RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780877|ref|YP_003065290.1| ATP-dependent Clp protease,
ATP-binding subunit protein [Candidatus Liberibacter asiaticus str.
psy62]
         (853 letters)



>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB.  Members
           of this protein family are the bacterial ATP-dependent
           chaperone ClpB. This protein belongs to the AAA family,
           ATPases associated with various cellular activities
           (pfam00004). This molecular chaperone does not act as a
           protease, but rather serves to disaggregate misfolded
           and aggregated proteins.
          Length = 852

 Score = 1319 bits (3416), Expect = 0.0
 Identities = 519/844 (61%), Positives = 656/844 (77%), Gaps = 7/844 (0%)

Query: 14  LQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQLKDYNQTVLSKIPK 73
           LQ+AQ+ AL + HQ + PEH+L   L+ E G    L+Q +G ++  L+   +  L K+PK
Sbjct: 9   LQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPK 68

Query: 74  VTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETGGIGESLKKCGLKF 133
           V+G G QVYLS  L  +L+ +E++A+K GD F+++E  LLA++ + G +G+ LK+ G   
Sbjct: 69  VSGPGGQVYLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGTLGKLLKEAGATA 128

Query: 134 SRLEESIKKLRKGRVADSVNAEQGFDALKKYCRDLTEEARNGKLDPVIGRDDEMRRAIQV 193
             LE +I  +R G+   S NAE  ++AL+KY RDLTE AR GKLDPVIGRD+E+RR IQV
Sbjct: 129 DALEAAINAVRGGQKVTSANAEDQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQV 188

Query: 194 LSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRG 253
           LSRRTKNNPVLIG+PGVGKTAI+EGLA RI+NGD+PESLK KRL+ALDMGALIAGAK+RG
Sbjct: 189 LSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRG 248

Query: 254 EFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDASNLLKPSLARGELHCIGA 313
           EFEERLK++L E+   +G+IILFIDELH LVGAGK +GAMDA N+LKP+LARGELHCIGA
Sbjct: 249 EFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGA 308

Query: 314 TTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSA 373
           TTLDEYRKYIEKD AL RRFQ + V EPTV DTISILRGLKERYE HH VRI+D A+V+A
Sbjct: 309 TTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAA 368

Query: 374 AVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEK 433
           A LS+RYITDRFLPDKAIDL+DEA+AR+RM+ID+KPE LDELDRRII L+IE+EALKKEK
Sbjct: 369 ATLSHRYITDRFLPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEK 428

Query: 434 DSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNELAIAQRQG 493
           D  SK RL +LEKEL+ LEE+   L  +W+  +  I  +  +K+ +E +R EL  A+R+G
Sbjct: 429 DEASKERLEDLEKELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREG 488

Query: 494 HFERAGELAYGLIPKTEKELDEAEKADS--TAEDMVQEVVTSDNIANIVSRWTGIPVDKM 551
              +A EL YG +P+ EK L  AE      T   +++E VT++ IA +VSRWTGIPV KM
Sbjct: 489 DLAKAAELQYGKLPELEKRLQAAEAKLGEETKPRLLREEVTAEEIAEVVSRWTGIPVSKM 548

Query: 552 LESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGK 611
           LE +REK L +E  + + V+GQ  AVE+VS+A+RR RAGL DP RP+GSF+FLGPTGVGK
Sbjct: 549 LEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGK 608

Query: 612 TELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPY 671
           TEL K+LA  LFDDE++M+RIDMSEYMEKHSV+RLIG+PPGYVGYEEGG LTEAVRR PY
Sbjct: 609 TELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPY 668

Query: 672 QVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLIIMTSNLGAEYLIEDGD- 730
            VVLFDE+EKAH DV N+LLQVLDDGRLTD QGRTVDFRNT+IIMTSNLG++++ E    
Sbjct: 669 SVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGG 728

Query: 731 ----SVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKEDMAKIVRIQLGRVLSLIKERNI 786
                + + VM ++R+ F+PEFLNR+DEI++F  L +E +A+IV IQLGR+   + ER I
Sbjct: 729 DDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKI 788

Query: 787 SMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTISDGDSIEVFVDDD 846
           +++  D  +D+L+  GYDP YGARPLKR IQR I+NPLA+++L+  ++DGD+I V V+  
Sbjct: 789 TLELSDAALDFLAEAGYDPVYGARPLKRAIQREIENPLAKKILAGEVADGDTIVVDVEGG 848

Query: 847 NLNF 850
            L F
Sbjct: 849 RLVF 852


>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
          Length = 857

 Score = 1002 bits (2592), Expect = 0.0
 Identities = 470/853 (55%), Positives = 620/853 (72%), Gaps = 5/853 (0%)

Query: 1   MNSDKYSDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQL 60
           M  D+ ++  +  L  AQ+ AL   +Q + P H++   L  E G+V  L+  +G +  QL
Sbjct: 1   MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQL 60

Query: 61  KDYNQTVLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETG 120
           +      LS++P+V G G  V  SQ L  +L+  +++A+K GD+F+++E F+LA +   G
Sbjct: 61  RTDINQALSRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRG 120

Query: 121 GIGESLKKCGLKFSRLEESIKKLRKGRVADSVNAEQGFDALKKYCRDLTEEARNGKLDPV 180
            + + LK  G   + + ++I+++R G   +   AE    ALKKY  DLTE A  GKLDPV
Sbjct: 121 TLADILKAAGATTANITQAIEQMRGGESVNDQGAEDQRQALKKYTIDLTERAEQGKLDPV 180

Query: 181 IGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMAL 240
           IGRD+E+RR IQVL RRTKNNPVLIG+PGVGKTAI+EGLA RIING++PE LKG+R++AL
Sbjct: 181 IGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL 240

Query: 241 DMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDASNLLK 300
           DMGAL+AGAK+RGEFEERLK +L ++  ++G +ILFIDELH +VGAGK DGAMDA N+LK
Sbjct: 241 DMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLK 300

Query: 301 PSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILRGLKERYEQH 360
           P+LARGELHC+GATTLDEYR+YIEKD AL RRFQ + V EP+V DTI+ILRGLKERYE H
Sbjct: 301 PALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELH 360

Query: 361 HKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRII 420
           H V+I+D A+V+AA LS+RYI DR LPDKAIDL+DEA++ +RMQID+KPE LD LDRRII
Sbjct: 361 HHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRII 420

Query: 421 CLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLE 480
            LK+E++AL KE D  SK RL  L +ELS  E +   L   W+  +  +     +K  LE
Sbjct: 421 QLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELE 480

Query: 481 SMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIV 540
             +  +  A+R G   R  EL YG IP+ EK+L  A + +     +++  VT   IA ++
Sbjct: 481 QAKIAIEQARRVGDLARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIAEVL 540

Query: 541 SRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGS 600
           +RWTGIPV +MLES+REK LR+E E+   VIGQ+ AVE+VSNA+RR RAGL DP RP+GS
Sbjct: 541 ARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGS 600

Query: 601 FMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGG 660
           F+FLGPTGVGKTEL K+LA  +FD +++M+RIDMSE+MEKHSVSRL+G+PPGYVGYEEGG
Sbjct: 601 FLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGG 660

Query: 661 ALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLIIMTSNL 720
            LTEAVRR PY V+L DE+EKAH DV NILLQVLDDGRLTD QGRTVDFRNT++IMTSNL
Sbjct: 661 YLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNL 720

Query: 721 GAEYLIE-----DGDSVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKEDMAKIVRIQLG 775
           G++ + E     D   + + V+G+V   F+PEF+NR+DE+++F  L ++ +A I +IQL 
Sbjct: 721 GSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQ 780

Query: 776 RVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTISD 835
           R+   ++ER   +   D+ +  LS  GYDP YGARPLKR IQ+ I+NPLA+++LS  +  
Sbjct: 781 RLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQILSGELVP 840

Query: 836 GDSIEVFVDDDNL 848
           G  I + V+DD +
Sbjct: 841 GKVIRLEVNDDRI 853


>gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
           Members of this protein family are homologs of ClpB, an
           ATPase associated with chaperone-related functions.
           These ClpB homologs, designated ClpV1, are a key
           component of the bacterial pathogenicity-associated type
           VI secretion system.
          Length = 852

 Score =  737 bits (1904), Expect = 0.0
 Identities = 331/868 (38%), Positives = 503/868 (57%), Gaps = 48/868 (5%)

Query: 7   SDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQLKDYNQT 66
           +   R  L+ A    +A+GH  +  EH L   L+     + ++++  G D+ +LK     
Sbjct: 2   NPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLAR 61

Query: 67  VLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAK-KSGDSFVTAEKFLLAMVMETGGIGES 125
            L K+P   G       S  L  +L ++  +A  + GD  + +   LLA++ +       
Sbjct: 62  ALDKLP--RGNTRTPVFSPHLVELLQEAWLLASLELGDGRIRSGHLLLALLTDPELRRLL 119

Query: 126 LKKCGLKFSRLE-ESIKKLRKGRVADSVNAEQ---------------GFDALKKYCRDLT 169
                   ++++ E++++     V  S  A                 G  AL +Y  DLT
Sbjct: 120 GSISPE-LAKIDREALREALPALVEGSAEASAAAADAGPAAAAAGAAGTSALDQYTTDLT 178

Query: 170 EEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIP 229
            +AR GK+DPV+GRDDE+R+ I +L RR +NNP+L G+ GVGKTA++EGLA RI  GD+P
Sbjct: 179 AQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVP 238

Query: 230 ESLKGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKT 289
            +L+  RL++LD+G L AGA  +GEFE RLKS++ E+++    IILFIDE H L+GAG  
Sbjct: 239 PALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQ 298

Query: 290 DGAMDASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISI 349
            G  DA+NLLKP+LARGEL  I ATT  EY+KY EKDPAL RRFQ + V EP     I +
Sbjct: 299 AGQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRM 358

Query: 350 LRGLKERYEQHHKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKP 409
           LRGL    E+HH V I D A+V+A  LS+RYI  R LPDKA+ L+D A ARV +  +  P
Sbjct: 359 LRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQNATP 418

Query: 410 EVLDELDRRIICLKIEKEALKKE--KDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQR 467
             L++L RRI  L++E +AL++E    +    RL EL  EL++LE +  +L  RWQ+ + 
Sbjct: 419 AALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQEK- 477

Query: 468 KILYVADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMV 527
                 +L + + ++R EL                   + + E  L  A       E +V
Sbjct: 478 ------ELVEAILALRAELEADADA--PADDDAALRAQLAELEAALASA----QGEEPLV 525

Query: 528 QEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRF 587
              V +  +A +V+ WTGIPV +M+  + E  L +   +++ VIGQ  A+E+++  +R  
Sbjct: 526 FPEVDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTA 585

Query: 588 RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI 647
           RAGL+DP++P+G F+ +GP+GVGKTE   +LA LL+  E ++I I+MSE+ E H+VSRL 
Sbjct: 586 RAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK 645

Query: 648 GSPPGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTV 707
           GSPPGYVGY EGG LTEAVRR PY VVL DE+EKAH DV  +  QV D G + D +GR +
Sbjct: 646 GSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREI 705

Query: 708 DFRNTLIIMTSNLGAEYLIE---------DGDSVHDKVMGIVRSAFKPEFLNRLDEIILF 758
           DF+NT+I++TSN G++ ++          D +++ + +   +   FKP FL R+  +I +
Sbjct: 706 DFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRM-TVIPY 764

Query: 759 EKLRKEDMAKIVRIQLGRVLSLIKER-NISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQ 817
             L  + +A IVR++L R+   +KE     + + + +++ +  R  +   GAR +  ++ 
Sbjct: 765 LPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILN 824

Query: 818 RYIQNPLAERVLSQTISDGDSIE-VFVD 844
           + +   L+ ++L + ++ G+ IE + +D
Sbjct: 825 QTLLPELSRQILER-LAAGEPIERIHLD 851


>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
           clpA. 
          Length = 731

 Score =  394 bits (1015), Expect = e-110
 Identities = 193/463 (41%), Positives = 280/463 (60%), Gaps = 25/463 (5%)

Query: 6   YSDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDI----AQLK 61
            S+ +  +L +A   A  + H+ +  EH+L   L D       +++  GGD+      L+
Sbjct: 1   ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSDAI--EILEECGGDVEALRKDLE 58

Query: 62  DYNQTVLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETGG 121
           DY +  L  I       A    +  +  +L ++    K +G   +     L+A+  E   
Sbjct: 59  DYLENNLPSIT--EENEADPEQTVGVQRVLQRALLHVKSAGKKEIGIGDILVALFDEEDS 116

Query: 122 IGE-SLKKCGLKFSRLEESI--------KKLRKGRVADSVNAEQGFDALKKYCRDLTEEA 172
                LK  G+    + E I         K R    A    A++  DAL+KY  DLTE+A
Sbjct: 117 HASYFLKSQGITRLDILEYISHGIPKDDGKNRDAEEAGKEEAKKQEDALEKYTVDLTEKA 176

Query: 173 RNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESL 232
           +NGK+DP+IGR+DE+ R IQVL RR KNNP+L+G+PGVGKTAI EGLA RI  G +PE+L
Sbjct: 177 KNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENL 236

Query: 233 KGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKT-DG 291
           K  ++ +LDMG+L+AG K+RG+FEERLK+++ EI  ++   ILFIDE+H +VGAG T  G
Sbjct: 237 KNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEI-EKEPNAILFIDEIHTIVGAGATSGG 295

Query: 292 AMDASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILR 351
           +MDASNLLKP+L+ G+L CIG+TT +EY+ + EKD AL+RRFQ + VGEP++ +T+ IL+
Sbjct: 296 SMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILK 355

Query: 352 GLKERYEQHHKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEV 411
           GLKE+YE+ H V+ SD AL +A  LS RYI DRFLPDKAID++DEA A  R++   K + 
Sbjct: 356 GLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKA 415

Query: 412 ---LDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSL 451
              + +++   +  K+    +K       + +L  LEK L + 
Sbjct: 416 NVSVKDIEN--VVAKMAHIPVKTVSVD-DREKLKNLEKNLKAK 455



 Score =  353 bits (907), Expect = 1e-97
 Identities = 149/316 (47%), Positives = 209/316 (66%), Gaps = 8/316 (2%)

Query: 531 VTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAG 590
           V+  +I N+V++   IPV  +   DREK   +E  +   + GQ  A++S+ ++++R RAG
Sbjct: 417 VSVKDIENVVAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVSSIKRSRAG 476

Query: 591 LQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSP 650
           L +P +P+GSF+F GPTGVGKTEL K LA  L      + R DMSEYMEKH+VSRLIG+P
Sbjct: 477 LGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL---GVHLERFDMSEYMEKHTVSRLIGAP 533

Query: 651 PGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFR 710
           PGYVG+E+GG LTEAVR+HP+ V+L DEIEKAH D++NILLQV+D   LTD+ GR  DFR
Sbjct: 534 PGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFR 593

Query: 711 NTLIIMTSNLGAEYLIED-----GDSVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKED 765
           N ++IMTSN GA  + +       ++V  K    ++  F PEF NRLD II F  L +E 
Sbjct: 594 NVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEV 653

Query: 766 MAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLA 825
           + KIV+  +  +   + E+NI ++  D    +L+ +GYD  +GARPL RVIQ  I+ PL+
Sbjct: 654 LEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQEEIKKPLS 713

Query: 826 ERVLSQTISDGDSIEV 841
           + +L   +  G S++V
Sbjct: 714 DEILFGKLKKGGSVKV 729


>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
           Provisional.
          Length = 758

 Score =  288 bits (738), Expect = 5e-78
 Identities = 126/257 (49%), Positives = 182/257 (70%), Gaps = 4/257 (1%)

Query: 150 DSVNAEQ--GFDALKKYCRDLTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGD 207
              + EQ  G + ++ +  +L + AR G +DP+IGR+ E+ RAIQVL RR KNNP+L+G+
Sbjct: 156 QPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGE 215

Query: 208 PGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIR 267
            GVGKTAI EGLA RI+ GD+PE +    + +LD+G+L+AG K+RG+FE+R K+LL ++ 
Sbjct: 216 SGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLE 275

Query: 268 SEDGEIILFIDELHVLVGAGKTDGA-MDASNLLKPSLARGELHCIGATTLDEYRKYIEKD 326
            +    ILFIDE+H ++GAG   G  +DA+NL+KP L+ G++  IG+TT  E+    EKD
Sbjct: 276 QDT-NSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKD 334

Query: 327 PALARRFQSLLVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSAAVLSNRYITDRFL 386
            ALARRFQ + + EP++ +T+ I+ GLK +YE HH VR +  A+ +A  L+ +YI DR L
Sbjct: 335 RALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHL 394

Query: 387 PDKAIDLMDEASARVRM 403
           PDKAID++DEA AR R+
Sbjct: 395 PDKAIDVIDEAGARARL 411



 Score =  287 bits (735), Expect = 1e-77
 Identities = 136/330 (41%), Positives = 209/330 (63%), Gaps = 12/330 (3%)

Query: 528 QEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRF 587
           ++ V   +I ++V+R   IP   + +SDR+    +   +   V GQ  A+E+++ A++  
Sbjct: 418 KKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMS 477

Query: 588 RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI 647
           RAGL    +P+GSF+F GPTGVGKTE+   L++ L      ++R DMSEYME+H+VSRLI
Sbjct: 478 RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYMERHTVSRLI 534

Query: 648 GSPPGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTV 707
           G+PPGYVG+++GG LT+AV +HP+ V+L DEIEKAH DV N+LLQV+D+G LTD+ GR  
Sbjct: 535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKA 594

Query: 708 DFRNTLIIMTSNLGAEY-------LIEDGDSVHDKVMGIVRSAFKPEFLNRLDEIILFEK 760
           DFRN +++MT+N G          LI   D+  D  M  ++  F PEF NRLD II F+ 
Sbjct: 595 DFRNVVLVMTTNAGVRETERKSIGLIHQ-DNSTD-AMEEIKKIFTPEFRNRLDNIIWFDH 652

Query: 761 LRKEDMAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYI 820
           L  + + ++V   +  + + + ++ +S++   +  DWL+ +GYD + GARP+ RVIQ  +
Sbjct: 653 LSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNL 712

Query: 821 QNPLAERVLSQTISDGDSIEVFVDDDNLNF 850
           + PLA  +L  ++ DG  + V +D +    
Sbjct: 713 KKPLANELLFGSLVDGGQVTVALDKEKNEL 742


>gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily).  This Pfam entry
           includes some of the AAA proteins not detected by the
           pfam00004 model.
          Length = 168

 Score =  286 bits (734), Expect = 2e-77
 Identities = 109/168 (64%), Positives = 128/168 (76%), Gaps = 8/168 (4%)

Query: 596 RPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVG 655
           RP+GSF+FLGPTGVGKTEL K+LA LLF DE ++IRIDMSEYME+HSVSRLIG+PPGYVG
Sbjct: 1   RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60

Query: 656 YEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLII 715
           YEEGG LTEAVRR PY +VL DEIEKAH  V N LLQ+L+ G LTD QGR VDFRNTL I
Sbjct: 61  YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120

Query: 716 MTSNLGAEYLIE--------DGDSVHDKVMGIVRSAFKPEFLNRLDEI 755
           MT N G+E + +        D + + + VM +++  F PEFL RL  I
Sbjct: 121 MTGNFGSEKISDASRLGKSPDYELLKELVMDLLKKGFIPEFLGRLPII 168


>gnl|CDD|151009 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
           protein.  This is the C-terminal domain of ClpB protein,
           referred to as the D2-small domain, and is a mixed
           alpha-beta structure. Compared with the D1-small domain
           (included in AAA, pfam00004) it lacks the long
           coiled-coil insertion, and instead of helix C4 contains
           a beta-strand (e3) that is part of a three stranded
           beta-pleated sheet. In Thermophilus the whole protein
           forms a hexamer with the D1-small and D2-small domains
           located on the outside of the hexamer, with the long
           coiled-coil being exposed on the surface. The D2-small
           domain is essential for oligomerisation, forming a tight
           interface with the D2-large domain of a neighbouring
           subunit and thereby providing enough binding energy to
           stabilize the functional assembly. The domain is
           associated with two Clp_N, pfam02861, at the N-terminus
           as well as AAA, pfam00004 and AAA_2, pfam07724.
          Length = 89

 Score =  108 bits (272), Expect = 7e-24
 Identities = 42/87 (48%), Positives = 61/87 (70%)

Query: 761 LRKEDMAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYI 820
           L KE++ +IV +QL R+   + ER I+++  D   DWL+ +GYDP YGARPL+R IQR I
Sbjct: 1   LSKEELRQIVDLQLKRLQKRLAERGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREI 60

Query: 821 QNPLAERVLSQTISDGDSIEVFVDDDN 847
           ++PLAE +LS  + +GD++ V VDD  
Sbjct: 61  EDPLAEEILSGELKEGDTVRVDVDDKL 87


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 70.5 bits (172), Expect = 2e-12
 Identities = 33/133 (24%), Positives = 53/133 (39%), Gaps = 7/133 (5%)

Query: 597 PMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGY 656
           P    + +GP G GKT L ++LAR L      +I ID  + +E+     L+    G    
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 657 EEGGA----LTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNT 712
             G           R+    V++ DEI          LL +L++ RL          +N 
Sbjct: 61  GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNL 117

Query: 713 LIIMTSNLGAEYL 725
            +I+T+N   +  
Sbjct: 118 TVILTTNDEKDLG 130



 Score = 41.2 bits (96), Expect = 0.001
 Identities = 33/152 (21%), Positives = 56/152 (36%), Gaps = 20/152 (13%)

Query: 198 TKNNPVLIGDPGVGKTAIIEGLASRI---------INGDIPESLKGKRLMALDMGALIAG 248
                +++G PG GKT +   LA  +         I+G+         ++   +  ++ G
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILE----EVLDQLLLIIVGG 56

Query: 249 AKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDA--SNLLKPSLARG 306
            K  G  E RL+  L   R      +L +DE+  L+ A +    +      LL    +  
Sbjct: 57  KKASGSGELRLRLALALARKLKP-DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115

Query: 307 ELHCIGATTLDEYRKYIEKDPALARRFQSLLV 338
            L  I  T  ++          L RRF   +V
Sbjct: 116 NLTVILTTNDEK----DLGPALLRRRFDRRIV 143


>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily).  This Pfam
           entry includes some of the AAA proteins not detected by
           the pfam00004 model.
          Length = 139

 Score = 62.3 bits (152), Expect = 5e-10
 Identities = 33/129 (25%), Positives = 54/129 (41%), Gaps = 16/129 (12%)

Query: 600 SFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGS--PPGYVGYE 657
             + +GP G GK+EL + LA  L +     ++  ++    +     L G           
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQ--LTRDTTE---EDLKGRRNIANGTTSW 55

Query: 658 EGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVD-------FR 710
             G L  A R    ++ + DEI +A+ DV N LL +LD+ RL   +G  +         +
Sbjct: 56  VDGPLVRAAREG--EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAK 113

Query: 711 NTLIIMTSN 719
              +I T N
Sbjct: 114 RFRLIATMN 122



 Score = 30.7 bits (70), Expect = 1.5
 Identities = 10/23 (43%), Positives = 16/23 (69%)

Query: 203 VLIGDPGVGKTAIIEGLASRIIN 225
           +L+G PG GK+ + E LA+ + N
Sbjct: 3   LLVGPPGTGKSELAERLAAALSN 25


>gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
           This model represents the ATPase subunit of HslVU, while
           the proteasome-related peptidase subunit is HslV.
           Residues 54-61 of the model contain a P-loop ATP-binding
           motif. Cys-287 of E. coli (position 308 in the seed
           alignment), studied in PubMed:98389714, is Ser in other
           members of the seed alignment.
          Length = 441

 Score = 44.8 bits (106), Expect = 9e-05
 Identities = 35/94 (37%), Positives = 52/94 (55%), Gaps = 10/94 (10%)

Query: 562 IETEISKSVIGQSAAVESVSNALR-RFR-----AGLQDPQRPMGSFMFLGPTGVGKTELV 615
           I  E+ K +IGQ  A +SV+ ALR R+R       L+D   P    M +GPTGVGKTE+ 
Sbjct: 6   IVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILM-IGPTGVGKTEIA 64

Query: 616 KSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGS 649
           + LA+L        I+++ +++ E   V R + S
Sbjct: 65  RRLAKLA---NAPFIKVEATKFTEVGYVGRDVES 95


>gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
           Provisional.
          Length = 443

 Score = 42.4 bits (101), Expect = 6e-04
 Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 7/63 (11%)

Query: 565 EISKSVIGQSAAVESVSNALR-RFR-----AGLQDPQRPMGSFMFLGPTGVGKTELVKSL 618
           E+ K +IGQ  A  +V+ ALR R+R       L+D   P    M +GPTGVGKTE+ + L
Sbjct: 12  ELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILM-IGPTGVGKTEIARRL 70

Query: 619 ARL 621
           A+L
Sbjct: 71  AKL 73


>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN.  Members of
           this family are the GvpN protein associated with the
           production of gas vesicles produced in some prokaryotes
           to give cells buoyancy. This family belongs to a larger
           family of ATPases (pfam07728).
          Length = 262

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 55/195 (28%), Positives = 85/195 (43%), Gaps = 45/195 (23%)

Query: 573 QSAAVESV-SNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR-------LLFD 624
           ++ AV+ V S ALR  ++G      P+      GP G GKT L   +AR       L+  
Sbjct: 3   ETDAVKRVTSRALRYLKSG-----YPV---HLRGPAGTGKTTLAMHVARKRDRPVMLING 54

Query: 625 DE---NSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEE-------GGALTEAVRRHPYQVV 674
           D     S +    + Y  K    + I +    V  E+          LT AV R  + +V
Sbjct: 55  DAELTTSDLVGSYAGYTRKKVHDQFIHN---VVKLEDIVRQNWVDNRLTLAV-REGFTLV 110

Query: 675 LFDEIEKAHSDVHNILLQVLDDGRL----TDSQGRTVD----FRNTLIIMTSNLGAEY-- 724
            +DE  ++  + +N+LL V ++G L         R VD    FR   +I TSN   EY  
Sbjct: 111 -YDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFR---VIFTSN-PVEYAG 165

Query: 725 LIEDGDSVHDKVMGI 739
           + E  D++ D+++ I
Sbjct: 166 VHETQDALLDRLITI 180


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 38/136 (27%), Positives = 64/136 (47%), Gaps = 16/136 (11%)

Query: 410 EVLDELDRRIICLKIEKEA---LKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQ 466
           E L+E  + +  LK + E    L +  + +    L E+EK LS LEE+ + +  R +E +
Sbjct: 276 EELEEKVKELKELKEKAEEYIKLSEFYEEYLD-ELREIEKRLSRLEEEINGIEERIKELE 334

Query: 467 RKILYVADLKKRLESMRNELA-IAQRQGHFERA-----------GELAYGLIPKTEKELD 514
            K   + +LKK+L+ +   L  + +R   +E A             L      K EKEL+
Sbjct: 335 EKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELE 394

Query: 515 EAEKADSTAEDMVQEV 530
           E EKA    E+ + ++
Sbjct: 395 ELEKAKEEIEEEISKI 410



 Score = 32.0 bits (73), Expect = 0.64
 Identities = 48/222 (21%), Positives = 85/222 (38%), Gaps = 45/222 (20%)

Query: 388 DKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFS--KGRLIELE 445
           ++ I   ++    V  +I+     L EL   +  L+ E + L++ K+     +  L  LE
Sbjct: 192 EELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLE 251

Query: 446 KELSSLEEKSHSLTLRWQEGQRKI------------------LYVA-------------D 474
                LEEK   L  R +E +++I                   Y+              +
Sbjct: 252 GSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELRE 311

Query: 475 LKKRLESMRNELAIAQRQ-----GHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQE 529
           ++KRL  +  E+   + +        ER  EL    + + EK L+E E+     E+   +
Sbjct: 312 IEKRLSRLEEEINGIEERIKELEEKEERLEELK-KKLKELEKRLEELEERHELYEEAKAK 370

Query: 530 VVTSDNIANIVSRWTGIPVDK---MLESDREKFLRIETEISK 568
               + +  +  R TG+  +K    LE   +    IE EISK
Sbjct: 371 K---EELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISK 409



 Score = 28.9 bits (65), Expect = 6.3
 Identities = 26/128 (20%), Positives = 58/128 (45%), Gaps = 18/128 (14%)

Query: 410 EVLDELDRRIICLK--IEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQR 467
           EV+ E+ RRI  L+  I++    +E     +  L E+ +E++ +  +   L       + 
Sbjct: 169 EVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPEL-------RE 221

Query: 468 KILYVADLKKRLESMRNELAIAQRQ-----GHFERAGELAYGLIPKTEKELDEAEKADST 522
           ++  +    K LE ++ E+   +++     G   +  E     I + E+ ++E +K    
Sbjct: 222 ELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEE----KIRELEERIEELKKEIEE 277

Query: 523 AEDMVQEV 530
            E+ V+E+
Sbjct: 278 LEEKVKEL 285


>gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I).  This model
           represents NtrC, a DNA-binding response regulator that
           is phosphorylated by NtrB and interacts with sigma-54.
           NtrC usually controls the expression of glutamine
           synthase, GlnA, and may be called GlnL, GlnG, etc.
          Length = 463

 Score = 39.0 bits (91), Expect = 0.005
 Identities = 64/231 (27%), Positives = 94/231 (40%), Gaps = 62/231 (26%)

Query: 563 ETEISKSVIGQSAAVESVSNALRRF-RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621
           E E S  +IG++ A++ V  A+ R  R+ +        + +  G +G GK ELV   AR 
Sbjct: 129 EAEDSAELIGEAPAMQEVFRAIGRLSRSDI--------TVLINGESGTGK-ELV---ARA 176

Query: 622 LFDD----ENSMIRIDMS----EYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQV 673
           L           I ++M+    + +E    S L G         E GA T A  R   + 
Sbjct: 177 LHRHSPRANGPFIALNMAAIPKDLIE----SELFG--------HEKGAFTGANTRRQGRF 224

Query: 674 ------VLF-DEIEKAHSDVHNILLQVLDDGRLTDSQGRT---VDFRNTLIIMTSNLGAE 723
                  LF DEI     D    LL+VL DG      GRT   VD R   I+  ++   E
Sbjct: 225 EQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVR---IVAATHQNLE 281

Query: 724 YLIEDGDSVHDKVMGIVRSAFKPEFLNRLDEI-ILFEKL--RKEDMAKIVR 771
            L+  G              F+ +  +RL+ I I    L  R+ED+ ++ R
Sbjct: 282 ALVRQG-------------KFREDLFHRLNVIRIHLPPLRERREDIPRLAR 319


>gnl|CDD|178741 PLN03200, PLN03200, cellulose synthase-interactive protein;
           Provisional.
          Length = 2102

 Score = 38.5 bits (90), Expect = 0.007
 Identities = 17/42 (40%), Positives = 25/42 (59%)

Query: 189 RAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPE 230
           +AI++LSR  ++ PV++GD     +  I  LA RIIN    E
Sbjct: 850 KAIEILSRLCRDQPVVLGDLIANASKCISSLADRIINSSSLE 891


>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily.  This
           subfamily of the AAA family ATPases includes two members
           each from three archaeal species. It also includes yeast
           CDC48 (cell division control protein 48) and the human
           ortholog, transitional endoplasmic reticulum ATPase
           (valosin-containing protein). These proteins in
           eukaryotes are involved in the budding and transfer of
           membrane from the transitional endoplasmic reticulum to
           the Golgi apparatus.
          Length = 733

 Score = 38.3 bits (89), Expect = 0.007
 Identities = 74/284 (26%), Positives = 117/284 (41%), Gaps = 62/284 (21%)

Query: 203 VLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRGEFEERLKSL 262
           +L G PG GKT + + +A+    G    S+ G  +M          +K+ GE EERL+ +
Sbjct: 216 LLYGPPGTGKTLLAKAVANEA--GAYFISINGPEIM----------SKYYGESEERLREI 263

Query: 263 LCEIRSEDGEIILFIDELHVLV-----GAGKTDGAMDAS--NLLKPSLARGELHCIGATT 315
             E   E+   I+FIDE+  +        G+ +  + A    L+     RG +  IGAT 
Sbjct: 264 FKEAE-ENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATN 322

Query: 316 LDEYRKYIEKDPALAR--RF-QSLLVGEPTVTDTISILR------------GLKERYEQH 360
             +       DPAL R  RF + +++  P       IL+             L +  E  
Sbjct: 323 RPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVT 377

Query: 361 HKVRISDSALVS--AAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRR 418
           H    +D A ++  AA+ + R    RF+ +  I+   E             EVL EL   
Sbjct: 378 HGFVGADLAALAKEAAMAALR----RFIREGKINFEAEEIPA---------EVLKELK-- 422

Query: 419 IICLKIEKEALKKEKDSFSKGRLIELEK----ELSSLEEKSHSL 458
            + +K   EALK  + S  +  L+E+      ++  LEE    L
Sbjct: 423 -VTMKDFMEALKMVEPSAIREVLVEVPNVRWSDIGGLEEVKQEL 465


>gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
           This model represents the well-conserved first ~ 365
           amino acids of the translation of the dnaX gene. The
           full-length product of the dnaX gene in the model
           bacterium E. coli is the DNA polymerase III tau subunit.
           A translational frameshift leads to early termination
           and a truncated protein subunit gamma, about 1/3 shorter
           than tau and present in roughly equal amounts. This
           frameshift mechanism is not necessarily universal for
           species with DNA polymerase III but appears conserved in
           the exterme thermophile Thermus thermophilis.
          Length = 355

 Score = 38.3 bits (90), Expect = 0.008
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 12/55 (21%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           + VIGQ   V+++ NA++          R   +++F GP G GKT    S+AR+ 
Sbjct: 14  EDVIGQEHIVQTLKNAIKN--------GRIAHAYLFSGPRGTGKT----SIARIF 56


>gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La.  This protein is induced
           by heat shock and other stresses in E. coli, B.
           subtilis, and other species. The yeast member,
           designated PIM1, is located in the mitochondrial matrix,
           required for mitochondrial function, and also induced by
           heat shock.
          Length = 775

 Score = 38.0 bits (89), Expect = 0.010
 Identities = 32/100 (32%), Positives = 46/100 (46%), Gaps = 15/100 (15%)

Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEG--- 659
            +GP GVGKT L KS+A+ L       +R  +         + + G    YVG   G   
Sbjct: 352 LVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGV---RDEAEIRGHRRTYVGAMPGRII 405

Query: 660 GALTEAVRRHPYQVVLFDEIEKAHSDVH----NILLQVLD 695
             L +A  ++P  + L DEI+K  S       + LL+VLD
Sbjct: 406 QGLKKAKTKNP--LFLLDEIDKIGSSFRGDPASALLEVLD 443


>gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
           (clpX).  A member of the ATP-dependent proteases, ClpX
           has ATP-dependent chaperone activity and is required for
           specific ATP-dependent proteolytic activities expressed
           by ClpPX. The gene is also found to be involved in
           stress tolerance in Bacillus subtilis and is essential
           for the efficient acquisition of genes specifying type
           IA and IB restriction.
          Length = 413

 Score = 37.8 bits (88), Expect = 0.012
 Identities = 72/316 (22%), Positives = 125/316 (39%), Gaps = 84/316 (26%)

Query: 570 VIGQSAAVESVSNA-------LRRFRAGLQDPQRPMG--SFMFLGPTGVGKTELVKSLAR 620
           VIGQ  A + +S A       L   +    D    +   + + +GPTG GKT L ++LAR
Sbjct: 79  VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLAR 138

Query: 621 LLFDDENSMIRI-DMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQV------ 673
           +L    N    I D +   E            GYVG +    L + ++   Y V      
Sbjct: 139 IL----NVPFAIADATTLTEA-----------GYVGEDVENILLKLLQAADYDVEKAQKG 183

Query: 674 -VLFDEIEK--------------AHSDVHNILLQVLDDGRLTD---SQGRTVDFRNTLII 715
            +  DEI+K              +   V   LL+++ +G + +     GR   ++  + I
Sbjct: 184 IIYIDEIDKISRKSENPSITRDVSGEGVQQALLKII-EGTVANVPPQGGRKHPYQEFIQI 242

Query: 716 MTSNL---------GAEYLI--------------------EDGDSVHDKVM-GIVRSAFK 745
            TSN+         G E +I                    E  D +       +V+    
Sbjct: 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLI 302

Query: 746 PEFLNRLDEIILFEKLRKEDMAKIVRIQLGRVL----SLIKERNISMDFDDQVIDWLSCR 801
           PEF+ RL  I   EKL +E +  I+      ++    +L K  N+ +DF+++ +  ++ +
Sbjct: 303 PEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKK 362

Query: 802 GYDPSYGARPLKRVIQ 817
             +   GAR L+ +++
Sbjct: 363 ALERKTGARGLRSIVE 378


>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 367

 Score = 37.5 bits (87), Expect = 0.013
 Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 27/137 (19%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL----F 623
             V+GQS    ++ NA+               + +F GP GVGKT   + LAR +    +
Sbjct: 17  DDVVGQSHITNTLLNAIEN--------NHLAQALLFCGPRGVGKTTCARILARKINQPGY 68

Query: 624 DDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHP----YQVVLFDEI 679
           DD N     ++ E ++  S +            ++   L + VR  P    Y++ + DE+
Sbjct: 69  DDPNEDFSFNIFE-LDAASNN----------SVDDIRNLIDQVRIPPQTGKYKIYIIDEV 117

Query: 680 EKAHSDVHNILLQVLDD 696
               S   N  L+ L++
Sbjct: 118 HMLSSAAFNAFLKTLEE 134


>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
           domain fusion protein; Reviewed.
          Length = 725

 Score = 37.3 bits (87), Expect = 0.015
 Identities = 51/167 (30%), Positives = 70/167 (41%), Gaps = 40/167 (23%)

Query: 178 DPVIGRDDEMRRAIQV--LSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGK 235
           D ++G    +RRAI+   +      + +L G PGVGKT     LA  I N          
Sbjct: 34  DHILGEGRLLRRAIKADRVG-----SLILYGPPGVGKTT----LARIIANH--------T 76

Query: 236 RLMALDMGALIAGAK-FRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMD 294
           R     + A++AG K  R E +   + L           ILFIDE+H    A +     D
Sbjct: 77  RAHFSSLNAVLAGVKDLRAEVDRAKERL----ERHGKRTILFIDEVHRFNKAQQ-----D 127

Query: 295 ASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARR-----FQSL 336
           A   L P +  G +  IGATT +    Y E + AL  R      +SL
Sbjct: 128 A---LLPWVENGTITLIGATTEN---PYFEVNKALVSRSRLFRLKSL 168



 Score = 30.0 bits (68), Expect = 2.9
 Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%)

Query: 598 MGSFMFLGPTGVGKTELVKSLARLL 622
           +GS +  GP GVGKT    +LAR++
Sbjct: 52  VGSLILYGPPGVGKT----TLARII 72


>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 484

 Score = 36.5 bits (84), Expect = 0.028
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 551 MLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVG 610
           M  +      +   +  + VI Q  A+ ++ NAL+  + G         +++F GP GVG
Sbjct: 1   MSGTHEVLSRKYRPQFFRDVIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVG 52

Query: 611 KTELVKSLARLL 622
           KT + + LA+ L
Sbjct: 53  KTTIARILAKRL 64


>gnl|CDD|165554 PHA03297, PHA03297, envelope glycoprotein L; Provisional.
          Length = 185

 Score = 36.2 bits (83), Expect = 0.036
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 210 VGKTAIIEGLASRIINGDIPESLKGKRLMALD 241
           V   A+I+GLA  + NG++P+  K K L ALD
Sbjct: 98  VNPFAVIQGLAEDVTNGNMPQDFKEKLLFALD 129


>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
           primarily archaeal type.  SMC (structural maintenance of
           chromosomes) proteins bind DNA and act in organizing and
           segregating chromosomes for partition. SMC proteins are
           found in bacteria, archaea, and eukaryotes. It is found
           in a single copy and is homodimeric in prokaryotes, but
           six paralogs (excluded from this family) are found in
           eukarotes, where SMC proteins are heterodimeric. This
           family represents the SMC protein of archaea and a few
           bacteria (Aquifex, Synechocystis, etc); the SMC of other
           bacteria is described by TIGR02168. The N- and
           C-terminal domains of this protein are well conserved,
           but the central hinge region is skewed in composition
           and highly divergent.
          Length = 1164

 Score = 36.2 bits (84), Expect = 0.040
 Identities = 34/184 (18%), Positives = 78/184 (42%), Gaps = 23/184 (12%)

Query: 394 MDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEE 453
            +E  A++  +ID     ++EL+R I   +  ++ L +E     K  L +L  EL  +++
Sbjct: 320 AEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE-LKEELEDLRAELEEVDK 378

Query: 454 KSHSLTLRWQEGQRKILYVADLKKRLESMRNELA--------IAQRQGHFERAGELAYGL 505
           +        ++ + K+     LK+ +  ++ EL         +++       A       
Sbjct: 379 EFAETRDELKDYREKL---EKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAK 435

Query: 506 IPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETE 565
           I + E+E ++        E  +++      +A  +S+      ++ L   +E++ R+E E
Sbjct: 436 INELEEEKEDKALEIKKQEWKLEQ------LAADLSK-----YEQELYDLKEEYDRVEKE 484

Query: 566 ISKS 569
           +SK 
Sbjct: 485 LSKL 488



 Score = 31.6 bits (72), Expect = 0.79
 Identities = 33/134 (24%), Positives = 64/134 (47%), Gaps = 8/134 (5%)

Query: 391 IDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSS 450
           +  +++    V+ ++      ++EL+  +  L+   EAL   +   S  R+ E++ ELS 
Sbjct: 746 LSSLEQEIENVKSELKELEARIEELEEDLHKLE---EALNDLEARLSHSRIPEIQAELSK 802

Query: 451 LEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNEL-----AIAQRQGHFERAGELAYGL 505
           LEE+   +  R +E ++K+  +   K+ LE    EL      + ++    E+  E   G 
Sbjct: 803 LEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGK 862

Query: 506 IPKTEKELDEAEKA 519
             + E+EL+E E A
Sbjct: 863 KEELEEELEELEAA 876



 Score = 31.2 bits (71), Expect = 1.3
 Identities = 30/145 (20%), Positives = 59/145 (40%), Gaps = 23/145 (15%)

Query: 409 PEVLDELDRRIICLKIEKEALKKEKDSF-------------SKGRLIELEKELSSLEEKS 455
           P  L  L  R+  LK E  +L+ E                 +  ++ E+EKE+  LE++ 
Sbjct: 673 PAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEE 732

Query: 456 HSLTLRWQEGQRKILY----VADLKKRLESMRNELAIAQRQGHFERA------GELAYGL 505
             L  R +E +  +      + ++K  L+ +   +   +   H            L++  
Sbjct: 733 EKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSR 792

Query: 506 IPKTEKELDEAEKADSTAEDMVQEV 530
           IP+ + EL + E+  S  E  ++E+
Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREI 817


>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
          Length = 424

 Score = 35.6 bits (83), Expect = 0.053
 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 573 QSAAVESVSNALRRF-RAGLQDPQRPMGSFMFLGPTGVGKT 612
           +  A   +   L       ++D  +  G    +GPTGVGKT
Sbjct: 195 ERTAWRYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKT 235


>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
           Provisional.
          Length = 412

 Score = 35.5 bits (83), Expect = 0.056
 Identities = 12/19 (63%), Positives = 16/19 (84%)

Query: 604 LGPTGVGKTELVKSLARLL 622
           +GPTG GKT L ++LAR+L
Sbjct: 114 IGPTGSGKTLLAQTLARIL 132


>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
          Length = 319

 Score = 35.5 bits (82), Expect = 0.058
 Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 4/53 (7%)

Query: 170 EEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLI--GDPGVGKTAIIEGLA 220
           E+ R  KLD ++G +D + R +QV++R   N P LI  G PG GKT  I  LA
Sbjct: 5   EKYRPTKLDDIVGNEDAVSR-LQVIAR-DGNMPNLILSGPPGTGKTTSILALA 55


>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 486

 Score = 35.2 bits (81), Expect = 0.067
 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 8/55 (14%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           K VIGQ   V  + NA++         QR   +++F GP G GKT + + LA++L
Sbjct: 16  KEVIGQEIVVRILKNAVKL--------QRVSHAYIFAGPRGTGKTTIARILAKVL 62


>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
           subunit McrB; Provisional.
          Length = 459

 Score = 35.1 bits (80), Expect = 0.074
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 8/86 (9%)

Query: 605 GPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI-GSPPGYVGYEEGGAL- 662
           GP GVGKT + + LA LL   E +  R++M ++ + +S    I G  P  VG+     + 
Sbjct: 201 GPPGVGKTFVARRLAYLL-TGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIF 259

Query: 663 ---TEAVRRHPYQVVLF--DEIEKAH 683
               +  +  P +  +F  DEI +A+
Sbjct: 260 YNFCQQAKEQPEKKYVFIIDEINRAN 285


>gnl|CDD|149505 pfam08477, Miro, Miro-like protein.  Mitochondrial Rho proteins
           (Miro-1 and Miro-2), are atypical Rho GTPases. They have
           a unique domain organisation, with tandem GTP-binding
           domains and two EF hand domains (pfam00036), that may
           bind calcium. They are also larger than classical small
           GTPases. It has been proposed that they are involved in
           mitochondrial homeostasis and apoptosis.
          Length = 118

 Score = 35.1 bits (81), Expect = 0.079
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 203 VLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFR----GEFEER 258
           V+IGD G GK++++  L       +IPE ++G  L    +              G  EE 
Sbjct: 3   VVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGGREEL 62

Query: 259 LKSLLCEIRSEDGEIILF 276
               +  +++ D  ++++
Sbjct: 63  KFEHIIFMKTADAILLVY 80


>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
           Members of this family from Pyrococcus horikoshii and
           Pyrococcus abyssi each contain a predicted intein.
          Length = 608

 Score = 34.8 bits (80), Expect = 0.088
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 11/57 (19%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDE 626
           VIGQ  AVE +  A ++ R           + + +G  GVGK+ L K++A LL D+E
Sbjct: 20  VIGQEEAVEIIKKAAKQKR-----------NVLLIGEPGVGKSMLAKAMAELLPDEE 65



 Score = 33.3 bits (76), Expect = 0.31
 Identities = 16/46 (34%), Positives = 31/46 (67%), Gaps = 6/46 (13%)

Query: 177 LDPVIGRDDEMRRAIQVLSRRTKN--NPVLIGDPGVGKTAIIEGLA 220
           +D VIG+++    A++++ +  K   N +LIG+PGVGK+ + + +A
Sbjct: 17  IDQVIGQEE----AVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA 58


>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 509

 Score = 34.7 bits (79), Expect = 0.089
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 8/55 (14%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           + VIGQ+  V ++SNAL        D Q    +++F G  GVGKT + + LA+ L
Sbjct: 16  QEVIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCL 62


>gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 614

 Score = 34.0 bits (78), Expect = 0.16
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR 620
           SV+GQ A   ++ NA+           +   +++F GP GVGKT   +  A+
Sbjct: 18  SVVGQEALTTTLKNAIAT--------NKLAHAYLFCGPRGVGKTTCARIFAK 61


>gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
           bacterial type.  SMC (structural maintenance of
           chromosomes) proteins bind DNA and act in organizing and
           segregating chromosomes for partition. SMC proteins are
           found in bacteria, archaea, and eukaryotes. This family
           represents the SMC protein of most bacteria. The smc
           gene is often associated with scpB (TIGR00281) and scpA
           genes, where scp stands for segregation and condensation
           protein. SMC was shown (in Caulobacter crescentus) to be
           induced early in S phase but present and bound to DNA
           throughout the cell cycle.
          Length = 1179

 Score = 33.9 bits (78), Expect = 0.17
 Identities = 31/154 (20%), Positives = 60/154 (38%), Gaps = 25/154 (16%)

Query: 395 DEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSF------------------ 436
            E  A +  Q++     L+EL+ ++  L  E   L+++ +                    
Sbjct: 308 RERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL 367

Query: 437 --SKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNELAIAQRQGH 494
              + RL ELE++L +L  K   L L+      +I  +    +RLE  R  L   + +  
Sbjct: 368 EELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERL-QQEIEEL 426

Query: 495 FERAGELAY----GLIPKTEKELDEAEKADSTAE 524
            ++  E         + + E+EL+E ++     E
Sbjct: 427 LKKLEEAELKELQAELEELEEELEELQEELERLE 460



 Score = 31.2 bits (71), Expect = 1.1
 Identities = 29/123 (23%), Positives = 54/123 (43%), Gaps = 9/123 (7%)

Query: 412 LDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILY 471
           L+EL   +   + E E L  E     + +L EL  E+S LEE+   L         +I  
Sbjct: 241 LEELQEELKEAEEELEELTAELQE-LEEKLEELRLEVSELEEEIEELQKELYALANEI-- 297

Query: 472 VADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAE-DMVQEV 530
            + L+++ + +R  LA  +RQ   E        L  +++ +    E A+   + + ++E 
Sbjct: 298 -SRLEQQKQILRERLANLERQ--LEELEAQLEEL--ESKLDELAEELAELEEKLEELKEE 352

Query: 531 VTS 533
           + S
Sbjct: 353 LES 355


>gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 585

 Score = 34.0 bits (78), Expect = 0.18
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 12/53 (22%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           ++GQ   V+++ NA+   R           +++F GP GVGKT    S AR+L
Sbjct: 18  LVGQEHVVQTLRNAIAEGRVA--------HAYLFTGPRGVGKT----STARIL 58


>gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 618

 Score = 33.2 bits (76), Expect = 0.26
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 8/52 (15%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           +GQ   V++++NAL +        QR   +++F G  GVGKT + + LA+ L
Sbjct: 19  VGQEHVVQALTNALTQ--------QRLHHAYLFTGTRGVGKTTVSRILAKSL 62


>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
          Length = 337

 Score = 33.4 bits (77), Expect = 0.27
 Identities = 16/55 (29%), Positives = 30/55 (54%)

Query: 169 TEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRI 223
           TE+ R   L+ ++G+D+ + R  + +      + ++ G PG GKTA +  LA  +
Sbjct: 6   TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL 60



 Score = 31.5 bits (72), Expect = 0.97
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 11/72 (15%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDD--EN 627
           ++GQ   VE     L R    +  P  P    +  GP G GKT  V++LAR L+ D  EN
Sbjct: 17  ILGQDEVVER----LSRA---VDSPNLP--HLLVQGPPGSGKTAAVRALARELYGDPWEN 67

Query: 628 SMIRIDMSEYME 639
           +    +++++ +
Sbjct: 68  NFTEFNVADFFD 79


>gnl|CDD|182809 PRK10884, PRK10884, SH3 domain-containing protein; Provisional.
          Length = 206

 Score = 33.1 bits (76), Expect = 0.28
 Identities = 15/61 (24%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 440 RLIELEKELSSLEEK----SHSLTLRWQEGQRKIL----YVADLKKRLESMRNELAIAQR 491
           R+ +LE ++ +L +K     ++   R  E Q+K+      +  LK+  + ++N+L +AQ+
Sbjct: 94  RVPDLENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQK 153

Query: 492 Q 492
           +
Sbjct: 154 K 154


>gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 944

 Score = 32.4 bits (74), Expect = 0.44
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 12/51 (23%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621
           +GQS  + +++NAL +        QR   +++F G  GVGKT    SLARL
Sbjct: 19  VGQSHVLHALTNALTQ--------QRLHHAYLFTGTRGVGKT----SLARL 57


>gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 700

 Score = 32.5 bits (74), Expect = 0.45
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 8/54 (14%)

Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           +++GQ   V ++++AL        + QR   +++F G  GVGKT L + LA+ L
Sbjct: 17  TLVGQEHVVRALTHAL--------EQQRLHHAYLFTGTRGVGKTTLSRILAKSL 62


>gnl|CDD|163452 TIGR03740, galliderm_ABC, gallidermin-class lantibiotic protection
           ABC transporter, ATP-binding subunit.  Model TIGR03731
           represents the family of all lantibiotics related to
           gallidermin, including epidermin, mutatin, and nisin.
           This protein family describes the ATP-binding subunit of
           a gallidermin/epidermin class lantibiotic protection
           transporter. It is largely restricted to
           gallidermin-family lantibiotic biosynthesis and export
           cassettes, but also occurs in orphan transporter
           cassettes in species that lack candidate lantibiotic
           precursor and synthetase genes.
          Length = 223

 Score = 32.4 bits (74), Expect = 0.53
 Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 14/94 (14%)

Query: 562 IETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621
           +ET+      G+  AV ++S  + +              +  LGP G GK+ L+K +  +
Sbjct: 1   LETKNLSKRFGKQTAVNNISLTVPKNSV-----------YGLLGPNGAGKSTLLKMITGI 49

Query: 622 LFDDENSMIRIDMSEYMEK--HSVSRLIGSPPGY 653
           L       I  D   +  K  H +  LI SPP Y
Sbjct: 50  LRPTSGE-IIFDGHPWTRKDLHKIGSLIESPPLY 82


>gnl|CDD|163576 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
           PQQ-dependent alcohol dehydrogenase system.  Members of
           this protein family are the ATP-binding subunit of an
           ABC transporter system that is associated with PQQ
           biosynthesis and PQQ-dependent alcohol dehydrogenases.
           While this family shows homology to several efflux ABC
           transporter subunits, the presence of a periplasmic
           substrate-binding protein and association with systems
           for catabolism of alcohols suggests a role in import
           rather than detoxification.
          Length = 236

 Score = 32.3 bits (74), Expect = 0.55
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 14/62 (22%)

Query: 572 GQSAAVESVSNALRRFRAGLQDPQRPMGSFM-FLGPTGVGKTELVKSLARLLFDDENSMI 630
           G   A++ VS  +R             G F+  LGP G GK+ L   L R L+  +   I
Sbjct: 12  GARRALDDVSFTVRP------------GEFVALLGPNGAGKSTLFSLLTR-LYVAQEGQI 58

Query: 631 RI 632
            +
Sbjct: 59  SV 60


>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
          Length = 637

 Score = 32.3 bits (74), Expect = 0.56
 Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 11/53 (20%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           VIGQ  AVE +  A ++ R             M +G  G GK+ L K++A LL
Sbjct: 33  VIGQEHAVEVIKKAAKQRR-----------HVMMIGSPGTGKSMLAKAMAELL 74


>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB.  Members of
           this protein are LonB, a paralog of the ATP-dependent
           protease La (LonA, TIGR00763). LonB proteins are found
           strictly, and almost universally, in endospore-forming
           bacteria. This protease was shown, in Bacillus subtilis,
           to be expressed specifically in the forespore, during
           sporulation, under control of sigma(F). The lonB gene,
           despite location immediately upstream of lonA, was shown
           to be monocistronic. LonB appears able to act on
           sigma(H) for post-translation control, but lonB mutation
           did not produce an obvious sporulation defect under the
           conditions tested. Note that additional paralogs of LonA
           and LonB occur in the Clostridium lineage and this model
           selects only one per species as the protein that
           corresponds to LonB in B. subtilis.
          Length = 531

 Score = 32.1 bits (73), Expect = 0.57
 Identities = 45/151 (29%), Positives = 64/151 (42%), Gaps = 36/151 (23%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKT-------ELVKSLAR 620
             +IGQ   ++++  AL     G  +PQ      +  GP GVGKT       E  K    
Sbjct: 65  DEIIGQEEGIKALKAAL----CG-PNPQH----VIIYGPPGVGKTAAARLVLEEAKKNPA 115

Query: 621 LLFDDENSMIRIDMS--EYMEKHSVSRLIGS----------PPGYVGYEE--GGALTEAV 666
             F +  + + ID +   + E+     LIGS          P G  G  +   GA+T A 
Sbjct: 116 SPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRA- 174

Query: 667 RRHPYQVVLF-DEIEKAHSDVHNILLQVLDD 696
               +  VLF DEI + H    N LL+VL+D
Sbjct: 175 ----HGGVLFIDEIGELHPVQMNKLLKVLED 201



 Score = 30.9 bits (70), Expect = 1.5
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 168 LTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTA 214
           L+E+ R    D +IG+++ ++     L      + ++ G PGVGKTA
Sbjct: 55  LSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTA 101


>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 451

 Score = 32.1 bits (73), Expect = 0.66
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 8/55 (14%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
             ++GQ A V  + NALR          R   +++F G  G GKT L +  A+ L
Sbjct: 17  SEILGQDAVVAVLKNALRF--------NRAAHAYLFSGIRGTGKTTLARIFAKAL 63


>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
          Length = 319

 Score = 31.8 bits (73), Expect = 0.71
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 9/56 (16%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDD 625
           ++GQ   VE     L+ +       ++ M   +F GP G GKT    +LAR L+ +
Sbjct: 19  IVGQEEIVER----LKSYVK-----EKNMPHLLFAGPPGTGKTTAALALARELYGE 65


>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
           protein; Provisional.
          Length = 398

 Score = 32.0 bits (73), Expect = 0.72
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 6/49 (12%)

Query: 593 DPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKH 641
           DP  P G  ++ GP G GKT L K++A        + IR+  SE+++K+
Sbjct: 177 DP--PRGVLLY-GPPGTGKTMLAKAVAH---HTTATFIRVVGSEFVQKY 219


>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
          Length = 880

 Score = 31.9 bits (73), Expect = 0.78
 Identities = 29/126 (23%), Positives = 54/126 (42%), Gaps = 25/126 (19%)

Query: 405 IDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQE 464
           I+   E ++EL+  +  L+ E E +++  +      L+E E  +  LEE+   L      
Sbjct: 470 IEEDRERVEELEAELEDLEEEVEEVEERLERAED--LVEAEDRIERLEERREDLEEL--- 524

Query: 465 GQRKILYVADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAE 524
                  +A+ ++ +E  R      + +   ERA EL        E E +E  +A + AE
Sbjct: 525 -------IAERRETIEEKRE-----RAEELRERAAEL--------EAEAEEKREAAAEAE 564

Query: 525 DMVQEV 530
           +  +E 
Sbjct: 565 EEAEEA 570


>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 576

 Score = 31.6 bits (72), Expect = 0.78
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 12/52 (23%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
            GQ     ++ NA+        D  R   +F+F G  GVGKT    S AR+L
Sbjct: 19  TGQEHVSRTLQNAI--------DTGRVAHAFLFTGARGVGKT----STARIL 58


>gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 709

 Score = 31.6 bits (71), Expect = 0.82
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           ++GQ   V+++ NAL        D  R   +++  G  GVGKT + + LA+ L
Sbjct: 18  LVGQEHVVKALQNAL--------DEGRLHHAYLLTGTRGVGKTTIARILAKSL 62


>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. 
          Length = 282

 Score = 31.5 bits (72), Expect = 0.89
 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 592 QDPQRPMGSFMFLGPTGVGK-TELVKSLARLLFDDENS---MIRID 633
            +     G    +GPTGVGK T L K  AR + +  N    +I  D
Sbjct: 188 DEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTD 233


>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 504

 Score = 31.3 bits (71), Expect = 1.0
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 12/53 (22%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           V+GQ    E +  ALR+ R G         +++F GP GVGKT    + ARL+
Sbjct: 16  VVGQEHVKEVLLAALRQGRLG--------HAYLFSGPRGVGKT----TTARLI 56


>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 546

 Score = 31.2 bits (70), Expect = 1.2
 Identities = 38/149 (25%), Positives = 61/149 (40%), Gaps = 43/149 (28%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL------- 622
           V GQ  A+ S+ +AL        + Q+   +++F G  GVGKT L + LA+ L       
Sbjct: 18  VAGQQHALNSLVHAL--------ETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT 69

Query: 623 -----------FDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHP- 670
                        + NS I     + +E  + SR         G EE   + + ++  P 
Sbjct: 70  AEPCNKCENCVAINNNSFI-----DLIEIDAASR--------TGVEETKEILDNIQYMPS 116

Query: 671 ---YQVVLFDEIEKAHSDVHNILLQVLDD 696
              Y+V L DE+        N LL+ L++
Sbjct: 117 QGRYKVYLIDEVHMLSKQSFNALLKTLEE 145


>gnl|CDD|180249 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
          Length = 646

 Score = 31.1 bits (71), Expect = 1.2
 Identities = 28/147 (19%), Positives = 57/147 (38%), Gaps = 21/147 (14%)

Query: 427 EALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRN-- 484
           E L K+ +      L ++EKE+  LEE+   L    +   +++       +RLE   N  
Sbjct: 85  EELIKDVEEE----LEKIEKEIKELEEEISEL----ENEIKELE---QEIERLEPWGNFD 133

Query: 485 -ELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIVSRW 543
            +L++     +         G +P+ + E  + E      E  +        +  +V + 
Sbjct: 134 LDLSLLLGFKYVSV----FVGTVPEDKLEELKLESDVENVEY-ISTDKGYVYVVVVVLKE 188

Query: 544 TGIPVDKMLESDREKFLRIETEISKSV 570
               V++ L+  +  F R+E E   + 
Sbjct: 189 LSDEVEEELK--KLGFERLELEEEGTP 213


>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
          Length = 413

 Score = 31.2 bits (72), Expect = 1.2
 Identities = 29/105 (27%), Positives = 40/105 (38%), Gaps = 25/105 (23%)

Query: 180 VIGRDDEMRRAIQVLSRRTKNNPVLI--GDPGVGKTAIIEGLASRIINGDIPESLKGKRL 237
           ++G    +RR I+           +I  G PG GKT +   +A                 
Sbjct: 20  LLGPGKPLRRMIE-----AGRLSSMILWGPPGTGKTTLARIIAGAT----------DAPF 64

Query: 238 MALDMGALIAGAK-FRGEFEERLKSLLCEIRSEDGEIILFIDELH 281
            AL   A+ +G K  R   EE       + RS     ILFIDE+H
Sbjct: 65  EALS--AVTSGVKDLREVIEE-----ARQRRSAGRRTILFIDEIH 102



 Score = 31.2 bits (72), Expect = 1.3
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 12/54 (22%)

Query: 570 VIGQSAAVESVSNALRR-FRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           V+GQ   +      LRR   AG       + S +  GP G GKT    +LAR++
Sbjct: 14  VVGQEHLLGPGK-PLRRMIEAGR------LSSMILWGPPGTGKT----TLARII 56


>gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 647

 Score = 31.0 bits (71), Expect = 1.3
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 12/53 (22%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           V+GQ   + +++NAL        D  R   +++F G  GVGKT    ++ARLL
Sbjct: 18  VVGQEHVLTALANAL--------DLGRLHHAYLFSGTRGVGKT----TIARLL 58


>gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 527

 Score = 30.9 bits (70), Expect = 1.3
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 8/52 (15%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           +GQ   V +++NAL +        QR   +++F G  GVGKT L + LA+ L
Sbjct: 19  VGQEHVVRALTNALEQ--------QRLHHAYLFTGTRGVGKTTLARILAKSL 62


>gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 598

 Score = 31.0 bits (71), Expect = 1.4
 Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 12/52 (23%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           IGQ A V +++NA   F  G     R   +FM  G  GVGKT    + AR+L
Sbjct: 27  IGQEAMVRTLTNA---FETG-----RIAQAFMLTGVRGVGKT----TTARIL 66


>gnl|CDD|182459 PRK10436, PRK10436, hypothetical protein; Provisional.
          Length = 462

 Score = 30.7 bits (70), Expect = 1.7
 Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 3/32 (9%)

Query: 581 SNALRRFRAGLQDPQRPMGSFMFLGPTGVGKT 612
              L +FR  LQ PQ   G  +  GPTG GKT
Sbjct: 204 PAQLAQFRQALQQPQ---GLILVTGPTGSGKT 232


>gnl|CDD|163043 TIGR02858, spore_III_AA, stage III sporulation protein AA.  Members
           of this protein are the stage III sporulation protein
           AA, encoded by one of several genes in the spoIIIA
           locus. It seems that this protein is found in a species
           if and only if that species is capable of endospore
           formation.
          Length = 270

 Score = 30.8 bits (70), Expect = 1.7
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 200 NNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAG 248
            N ++I  P  GKT ++  LA  +  G     L+GK++  +D  + IAG
Sbjct: 112 LNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVDERSEIAG 160


>gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 584

 Score = 30.6 bits (69), Expect = 1.9
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           V+GQ    E +S+AL        D  R   +++F GP G GKT   + LAR L
Sbjct: 15  VVGQEHVTEPLSSAL--------DAGRINHAYLFSGPRGCGKTSSARILARSL 59


>gnl|CDD|184302 PRK13752, PRK13752, putative transcriptional regulator MerR;
           Provisional.
          Length = 144

 Score = 30.6 bits (69), Expect = 1.9
 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 562 IETEISKSVIGQSAAVESVSNALRRF--RAGL-QDPQRPMGSFMFLGPTGVGKTELVKSL 618
           +E  +    IG  A    V+    RF  R GL  +P +P GS    G   V +   VKS 
Sbjct: 1   MENNLENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSA 60

Query: 619 ARLLF--DDENSMIRIDMSEYMEKHS 642
            RL F  D+   ++R++   + E+ S
Sbjct: 61  QRLGFSLDEIAELLRLEDGTHCEEAS 86


>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
           Provisional.
          Length = 482

 Score = 30.7 bits (70), Expect = 1.9
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 5/51 (9%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR 620
           V+G   A E +   +  +  G   P++ +   +  GP GVGKT L  +LA 
Sbjct: 16  VVGNEKAKEQLREWIESWLKG--KPKKAL---LLYGPPGVGKTSLAHALAN 61



 Score = 29.1 bits (66), Expect = 4.9
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 167 DLTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNP----VLIGDPGVGKTAIIEGLA 220
              E+ R   L  V+G +    +  + +    K  P    +L G PGVGKT++   LA
Sbjct: 3   PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60


>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
           Provisional.
          Length = 588

 Score = 30.3 bits (69), Expect = 1.9
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 12/62 (19%)

Query: 572 GQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIR 631
                VE VS     F A      +P  +   +GPTG GK+ L+  L R +FD ++  I 
Sbjct: 346 NSRQGVEDVS-----FEA------KPGQTVAIVGPTGAGKSTLINLLQR-VFDPQSGRIL 393

Query: 632 ID 633
           ID
Sbjct: 394 ID 395


>gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
          Length = 345

 Score = 30.6 bits (70), Expect = 2.0
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 605 GPTGVGKTELVKSLARL 621
           G TG GKTEL+++LA  
Sbjct: 148 GNTGSGKTELLQALANA 164


>gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional.
          Length = 3095

 Score = 30.3 bits (68), Expect = 2.1
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%)

Query: 455  SHSLTLRWQEGQRKILY------VADLKKRLESMRNELAIAQ 490
            SH LT+R  E     +Y      +  L+ RL  +++ELA+A+
Sbjct: 1756 SHDLTVRIDESGPMTIYAERIDALVRLENRLAELKSELALAE 1797


>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
          Length = 298

 Score = 30.2 bits (69), Expect = 2.4
 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 13/56 (23%)

Query: 203 VLIGDPGVGKT----AIIEGLASRIINGDIPESL-KGK------RLMALDMGALIA 247
           VL G  GVGK+    A+   L  +   G+I E+L +GK       L  L  G L+ 
Sbjct: 168 VLAGQSGVGKSTLLNALAPDLELKT--GEISEALGRGKHTTTHVELYDLPGGGLLI 221


>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
           Provisional.
          Length = 638

 Score = 30.0 bits (68), Expect = 2.4
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 675 LF-DEIEKAHSDVHNILLQVLDDGRLTDSQGR---TVDFRNTLIIMTSNLGAEYLIEDG 729
           LF +++E    ++ + LLQVL  G +T    R    VD R   +I T+      L+E  
Sbjct: 420 LFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVR---VIATTTADLAMLVEQN 475


>gnl|CDD|150950 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
           Fmp27_WPPW is a conserved domain of a family of proteins
           involved in RNA polymerase II transcription initiation.
           It contains characteristic HQR and WPPW sequence motifs.
           and is towards the C-terminal in members which contain
           Fmp27_SW pfam10305.
          Length = 470

 Score = 30.0 bits (68), Expect = 2.5
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 440 RLIELEKELSSLEEKSHSLTLRWQEGQRKIL-----YVADLKKRLESMRNEL 486
           RL +LE+++  LEEK   L L   E  +  L      ++ LK+RLE +   L
Sbjct: 169 RLKQLEEQIKKLEEKLGDLELNDDEELQSDLEELEKELSVLKERLEFLEKLL 220


>gnl|CDD|152161 pfam11725, AvrE, Pathogenicity factor.  This family is secreted by
            gram-negative Gammaproteobacteria such as Pseudomonas
            syringae of tomato and the fire blight plant pathogen
            Erwinia amylovora, amongst others. It is an essential
            pathogenicity factor of approximately 198 kDa. Its
            injection into the host-plant is dependent upon the
            bacterial type III or Hrp secretion system. The family is
            long and carries a number of predicted functional
            regions, including an ERMS or endoplasmic reticulum
            membrane retention signal at both the C- and the
            N-termini, a leucine-zipper motif from residues 539-560,
            and a nuclear localisation signal at 1358-1361. this
            conserved AvrE-family of effectors is among the few that
            are required for full virulence of many phytopathogenic
            pseudomonads, erwinias and pantoeas.
          Length = 1771

 Score = 30.1 bits (68), Expect = 2.7
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 9/67 (13%)

Query: 473  ADLKKRLESMRNEL---------AIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTA 523
            A+L K LE  R EL          + Q+QG     GE+     PK  K L ++   + + 
Sbjct: 964  AELVKDLEQFREELENHSTTAAILLGQQQGVLNSHGEINKPFKPKKSKALGQSFNVNRSG 1023

Query: 524  EDMVQEV 530
             D+ +E+
Sbjct: 1024 HDLSKEL 1030


>gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 830

 Score = 29.8 bits (67), Expect = 2.8
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 8/54 (14%)

Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           S++GQ   V ++++AL        D  R   +++F G  GVGKT L +  A+ L
Sbjct: 17  SLVGQEHVVRALTHAL--------DGGRLHHAYLFTGTRGVGKTTLSRIFAKAL 62


>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit.  At position
           126-127 of the seed alignment, this family lacks the HM
           motif of gamma/tau; at 132 it has a near-invariant A vs.
           an invariant F in gamma/tau.
          Length = 188

 Score = 29.9 bits (68), Expect = 2.8
 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 20/107 (18%)

Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI--GSPPGYVGYE-EG 659
           F GP GVGK  L  +LA+ L  ++         E   +    RLI  G+ P     E EG
Sbjct: 19  FAGPEGVGKELLALALAKALLCEQPGGG-----EPCGECPSCRLIEAGNHPDLHRLEPEG 73

Query: 660 GALT-EAVRRH-----------PYQVVLFDEIEKAHSDVHNILLQVL 694
            ++  + VR               +VV+ ++ E+ +    N LL+ L
Sbjct: 74  QSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTL 120


>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
           Provisional.
          Length = 255

 Score = 30.0 bits (68), Expect = 2.9
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 604 LGPTGVGKTELVKSLARLL 622
           +GP G GK+ L+K  ARLL
Sbjct: 34  IGPNGCGKSTLLKCFARLL 52


>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
          Length = 506

 Score = 29.9 bits (67), Expect = 3.0
 Identities = 34/121 (28%), Positives = 59/121 (48%), Gaps = 24/121 (19%)

Query: 177 LDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKR 236
           L  VIG++ + +R +++ +    +N +LIG PG GKT     LASR ING +P+    + 
Sbjct: 190 LSDVIGQE-QGKRGLEI-TAAGGHNLLLIGPPGTGKTM----LASR-INGLLPDLSNEEA 242

Query: 237 LMALDMGALIAGAKFRGEFEER------LKSLLCEIRS-----EDGEI------ILFIDE 279
           L +  + +L+     + ++ +R        + L  +         GEI      +LF+DE
Sbjct: 243 LESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDE 302

Query: 280 L 280
           L
Sbjct: 303 L 303


>gnl|CDD|163225 TIGR03348, VI_IcmF, type VI secretion protein IcmF.  Members of
           this protein family are IcmF homologs and tend to be
           associated with type VI secretion systems.
          Length = 1169

 Score = 29.6 bits (67), Expect = 3.2
 Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 16/65 (24%)

Query: 168 LTEEARNGKLDPVIGRDDE-------MRRAIQVLSRRTKNNP---------VLIGDPGVG 211
           L   A   KL      + E          A+ +L R               ++IG PG G
Sbjct: 64  LAALAAPTKLKADAAAEAEIRELRARFNEALALLKRSRLGGRRYLYDLPWYLVIGPPGSG 123

Query: 212 KTAII 216
           KT ++
Sbjct: 124 KTTLL 128


>gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E.  This
           family describes GspE, the E protein of the type II
           secretion system, also called the main terminal branch
           of the general secretion pathway. This model separates
           GspE from the PilB protein of type IV pilin
           biosynthesis.
          Length = 486

 Score = 29.7 bits (67), Expect = 3.6
 Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 584 LRRFRAGLQDPQRPMGSFMFLGPTGVGK-TELVKSLARLLFDDENSMIRIDMSEY 637
           L RF   ++   RP G  +  GPTG GK T L  +L+RL   + N +   D  EY
Sbjct: 231 LSRFERLIR---RPHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY 282


>gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter
           ATP-binding subunit.  This model describes daunorubicin
           resistance ABC transporter, ATP binding subunit in
           bacteria and archaea. This model is restricted in its
           scope to preferentially recognize the ATP binding
           subunit associated with effux of the drug, daunorubicin.
           This transport system belong to the larger ATP-Binding
           Cassette (ABC) transporter superfamily. The
           characteristic feature of these transporter is the
           obligatory coupling of ATP hydrolysis to substrate
           translocation. The minimal configuration of bacterial
           ABC transport system: an ATPase or ATP binding subunit;
           An integral membrane protein; a hydrophilic polypetpide,
           which likely functions as substrate binding protein. In
           eukaryotes proteins of similar function include p-gyco
           proteins, multidrug resistance protein etc.
          Length = 302

 Score = 29.7 bits (67), Expect = 3.6
 Identities = 12/22 (54%), Positives = 14/22 (63%)

Query: 601 FMFLGPTGVGKTELVKSLARLL 622
           F FLGP G GKT  ++ L  LL
Sbjct: 22  FGFLGPNGAGKTTTIRMLTTLL 43


>gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 620

 Score = 29.5 bits (67), Expect = 4.0
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 12/53 (22%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           ++GQ A   ++ NAL           R   +++F GP G GKT    S AR+L
Sbjct: 18  LVGQEAIATTLKNALIS--------NRIAPAYLFTGPRGTGKT----SSARIL 58


>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
           utilisation.  Members of this family function in
           ethanolamine and propanediol degradation pathways,
           however the exact roles of these proteins is poorly
           understood.
          Length = 143

 Score = 29.5 bits (67), Expect = 4.0
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 598 MGSFMFLGPTGVGKTELVKSL 618
           M   M +G +G GKT L ++L
Sbjct: 1   MKKIMLIGRSGCGKTTLTQAL 21


>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
           Provisional.
          Length = 784

 Score = 29.5 bits (66), Expect = 4.0
 Identities = 31/98 (31%), Positives = 48/98 (48%), Gaps = 11/98 (11%)

Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSR-LIGSPPGYVGYEEGGA 661
            +GP GVGKT L +S+A+        M    + +  E     R  IGS PG +  +    
Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQK---- 409

Query: 662 LTEAVRRHPYQVVLFDEIEKAHSDVH----NILLQVLD 695
           + +   ++P  + L DEI+K  SD+     + LL+VLD
Sbjct: 410 MAKVGVKNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445


>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
          Length = 174

 Score = 29.5 bits (67), Expect = 4.1
 Identities = 12/18 (66%), Positives = 13/18 (72%)

Query: 605 GPTGVGKTELVKSLARLL 622
           GP GVGKT LV  +A LL
Sbjct: 7   GPPGVGKTTLVLKIAELL 24


>gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding protein;
           Provisional.
          Length = 253

 Score = 29.0 bits (65), Expect = 4.5
 Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%)

Query: 591 LQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           L+ PQ   G F  +GP+G GK+ L+++  RLL
Sbjct: 25  LKIPQN--GVFALMGPSGCGKSTLLRTFNRLL 54


>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
          Length = 205

 Score = 29.3 bits (67), Expect = 4.8
 Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 14/44 (31%)

Query: 601 FMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVS 644
            +  GP+G GK+    +L + L + + ++          + SVS
Sbjct: 8   IVLSGPSGAGKS----TLVKALLERDPNL----------QLSVS 37


>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 605

 Score = 29.0 bits (65), Expect = 4.8
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 8/55 (14%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           K +IGQ    + + NA+           +   +++F GP G+GKT + K  A+ +
Sbjct: 16  KQIIGQELIKKILVNAILN--------NKLTHAYIFSGPRGIGKTSIAKIFAKAI 62


>gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein;
           Provisional.
          Length = 623

 Score = 29.1 bits (65), Expect = 4.8
 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 9/66 (13%)

Query: 775 GR-VLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTI 833
           GR +L L++ +   + F+ Q ID L           + L+R IQ   Q+P A     QT+
Sbjct: 367 GRALLRLVESQGGEIIFNGQRIDTL------SPGKLQALRRDIQFIFQDPYASLDPRQTV 420

Query: 834 SDGDSI 839
             GDSI
Sbjct: 421 --GDSI 424


>gnl|CDD|163076 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
           protein.  Members of this protein family are found
           exclusively in the archaea. This set of DNA binding
           proteins shows homology to the origin recognition
           complex subunit 1/cell division control protein 6 family
           in eukaryotes. Several members may be found in genome
           and interact with each other.
          Length = 365

 Score = 29.1 bits (66), Expect = 4.9
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 178 DPVIGRDDE---MRRAIQ-VLSRRTKNNPVLIGDPGVGKTAIIEGLASRI 223
           D ++ RD++   + +A++ +L     +N  + G  G GKTA+ + +   +
Sbjct: 15  DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64


>gnl|CDD|163168 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase.  The
           Escherichia coli YbbB protein was shown to encode a
           selenophosphate-dependent tRNA 2-selenouridine synthase,
           essential for modification of some tRNAs to replace a
           sulfur atom with selenium. This enzyme works with SelD,
           the selenium donor protein, which also acts in
           selenocysteine incorporation. Although the members of
           this protein family show a fairly deep split, sequences
           from both sides of the split are supported by
           co-occurence with, and often proximity to, the selD
           gene.
          Length = 311

 Score = 29.1 bits (66), Expect = 5.0
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 605 GPTGVGKTELVKSLARL 621
           G TG GKTEL+ +LA  
Sbjct: 134 GMTGSGKTELLHALANA 150


>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family.  In a
           subset of endospore-forming members of the Firmcutes,
           members of this protein family are found, several to a
           genome. Two very strongly conserved sequences regions
           are separated by a highly variable linker region. Much
           of the linker region was excised from the seed alignment
           for this model. A characterized member is the
           prespore-specific transcription RsfA from Bacillus
           subtilis, previously called YwfN, which is controlled by
           sigma factor F and seems to fine-tune expression of some
           genes in the sigma-F regulon. A paralog in Bacillus
           subtilis is designated YlbO.
          Length = 161

 Score = 29.0 bits (65), Expect = 5.2
 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 5/64 (7%)

Query: 422 LKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLES 481
           L+ E E LK + +S  K R  ELEKEL  L ++  ++    +E  + ++ + D  ++L  
Sbjct: 102 LQKENERLKNQNESLQK-RNEELEKELEKLRQRLSTI----EEDYQTLIDIMDRARKLAV 156

Query: 482 MRNE 485
           + ++
Sbjct: 157 VEDD 160


>gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 563

 Score = 29.0 bits (65), Expect = 5.5
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%)

Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           S+ GQ   VE++ +++   +           +++F GP GVGKT   ++ AR L
Sbjct: 17  SLEGQDFVVETLKHSIESNKIA--------NAYIFSGPRGVGKTSSARAFARCL 62


>gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
          Length = 484

 Score = 28.8 bits (65), Expect = 5.8
 Identities = 12/21 (57%), Positives = 13/21 (61%)

Query: 599 GSFMFLGPTGVGKTELVKSLA 619
           G F  +GPTGVGKT     LA
Sbjct: 257 GVFALMGPTGVGKTTTTAKLA 277


>gnl|CDD|179742 PRK04123, PRK04123, ribulokinase; Provisional.
          Length = 548

 Score = 28.7 bits (65), Expect = 6.1
 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 4/44 (9%)

Query: 651 PGYVGYEEG----GALTEAVRRHPYQVVLFDEIEKAHSDVHNIL 690
           PG +GYE G    G +     R        DE E     +  +L
Sbjct: 322 PGLIGYEAGQSAVGDIFAWFARLLVPPEYKDEAEARGKQLLELL 365


>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
           activities (AAA).  This Pfam entry includes some of the
           AAA proteins not detected by the pfam00004 model.
          Length = 131

 Score = 28.7 bits (65), Expect = 6.2
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 605 GPTGVGKTELVKSLARLL 622
           G  G+ KT L ++LAR L
Sbjct: 6   GVPGLAKTLLARTLARSL 23


>gnl|CDD|184901 PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional.
          Length = 1000

 Score = 28.8 bits (65), Expect = 6.3
 Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 15/74 (20%)

Query: 470 LYVADLKKRLESMRNELA----------IAQRQGHFERAGELAYGLIPKTEKE-LDEAE- 517
           L+ ADLK  LE+   +L           +A +    +   E    L+P + +E LD A  
Sbjct: 647 LFKADLKTPLETFVEKLKSVTYFEALGSLADKVERIKAHAEELAALLPLSARETLDRAAE 706

Query: 518 --KADSTAEDMVQE 529
             K D     MV E
Sbjct: 707 LCKFD-LVSQMVNE 719


>gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 702

 Score = 28.9 bits (64), Expect = 6.4
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 8/53 (15%)

Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
           ++GQ+    ++S+AL R R           +++F G  GVGKT + + LA+ L
Sbjct: 17  LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCL 61


>gnl|CDD|185619 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
            Provisional.
          Length = 2722

 Score = 28.6 bits (64), Expect = 6.6
 Identities = 14/53 (26%), Positives = 22/53 (41%)

Query: 90   ILSKSEEIAKKSGDSFVTAEKFLLAMVMETGGIGESLKKCGLKFSRLEESIKK 142
            I   SE+I K+  +S   AE+F      E       +K+   K  + +E   K
Sbjct: 1292 ISIDSEKILKEILNSTKKAEEFSNDAKKELEKTDNLIKQVEAKIEQAKEHKNK 1344


>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein.  This model
           describes glucan exporter ATP binding protein in
           bacteria. It belongs to the larger ABC transporter
           superfamily with the characteristic ATP binding motif.
           The In general, this protein is in some ways implicated
           in osmoregulation and suggested to participate in the
           export of glucan from the cytoplasm to periplasm. The
           cyclic beta-1,2-glucan in the bactrerial periplasmic
           space is suggested to confer the property of high
           osmolority. It has also been demonstrated that mutants
           in this loci have lost functions of virulence and
           motility. It is unclear as to how virulence and
           osmoadaptaion are related.
          Length = 585

 Score = 28.7 bits (64), Expect = 6.6
 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)

Query: 604 LGPTGVGKTELVKSLARLLFDDENSMIRID 633
           +GPTG GKT L+  L R ++D     I ID
Sbjct: 367 VGPTGAGKTTLINLLQR-VYDPTVGQILID 395


>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
           RuvA specifically binds Holliday junctions as a sandwich
           of two tetramers and maintains the configuration of the
           junction. It forms a complex with two hexameric rings of
           RuvB, the subunit that contains helicase activity. The
           complex drives ATP-dependent branch migration of the
           Holliday junction recombination intermediate. The
           endonuclease RuvC resolves junctions.
          Length = 305

 Score = 28.8 bits (65), Expect = 6.8
 Identities = 34/130 (26%), Positives = 52/130 (40%), Gaps = 27/130 (20%)

Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMI 630
           IGQ    E V   L+ F    +  Q  +   +  GP G+GKT    +LA ++ ++    +
Sbjct: 7   IGQ----EKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKT----TLAHIIANEMGVNL 58

Query: 631 RIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQVVLF-DEIEKAHSDVHNI 689
           +I     +EK          PG    +    LT          VLF DEI +    V  +
Sbjct: 59  KITSGPALEK----------PG----DLAAILTNLEEGD----VLFIDEIHRLSPAVEEL 100

Query: 690 LLQVLDDGRL 699
           L   ++D RL
Sbjct: 101 LYPAMEDFRL 110


>gnl|CDD|181314 PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated.
          Length = 339

 Score = 28.7 bits (65), Expect = 6.9
 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 9/37 (24%)

Query: 570 VIGQSAA---------VESVSNALRRFRAGLQDPQRP 597
           V+G SAA         V +V++AL+R RA L +    
Sbjct: 167 VLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPS 203


>gnl|CDD|152140 pfam11704, Folliculin, Vesicle coat protein involved in Golgi to
           plasma membrane transport.  In yeast cells this family
           functions in the regulated delivery of Gap1p (a general
           amino acid permease) to the cell surface, perhaps as a
           component of a post-Golgi secretory-vesicle coat
           complex. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal
           dominant disorder characterized by hamartomas of skin
           follicles, lung cysts, spontaneous pneumothorax, and
           renal cell carcinoma. Folliculin is the protein from the
           BHD4 gene and is found to have no significant homology
           to any other human proteins. It is expressed in most
           tissues. These same symptoms also occur in TSC or
           tuberous sclerosis complex, suggesting that the same
           pathway is involved, and it is likely that the target is
           the down-stream Tor2 - an essential gene. Folliculin
           appears to bind Tor2, and down-regulation of Tor2
           activity leads to up-regulation of nitrogen responsive
           genes including membrane transporters and amino acid
           permeases.
          Length = 168

 Score = 28.4 bits (64), Expect = 7.1
 Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 14/82 (17%)

Query: 259 LKSLLCEIRSEDGEIILFIDEL--HVLVGAGKTDGAMDASNLLKPSLARG--ELHCIGAT 314
           ++SL CE    DG  + F D +  +VL    K          LK   ARG    + +   
Sbjct: 24  VRSLSCETMGYDGGPLFFGDAIRGYVLSYGFK----------LKDPNARGNERRYSLIVL 73

Query: 315 TLDEYRKYIEKDPALARRFQSL 336
             D+  K +   P +A  F  +
Sbjct: 74  ADDKMSKLLNNWPFIAEYFGKI 95


>gnl|CDD|132269 TIGR03225, benzo_boxB, benzoyl-CoA oxygenase, B subunit.  Members
           of this protein family are BoxB, the B subunit of
           benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts
           in an aerobic pathway of benzoate catabolism via
           coenzyme A ligation.
          Length = 471

 Score = 28.6 bits (64), Expect = 7.7
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 144 RKGRVADSVNAEQGFDALKKYCR-DLTEEARNGKL-DPVIGRDDEMRRAIQVLSRRTKNN 201
           R G++  +  AE GFD L + CR  LTEEA +  + +  +GR   + R  QV+     ++
Sbjct: 211 RDGKMQLAALAESGFDPLSRTCRFMLTEEAHHMFVGESGVGR--VIERTCQVMKENGTDD 268

Query: 202 PVLIGDPGV 210
           P  I   GV
Sbjct: 269 PYRIRALGV 277


>gnl|CDD|177536 PHA03132, PHA03132, thymidine kinase; Provisional.
          Length = 580

 Score = 28.6 bits (64), Expect = 8.1
 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 601 FMFL-GPTGVGKTELVKSLARLLFD 624
           F+FL G  GVGKT L+  +  +L D
Sbjct: 259 FLFLEGVMGVGKTTLLNHMRGILGD 283


>gnl|CDD|173186 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
          Length = 767

 Score = 28.2 bits (63), Expect = 8.3
 Identities = 11/21 (52%), Positives = 12/21 (57%)

Query: 599 GSFMFLGPTGVGKTELVKSLA 619
           G    +GPTGVGKT     LA
Sbjct: 186 GVLALVGPTGVGKTTTTAKLA 206


>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
           subunit.  This model describes 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
           transporter is the obligatory coupling of ATP hydrolysis
           to substrate translocation. The minimal configuration of
           bacterial ABC transport system: an ATPase or ATP binding
           subunit; An integral membrane protein; a hydrophilic
           polypetpide, which likely functions as substrate binding
           protein. Functionally, this transport system is involved
           in osmoregulation. Under conditions of stress, the
           organism recruits these transport system to accumulate
           glycine betaine and other solutes which offer
           osmo-protection. It has been demonstrated that glycine
           betaine uptake is accompanied by symport with sodium
           ions. The locus has been named variously as proU or
           opuA. A gene library from L.lactis functionally
           complements an E.coli proU mutant. The comlementing
           locus is similar to a opuA locus in B.sutlis. This
           clarifies the differences in nomenclature.
          Length = 363

 Score = 28.3 bits (63), Expect = 8.7
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 601 FMFLGPTGVGKTELVKSLARLL 622
           F+ +G +G GK+  V+ L RL+
Sbjct: 22  FVIMGLSGSGKSTTVRMLNRLI 43


>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG.  This model
           represents UreG, a GTP hydrolase that acts in the
           assembly of the nickel metallocenter of urease. It is
           found only in urease-positive species, although some
           urease-positive species (e.g. Bacillus subtilis) lack
           this protein. A similar protein, hypB, is an accessory
           protein for expression of hydrogenase, which also uses
           nickel.
          Length = 199

 Score = 28.3 bits (63), Expect = 8.8
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 10/69 (14%)

Query: 605 GPTGVGKTELVKSLARLLFDD------ENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEE 658
           GP G GKT L+++L R L          N +   + +E++ K+S       P   +G E 
Sbjct: 8   GPVGSGKTALIEALTRALRQKYQLAVITNDIYTQEDAEFLVKNSAL----PPERILGVET 63

Query: 659 GGALTEAVR 667
           GG    A+R
Sbjct: 64  GGCPHTAIR 72


>gnl|CDD|184315 PRK13768, PRK13768, GTPase; Provisional.
          Length = 253

 Score = 28.3 bits (64), Expect = 8.9
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 603 FLGPTGVGKTELVKSLARLL 622
           FLG  G GKT L K+L+  L
Sbjct: 7   FLGTAGSGKTTLTKALSDWL 26


>gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine
           dehydrogenase I; Provisional.
          Length = 819

 Score = 28.2 bits (64), Expect = 9.4
 Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 9/64 (14%)

Query: 385 FLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIEL 444
           +L  K IDL      RV    +++  +LDE     I L   +E L +  + F   RLI L
Sbjct: 490 WLKKKNIDL------RVCGIANSRKMLLDE---HGIDLDNWREELAEAGEPFDLDRLIRL 540

Query: 445 EKEL 448
            KE 
Sbjct: 541 VKEY 544


>gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain.  This is a family of PrkA
           bacterial and archaeal serine kinases approximately 630
           residues long. This is the N-terminal AAA domain.
          Length = 361

 Score = 28.0 bits (63), Expect = 9.5
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622
               G   A+E   N  +    GL++ ++       LGP G GK+ LV+ L R L
Sbjct: 51  HDFFGMEEAIERFVNYFKSAAQGLEERKQ---ILYLLGPVGGGKSSLVECLKRGL 102


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.317    0.136    0.375 

Gapped
Lambda     K      H
   0.267   0.0738    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 14,199,078
Number of extensions: 990255
Number of successful extensions: 3141
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3059
Number of HSP's successfully gapped: 226
Length of query: 853
Length of database: 5,994,473
Length adjustment: 102
Effective length of query: 751
Effective length of database: 3,790,457
Effective search space: 2846633207
Effective search space used: 2846633207
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: 61 (27.3 bits)