (BtuD) are in
           close contact with each other, as are the two
           membrane-spanning subunits (BtuC); this arrangement is
           distinct from that observed for the E. coli lipid
           flippase MsbA.  The BtuC subunits provide 20
           transmembrane helices grouped around a translocation
           pathway that is closed to the cytoplasm by a gate
           region, whereas the dimer arrangement of the BtuD
           subunits resembles the ATP-bound form of the Rad50 DNA
           repair enzyme.  A prominent cytoplasmic loop of BtuC
           forms the contact region with the ATP-binding cassette
           and represent a conserved motif among the ABC
           transporters..
          Length = 180

 Score = 28.5 bits (64), Expect = 4.1
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 255 ISGGTGSGKTTLLNCLTRYI 274
           I G  G+GK+TLL  L   +
Sbjct: 30  ILGPNGAGKSTLLKTLAGLL 49


>gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute
           Transporters-like subgroup.  This family is comprised of
           proteins involved in the transport of apparently
           unrelated solutes and proteins specific for di- and
           oligosaccharides and polyols.  ABC transporters are a
           large family of proteins involved in the transport of a
           wide variety of different compounds, like sugars, ions,
           peptides and more complex organic molecules.  The
           nucleotide-binding domain shows the highest similarity
           between all members of the family.   ABC transporters
           are a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 213

 Score = 28.6 bits (64), Expect = 4.2
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           + + G +G GKTTLL  +      D 
Sbjct: 29  LALLGPSGCGKTTLLRLIAGLERPDS 54


>gnl|CDD|31412 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 408

 Score = 28.6 bits (64), Expect = 4.2
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYID 275
           N+L+ G TGSGKT L   L + ++
Sbjct: 99  NILLIGPTGSGKTLLAQTLAKILN 122


>gnl|CDD|35964 KOG0745, KOG0745, KOG0745, Putative ATP-dependent Clp-type protease
           (AAA+ ATPase superfamily) [Posttranslational
           modification, protein turnover, chaperones].
          Length = 564

 Score = 28.4 bits (63), Expect = 4.3
 Identities = 14/24 (58%), Positives = 16/24 (66%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYID 275
           NVL+ G TGSGKT L   L R +D
Sbjct: 228 NVLLLGPTGSGKTLLAQTLARVLD 251


>gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
           [Inorganic ion transport and metabolism].
          Length = 235

 Score = 28.3 bits (63), Expect = 4.4
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVR 298
           VL+ G  GSGK+TLL  L   +      V  +       +    +R
Sbjct: 33  VLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLELR 78


>gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction
           only].
          Length = 849

 Score = 28.4 bits (63), Expect = 4.5
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 4/51 (7%)

Query: 237 AEGARLLQIIGRIR----CNVLISGGTGSGKTTLLNCLTRYIDKDERIVTC 283
            E A+LL    R+       VL++G +G GK+ L+N + + I +       
Sbjct: 7   TELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIK 57


>gnl|CDD|73003 cd03244, ABCC_MRP_domain2, Domain 2 of the ABC subfamily C.  This
           family is also known as MRP (mulrtidrug
           resisitance-associated protein).  Some of the MRP
           members have five additional transmembrane segments in
           their N-terminus, but the function of these additional
           membrane-spanning domains is not clear.  The MRP was
           found in the multidrug-resistance lung cancer cell in
           which p-glycoprotein was not overexpressed.  MRP exports
           glutathione by drug stimulation, as well as, certain
           substrates in conjugated forms with anions, such as
           glutathione, glucuronate, and sulfate..
          Length = 221

 Score = 28.5 bits (64), Expect = 4.5
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 255 ISGGTGSGKTTLLNCLTRYID 275
           I G TGSGK++LL  L R ++
Sbjct: 35  IVGRTGSGKSSLLLALFRLVE 55


>gnl|CDD|72999 cd03240, ABC_Rad50, The catalytic domains of Rad50 are similar to
           the ATP-binding cassette of ABC transporters, but are
           not associated with membrane-spanning domains.  The
           conserved ATP-binding motifs common to Rad50 and the ABC
           transporter family include the Walker A and Walker B
           motifs, the Q loop, a histidine residue in the switch
           region, a D-loop, and a conserved LSGG sequence.  This
           conserved sequence, LSGG, is the most specific and
           characteristic motif of this family and is thus known as
           the ABC signature sequence..
          Length = 204

 Score = 28.2 bits (63), Expect = 4.6
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 254 LISGGTGSGKTTLLNCL 270
           LI G  G+GKTT++  L
Sbjct: 26  LIVGQNGAGKTTIIEAL 42


>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
           betaine/L-proline ATP binding subunit in bacteria and
           its equivalents in archaea.  This transport system
           belong to the larger ATP-Binding Cassette (ABC)
           transporter superfamily.  The characteristic feature of
           these transporters is the obligatory coupling of ATP
           hydrolysis to substrate translocation.  ABC transporters
           are a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 269

 Score = 28.2 bits (63), Expect = 4.8
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 255 ISGGTGSGKTTLLNCLTRYID 275
           I G +GSGK+TLL C+ R I+
Sbjct: 55  IMGLSGSGKSTLLRCINRLIE 75


>gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins
           belongs to a multisubunit transporter involved in drug
           resistance (BcrA and DrrA), nodulation, lipid transport,
           and lantibiotic immunity.  In bacteria and archaea,
           these transporters usually include an ATP-binding
           protein and one or two integral membrane proteins.
           Eukaryote systems of the ABCA subfamily display ABC
           domains that are quite similar to this family.  The
           ATP-binding domain shows the highest similarity between
           all members of the ABC transporter family.  ABC
           transporters are a subset of nucleotide hydrolases that
           contain a signature motif, Q-loop, and H-loop/switch
           region, in addition to, the Walker A motif/P-loop and
           Walker B motif commonly found in a number of ATP- and
           GTP-binding and hydrolyzing proteins..
          Length = 173

 Score = 28.5 bits (64), Expect = 4.9
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 257 GGTGSGKTTLLNCLTRYIDKDE 278
           G  G+GKTTL+  +   +  D 
Sbjct: 33  GPNGAGKTTLIKIILGLLKPDS 54


>gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
           involved in the metabolism of nicotinamide adenine
           dinucleotide (NAD+). This enzyme catalyzes the
           phosphorylation of nicotinamide riboside (NR) to form
           nicotinamide mononucleotide (NMN). It defines the NR
           salvage pathway of NAD+ biosynthesis in addition to the
           pathways through nicotinic acid mononucleotide (NaMN).
           This enzyme can also phosphorylate the anticancer drug
           tiazofurin, which is an analog of nicotinamide
           riboside..
          Length = 187

 Score = 28.3 bits (63), Expect = 5.2
 Identities = 13/22 (59%), Positives = 14/22 (63%)

Query: 253 VLISGGTGSGKTTLLNCLTRYI 274
           V ISG T SGKTTL   L R +
Sbjct: 2   VGISGVTNSGKTTLAKLLQRIL 23


>gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
           and repair].
          Length = 845

 Score = 28.0 bits (62), Expect = 5.4
 Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 235 VTAEGARLLQIIGRIRCNVLISGGTGSGKTTLL 267
           VTA    +L+ I + +  V+I G TGSGKTT L
Sbjct: 51  VTAVRDEILKAIEQNQV-VIIVGETGSGKTTQL 82


>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
           thymidylate kinase, catalyzes the phosphorylation of
           thymidine monophosphate (TMP) to thymidine diphosphate
           (TDP) utilizing ATP as its preferred phophoryl donor.
           TMPK represents the rate-limiting step in either de novo
           or salvage biosynthesis of thymidine triphosphate
           (TTP)..
          Length = 200

 Score = 27.9 bits (62), Expect = 5.5
 Identities = 10/34 (29%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDER--IVTCE 284
           ++  G  G+GKTTL+  L   ++      ++T E
Sbjct: 3   IVFEGIDGAGKTTLIELLAERLEARGYEVVLTRE 36


>gnl|CDD|29993 cd01127, TrwB, Bacterial conjugation protein TrwB,  ATP binding
           domain. TrwB is a homohexamer encoded by conjugative
           plasmids in Gram-negative bacteria. TrwB also has an all
           alpha domain which has been hypothesized to be
           responsible for DNA binding. TrwB is a component of Type
           IV secretion and is responsible for the horizontal
           transfer of DNA between bacteria..
          Length = 410

 Score = 27.9 bits (62), Expect = 5.5
 Identities = 10/23 (43%), Positives = 14/23 (60%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYI 274
           + +I G TG+GKTT +  L   I
Sbjct: 44  HTMIIGTTGTGKTTQIRELLASI 66


>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette
           transporter (Pat) is involved in the import of very
           long-chain fatty acids (VLCFA) into the peroxisome.  The
           peroxisomal membrane forms a permeability barrier for a
           wide variety of metabolites required for and formed
           during fatty acid beta-oxidation.  To communicate with
           the cytoplasm and mitochondria, peroxisomes need
           dedicated proteins to transport such hydrophilic
           molecules across their membranes.  X-linked
           adrenoleukodystrophy (X-ALD) is caused by mutations in
           the ALD gene, which encodes ALDP (adrenoleukodystrophy
           protein ), a peroxisomal integral membrane protein that
           is a member of the ATP-binding cassette (ABC)
           transporter protein family.  The disease is
           characterized by a striking and unpredictable variation
           in phenotypic expression.  Phenotypes include the
           rapidly progressive childhood cerebral form (CCALD), the
           milder adult form, adrenomyeloneuropathy (AMN), and
           variants without neurologic involvement (i.e.
           asymptomatic)..
          Length = 166

 Score = 28.2 bits (63), Expect = 5.7
 Identities = 7/16 (43%), Positives = 13/16 (81%)

Query: 252 NVLISGGTGSGKTTLL 267
            +LI+G +G+GK++L 
Sbjct: 29  RLLITGPSGTGKSSLF 44


>gnl|CDD|133265 cd01862, Rab7, Rab7 subfamily.  Rab7 is a small Rab GTPase that
           regulates vesicular traffic from early to late endosomal
           stages of the endocytic pathway.  The yeast Ypt7 and
           mammalian Rab7 are both involved in transport to the
           vacuole/lysosome, whereas Ypt7 is also required for
           homotypic vacuole fusion.  Mammalian Rab7 is an
           essential participant in the autophagic pathway for
           sequestration and targeting of cytoplasmic components to
           the lytic compartment. Mammalian Rab7 is also proposed
           to function as a tumor suppressor. GTPase activating
           proteins (GAPs) interact with GTP-bound Rab and
           accelerate the hydrolysis of GTP to GDP. Guanine
           nucleotide exchange factors (GEFs) interact with
           GDP-bound Rabs to promote the formation of the GTP-bound
           state.  Rabs are further regulated by guanine nucleotide
           dissociation inhibitors (GDIs), which facilitate Rab
           recycling by masking C-terminal lipid binding and
           promoting cytosolic localization.  Most Rab GTPases
           contain a lipid modification site at the C-terminus,
           with sequence motifs CC, CXC, or CCX. Lipid binding is
           essential for membrane attachment, a key feature of most
           Rab proteins. Due to the presence of truncated sequences
           in this CD, the lipid modification site is not available
           for annotation.
          Length = 172

 Score = 28.0 bits (63), Expect = 5.9
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 20/55 (36%)

Query: 253 VLISGGTGSGKTTLLN------------------CLTRYIDKDERIVTCE--DTA 287
           V+I G +G GKT+L+N                   LT+ +  D+++VT +  DTA
Sbjct: 3   VIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDKLVTLQIWDTA 57


>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form
           of molybdenum cofactor (Moco) which is associated with
           the metabolism of nitrogen, carbon and sulfur by redox
           active enzymes. In E. coli, the synthesis of Moco
           involves genes from several loci: moa, mob, mod, moe and
           mog. The mob locus contains mobA and mobB genes. MobB
           catalyzes the attachment of the guanine dinucleotide to
           molybdopterin..
          Length = 159

 Score = 27.9 bits (62), Expect = 6.1
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 255 ISGGTGSGKTTLLNCLTRYI 274
             G +GSGKTTLL  L   +
Sbjct: 6   FVGYSGSGKTTLLEKLIPAL 25


>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
           ATPase domains [General function prediction only].
          Length = 530

 Score = 27.9 bits (62), Expect = 6.5
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAEL 289
           + I G  G+GK+TLL  L   +      V   +T ++
Sbjct: 351 IAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKI 387


>gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
           component [General function prediction only].
          Length = 263

 Score = 27.9 bits (62), Expect = 6.5
 Identities = 9/25 (36%), Positives = 14/25 (56%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKD 277
           V + G  G+GK+TLLN +   +   
Sbjct: 35  VTVIGSNGAGKSTLLNAIAGDLKPT 59


>gnl|CDD|35342 KOG0120, KOG0120, KOG0120, Splicing factor U2AF, large subunit (RRM
           superfamily) [RNA processing and modification].
          Length = 500

 Score = 27.7 bits (61), Expect = 6.7
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 72  MIDITQLSQYDSQSARDEIATLMNEIVSVKKITMSLDEQLDLFEDLCNDILGYGPLQPL- 130
            +    L          E+  L N  V         +E  ++ ED+  +   +G ++ + 
Sbjct: 383 QVPGIPLLMTQMAGIPTEVLCLTN--VVTPDELKDDEEYEEILEDVRTECAKFGAVRSVE 440

Query: 131 IARDDIADIMVNGSNKVFIE 150
           I R    +  V G+ KVF+E
Sbjct: 441 IPRPYPDENPVPGTGKVFVE 460


>gnl|CDD|73038 cd03279, ABC_sbcCD, SbcCD and other Mre11/Rad50 (MR) complexes are
           implicated in the metabolism of DNA ends. They cleave
           ends sealed by hairpin structures and are thought to
           play a role in removing protein bound to DNA termini..
          Length = 213

 Score = 27.9 bits (62), Expect = 6.7
 Identities = 10/18 (55%), Positives = 15/18 (83%)

Query: 254 LISGGTGSGKTTLLNCLT 271
           LI G TG+GK+T+L+ +T
Sbjct: 32  LICGPTGAGKSTILDAIT 49


>gnl|CDD|30199 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in
           the Benson-Calvin cycle in chloroplasts or
           photosynthetic prokaryotes. This enzyme catalyzes the
           phosphorylation of D-ribulose 5-phosphate to form
           D-ribulose 1, 5-biphosphate, using ATP and NADPH
           produced by the primary reactions of photosynthesis..
          Length = 273

 Score = 27.9 bits (62), Expect = 6.8
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285
           ++G +G GK+T L  LT     D   V C D
Sbjct: 4   VAGDSGCGKSTFLRRLTSLFGSDLVTVICLD 34


>gnl|CDD|73180 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
           also known as guanylate kinase (GKase), catalyzes the
           reversible phosphoryl transfer from adenosine
           triphosphate (ATP) to guanosine monophosphate (GMP) to
           yield adenosine diphosphate (ADP) and guanosine
           diphosphate (GDP). It plays an essential role in the
           biosynthesis of guanosine triphosphate (GTP). This
           enzyme is also important for the activation of some
           antiviral and anticancer agents, such as acyclovir,
           ganciclovir, carbovir, and thiopurines..
          Length = 137

 Score = 27.8 bits (62), Expect = 6.9
 Identities = 9/20 (45%), Positives = 14/20 (70%)

Query: 253 VLISGGTGSGKTTLLNCLTR 272
           +++SG +G GK+TLL  L  
Sbjct: 2   IVLSGPSGVGKSTLLKRLLE 21


>gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding
           components of the bacterial periplasmic histidine and
           glutamine permeases, repectively.  Histidine permease is
           a multisubunit complex containing the HisQ and HisM
           integral membrane subunits and two copies of HisP.  HisP
           has properties intermediate between those of integral
           and peripheral membrane proteins and is accessible from
           both sides of the membrane, presumably by its
           interaction with HisQ and HisM.  The two HisP subunits
           form a homodimer within the complex.  The domain
           structure of the amino acid uptake systems is typical
           for prokaryote extracellular solute binding
           protein-dependent uptake systems.  All of the amino acid
           uptake systems also have at least one, and in a few
           cases, two extracellular solute binding proteins located
           in the periplasm of Gram-negative bacteria, or attached
           to the cell membrane of Gram-positive bacteria.  The
           best-studied member of the PAAT (polar amino acid
           transport) family is the HisJQMP system of S.
           typhimurium, where HisJ is the extracellular solute
           binding proteins and HisP is the ABC protein..
          Length = 213

 Score = 27.8 bits (62), Expect = 6.9
 Identities = 11/20 (55%), Positives = 15/20 (75%)

Query: 253 VLISGGTGSGKTTLLNCLTR 272
           V+I G +GSGK+TLL C+  
Sbjct: 29  VVIIGPSGSGKSTLLRCINL 48


>gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2
           [Replication, recombination and repair].
          Length = 333

 Score = 27.6 bits (61), Expect = 7.0
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)

Query: 242 LLQIIGRIR--CNVLISGGTGSGKTTLLNCLTR 272
            L +I +     N++ISG  G+GKTT + CL R
Sbjct: 38  RLSVIAKEGNMPNLIISGPPGTGKTTSILCLAR 70


>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
           ATPase component [Amino acid transport and metabolism].
          Length = 386

 Score = 27.6 bits (61), Expect = 7.0
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 254 LISGGTGSGKTTLLNCLTRYID 275
           +I G +GSGK+TL+  L R I+
Sbjct: 58  VIMGLSGSGKSTLVRLLNRLIE 79


>gnl|CDD|33913 COG4172, COG4172, ABC-type uncharacterized transport system,
           duplicated ATPase component [General function prediction
           only].
          Length = 534

 Score = 27.9 bits (62), Expect = 7.1
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 368 RMEAMIAMGGFTLPSQMVREIITSSLDVIVQTQRLRDGSRRITNICEIVGMEGNVIITQD 427
           R   MIAM     P  ++ +  T++LDV VQ Q L      +  +   +GM   + IT D
Sbjct: 163 RQRVMIAMALANEPDLLIADEPTTALDVTVQAQIL----DLLKELQAELGM-AILFITHD 217

Query: 428 L 428
           L
Sbjct: 218 L 218


>gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC
           superfamily (involved in peroxisome organization and
           biogenesis) [Lipid transport and metabolism, General
           function prediction only].
          Length = 659

 Score = 27.6 bits (61), Expect = 7.5
 Identities = 11/19 (57%), Positives = 15/19 (78%)

Query: 252 NVLISGGTGSGKTTLLNCL 270
           N+LI+G +G GKT+LL  L
Sbjct: 463 NLLITGPSGCGKTSLLRVL 481


>gnl|CDD|146630 pfam04097, Nic96, Nup93/Nic96.  Nup93/Nic96 is a component of the
           nuclear pore complex. It is required for the correct
           assembly of the nuclear pore complex. In Saccharomyces
           cerevisiae, Nic96 has been shown to be involved in the
           distribution and cellular concentration of the GTPase
           Gsp1. The structure of Nic96 has revealed a mostly alpha
           helical structure.
          Length = 602

 Score = 27.6 bits (62), Expect = 7.6
 Identities = 20/94 (21%), Positives = 31/94 (32%), Gaps = 18/94 (19%)

Query: 106 SLDEQLDLFEDLCNDILGYGPLQPLIARDD---IADIMVNGS-NKVFIEVNGKTVETGIN 161
                  L  +   +++       L  R+    + DI  +G+     IE   K     I 
Sbjct: 346 KDKTGRSLCHEALRELV-------LETREFDLLLGDINPDGARIPGLIERRLKL----IK 394

Query: 162 FRDNEQLLSVCQRIVNQVGRRVDESSPICDARLL 195
             D E+ L   + I  Q     D+     DA LL
Sbjct: 395 LEDEEEFL---RTITEQAAEEADDRGRFEDAILL 425


>gnl|CDD|38518 KOG3308, KOG3308, KOG3308, Uncharacterized protein of the uridine
           kinase family [Nucleotide transport and metabolism].
          Length = 225

 Score = 27.7 bits (61), Expect = 7.7
 Identities = 14/28 (50%), Positives = 15/28 (53%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDERI 280
           V ISG T SGKTTL   L R+      I
Sbjct: 7   VGISGCTNSGKTTLAKSLHRFFPGCSLI 34


>gnl|CDD|31398 COG1205, COG1205, Distinct helicase family with a unique C-terminal
           domain including a metal-binding cysteine cluster
           [General function prediction only].
          Length = 851

 Score = 27.7 bits (61), Expect = 7.7
 Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 11/95 (11%)

Query: 175 IVNQVGRRVDESSPICDARLLDGSRVNVIIPPLALDGPTLTIRKFKKDKLTLDHLVSFGA 234
                           DA   +GS +    P +       +     +D+     LV  G 
Sbjct: 11  RSAFKFITEYLEDEFKDAEGQEGSILRD--PEIEARPGKTSEFPELRDESLKSALVKAGI 68

Query: 235 VT-----AEGARLLQIIGRIRCNVLISGGTGSGKT 264
                   +  RL++  GR   NV+++ GTGSGKT
Sbjct: 69  ERLYSHQVDALRLIRE-GR---NVVVTTGTGSGKT 99


>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
           metabolism].
          Length = 208

 Score = 27.5 bits (61), Expect = 7.7
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDK 276
           ++I G  G+GKTT    L   +++
Sbjct: 6   IVIEGIDGAGKTTQAELLKERLEE 29


>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase.  Members of this family
           include the DEAD and DEAH box helicases. Helicases are
           involved in unwinding nucleic acids. The DEAD box
           helicases are involved in various aspects of RNA
           metabolism, including nuclear transcription, pre mRNA
           splicing, ribosome biogenesis, nucleocytoplasmic
           transport, translation, RNA decay and organellar gene
           expression.
          Length = 167

 Score = 27.6 bits (62), Expect = 7.7
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 251 CNVLISGGTGSGKTT 265
            +VL+   TGSGKT 
Sbjct: 15  KDVLVQAPTGSGKTL 29


>gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase
           component/photorepair protein PhrA [Inorganic ion
           transport and metabolism].
          Length = 257

 Score = 27.5 bits (61), Expect = 8.0
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 252 NVLISGGTGSGKTTLLNCLTRY 273
           +  I G  G+GKTTLL+ LT  
Sbjct: 59  HWAIVGPNGAGKTTLLSLLTGE 80


>gnl|CDD|73012 cd03253, ABCC_ATM1_transporter, ATM1 is an ABC transporter that is
           expressed in the mitochondria.  Although the specific
           function of ATM1 is unknown, its disruption results in
           the accumulation of excess mitochondrial iron, loss of
           mitochondrial cytochromes, oxidative damage to
           mitochondrial DNA, and decreased levels of cytosolic
           heme proteins.  ABC transporters are a large family of
           proteins involved in the transport of a wide variety of
           different compounds, like sugars, ions, peptides, and
           more complex organic molecules.  The nucleotide binding
           domain shows the highest similarity between all members
           of the family.  ABC transporters are a subset of
           nucleotide hydrolases that contain a signature motif,
           Q-loop, and H-loop/switch region, in addition to, the
           Walker A motif/P-loop and Walker B motif commonly found
           in a number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 236

 Score = 27.5 bits (61), Expect = 8.2
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 253 VLISGGTGSGKTTLLNCLTRYIDKDE 278
           V I G +GSGK+T+L  L R+ D   
Sbjct: 30  VAIVGPSGSGKSTILRLLFRFYDVSS 55


>gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the transport
           of a variety of lipid compounds.  Mutations of members
           of ABCA subfamily are associated with human genetic
           diseases, such as, familial high-density lipoprotein
           (HDL) deficiency, neonatal surfactant deficiency,
           degenerative retinopathies, and congenital
           keratinization disorders.  The ABCA1 protein is involved
           in disorders of cholesterol transport and high-density
           lipoprotein (HDL) biosynthesis.  The ABCA4 (ABCR)
           protein transports vitamin A derivatives in the outer
           segments of photoreceptor cells, and therefore, performs
           a crucial step in the visual cycle.  The ABCA genes are
           not present in yeast.  However, evolutionary studies of
           ABCA genes indicate that they arose as transporters that
           subsequently duplicated and that certain sets of ABCA
           genes were lost in different eukaryotic lineages..
          Length = 220

 Score = 27.4 bits (61), Expect = 8.2
 Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)

Query: 251 CNVLISGGTGSGKTTLLNCLT 271
              L+ G  G+GKTT L  LT
Sbjct: 30  IFGLL-GHNGAGKTTTLKMLT 49


>gnl|CDD|31860 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
           proteins [Cell division and chromosome partitioning].
          Length = 858

 Score = 27.5 bits (60), Expect = 8.3
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 252 NVLISGGTGSGKTTLLNCLT 271
           ++LI+G TGSGK+  LN + 
Sbjct: 532 HLLIAGATGSGKSVALNTMI 551


>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like.  This
           family includes several distinct subfamilies (TrmE/ThdF,
           FeoB, YihA (EngG), Era, and EngA/YfgK) that generally
           show sequence conservation in the region between the
           Walker A and B motifs (G1 and G3 box motifs), to the
           exclusion of other GTPases. TrmE is ubiquitous in
           bacteria and is a widespread mitochondrial protein in
           eukaryotes, but is absent from archaea. The yeast member
           of TrmE family, MSS1, is involved in mitochondrial
           translation; bacterial members are often present in
           translation-related operons.  FeoB represents an unusual
           adaptation of GTPases for high-affinity iron (II)
           transport. YihA (EngB) family of GTPases is typified by
           the E. coli YihA, which is an essential protein involved
           in cell division control.  Era is characterized by a
           distinct derivative of the KH domain (the pseudo-KH
           domain) which is located C-terminal to the GTPase
           domain.  EngA and its orthologs are composed of two
           GTPase domains and, since the sequences of the two
           domains are more similar to each other than to other
           GTPases, it is likely that an ancient gene duplication,
           rather than a fusion of evolutionarily distinct GTPases,
           gave rise to this family.
          Length = 163

 Score = 27.7 bits (62), Expect = 8.3
 Identities = 8/16 (50%), Positives = 11/16 (68%)

Query: 257 GGTGSGKTTLLNCLTR 272
           G T +GK++LLN L  
Sbjct: 3   GRTNAGKSSLLNALLG 18


>gnl|CDD|133367 cd04167, Snu114p, Snu114p subfamily.  Snu114p is one of several
           proteins that make up the U5 small nuclear
           ribonucleoprotein (snRNP) particle.  U5 is a component
           of the spliceosome, which catalyzes the splicing of
           pre-mRNA to remove introns.  Snu114p is homologous to
           EF-2, but typically contains an additional N-terminal
           domain not found in Ef-2.  This protein is part of the
           GTP translation factor family and the Ras superfamily,
           characterized by five G-box motifs.
          Length = 213

 Score = 27.6 bits (62), Expect = 8.6
 Identities = 10/22 (45%), Positives = 13/22 (59%)

Query: 252 NVLISGGTGSGKTTLLNCLTRY 273
           NV I+G    GKT+LL+ L   
Sbjct: 2   NVAIAGHLHHGKTSLLDMLIEQ 23


>gnl|CDD|34240 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
           permease components [Secondary metabolites biosynthesis,
           transport, and catabolism / Inorganic ion transport and
           metabolism].
          Length = 546

 Score = 27.6 bits (61), Expect = 8.7
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 253 VLISGGTGSGKTTLLNCLT 271
           V + GG GSGK+TL   LT
Sbjct: 352 VFLIGGNGSGKSTLAMLLT 370


>gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation,
           ribosomal structure and biogenesis].
          Length = 971

 Score = 27.3 bits (60), Expect = 8.8
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 242 LLQIIGRIRCNVLISGGTGSGKTTLLNCLTRY 273
           L+    RIR NV + G    GKT L++ L   
Sbjct: 121 LMDNPERIR-NVGLVGHLHHGKTALMDLLVEQ 151


>gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 352

 Score = 27.5 bits (61), Expect = 8.9
 Identities = 10/31 (32%), Positives = 16/31 (51%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDERIVTCED 285
           + G +GSGKT+L+N +      DE  +    
Sbjct: 29  LFGPSGSGKTSLINMIAGLTRPDEGRIELNG 59


>gnl|CDD|73020 cd03261, ABC_Org_Solvent_Resistant, ABC (ATP-binding cassette)
           transport system involved in resistant to organic
           solvents; ABC transporters are a large family of
           proteins involved in the transport of a wide variety of
           different compounds, like sugars, ions, peptides, and
           more complex organic molecules.  The nucleotide binding
           domain shows the highest similarity between all members
           of the family.  ABC transporters are a subset of
           nucleotide hydrolases that contain a signature motif,
           Q-loop, and H-loop/switch region, in addition to, the
           Walker A motif/P-loop and Walker B motif commonly found
           in a number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 235

 Score = 27.4 bits (61), Expect = 9.0
 Identities = 15/51 (29%), Positives = 23/51 (45%)

Query: 252 NVLISGGTGSGKTTLLNCLTRYIDKDERIVTCEDTAELQLQQPHVVRLETR 302
            + I G +GSGK+TLL  +   +  D   V  +      L +  + RL  R
Sbjct: 28  ILAIIGPSGSGKSTLLRLIVGLLRPDSGEVLIDGEDISGLSEAELYRLRRR 78


>gnl|CDD|31846 COG1660, COG1660, Predicted P-loop-containing kinase [General
           function prediction only].
          Length = 286

 Score = 27.5 bits (61), Expect = 9.0
 Identities = 7/18 (38%), Positives = 13/18 (72%)

Query: 253 VLISGGTGSGKTTLLNCL 270
           V+++G +G+GK+  L  L
Sbjct: 4   VIVTGLSGAGKSVALRVL 21


>gnl|CDD|133354 cd04154, Arl2, Arl2 subfamily.  Arl2 (Arf-like 2) GTPases are
           members of the Arf family that bind GDP and GTP with
           very low affinity.  Unlike most Arf family proteins,
           Arl2 is not myristoylated at its N-terminal helix.  The
           protein PDE-delta, first identified in photoreceptor rod
           cells, binds specifically to Arl2 and is structurally
           very similar to RhoGDI.  Despite the high structural
           similarity between Arl2 and Rho proteins and between
           PDE-delta and RhoGDI, the interactions between the
           GTPases and their effectors are very different.  In its
           GTP bound form, Arl2 interacts with the protein Binder
           of Arl2 (BART), and the complex is believed to play a
           role in mitochondrial adenine nucleotide transport.  In
           its GDP bound form, Arl2 interacts with tubulin- folding
           Cofactor D; this interaction is believed to play a role
           in regulation of microtubule dynamics that impact the
           cytoskeleton, cell division, and cytokinesis.
          Length = 173

 Score = 27.2 bits (61), Expect = 9.2
 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)

Query: 242 LLQIIGRIR-----CNVLISGGTGSGKTTLLNCL 270
           LL II + +       +LI G   +GKTT+L  L
Sbjct: 1   LLTIIRKQKLKEREMRILILGLDNAGKTTILKKL 34


>gnl|CDD|31324 COG1127, Ttg2A, ABC-type transport system involved in resistance to
           organic solvents, ATPase component [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 263

 Score = 27.4 bits (61), Expect = 9.3
 Identities = 11/24 (45%), Positives = 16/24 (66%)

Query: 255 ISGGTGSGKTTLLNCLTRYIDKDE 278
           I GG+GSGK+TLL  +   +  D+
Sbjct: 39  ILGGSGSGKSTLLRLILGLLRPDK 62


>gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component
           [Carbohydrate transport and metabolism].
          Length = 500

 Score = 27.4 bits (61), Expect = 9.4
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)

Query: 231 SFGAVTA-EGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLT 271
           SFG V A +G  L    G +     + G  G+GK+TL+  L+
Sbjct: 17  SFGGVKALDGVSLTVRPGEVHA---LLGENGAGKSTLMKILS 55


>gnl|CDD|34537 COG4928, COG4928, Predicted P-loop ATPase [General function
           prediction only].
          Length = 646

 Score = 27.2 bits (60), Expect = 9.6
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 224 LTLDHLVSFG--AVTAEGARLLQIIGRIRCNVLISGGTGSGKTTLLNCLTRYIDKDERIV 281
           L+ +   SFG       G   +  +      V+ SG  G+GK+TL N L+        I+
Sbjct: 24  LSGEPRDSFGRSGGWGNGKSSICKLAPRGILVVASGEWGTGKSTLSNNLSSEERSPYEIL 83

Query: 282 TCEDTAEL 289
             +  A L
Sbjct: 84  IVKFNAWL 91


>gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
           ATPase components [Amino acid transport and metabolism].
          Length = 352

 Score = 27.2 bits (60), Expect = 9.9
 Identities = 8/14 (57%), Positives = 10/14 (71%)

Query: 257 GGTGSGKTTLLNCL 270
           G +G GKTTLL  +
Sbjct: 38  GPSGCGKTTLLRMI 51


>gnl|CDD|133297 cd01897, NOG, NOG1 is a nucleolar GTP-binding protein present in
           eukaryotes ranging from trypanosomes to humans.  NOG1 is
           functionally linked to ribosome biogenesis and found in
           association with the nuclear pore complexes and
           identified in many preribosomal complexes.  Thus,
           defects in NOG1 can lead to defects in 60S biogenesis.
           The S. cerevisiae NOG1 gene is essential for cell
           viability, and mutations in the predicted G motifs
           abrogate function.  It is a member of the ODN family of
           GTP-binding proteins that also includes the bacterial
           Obg and DRG proteins.
          Length = 168

 Score = 27.1 bits (61), Expect = 10.0
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 253 VLISGGTGSGKTTLLNCLTR 272
           ++I+G    GK++L+N LTR
Sbjct: 3   LVIAGYPNVGKSSLVNKLTR 22


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.136    0.380 

Gapped
Lambda     K      H
   0.267   0.0724    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,554,329
Number of extensions: 295997
Number of successful extensions: 1379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1355
Number of HSP's successfully gapped: 213
Length of query: 483
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 385
Effective length of database: 4,146,055
Effective search space: 1596231175
Effective search space used: 1596231175
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)