RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780829|ref|YP_003065242.1| ATP-dependent protease
ATP-binding subunit [Candidatus Liberibacter asiaticus str. psy62]
         (437 letters)



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

 Score =  708 bits (1830), Expect = 0.0
 Identities = 252/443 (56%), Positives = 331/443 (74%), Gaps = 13/443 (2%)

Query: 6   NFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG 65
             +PREIVSELD+YIIGQ DAKRAVAIALRNRWRR QLP +LRDE+ PKNIL++GPTGVG
Sbjct: 3   ELTPREIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVG 62

Query: 66  KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQ 125
           KT I+RRLA+LA APFIKVE TKFTE+GYVGR+VE IIRDLV++A+ +VRE +R++VRE+
Sbjct: 63  KTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVREK 122

Query: 126 ASINAEERILDALVGK-----------TATSNTREVFRKKLRDGEISDKEIDIEVADTSS 174
           A   AEERILDAL+                S TR+ FRKKLR+GE+ DKEI+IEVA+ + 
Sbjct: 123 AEEAAEERILDALLPPAKNNWGEEEEKEEISATRQKFRKKLREGELDDKEIEIEVAEAAP 182

Query: 175 DISNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVH 234
            +     PG   + I  L ++F  +    +KKK ++ V++    L+ +E+ +LIDM+ + 
Sbjct: 183 MMEIMGPPGMEEMTI-QLQDMFGNLGP-KKKKKRKLKVKEARKILIEEEAAKLIDMEEIK 240

Query: 235 RDSIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTD 294
           +++I+ VE  GIVF+DE DKI AR   +G  VSREGVQRDLLPLVEGS+VSTKYG + TD
Sbjct: 241 QEAIERVEQNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTD 300

Query: 295 HILFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMK 354
           HILFIASGAFHVS+P+DL+PE+QGRFP+RV L +L + DF  ILT+ +++LI QY+ L+ 
Sbjct: 301 HILFIASGAFHVSKPSDLIPELQGRFPIRVELDALTEEDFVRILTEPKASLIKQYQALLA 360

Query: 355 TEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVI 414
           TEG+ L+FT+D+I  +A++A  +N    +IGARRL TVME++LEDISF A D+  +TV I
Sbjct: 361 TEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDMSGETVTI 420

Query: 415 DAEYVRLHIGDFPSETDMYHFIL 437
           DA YV   +GD   + D+  +IL
Sbjct: 421 DAAYVDEKLGDLVKDEDLSRYIL 443


>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 =  512 bits (1319), Expect = e-146
 Identities = 224/441 (50%), Positives = 318/441 (72%), Gaps = 12/441 (2%)

Query: 8   SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67
           +PREIV+ELD+YIIGQ +AK++VAIALRNR+RR QL  +L+DE+ PKNIL++GPTGVGKT
Sbjct: 2   TPREIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKT 61

Query: 68  AISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQAS 127
            I+RRLA+LA APFIKVE TKFTE+GYVGR+VE ++RDL D A+ +V+E   ++VR++A 
Sbjct: 62  EIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAVKLVKEEAIEKVRDRAE 121

Query: 128 INAEERILDALV-----------GKTATSNTREVFRKKLRDGEISDKEIDIEVADTSSDI 176
             AEERI+D L+            +    + RE FRKKLR+GE+ DKEI+I+V+      
Sbjct: 122 ELAEERIVDVLLPPAKNQWGQTEQQQEPESAREAFRKKLREGELDDKEIEIDVSAKMPSG 181

Query: 177 SNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRD 236
                P G     + L  LF  + G  +KKK ++ ++     L+ +E+ +L+D + + ++
Sbjct: 182 IEIMAPPGMEEMTMQLQSLFQNLGGQ-KKKKRKLKIKDAKKALIAEEAAKLVDPEEIKQE 240

Query: 237 SIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHI 296
           +I  VE  GI+F+DE DKI  +   +G  VSREGVQRDLLP+VEGS+V+TKYG + TDHI
Sbjct: 241 AIDAVEQSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHI 300

Query: 297 LFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTE 356
           LFIA+GAF +++P+DL+PE+QGRFP+RV L++L   DF  ILT+ +++LI QYK LMKTE
Sbjct: 301 LFIAAGAFQLAKPSDLIPELQGRFPIRVELQALTTDDFERILTEPKNSLIKQYKALMKTE 360

Query: 357 GIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDA 416
           G+ ++F++++I  +A++A N+N    +IGARRL TV+ER+LEDISF A DL  + + IDA
Sbjct: 361 GVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLEDISFEAPDLSGQNITIDA 420

Query: 417 EYVRLHIGDFPSETDMYHFIL 437
           +YV   +G   ++ D+  FIL
Sbjct: 421 DYVSKKLGALVADEDLSRFIL 441


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

 Score =  121 bits (305), Expect = 4e-28
 Identities = 70/232 (30%), Positives = 112/232 (48%), Gaps = 63/232 (27%)

Query: 245 GIVFLDEFDKIVARDSGNGIG---VSREGVQRDLLPLVEGSSVS-----------TKYGS 290
           GIV++DE DKI AR S N      VS EGVQ+ LL ++EG+  S            ++  
Sbjct: 175 GIVYIDEIDKI-ARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQ 233

Query: 291 INTDHILFIASGAF------------------------------------HVSRPADLL- 313
           ++T +ILFI  GAF                                     V  P DL+ 
Sbjct: 234 VDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQV-EPEDLIK 292

Query: 314 ----PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDA 369
               PE  GR PV   L+ L++     ILT+ ++ L+ QY++L + +G+ L+FT+++++A
Sbjct: 293 FGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEA 352

Query: 370 LADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQE-KTVVIDAEYVR 420
           +A  A+   +     GAR L++++E +L D+ F     ++ + VVI  E V 
Sbjct: 353 IAKKAIERKT-----GARGLRSILEEILLDVMFELPSREDVEKVVITKEVVE 399



 Score =  105 bits (264), Expect = 3e-23
 Identities = 45/105 (42%), Positives = 68/105 (64%), Gaps = 2/105 (1%)

Query: 8   SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRD--ELMPKNILLVGPTGVG 65
           +P+EI + LD+Y+IGQ+ AK+ +++A+ N ++R +      D  EL   NILL+GPTG G
Sbjct: 61  TPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSG 120

Query: 66  KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
           KT +++ LAR+   PF   + T  TE GYVG +VE I+  L+  A
Sbjct: 121 KTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAA 165


>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 =  101 bits (253), Expect = 4e-22
 Identities = 71/229 (31%), Positives = 107/229 (46%), Gaps = 61/229 (26%)

Query: 245 GIVFLDEFDKIVARDSGNGI--GVSREGVQRDLLPLVEGS--SVSTKYG---------SI 291
           GI+++DE DKI  +     I   VS EGVQ+ LL ++EG+  +V  + G          I
Sbjct: 183 GIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQI 242

Query: 292 NTDHILFIASGAF---------------------------------HVSRPADLL----- 313
           +T +ILFI  GAF                                     P DL+     
Sbjct: 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLI 302

Query: 314 PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDALADV 373
           PE  GR PV   L+ L++     ILT  ++ L+ QY+ L K + + LDF E+++ A+A  
Sbjct: 303 PEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKK 362

Query: 374 AVNLNSTVGDIGARRLQTVMERVLEDISF---SASDLQEKTVVIDAEYV 419
           A+   +     GAR L++++E +L D+ F   S  DL++  VVI  E V
Sbjct: 363 ALERKT-----GARGLRSIVEGLLLDVMFDLPSLEDLEK--VVITKETV 404



 Score = 90.6 bits (225), Expect = 7e-19
 Identities = 45/107 (42%), Positives = 67/107 (62%), Gaps = 4/107 (3%)

Query: 8   SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLP----ADLRDELMPKNILLVGPTG 63
           +P+EI + LD Y+IGQ+ AK+ +++A+ N ++R        +D   EL   NILL+GPTG
Sbjct: 67  TPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTG 126

Query: 64  VGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
            GKT +++ LAR+   PF   + T  TE GYVG +VE I+  L+  A
Sbjct: 127 SGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAA 173


>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 = 83.0 bits (206), Expect = 2e-16
 Identities = 40/187 (21%), Positives = 65/187 (34%), Gaps = 60/187 (32%)

Query: 176 ISNFDIPGGASVGILNLSELFSKVMGSGRKKKIR--MSVQKCYPELMRDESDRLIDMDTV 233
           I +F   G   VG   L++  ++++    +  IR  MS      E M    +  +     
Sbjct: 3   IGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMS------EYM---EEHSVSRLIG 53

Query: 234 HRDSIQMVEN------------YGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEG 281
                   E             Y IV +DE +K               GVQ DLL ++EG
Sbjct: 54  APPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHP------------GVQNDLLQILEG 101

Query: 282 SSVSTKYGS-INTDHILFIASGAFHVSRPAD------------------------LLPEI 316
            +++ K G  ++  + LFI +G F   + +D                         +PE 
Sbjct: 102 GTLTDKQGRKVDFRNTLFIMTGNFGSEKISDASRLGKSPDYELLKELVMDLLKKGFIPEF 161

Query: 317 QGRFPVR 323
            GR P+ 
Sbjct: 162 LGRLPII 168



 Score = 40.3 bits (95), Expect = 0.001
 Identities = 14/40 (35%), Positives = 26/40 (65%), Gaps = 3/40 (7%)

Query: 55 NILLVGPTGVGKTAISRRLARLAG---APFIKVEVTKFTE 91
          + L +GPTGVGKT +++ LA L        I+++++++ E
Sbjct: 5  SFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME 44


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

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 18/94 (19%)

Query: 15  ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPK-NILLVGPTGVGKTAISRRL 73
            L   I GQ +A  ++  +++ R R     A L +   P  + L  GPTGVGKT ++++L
Sbjct: 451 NLKAKIFGQDEAIDSLVSSIK-RSR-----AGLGNPNKPVGSFLFTGPTGVGKTELAKQL 504

Query: 74  ARLAGAPFIKVEVTKFTE-----------IGYVG 96
           A   G    + +++++ E            GYVG
Sbjct: 505 AEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVG 538



 Score = 30.8 bits (70), Expect = 0.77
 Identities = 14/22 (63%), Positives = 15/22 (68%)

Query: 55  NILLVGPTGVGKTAISRRLARL 76
           N LLVG  GVGKTAI+  LA  
Sbjct: 205 NPLLVGEPGVGKTAIAEGLALR 226


>gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
           HflB(FtsH) is a pleiotropic protein required for correct
           cell division in bacteria. It has ATP-dependent zinc
           metalloprotease activity. It was formerly designated
           cell division protein FtsH.
          Length = 495

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 7/77 (9%)

Query: 34  LRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93
           L+N  +  +L A +     PK +LLVGP G GKT +++ +A  AG PF  +  + F E+ 
Sbjct: 74  LKNPSKFTKLGAKI-----PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM- 127

Query: 94  YVGRNVEQIIRDLVDVA 110
           +VG    + +RDL + A
Sbjct: 128 FVGVGASR-VRDLFEQA 143


>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
          Length = 184

 Score = 42.2 bits (100), Expect = 3e-04
 Identities = 15/38 (39%), Positives = 22/38 (57%)

Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
             R  L  + ++LVG  G GK+ + RRLA + G PF+
Sbjct: 2  ERARAALGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL 39


>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
          Length = 175

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 51 LMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
          L   NI+L+G  G GK+ I R LA+  G  FI
Sbjct: 2  LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFI 33


>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
          Length = 644

 Score = 40.8 bits (95), Expect = 6e-04
 Identities = 31/94 (32%), Positives = 49/94 (52%), Gaps = 10/94 (10%)

Query: 20  IIGQQDAKRAVAIA---LRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARL 76
           + G  +AK  VA     LR   R Q+L   +     PK +L+VGP G GKT +++ +A  
Sbjct: 154 VAGCDEAKEEVAELVEYLREPSRFQKLGGKI-----PKGVLMVGPPGTGKTLLAKAIAGE 208

Query: 77  AGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110
           A  PF  +  + F E+ +VG    + +RD+ + A
Sbjct: 209 AKVPFFTISGSDFVEM-FVGVGASR-VRDMFEQA 240


>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
           Provisional.
          Length = 389

 Score = 40.6 bits (96), Expect = 7e-04
 Identities = 37/107 (34%), Positives = 54/107 (50%), Gaps = 25/107 (23%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE----VTKFTEIGYVGRNVEQIIRDLVD 108
           PK +LL GP G GKT +++ +A    A FI+V     V KF  IG   R    ++R+L +
Sbjct: 165 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKF--IGEGAR----LVRELFE 218

Query: 109 VAINIVRESRRDEVREQASINAEERILDALVGK---TATSNTREVFR 152
           +A    RE      +  + I  +E  +DA+  K   + TS  REV R
Sbjct: 219 LA----RE------KAPSIIFIDE--IDAIAAKRTDSGTSGDREVQR 253



 Score = 29.0 bits (66), Expect = 2.7
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPL 278
           I+F+DE D I A+ + +G    RE VQR L+ L
Sbjct: 227 IIFIDEIDAIAAKRTDSGTSGDRE-VQRTLMQL 258


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

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 10/89 (11%)

Query: 15  ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73
           EL   +IGQ +A  AV+ A+R R R     A L D   P  + L +GPTGVGKT + + L
Sbjct: 565 ELHHRVIGQNEAVEAVSNAIR-RSR-----AGLSDPNRPIGSFLFLGPTGVGKTELCKAL 618

Query: 74  ARL---AGAPFIKVEVTKFTEIGYVGRNV 99
           A     +    +++++++F E   V R V
Sbjct: 619 ANFMFDSDDAMVRIDMSEFMEKHSVSRLV 647


>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 = 40.3 bits (95), Expect = 0.001
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 7/61 (11%)

Query: 15  ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73
            L   ++GQ +A  AV+ A+R R R     A L D   P  + L +GPTGVGKT +++ L
Sbjct: 562 VLHERVVGQDEAVEAVSDAIR-RSR-----AGLSDPNRPIGSFLFLGPTGVGKTELAKAL 615

Query: 74  A 74
           A
Sbjct: 616 A 616



 Score = 27.2 bits (61), Expect = 9.2
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 55  NILLVGPTGVGKTAISRRLAR 75
           N +L+G  GVGKTAI   LA+
Sbjct: 196 NPVLIGEPGVGKTAIVEGLAQ 216


>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 = 39.5 bits (92), Expect = 0.002
 Identities = 38/138 (27%), Positives = 64/138 (46%), Gaps = 21/138 (15%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE----VTKFTEIGYVGRNVEQIIRDLVD 108
           PK +LL GP G GKT +++ +A  AGA FI +     ++K+   G     + +I ++  +
Sbjct: 212 PKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKY--YGESEERLREIFKEAEE 269

Query: 109 VAINIVRESRRDEV---REQASINAEERI-------LDALVGK-----TATSNTREVFRK 153
            A +I+     D +   RE+ +   E+R+       +D L G+        +N  +    
Sbjct: 270 NAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

Query: 154 KLRDGEISDKEIDIEVAD 171
            LR     D+EI I V D
Sbjct: 330 ALRRPGRFDREIVIRVPD 347



 Score = 34.9 bits (80), Expect = 0.044
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKV 84
           PK +LL GP G GKT +++ +A  +GA FI V
Sbjct: 487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAV 518


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

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 10  REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAI 69
           RE++ +L       +DA R +  AL      +    ++ ++     I LVGPTGVGKT  
Sbjct: 154 RELLEKLPERA-DAEDAWRWLREALEKMLPVKPEEDEILEQ--GGVIALVGPTGVGKTTT 210

Query: 70  SRRLARLAG 78
              LA+LA 
Sbjct: 211 ---LAKLAA 216


>gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
          transferase; Reviewed.
          Length = 307

 Score = 39.0 bits (92), Expect = 0.003
 Identities = 13/24 (54%), Positives = 18/24 (75%)

Query: 52 MPKNILLVGPTGVGKTAISRRLAR 75
           PK I++VGPT  GKTA++  LA+
Sbjct: 3  KPKVIVIVGPTASGKTALAIELAK 26


>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 = 38.5 bits (89), Expect = 0.003
 Identities = 16/34 (47%), Positives = 20/34 (58%)

Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
           + IL+VGP G GKT ++R LAR  G P   V  
Sbjct: 2  GEVILIVGPPGSGKTTLARALARELGPPGGGVIY 35


>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 = 38.4 bits (90), Expect = 0.003
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 55  NILLVGPTGVGKTAISRRLA-RLAGAPFIKVEVTKFTEIGYV--GRNVEQIIRDLVD-VA 110
            +LLVGP G GK+ ++ RLA  L+  P   V++T+ T    +   RN+       VD   
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60

Query: 111 INIVRESR 118
           +   RE  
Sbjct: 61  VRAAREGE 68


>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein.  The N-terminal
           end matches very strongly a pfam Mg_chelatase domain.
          Length = 499

 Score = 37.5 bits (87), Expect = 0.007
 Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 16/54 (29%)

Query: 20  IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73
           I GQQ AKRA+ IA                     N+LL GP G GKT ++ RL
Sbjct: 194 IKGQQHAKRALEIAAAGG----------------HNLLLFGPPGSGKTMLASRL 231


>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 = 37.3 bits (87), Expect = 0.009
 Identities = 13/40 (32%), Positives = 24/40 (60%)

Query: 47  LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
           LR ++    + LVGP GVGKT++ + +A+     F++  +
Sbjct: 341 LRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSL 380


>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 = 36.8 bits (86), Expect = 0.010
 Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 9/54 (16%)

Query: 16  LDRYIIGQQDAKRAVAIALRN-RWRRQQLPADLRDELMPKNI-LLVGPTGVGKT 67
           L   +IGQ  A  A+A  +R  R       A L D   P  + LLVGP+GVGKT
Sbjct: 564 LAERVIGQDHALEAIAERIRTAR-------AGLEDPRKPLGVFLLVGPSGVGKT 610



 Score = 27.6 bits (62), Expect = 7.3
 Identities = 11/21 (52%), Positives = 13/21 (61%)

Query: 55  NILLVGPTGVGKTAISRRLAR 75
           N +L G  GVGKTA+   LA 
Sbjct: 210 NPILTGEAGVGKTAVVEGLAL 230


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

 Score = 36.8 bits (86), Expect = 0.011
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 10/71 (14%)

Query: 10  REIVSEL-DRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNIL-LVGPTGVGKT 67
            +++  L +     ++ A R +   L N      +P  + D L    ++ LVGPTGVGKT
Sbjct: 181 EKLLKLLLEHMPPRERTAWRYLLELLAN-----MIPVRVEDILKQGGVVALVGPTGVGKT 235

Query: 68  AISRRLARLAG 78
                LA+LA 
Sbjct: 236 TT---LAKLAA 243


>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family.  Many
           proteins may score above the trusted cutoff because an
           internal.
          Length = 364

 Score = 36.3 bits (84), Expect = 0.018
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIR 104
           PK +LL GP G GKT +++ +A    A FI+V  ++     IG   R V +I  
Sbjct: 156 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFE 209



 Score = 28.2 bits (63), Expect = 4.3
 Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLV 279
           I+F+DE D I A+ + +G    RE VQR L+ L+
Sbjct: 218 IIFIDEIDAIAAKRTDSGTSGDRE-VQRTLMQLL 250


>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
          Length = 171

 Score = 36.2 bits (84), Expect = 0.018
 Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKV--EVTKFTE 91
          KNI+L+G  G GKT + +R+A      FI    E+ K T 
Sbjct: 2  KNIVLIGFMGTGKTTVGKRVATTLSFGFIDTDKEIEKMTG 41


>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 = 36.1 bits (84), Expect = 0.019
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 13/75 (17%)

Query: 53  PKNILLVGPTGVGKTAISR----RLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108
           P N+ + G TG GKTA+++     L   A          +   +  V  N  QI+  L  
Sbjct: 40  PSNVFIYGKTGTGKTAVTKYVMKELEEAAE--------DRDVRVVTVYVNC-QILDTLYQ 90

Query: 109 VAINIVRESRRDEVR 123
           V + +  + R     
Sbjct: 91  VLVELANQLRGSGEE 105


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

 Score = 35.8 bits (82), Expect = 0.020
 Identities = 17/30 (56%), Positives = 22/30 (73%)

Query: 47  LRDELMPKNILLVGPTGVGKTAISRRLARL 76
           L+   + KNI+L GP GVGKT ++RRLA L
Sbjct: 188 LKRLTIKKNIILQGPPGVGKTFVARRLAYL 217


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

 Score = 35.5 bits (82), Expect = 0.024
 Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 9/87 (10%)

Query: 21  IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAP 80
           I +Q+ + AV + L      +Q+  D      P+ +LL GP G GKT +++ +A    A 
Sbjct: 152 IQKQEIREAVELPLTCPELYEQIGID-----PPRGVLLYGPPGTGKTMLAKAVAHHTTAT 206

Query: 81  FIKVEVTKFTEIGYVG---RNVEQIIR 104
           FI+V  ++F +  Y+G   R V  + R
Sbjct: 207 FIRVVGSEFVQ-KYLGEGPRMVRDVFR 232


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

 Score = 34.8 bits (80), Expect = 0.040
 Identities = 14/41 (34%), Positives = 26/41 (63%)

Query: 57  LLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGR 97
           L  GPTGVGKT ++ +L++  G   ++ +++++ E   V R
Sbjct: 492 LFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSR 532



 Score = 30.6 bits (69), Expect = 0.84
 Identities = 14/20 (70%), Positives = 16/20 (80%)

Query: 55  NILLVGPTGVGKTAISRRLA 74
           N LLVG +GVGKTAI+  LA
Sbjct: 209 NPLLVGESGVGKTAIAEGLA 228


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

 Score = 33.1 bits (77), Expect = 0.13
 Identities = 12/30 (40%), Positives = 19/30 (63%)

Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV 84
          +++L GP G GKT ++R +A    APF  +
Sbjct: 38 SMILWGPPGTGKTTLARIIAGATDAPFEAL 67


>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
          Length = 169

 Score = 33.2 bits (76), Expect = 0.15
 Identities = 14/29 (48%), Positives = 16/29 (55%)

Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFI 82
            I LVG  G GKT + + LAR  G  FI
Sbjct: 2  ARIFLVGYMGAGKTTLGKALARELGLSFI 30


>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
          Length = 259

 Score = 32.8 bits (75), Expect = 0.17
 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 3/36 (8%)

Query: 55  NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90
           NI+L+GP+GVGKT ++  L   A    IK    +FT
Sbjct: 104 NIVLLGPSGVGKTHLAIALGYEAVRAGIK---VRFT 136


>gnl|CDD|179921 PRK05057, aroK, shikimate kinase I; Reviewed.
          Length = 172

 Score = 32.8 bits (75), Expect = 0.20
 Identities = 13/22 (59%), Positives = 17/22 (77%)

Query: 54 KNILLVGPTGVGKTAISRRLAR 75
          +NI LVGP G GK+ I R+LA+
Sbjct: 5  RNIFLVGPMGAGKSTIGRQLAQ 26


>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 = 32.7 bits (75), Expect = 0.21
 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 9/54 (16%)

Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74
          IGQ+  K  + + +          A +R E    ++LL GP G+GKT ++  +A
Sbjct: 7  IGQEKVKEQLQLFIE--------AAKMRQE-ALDHLLLYGPPGLGKTTLAHIIA 51


>gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed.
          Length = 171

 Score = 32.2 bits (74), Expect = 0.27
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI 82
          M + + LVG  G GKT +   LA+  G  F+
Sbjct: 1  MTQPLFLVGARGCGKTTVGMALAQALGYRFV 31


>gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
           Members of this protein family resemble the widely
           distributed ATP-dependent protease La, also called Lon
           and LonA. It resembles even more closely LonB, which is
           a LonA paralog found in genomes if and only if the
           species is capable of endospore formation (as in
           Bacillus subtilis, Clostridium tetani, and select other
           members of the Firmicutes) and expressed specifically in
           the forespore compartment. Members of this family are
           restricted to a subset of spore-forming species, and are
           very likely to participate in the program of endospore
           formation. We propose the designation LonC.
          Length = 615

 Score = 32.1 bits (73), Expect = 0.31
 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 6/44 (13%)

Query: 53  PKNILLVGPTGVGKTAISR----RLARLAGAPFIKVEVTKFTEI 92
           P++I+L GP GVGKT  +R       +L   PF   E   F E+
Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPF--AEDAPFVEV 216


>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
          Length = 420

 Score = 31.8 bits (72), Expect = 0.33
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 13/78 (16%)

Query: 3   LTFNFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLR----DELMPKNIL- 57
           L+  FSP      L R+++ +  A R    +L+       L  +LR    DE++ +  + 
Sbjct: 142 LSAGFSP-----LLSRHLLEKLPADRDFEQSLK--KTISLLTLNLRTIGGDEIIEQGGVY 194

Query: 58  -LVGPTGVGKTAISRRLA 74
            L+GPTGVGKT  + +LA
Sbjct: 195 ALIGPTGVGKTTTTAKLA 212


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

 Score = 32.1 bits (73), Expect = 0.33
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 14/75 (18%)

Query: 7   FSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADL-----RDELMPKN--ILLV 59
           FS +   + L+R  +G  D   A+A      W R +L   L      D L+ +   + LV
Sbjct: 139 FSGQLARALLERLPVGY-DRPAAMA------WIRNELATHLPVLRDEDALLAQGGVLALV 191

Query: 60  GPTGVGKTAISRRLA 74
           GPTGVGKT  + +LA
Sbjct: 192 GPTGVGKTTTTAKLA 206


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

 Score = 31.9 bits (72), Expect = 0.35
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 16/57 (28%)

Query: 20  IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARL 76
           +IGQ+  KR + I                      N+LL+GP G GKT ++ R+  L
Sbjct: 193 VIGQEQGKRGLEITAAG----------------GHNLLLIGPPGTGKTMLASRINGL 233


>gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
          glucokinase family.  This model represents a subfamily
          of proteins that includes thermoresistant and
          thermosensitve isozymes of gluconate kinase
          (gluconokinase) in E. coli and other related proteins;
          members of this family are often named by similarity to
          the thermostable isozyme. These proteins show homology
          to shikimate kinases and adenylate kinases but not to
          gluconate kinases from the FGGY family of carbohydrate
          kinases.
          Length = 163

 Score = 32.0 bits (73), Expect = 0.36
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82
           +L+G  G GK+ I+  LA   GA FI
Sbjct: 1  FVLMGVAGSGKSTIASALAHRLGAKFI 27


>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 388

 Score = 31.8 bits (72), Expect = 0.38
 Identities = 15/30 (50%), Positives = 19/30 (63%)

Query: 49  DELMPKNILLVGPTGVGKTAISRRLARLAG 78
           D L  +  +LVGPTGVGKT    +LA + G
Sbjct: 170 DNLKKRVFILVGPTGVGKTTTIAKLAAIYG 199


>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
          Length = 394

 Score = 31.4 bits (72), Expect = 0.43
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86
          P N+L+ GP G GKT   +++        +KV  
Sbjct: 55 PLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVY 88


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

 Score = 31.5 bits (72), Expect = 0.46
 Identities = 11/17 (64%), Positives = 14/17 (82%)

Query: 58  LVGPTGVGKTAISRRLA 74
           L+GPTGVGKT  + +LA
Sbjct: 261 LMGPTGVGKTTTTAKLA 277


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

 Score = 31.4 bits (71), Expect = 0.50
 Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 56  ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT----EIGYVGRNVEQIIRDLVD 108
           +L  GP GVGKT  +R LAR    P        F+    E+     N    IR+L+D
Sbjct: 42  LLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLID 98


>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
          Length = 328

 Score = 31.2 bits (71), Expect = 0.52
 Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 3/34 (8%)

Query: 41 QQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74
          QQL    R    P   LL GP G+GK A++ RLA
Sbjct: 13 QQLAGRGR---HPHAYLLHGPAGIGKRALAERLA 43


>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
          Length = 325

 Score = 31.4 bits (71), Expect = 0.54
 Identities = 11/26 (42%), Positives = 14/26 (53%)

Query: 50 ELMPKNILLVGPTGVGKTAISRRLAR 75
          E  P   L  G  G+GKTA +R  A+
Sbjct: 18 ERRPNAWLFAGKKGIGKTAFARFAAQ 43


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

 Score = 31.3 bits (72), Expect = 0.55
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 40  RQQLPADLRDELMPKN-ILLVGPTGVGKTAISRRLARLAGAPFI 82
           R+ +   L +       ++L G TG GKT + + LA  AGA  +
Sbjct: 127 RRFVIDTLEEAPAQFPLVVLGGNTGSGKTELLQALAN-AGAQVL 169


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

 Score = 31.1 bits (71), Expect = 0.61
 Identities = 13/27 (48%), Positives = 16/27 (59%)

Query: 49 DELMPKNILLVGPTGVGKTAISRRLAR 75
          D     ++L+ GP G GKTA  R LAR
Sbjct: 32 DSPNLPHLLVQGPPGSGKTAAVRALAR 58


>gnl|CDD|180779 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
          Length = 342

 Score = 30.9 bits (70), Expect = 0.61
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 4/38 (10%)

Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          W R Q    LR  L P  +LL G  G+GK   ++ LA+
Sbjct: 10 WNRLQ---ALRARL-PHALLLHGQAGIGKLDFAQHLAQ 43


>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 = 30.9 bits (70), Expect = 0.62
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 26/86 (30%)

Query: 20  IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLA-- 77
           IIGQ++  +A+  AL         P        P+++++ GP GVGKTA +R +   A  
Sbjct: 67  IIGQEEGIKALKAALCG-------PN-------PQHVIIYGPPGVGKTAAARLVLEEAKK 112

Query: 78  --------GAPFIKVEVT--KFTEIG 93
                   GA F++++ T  +F E G
Sbjct: 113 NPASPFKEGAAFVEIDATTARFDERG 138


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

 Score = 30.7 bits (69), Expect = 0.78
 Identities = 11/27 (40%), Positives = 20/27 (74%)

Query: 58  LVGPTGVGKTAISRRLARLAGAPFIKV 84
           LVGP GVGKT++ + +A+  G  ++++
Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRM 380


>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
          Reviewed.
          Length = 712

 Score = 30.5 bits (69), Expect = 0.80
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 60 GPTGVGKTAISRRLARLAGAPFI 82
          GP GVGK+++SR LA+  G  ++
Sbjct: 8  GPAGVGKSSVSRALAQYLGYAYL 30


>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
           protein; Provisional.
          Length = 438

 Score = 30.5 bits (69), Expect = 0.86
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKV 84
           PK ++L GP G GKT +++ +A    A F++V
Sbjct: 217 PKGVILYGPPGTGKTLLAKAVANETSATFLRV 248


>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 = 30.7 bits (70), Expect = 0.88
 Identities = 13/36 (36%), Positives = 17/36 (47%)

Query: 40 RQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
           QQL   L    +    L  GP GVGK  ++  LA+
Sbjct: 1  YQQLKRALEKGRLAHAYLFAGPEGVGKELLALALAK 36


>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 = 30.3 bits (69), Expect = 0.92
 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)

Query: 56  ILLVGPTGVGKTAISRRLARLAGAPFIKVE 85
           I+L G TG GKT +   LA  AGA  + +E
Sbjct: 130 IVLGGMTGSGKTELLHALAN-AGAQVLDLE 158


>gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA).  Catalyzes
          the first step in the modification of an adenosine near
          the anticodon to 2-methylthio-N6-isopentyladenosine.
          Length = 287

 Score = 30.4 bits (69), Expect = 0.94
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVE 85
          I ++GPT VGK+ ++ +LA+   A  I V+
Sbjct: 2  IFIMGPTAVGKSQLAIQLAKKLNAEIISVD 31


>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
          Length = 327

 Score = 30.4 bits (69), Expect = 0.97
 Identities = 11/27 (40%), Positives = 14/27 (51%)

Query: 58 LVGPTGVGKTAISRRLARLAGAPFIKV 84
          + G +G GKT   R LA L G   + V
Sbjct: 13 VAGDSGCGKTTFLRGLADLLGEELVTV 39


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

 Score = 30.3 bits (69), Expect = 1.00
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 10/56 (17%)

Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          ++G + AK  +       W + +           K +LL GP GVGKT+++  LA 
Sbjct: 16 VVGNEKAKEQL-REWIESWLKGK---------PKKALLLYGPPGVGKTSLAHALAN 61


>gnl|CDD|173382 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
          Length = 229

 Score = 30.1 bits (68), Expect = 1.0
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 9/90 (10%)

Query: 53  PKNILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIRDL 106
           P  I+L G  GVGK   +  L++      I +      E+   T I   G+ +++++   
Sbjct: 6   PLKIVLFGAPGVGKGTFAEILSKKENLKHINMGNILREEIKAKTTI---GKEIQKVVTSG 62

Query: 107 VDVAINIVRESRRDEVREQASINAEERILD 136
             V  N+V    +DE+ +      +  ILD
Sbjct: 63  NLVPDNLVIAIVKDEIAKVTDDCFKGFILD 92


>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 = 29.9 bits (68), Expect = 1.4
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 54 KNILLVGPTGVGKTAISRRL 73
          K I+L+G +G GKT +++ L
Sbjct: 2  KKIMLIGRSGCGKTTLTQAL 21


>gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed.
          Length = 352

 Score = 30.0 bits (68), Expect = 1.4
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 28  RAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73
           + + I++      + L   LR+    K  ++ GP+GVGK+++  RL
Sbjct: 151 QPLFISVETGIGLEALLEQLRN----KITVVAGPSGVGKSSLINRL 192


>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 = 29.4 bits (67), Expect = 1.6
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVT 87
          +LL G  G+ KT ++R LAR  G  F +++ T
Sbjct: 2  VLLEGVPGLAKTLLARTLARSLGLDFRRIQFT 33


>gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase.  In the Actinobacteria, as
           shown for Mycobacterium tuberculosis, some proteins are
           modified by ligation between an epsilon-amino group of a
           lysine side chain and the C-terminal carboxylate of the
           ubiquitin-like protein Pup. This modification leads to
           protein degradation by the archaeal-like proteasome
           found in the Actinobacteria. Members of this protein
           family belong to the AAA family of ATPases and tend to
           be clustered with the genes for Pup, the Pup ligase
           PafA, and structural components of the proteasome. This
           protein forms hexameric rings with ATPase activity.
          Length = 512

 Score = 29.7 bits (67), Expect = 1.7
 Identities = 12/22 (54%), Positives = 16/22 (72%)

Query: 53  PKNILLVGPTGVGKTAISRRLA 74
           PK +LL GP G GKT I++ +A
Sbjct: 216 PKGVLLYGPPGCGKTLIAKAVA 237


>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 = 29.3 bits (67), Expect = 2.1
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 5/50 (10%)

Query: 350 KELMKTEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLED 399
           ++ +   GI L+ T+ + D LA+   +        GAR L+  ++R +ED
Sbjct: 18  QKRLAERGITLELTDAAKDWLAEKGYDPEY-----GARPLRRAIQREIED 62


>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 = 29.4 bits (66), Expect = 2.2
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 58 LVGPTGVGKTAISRRLARLAGAPFI 82
          L GP G GKT ++  +AR    P +
Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRPVM 50


>gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
          Provisional.
          Length = 491

 Score = 29.0 bits (65), Expect = 2.4
 Identities = 12/20 (60%), Positives = 17/20 (85%)

Query: 52 MPKNILLVGPTGVGKTAISR 71
          +P++ILLVG +GVGKT  +R
Sbjct: 34 IPQSILLVGASGVGKTTCAR 53


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

 Score = 28.9 bits (66), Expect = 2.5
 Identities = 9/25 (36%), Positives = 17/25 (68%), Gaps = 2/25 (8%)

Query: 51 LMPKNILLV--GPTGVGKTAISRRL 73
          +M + +L+V  GP+G GK+ + + L
Sbjct: 1  MMRRGLLIVLSGPSGAGKSTLVKAL 25


>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 = 29.0 bits (65), Expect = 2.7
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 19/76 (25%)

Query: 4  TFNFSPREIVSELDRYI---IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVG 60
             F   E +   +R I   IGQ++A   +  A + +                +N+LL+G
Sbjct: 1  GIKFETTEEIPVPERLIDQVIGQEEAVEIIKKAAKQK----------------RNVLLIG 44

Query: 61 PTGVGKTAISRRLARL 76
            GVGK+ +++ +A L
Sbjct: 45 EPGVGKSMLAKAMAEL 60


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

 Score = 28.9 bits (65), Expect = 2.7
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFI 82
          +++L GP GVGKT ++R +A    A F 
Sbjct: 54 SLILYGPPGVGKTTLARIIANHTRAHFS 81


>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
           regulator; Reviewed.
          Length = 309

 Score = 28.8 bits (65), Expect = 2.7
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 42  QLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91
            +    R     + I L+G  G GK+ + R LA   G PF  VE+ +  E
Sbjct: 122 GMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPF--VELNREIE 169


>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
          Length = 374

 Score = 28.9 bits (64), Expect = 2.8
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 7/44 (15%)

Query: 38  WRRQQLPADL-----RDELMPKN--ILLVGPTGVGKTAISRRLA 74
           W +  L A+L      D LM +     L+GPTGVGKT  + +LA
Sbjct: 115 WAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAKLA 158


>gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein;
           Provisional.
          Length = 252

 Score = 28.6 bits (64), Expect = 2.9
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 50  ELMPKNIL-LVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108
           +  P  I  L+GP+G GK+ + R + R+     +  EVT    I Y G N+     D VD
Sbjct: 27  DFYPNEITALIGPSGSGKSTLLRSINRMND---LNPEVTITGSIVYNGHNIYSPRTDTVD 83

Query: 109 V 109
           +
Sbjct: 84  L 84


>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
          Length = 773

 Score = 28.7 bits (65), Expect = 3.1
 Identities = 12/17 (70%), Positives = 15/17 (88%)

Query: 54 KNILLVGPTGVGKTAIS 70
          KN L+V PTG+GKTAI+
Sbjct: 30 KNTLVVLPTGLGKTAIA 46


>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 = 28.4 bits (64), Expect = 3.4
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 56  ILLVGPTGVGKTAISRRLARL 76
           + L+GP G GK+++   L R 
Sbjct: 81  LYLLGPVGGGKSSLVECLKRG 101


>gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin.  This family consists of
          several bacterial zeta toxin proteins. Zeta toxin is
          thought to be part of a postregulational killing system
          in bacteria. It relies on antitoxin/toxin systems that
          secure stable inheritance of low and medium copy number
          plasmids during cell division and kill cells that have
          lost the plasmid.
          Length = 191

 Score = 28.4 bits (64), Expect = 3.4
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          +D   +  P  +LL G  G GKT ++R L  
Sbjct: 4  SDKPPQERPVAVLLGGQPGAGKTELARALLE 34


>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 = 28.7 bits (65), Expect = 3.5
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 15/57 (26%)

Query: 20 IIGQQDAKRAVAIALRNRWRRQQL-PADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          +IGQ+     +   L+N  +  ++  A           L  GP G GKT+I+R  A+
Sbjct: 16 VIGQE----HIVQTLKNAIKNGRIAHA----------YLFSGPRGTGKTSIARIFAK 58


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

 Score = 28.6 bits (64), Expect = 3.6
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 15/57 (26%)

Query: 33 ALRNRWRRQQLPAD----------LRDELMPKNI----LLVGPTGVGKTAISRRLAR 75
           L  +WR Q   A+          LR+ +    +    L  GP GVGKT+ +R LA+
Sbjct: 5  VLYRKWRSQTF-AELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAK 60


>gnl|CDD|152439 pfam12004, DUF3498, Domain of unknown function (DUF3498).  This
           presumed domain is functionally uncharacterized. This
           domain is found in eukaryotes. This domain is typically
           between 433 to 538 amino acids in length. This domain is
           found associated with pfam00616, pfam00168. This domain
           has two conserved sequence motifs: DLQ and PLSFQNP.
          Length = 489

 Score = 28.1 bits (62), Expect = 4.0
 Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 3/36 (8%)

Query: 116 ESRRDEVREQASINAEERILDALVGKTAT---SNTR 148
           E ++D    QA ++++++I+DA   + A+   +NTR
Sbjct: 442 ELKKDHADMQAVVDSKQKIIDAQERRIASLDAANTR 477


>gnl|CDD|181814 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
          Length = 488

 Score = 28.4 bits (64), Expect = 4.2
 Identities = 27/81 (33%), Positives = 35/81 (43%), Gaps = 18/81 (22%)

Query: 107 VDVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEID 166
           VD AIN VR++    +   A I  EE  +DA+ G T      EV   KL  G   D+   
Sbjct: 415 VDAAINAVRKA----LSGVADIELEEYHVDAITGGTDALVEVEV---KLSRG---DRV-- 462

Query: 167 IEVADTSSDISNFDIPGGASV 187
           + V    +DI        ASV
Sbjct: 463 VTVRGADADIIM------ASV 477


>gnl|CDD|184809 PRK14738, gmk, guanylate kinase; Provisional.
          Length = 206

 Score = 28.2 bits (63), Expect = 4.3
 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)

Query: 45 ADLRDELMPKNILLV--GPTGVGKTAISRRLARLAGAPF 81
                   K +L+V  GP+GVGK A+  R+ R    PF
Sbjct: 3  NPWLFNKPAKPLLVVISGPSGVGKDAVLARM-RERKLPF 40


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

 Score = 28.2 bits (63), Expect = 4.5
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 13/56 (23%)

Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          ++GQ     A+   L+N     +L             L  GP GVGKT  +R  A+
Sbjct: 19 VVGQ----EALTTTLKNAIATNKLA---------HAYLFCGPRGVGKTTCARIFAK 61


>gnl|CDD|181017 PRK07529, PRK07529, AMP-binding domain protein; Validated.
          Length = 632

 Score = 28.0 bits (63), Expect = 4.5
 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 16/67 (23%)

Query: 119 RDEVREQASINAEERILDAL----VGKT--------ATSNTREVFRKKLRDGEISDKEID 166
           RD + E+A++    RILDAL    VGK         A    R V R  LRD  +  + +D
Sbjct: 532 RDHIAERAAVPKHVRILDALPKTAVGKIFKPALRRDAI---RRVLRAALRDAGVEAEVVD 588

Query: 167 IEVADTS 173
           + V D  
Sbjct: 589 V-VEDGR 594


>gnl|CDD|162762 TIGR02208, lipid_A_msbB, lipid A biosynthesis
           (KDO)2-(lauroyl)-lipid IVA acyltransferase.  This family
           consists of MsbB in E. coli and closely related proteins
           in other species. MsbB is homologous to HtrB (TIGR02207)
           and acts immediately after it in the biosynthesis of
           KDO-2 lipid A (also called Re LPS and Re endotoxin).
           These two enzymes act after creation of KDO-2 lipid IV-A
           by addition of the KDO sugars.
          Length = 305

 Score = 28.2 bits (63), Expect = 4.6
 Identities = 8/34 (23%), Positives = 17/34 (50%)

Query: 196 FSKVMGSGRKKKIRMSVQKCYPELMRDESDRLID 229
           F   +    + + R+++  C+PE    E + +ID
Sbjct: 45  FVGPIAKKPRGRARINLSACFPEKSEAERETIID 78


>gnl|CDD|184589 PRK14248, PRK14248, phosphate ABC transporter ATP-binding protein;
           Provisional.
          Length = 268

 Score = 28.0 bits (62), Expect = 5.1
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 12/62 (19%)

Query: 58  LVGPTGVGKTAISRRLARLAGA-PFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRE 116
           L+GP+G GK+   R + R+    P  + E     EI Y G N+       +D  IN+V  
Sbjct: 52  LIGPSGCGKSTFLRSINRMNDLIPSARSE----GEILYEGLNI-------LDSNINVVNL 100

Query: 117 SR 118
            R
Sbjct: 101 RR 102


>gnl|CDD|178749 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
          Length = 1153

 Score = 27.9 bits (62), Expect = 5.1
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 24/106 (22%)

Query: 60  GPTGVGKTAISRRL-----ARLAGAPFI-KVEVTKFTEIGYVGRNVEQI----------- 102
           G +G+GKT I+R L      +   + FI +  ++K  EI Y   N +             
Sbjct: 214 GSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEI-YSSANPDDYNMKLHLQRAFL 272

Query: 103 --IRDLVDVAINIVRESRRDEVREQASINA----EERILDALVGKT 142
             I D  D+ I  +          +  I      ++ +LDAL G+T
Sbjct: 273 SEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQT 318


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

 Score = 28.0 bits (62), Expect = 5.3
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 57 LLVGPTGVGKTAISRRLAR 75
          +  GP GVGKT I+R LA+
Sbjct: 44 IFFGPRGVGKTTIARILAK 62


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

 Score = 27.8 bits (61), Expect = 5.4
 Identities = 12/19 (63%), Positives = 14/19 (73%)

Query: 57 LLVGPTGVGKTAISRRLAR 75
          LL G  GVGKT I+R LA+
Sbjct: 42 LLTGTRGVGKTTIARILAK 60


>gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase.
          Length = 261

 Score = 27.9 bits (62), Expect = 5.6
 Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)

Query: 53 PKNILLV--GPTGVGKTAISRRLARLAGAPFI 82
           +N+  V  G  GVGK   + RL++L G P I
Sbjct: 27 GRNVNWVFLGCPGVGKGTYASRLSKLLGVPHI 58


>gnl|CDD|183705 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 559

 Score = 27.7 bits (61), Expect = 5.6
 Identities = 12/21 (57%), Positives = 14/21 (66%)

Query: 56  ILLVGPTGVGKTAISRRLARL 76
           I LVGPTG GKT    +LA+ 
Sbjct: 353 IALVGPTGAGKTTTIAKLAQR 373


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

 Score = 27.9 bits (62), Expect = 5.7
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 57 LLVGPTGVGKTAISRRLAR 75
          L  G  GVGKT +SR LA+
Sbjct: 42 LFTGTRGVGKTTLSRILAK 60


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

 Score = 27.8 bits (62), Expect = 5.7
 Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 16/57 (28%)

Query: 20 IIGQQDA-KRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75
          I+G +DA  R   IA              RD  MP N++L GP G GKT     LA 
Sbjct: 15 IVGNEDAVSRLQVIA--------------RDGNMP-NLILSGPPGTGKTTSILALAH 56


>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus.  This family consists of the
          C-terminal region of several eukaryotic and archaeal
          RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
          or TIP49b) proteins. The N-terminal domain contains the
          pfam00004 domain. In zebrafish, the liebeskummer (lik)
          mutation, causes development of hyperplastic embryonic
          hearts. lik encodes Reptin, a component of a
          DNA-stimulated ATPase complex. Beta-catenin and Pontin,
          a DNA-stimulated ATPase that is often part of complexes
          with Reptin, are in the same genetic pathways. The
          Reptin/Pontin ratio serves to regulate heart growth
          during development, at least in part via the
          beta-catenin pathway. TBP-interacting protein 49
          (TIP49) was originally identified as a TBP-binding
          protein, and two related proteins are encoded by
          individual genes, tip49a and b. Although the function
          of this gene family has not been elucidated, they are
          supposed to play a critical role in nuclear events
          because they interact with various kinds of nuclear
          factors and have DNA helicase activities.TIP49a has
          been suggested to act as an autoantigen in some
          patients with autoimmune diseases.
          Length = 395

 Score = 27.7 bits (62), Expect = 6.0
 Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 2/30 (6%)

Query: 54 KNILLVGPTGVGKTAISRRLARLAGA--PF 81
          + +L+ GP G GKTA++  +++  G   PF
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPF 80


>gnl|CDD|177388 PHA02554, 13, neck protein; Provisional.
          Length = 311

 Score = 27.8 bits (62), Expect = 6.1
 Identities = 18/51 (35%), Positives = 21/51 (41%), Gaps = 16/51 (31%)

Query: 66  KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRE 116
           K  I RRL    GAP I VEVT            E  I D +  A+ +  E
Sbjct: 12  KDYILRRL----GAPIINVEVT------------EDQIYDCIQRALELYGE 46


>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
          Length = 329

 Score = 27.6 bits (62), Expect = 6.1
 Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 4/24 (16%)

Query: 54  KNILLVGPTGVGKT----AISRRL 73
           +N+L  G TG GKT     I++ L
Sbjct: 184 ENLLFYGNTGTGKTFLSNCIAKEL 207


>gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
          Length = 365

 Score = 27.7 bits (62), Expect = 6.2
 Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)

Query: 57 LLVGPTGVGKTAISRRLAR--LAGAP 80
          L+ GP G+GK  ++ R+AR  LA  P
Sbjct: 45 LIGGPQGIGKATLAYRMARFLLATPP 70


>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
           Provisional.
          Length = 344

 Score = 27.6 bits (61), Expect = 6.4
 Identities = 11/18 (61%), Positives = 14/18 (77%)

Query: 56  ILLVGPTGVGKTAISRRL 73
           +LL GPTG GKT +S+ L
Sbjct: 165 MLLCGPTGSGKTTMSKTL 182


>gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase.  Members of this family
          are the enzyme guanylate kinase, also called GMP
          kinase. This enzyme transfers a phosphate from ATP to
          GMP, yielding ADP and GDP.
          Length = 180

 Score = 27.4 bits (62), Expect = 7.0
 Identities = 8/18 (44%), Positives = 14/18 (77%)

Query: 56 ILLVGPTGVGKTAISRRL 73
          I++ GP+GVGK+ + + L
Sbjct: 4  IVISGPSGVGKSTLVKAL 21


>gnl|CDD|184728 PRK14530, PRK14530, adenylate kinase; Provisional.
          Length = 215

 Score = 27.4 bits (61), Expect = 7.0
 Identities = 10/24 (41%), Positives = 12/24 (50%)

Query: 51 LMPKNILLVGPTGVGKTAISRRLA 74
          +    ILL+G  G GK   S  LA
Sbjct: 1  MSQPRILLLGAPGAGKGTQSSNLA 24


>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
           protein TraD.  The TraD protein performs an essential
           coupling function in conjugative type IV secretion
           systems. This protein sits at the inner membrane in
           contact with the assembled pilus and its scaffold as
           well as the relaxosome-plasmid DNA complex (through
           TraM).
          Length = 566

 Score = 27.4 bits (61), Expect = 7.0
 Identities = 10/22 (45%), Positives = 15/22 (68%)

Query: 54  KNILLVGPTGVGKTAISRRLAR 75
           ++IL+ G TG GK+   R+L R
Sbjct: 177 QHILIHGTTGSGKSVAIRKLLR 198


>gnl|CDD|183360 PRK11889, flhF, flagellar biosynthesis regulator FlhF; Provisional.
          Length = 436

 Score = 27.3 bits (60), Expect = 7.0
 Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 16/102 (15%)

Query: 54  KNILLVGPTGVGKTAISRRLA-----RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108
           + I L+GPTGVGKT    ++A     +     FI  + ++   +  +   V+ I  +++ 
Sbjct: 242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA 301

Query: 109 VAINIVRESRRDEVREQASIN--AEERILDALVGKTATSNTR 148
           V         RDE     ++    EE  +D ++  TA  N R
Sbjct: 302 V---------RDEAAMTRALTYFKEEARVDYILIDTAGKNYR 334


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

 Score = 27.4 bits (61), Expect = 7.3
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 57 LLVGPTGVGKTAISRRLAR 75
          L  G  GVGKT +SR LA+
Sbjct: 42 LFTGTRGVGKTTVSRILAK 60


>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 = 27.5 bits (61), Expect = 7.4
 Identities = 20/106 (18%), Positives = 39/106 (36%), Gaps = 11/106 (10%)

Query: 54  KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINI 113
           + + +VGPTG GKT +   L R        V      +I   G ++  + R+ +  +I  
Sbjct: 362 QTVAIVGPTGAGKTTLINLLQR--------VYDPTVGQILIDGIDINTVTRESLRKSIAT 413

Query: 114 VRESR---RDEVREQASINAEERILDALVGKTATSNTREVFRKKLR 156
           V +        +RE   +  E    + +      +   +   K+  
Sbjct: 414 VFQDAGLFNRSIRENIRLGREGATDEEVYEAAKAAAAHDFILKRSN 459


>gnl|CDD|162313 TIGR01351, adk, adenylate kinases.  Adenylate kinase (EC 2.7.4.3)
           converts ATP + AMP to ADP + ADP, that is, uses ATP as a
           phosphate donor for AMP. Most members of this family are
           known or believed to be adenylate kinase. However, some
           members accept other nucleotide triphosphates as donors,
           may be unable to use ATP, and may fail to complement
           adenylate kinase mutants. An example of a
           nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
           is a GTP:AMP phosphotransferase. This family is
           designated subfamily rather than equivalog for this
           reason.
          Length = 210

 Score = 27.6 bits (62), Expect = 7.5
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 13/72 (18%)

Query: 55  NILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIR--DL 106
            ++L+GP G GK   ++R+A   G P I        E+   T +   G+  ++ +   +L
Sbjct: 1   RLVLLGPPGSGKGTQAKRIAEKYGLPHISTGDLLRAEIKAGTPL---GKKAKEYMEKGEL 57

Query: 107 V--DVAINIVRE 116
           V  ++   +V+E
Sbjct: 58  VPDEIVNQLVKE 69


>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
           AtoC; Provisional.
          Length = 457

 Score = 27.5 bits (61), Expect = 7.6
 Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 3/33 (9%)

Query: 55  NILLVGPTGVGKTAISRRL---ARLAGAPFIKV 84
           ++L+ G +G GK  I+R +   +R A  PFIKV
Sbjct: 168 SVLISGESGTGKELIARAIHYNSRRAKGPFIKV 200


>gnl|CDD|130495 TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type
          II.  Note that the Type I HAD enzymes have not yet been
          fully characterized, but clearly utilize a
          substantially different catalytic mechanism and are
          thus unlikely to be related.
          Length = 198

 Score = 27.3 bits (61), Expect = 7.9
 Identities = 8/29 (27%), Positives = 11/29 (37%)

Query: 24 QDAKRAVAIALRNRWRRQQLPADLRDELM 52
           +       AL   WR++QL       LM
Sbjct: 23 AELYGGRGEALSQLWRQKQLEYSWLRTLM 51


>gnl|CDD|179573 PRK03372, ppnK, inorganic polyphosphate/ATP-NAD kinase;
           Provisional.
          Length = 306

 Score = 27.2 bits (61), Expect = 8.2
 Identities = 13/26 (50%), Positives = 14/26 (53%)

Query: 64  VGKTAISRRLARLAGAPFIKVEVTKF 89
           V + A   RLARL  APF    V KF
Sbjct: 269 VRRGATPVRLARLDSAPFTDRLVRKF 294


>gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
          Length = 248

 Score = 27.2 bits (61), Expect = 8.3
 Identities = 16/30 (53%), Positives = 18/30 (60%), Gaps = 4/30 (13%)

Query: 50 ELMPKNIL-LVGPTGVGKTAISRRLARLAG 78
          E+    IL LVGP G GK   S  LAR+AG
Sbjct: 18 EVRAGEILHLVGPNGAGK---STLLARMAG 44


>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. 
          Length = 201

 Score = 27.1 bits (60), Expect = 8.6
 Identities = 7/16 (43%), Positives = 11/16 (68%)

Query: 54 KNILLVGPTGVGKTAI 69
          ++++L  PTG GKT  
Sbjct: 25 RDVILAAPTGSGKTLA 40


>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
          Length = 251

 Score = 27.4 bits (61), Expect = 8.7
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 40 RQQLPADLRDELMPKNIL-LVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYV 95
          ++++ +D+  EL P  IL L+GP G GK+ + R +  L       ++      IGYV
Sbjct: 16 QRRVLSDVSLELKPGKILTLLGPNGAGKSTLVRVVLGLVAPDEGVIKRNGKLRIGYV 72


>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases.  Rab GTPases are
          implicated in vesicle trafficking.
          Length = 164

 Score = 27.1 bits (61), Expect = 9.1
 Identities = 8/20 (40%), Positives = 14/20 (70%)

Query: 56 ILLVGPTGVGKTAISRRLAR 75
          I+L+G +GVGK+++  R   
Sbjct: 3  IILIGDSGVGKSSLLSRFTD 22


>gnl|CDD|152127 pfam11691, DUF3288, Protein of unknown function (DUF3288).  This
           family of proteins with unknown function appears to be
           restricted to Cyanobacteria.
          Length = 90

 Score = 27.2 bits (61), Expect = 9.6
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 385 GARRLQTVMERVLEDISFSASDLQEKT 411
           GA  LQ  +E+VL+    +  +L E+T
Sbjct: 43  GAEDLQRDLEKVLKLWGLTEEELFERT 69


>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 432

 Score = 27.2 bits (60), Expect = 9.6
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 5/53 (9%)

Query: 54  KNILLVGPTGVGKTAISRRLARLAGAPFIKV--EVTKFTEIGYVGRNVEQIIR 104
           K +  VGPTG GKT     +A+LA   F+ +   V+ +T   Y    +EQ+ R
Sbjct: 224 KVVFFVGPTGSGKTT---SIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKR 273


>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
          Provisional.
          Length = 351

 Score = 27.0 bits (60), Expect = 9.8
 Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 58 LVGPTGVGKTAISRRLARL----AGAPFIKVE-VTK 88
          L+GP+G GKT + R +A L     G  FI  E VT 
Sbjct: 37 LLGPSGCGKTTVLRLVAGLEKPTEGQIFIDGEDVTH 72


  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
   0.319    0.137    0.376 

Gapped
Lambda     K      H
   0.267   0.0662    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,232,501
Number of extensions: 494314
Number of successful extensions: 1646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1625
Number of HSP's successfully gapped: 192
Length of query: 437
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 341
Effective length of database: 3,920,105
Effective search space: 1336755805
Effective search space used: 1336755805
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)