RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780709|ref|YP_003065122.1| cell division protein
[Candidatus Liberibacter asiaticus str. psy62]
         (321 letters)



>gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein
           FtsY; Provisional.
          Length = 318

 Score =  399 bits (1027), Expect = e-112
 Identities = 145/303 (47%), Positives = 206/303 (67%), Gaps = 2/303 (0%)

Query: 5   KVASESLSWIRKLTKGFASTSLKLKEGITDIISSRRLDDGVREELEDLLIRSDIGVAVAQ 64
           K   +   W  +L KG + T     EGI  + + +++D+ + EELE+LLI +D+GV   +
Sbjct: 8   KKKEKKEGWFERLKKGLSKTRENFGEGINGLFAKKKIDEDLLEELEELLIEADVGVETTE 67

Query: 65  KIVEELLTKRYAKDVSVQRVLYDV-SELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVG 123
           +I+EEL  +   K++     L ++  E + ++L P+ KP N     +P VILVVGVNGVG
Sbjct: 68  EIIEELRERVKRKNLKDPEELKELLKEELAEILEPVEKPLN-IEEKKPFVILVVGVNGVG 126

Query: 124 KTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAY 183
           KTT IGKL+ K    G KV+LAAGDTFR+AAI+QL++W +R     +  + G+D A++A+
Sbjct: 127 KTTTIGKLAHKYKAQGKKVLLAAGDTFRAAAIEQLQVWGERVGVPVIAQKEGADPASVAF 186

Query: 184 EAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQ 243
           +A + A+A+ +DVLIIDTAGRLHN + LM  + K+ RV+K+ DP APH VL VLDATTGQ
Sbjct: 187 DAIQAAKARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQ 246

Query: 244 NALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVA 303
           NAL Q + FH   G TG+I+TK+DGTA+GG +  I     IP+ F+GVGEGI+DL+PF A
Sbjct: 247 NALSQAKAFHEAVGLTGIILTKLDGTAKGGVVFAIADELGIPIKFIGVGEGIDDLQPFDA 306

Query: 304 KDF 306
           ++F
Sbjct: 307 EEF 309


>gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY. 
           There is a weak division between FtsY and SRP54; both
           are GTPases. In E.coli, ftsY is an essential gene
           located in an operon with cell division genes ftsE and
           ftsX, but its apparent function is as the signal
           recognition particle docking protein.
          Length = 272

 Score =  287 bits (737), Expect = 2e-78
 Identities = 125/267 (46%), Positives = 180/267 (67%), Gaps = 2/267 (0%)

Query: 41  LDDGVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDVSVQRVLYD-VSELIHKMLMPL 99
            D+   EELE++L+ SD+G  V +KI+E L  +   K V    +L + + E + ++L   
Sbjct: 2   DDEDFFEELEEILLESDVGYEVVEKIIEALKKELKGKKVKDAELLKEILKEYLKEILKET 61

Query: 100 SKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLK 159
                 +  ++P+VIL VGVNGVGKTT I KL+ K+   G  V+LAAGDTFR+AAI+QL+
Sbjct: 62  DLELIVE-ENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLE 120

Query: 160 IWADRTSADFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMI 219
            WA R   D +  + G+D AA+A++A ++A+A+ +DV++IDTAGRL N   LM  + K+ 
Sbjct: 121 EWAKRLGVDVIKQKEGADPAAVAFDAIQKAKARNIDVVLIDTAGRLQNKVNLMDELKKIK 180

Query: 220 RVLKRLDPHAPHSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIV 279
           RV+K++D  AP  VL VLDATTGQNAL Q ++F+   G TG+I+TK+DGTA+GG ++ I 
Sbjct: 181 RVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFNEAVGLTGIILTKLDGTAKGGIILSIA 240

Query: 280 VTHKIPVYFLGVGEGINDLEPFVAKDF 306
              K+P+ F+GVGE I+DL PF A  F
Sbjct: 241 YELKLPIKFIGVGEKIDDLAPFDADWF 267


>gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional.
          Length = 336

 Score =  207 bits (530), Expect = 2e-54
 Identities = 111/295 (37%), Positives = 163/295 (55%), Gaps = 24/295 (8%)

Query: 27  KLKEGITDIISSRRLD----DGVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDVSVQ 82
           K K G  D      +     + + EELE  L+ SD+ + VA++I+E L  K   K V   
Sbjct: 44  KEKPGFFDKAKITEIKEKDIEDLLEELELELLESDVALEVAEEILESLKEKLVGKKV--- 100

Query: 83  RVLYDVSELIHKMLMP-----LSKPFNWDF------SHRPHVILVVGVNGVGKTTVIGKL 131
           +   DV E++   L       LS    +D         +P VI+ VGVNG GKTT I KL
Sbjct: 101 KRGEDVEEIVKNALKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKL 160

Query: 132 SKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQA 191
           +  +   G  V++AAGDTFR+ AI+QL+  A+R     +  + G+D AA+AY+A + A+A
Sbjct: 161 AYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIEHAKA 220

Query: 192 KKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQVEM 251
           + +DV++IDTAGR+H ++ LM  + K++RV K      P  V+ V DA  G +A+ Q   
Sbjct: 221 RGIDVVLIDTAGRMHTDANLMDELKKIVRVTK------PDLVIFVGDALAGNDAVEQARE 274

Query: 252 FHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVAKDF 306
           F+   G  G+I+TK+D  A+GG  + I      P+ FLGVG+G +DL PF    F
Sbjct: 275 FNEAVGIDGVILTKVDADAKGGAALSIAYVIGKPILFLGVGQGYDDLIPFDPDWF 329


>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
           Provisional.
          Length = 437

 Score =  182 bits (464), Expect = 1e-46
 Identities = 99/298 (33%), Positives = 155/298 (52%), Gaps = 25/298 (8%)

Query: 27  KLKEGITDIISSRRLD-DGVREELEDL---LIRSDIGVAVA----QKIVEELLTKRYAKD 78
            L++ +  +    R+D   V+E ++D+   L+++D+ V +     + I E  L +   K 
Sbjct: 4   SLRDALKKLAGKSRIDEKTVKEVVKDIQRALLQADVNVKLVKELSKSIKERALEEEPPKG 63

Query: 79  VSVQ----RVLYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKK 134
           ++ +    +++Y+  EL+   L+            +P  I++VG+ G GKTT   KL++ 
Sbjct: 64  LTPREHVIKIVYE--ELVK--LLGEETEPL-VLPLKPQTIMLVGLQGSGKTTTAAKLARY 118

Query: 135 MSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQAKKV 194
               GLKV L A DT+R AA DQLK  A++    F       DA  +A E  ++   KK 
Sbjct: 119 FKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEKF--KKA 176

Query: 195 DVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQVEMFHA 254
           DV+I+DTAGR      L+  + ++   +K      P  VL V+DAT GQ A  Q + FH 
Sbjct: 177 DVIIVDTAGRHALEEDLIEEMKEIKEAVK------PDEVLLVIDATIGQQAKNQAKAFHE 230

Query: 255 VAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVAKDFSAVITG 312
             G  G+I+TK+DGTA+GGG +  V     P+ F+G GE I+DLE F    F + + G
Sbjct: 231 AVGIGGIIITKLDGTAKGGGALSAVAETGAPIKFIGTGEKIDDLERFDPDRFISRLLG 288


>gnl|CDD|162133 TIGR00959, ffh, signal recognition particle protein.  This model
           represents Ffh (Fifty-Four Homolog), the protein
           component that forms the bacterial (and organellar)
           signal recognition particle together with a 4.5S RNA.
           Ffh is a GTPase homologous to eukaryotic SRP54 and also
           to the GTPase FtsY (TIGR00064) that is the receptor for
           the signal recognition particle.
          Length = 428

 Score =  176 bits (449), Expect = 6e-45
 Identities = 92/294 (31%), Positives = 151/294 (51%), Gaps = 17/294 (5%)

Query: 21  FASTSLKLKEGITDIISSRRLDD-GVREELEDL---LIRSDIGVAVAQKIVEELLTKRYA 76
           F S S +L+     +     + +  ++E L ++   L+ +D+ + V +  ++++  K   
Sbjct: 1   FESLSERLQRIFKKLSGRGTITEKNIKEALREIRLALLEADVNLQVVKDFIKKVKEKALG 60

Query: 77  KDVSV-----QRVLYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
           ++V       Q+ +  V E +  +L   +   N      P VIL+VG+ G GKTT  GKL
Sbjct: 61  QEVLKSLSPGQQFIKIVHEELVAILGGENASLNLA-KKPPTVILMVGLQGSGKTTTCGKL 119

Query: 132 SKKM-SDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQ 190
           +  +    G KV+L A D +R AAI+QLK+   +          G     +A  A + A+
Sbjct: 120 AYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRALEYAK 179

Query: 191 AKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQVE 250
               DV+I+DTAGRL  +  LM  +  +  +L       P  +L V+DA TGQ+A+   +
Sbjct: 180 ENGFDVVIVDTAGRLQIDEELMEELAAIKEILN------PDEILLVVDAMTGQDAVNTAK 233

Query: 251 MFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGINDLEPFVAK 304
            F+   G TG+++TK+DG ARGG  + +      P+ F+GVGE I+DLEPF  +
Sbjct: 234 TFNERLGLTGVVLTKLDGDARGGAALSVRSVTGKPIKFIGVGEKIDDLEPFHPE 287


>gnl|CDD|182793 PRK10867, PRK10867, signal recognition particle protein;
           Provisional.
          Length = 433

 Score =  168 bits (429), Expect = 2e-42
 Identities = 80/193 (41%), Positives = 114/193 (59%), Gaps = 9/193 (4%)

Query: 111 PHVILVVGVNGVGKTTVIGKLSKKMSD-AGLKVMLAAGDTFRSAAIDQLKIWADRTSADF 169
           P VI++VG+ G GKTT  GKL+K +      KV+L A D +R AAI+QLK   ++     
Sbjct: 100 PTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPV 159

Query: 170 VCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHA 229
             S  G D   +A  A ++A+    DV+I+DTAGRLH +  LM  +  +   +       
Sbjct: 160 FPSGDGQDPVDIAKAALEEAKENGYDVVIVDTAGRLHIDEELMDELKAIKAAVN------ 213

Query: 230 PHSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPI-VVTHKIPVYF 288
           P  +L V+DA TGQ+A+   + F+   G TG+I+TK+DG ARGG  + I  VT K P+ F
Sbjct: 214 PDEILLVVDAMTGQDAVNTAKAFNEALGLTGVILTKLDGDARGGAALSIRAVTGK-PIKF 272

Query: 289 LGVGEGINDLEPF 301
           +G GE ++DLEPF
Sbjct: 273 IGTGEKLDDLEPF 285


>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
           This model represents examples from the eukaryotic
           cytosol of the signal recognition particle protein
           component, SRP54. This GTP-binding protein is a
           component of the eukaryotic signal recognition particle,
           along with several other protein subunits and a 7S RNA.
           Some species, including Arabidopsis, have several
           closely related forms. The extreme C-terminal region is
           glycine-rich and lower in complexity, poorly conserved
           between species, and excluded from this model.
          Length = 429

 Score =  134 bits (339), Expect = 2e-32
 Identities = 82/279 (29%), Positives = 133/279 (47%), Gaps = 24/279 (8%)

Query: 48  ELEDLLIRSDIGVAVAQKIVE--------ELLTKRYAKDVSVQRVLYDVSELIHKMLMPL 99
           E+   L+ SD+ + + +++ E        E +     K   +Q  ++   EL   ++ P 
Sbjct: 33  EICTALLESDVNIKLVRQLRENIKKAINLEEMASGLNKRKMIQHAVFK--ELC-NLVDPG 89

Query: 100 SKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLK 159
            + F      + +VI+ VG+ G GKTT   KL+      G K  L   DTFR+ A DQLK
Sbjct: 90  VEAFTPK-KGKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTFRAGAFDQLK 148

Query: 160 IWADRTSADFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSIL---MAGIG 216
             A +    F  S   SD   +A E  ++ + +  D++I+DT+GR      L   M  + 
Sbjct: 149 QNATKARIPFYGSYTESDPVKIASEGVEKFKKENFDIIIVDTSGRHKQEDSLFEEMLQVA 208

Query: 217 KMIRVLKRLDPHAPHSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLI 276
           + I+         P +++ V+D + GQ A  Q + F        +I+TK+DG A+GGG +
Sbjct: 209 EAIQ---------PDNIIFVMDGSIGQAAEAQAKAFKDSVDVGSVIITKLDGHAKGGGAL 259

Query: 277 PIVVTHKIPVYFLGVGEGINDLEPFVAKDFSAVITGCLD 315
             V   K P+ F+G GE I+D E F  + F + + G  D
Sbjct: 260 SAVAATKSPIIFIGTGEHIDDFEIFKTQPFISKLLGMGD 298


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

 Score = 90.7 bits (226), Expect = 4e-19
 Identities = 75/274 (27%), Positives = 122/274 (44%), Gaps = 31/274 (11%)

Query: 28  LKEGITDIISSRRLD---DGVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDVSVQRV 84
           LK  + D +S  R          EL   L RS +   +A+K+++ LL     ++ +  R 
Sbjct: 142 LKNLLEDQLSGLRQVERIPPEFAELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRY 201

Query: 85  LYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMS--DAGLKV 142
           L    EL+  M+         D   +  V+ +VG  GVGKTT + KL+ + +      KV
Sbjct: 202 LL---ELLANMI----PVRVEDILKQGGVVALVGPTGVGKTTTLAKLAARYALLYGKKKV 254

Query: 143 MLAAGDTFRSAAIDQLKIWADRTSADF-VCSEIGSDAAALAYEAFKQA--QAKKVDVLII 199
            L   DT+R  A++QLK +A        V  +          +   +A  Q +  DV++I
Sbjct: 255 ALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDP---------KELAKALEQLRDCDVILI 305

Query: 200 DTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQ-VEMFHAVAGT 258
           DTAGR   +  L+  +  +I          P  V  VL ATT    L+   + F  +   
Sbjct: 306 DTAGRSQRDKRLIEELKALIEFSG-----EPIDVYLVLSATTKYEDLKDIYKHFSRL-PL 359

Query: 259 TGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVG 292
            GLI TK+D T+  G ++ +++   +P+ +L  G
Sbjct: 360 DGLIFTKLDETSSLGSILSLLIESGLPISYLTNG 393


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

 Score = 77.0 bits (190), Expect = 6e-15
 Identities = 51/181 (28%), Positives = 83/181 (45%), Gaps = 19/181 (10%)

Query: 28  LKEGITDIISSRRLD--DGVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDVSVQRVL 85
           L+E +  +++       D    +L + L+R+ +   +A++++E+L     A      R L
Sbjct: 116 LRELLERLLAGLAWLQRDPEGAKLLERLLRAGVSPELARELLEKL--PERADAEDAWRWL 173

Query: 86  YDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKK--MSDAGLKVM 143
               E + KML    KP   +   +  VI +VG  GVGKTT + KL+ +  +     KV 
Sbjct: 174 ---REALEKML--PVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVA 228

Query: 144 LAAGDTFRSAAIDQLKIWADRTSADF-VCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTA 202
           L   DT+R  A++QLK +A        V  +      AL     K       D+++IDTA
Sbjct: 229 LITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLRDK-------DLILIDTA 281

Query: 203 G 203
           G
Sbjct: 282 G 282


>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
           Provisional.
          Length = 407

 Score = 60.9 bits (147), Expect = 4e-10
 Identities = 53/197 (26%), Positives = 90/197 (45%), Gaps = 16/197 (8%)

Query: 104 NWDFS-HRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWA 162
           ++D S HR  +I ++G  GVGKTT + KL  ++      V     DTFRS A++Q + +A
Sbjct: 200 SFDLSNHR--IISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYA 257

Query: 163 DRTSADFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVL 222
           D+   + +   + +  A L            VD ++IDT GR +     ++ I     V+
Sbjct: 258 DKLDVELI---VATSPAELEEAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTDVV 314

Query: 223 KRLDPHAPHSVLQVLDATTGQNALRQVEMFHAVAG--TTGLIMTKMDGTARGGGLIPIVV 280
                   H  L     ++G  +   + +   +A     G I+TKMD T R G L  ++ 
Sbjct: 315 --------HPDLTCFTFSSGMKSADVMTILPKLAEIPIDGFIITKMDETTRIGDLYTVMQ 366

Query: 281 THKIPVYFLGVGEGIND 297
              +PV ++  G+ I +
Sbjct: 367 ETNLPVLYMTDGQNITE 383


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

 Score = 60.4 bits (146), Expect = 7e-10
 Identities = 54/187 (28%), Positives = 78/187 (41%), Gaps = 17/187 (9%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMS-DAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVC 171
           V+  VG  G GKTT I KL+ K     G  V L   D +R AAI+QLK +AD     F  
Sbjct: 225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKRYADTMGMPFY- 283

Query: 172 SEIGSDAAALAYEAFKQAQAKKVDVLI-IDTAGRLHNNSILMAGIGKMIRVLKRLDPHAP 230
                       + FK+  A+    LI IDTAG  H N   +  +          D    
Sbjct: 284 -------PVKDIKKFKETLARDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKD---- 332

Query: 231 HSV--LQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYF 288
            SV  L VL +T+  +    V   +       +++TK+D     G  + +  T+     +
Sbjct: 333 -SVENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTKLDEADFLGSFLELADTYSKSFTY 391

Query: 289 LGVGEGI 295
           L VG+ +
Sbjct: 392 LSVGQEV 398


>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 = 59.7 bits (144), Expect = 1e-09
 Identities = 32/146 (21%), Positives = 53/146 (36%), Gaps = 8/146 (5%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADF 169
              VIL+VG  G GKTT+   L++++   G  V+   G+      +DQL +         
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLL------IIV 54

Query: 170 VCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHA 229
              +           A   A+  K DVLI+D    L +       +  ++  L+ L    
Sbjct: 55  GGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLL--LLEELRLLLLLK 112

Query: 230 PHSVLQVLDATTGQNALRQVEMFHAV 255
               L V+  T  +  L    +    
Sbjct: 113 SEKNLTVILTTNDEKDLGPALLRRRF 138


>gnl|CDD|75717 PRK06731, flhF, flagellar biosynthesis regulator FlhF; Validated.
          Length = 270

 Score = 57.1 bits (137), Expect = 6e-09
 Identities = 54/236 (22%), Positives = 101/236 (42%), Gaps = 13/236 (5%)

Query: 64  QKIVEELLTKRYAKDVSV--QRVLYDVSELIHKMLMPLSKPFNWD--FSHRPHVILVVGV 119
           Q  VE+     YA+ + V  +       E+I  +L  +S  FN +  F      I ++G 
Sbjct: 24  QNDVEQYFIHAYAEKLKVKFENATMITEEVIEYILEDMSSHFNTENVFEKEVQTIALIGP 83

Query: 120 NGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAA 179
            GVGKTT + K++ +       V     D  R   + QL+ +      + +      D A
Sbjct: 84  TGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVR---DEA 140

Query: 180 ALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDA 239
           A+        +  +VD ++IDTAG+ +  S     + +MI  + +++P   +  L +  +
Sbjct: 141 AMTRALTYFKEEARVDYILIDTAGKNYRAS---ETVEEMIETMGQVEPD--YICLTLSAS 195

Query: 240 TTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGI 295
              ++ +  +  F  +    G++ TK D TA  G L+ I      P+  +  G+ +
Sbjct: 196 MKSKDMIEIITNFKDIH-IDGIVFTKFDETASSGELLKIPAVSSAPIVLMTDGQDV 250


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

 Score = 57.0 bits (137), Expect = 6e-09
 Identities = 56/239 (23%), Positives = 101/239 (42%), Gaps = 18/239 (7%)

Query: 64  QKIVEELLTKRYAKDVSVQ---RVLYDVSELIHKMLMPLSKPFNWD--FSHRPHVILVVG 118
           Q  VE+     YA+ + V+     +    E+I  +L  +   FN +  F      I ++G
Sbjct: 189 QNDVEQYFIHAYAEKLKVKFENATMITEEEVIEYILEDMRSHFNTENVFEKEVQTIALIG 248

Query: 119 VNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDA 178
             GVGKTT + K++ +       V     D  R   + QL+ +      + +      D 
Sbjct: 249 PTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVR---DE 305

Query: 179 AAL--AYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQV 236
           AA+  A   FK  +  +VD ++IDTAG+ +  S     + +MI  + +++   P  +   
Sbjct: 306 AAMTRALTYFK--EEARVDYILIDTAGKNYRAS---ETVEEMIETMGQVE---PDYICLT 357

Query: 237 LDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEGI 295
           L A+     + ++          G++ TK D TA  G L+ I      P+  +  G+ +
Sbjct: 358 LSASMKSKDMIEIITNFKDIHIDGIVFTKFDETASSGELLKIPAVSSAPIVLMTDGQDV 416


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

 Score = 56.3 bits (136), Expect = 1e-08
 Identities = 50/193 (25%), Positives = 88/193 (45%), Gaps = 31/193 (16%)

Query: 113 VILVVGVNGVGKTTVIGKLSKK--MSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFV 170
           V+ +VG  GVGKTT   KL+ +    +   ++ L   D+FR  A++QL+I+        V
Sbjct: 187 VLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILG---V 243

Query: 171 CSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAG------RLHNNSILMAGIGK-MIRVLK 223
                 DAA L + A      K +  ++IDT G       +     ++ G+G+ + R+L 
Sbjct: 244 PVHAVKDAADLRF-ALAALGDKHL--VLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLL- 299

Query: 224 RLDPHAPHSVLQVLDATTGQNALRQV--EMFHAVAG-TTGLIMTKMDGTARGGGLIPIVV 280
                       +L+A +  + L +V     H       G I+TK+D     G  +  V+
Sbjct: 300 ------------LLNAASHGDTLNEVVHAYRHGAGEDVDGCIITKLDEATHLGPALDTVI 347

Query: 281 THKIPVYFLGVGE 293
            H++PV+++  G+
Sbjct: 348 RHRLPVHYVSTGQ 360


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

 Score = 56.3 bits (135), Expect = 1e-08
 Identities = 51/197 (25%), Positives = 90/197 (45%), Gaps = 23/197 (11%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKK--MSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSA 167
           R  V  ++G  GVGKTT   KL+ +  M     KV L   D++R    +QL+I+      
Sbjct: 136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGV 195

Query: 168 DFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDP 227
                + G D           A+ +   +++IDT G    +      +   I +L   D 
Sbjct: 196 PVHAVKDGGDLQ------LALAELRNKHMVLIDTIGMSQRDRT----VSDQIAMLHGAD- 244

Query: 228 HAPHSVLQVLDATTGQNALRQV-EMFHAVAGT--------TGLIMTKMDGTARGGGLIPI 278
             P   L +L+AT+  + L +V + + + AG          G I+TK+D  +  GG++  
Sbjct: 245 -TPVQRLLLLNATSHGDTLNEVVQAYRSAAGQPKAALPDLAGCILTKLDEASNLGGVLDT 303

Query: 279 VVTHKIPVYFLGVGEGI 295
           V+ +K+PV+++  G+ +
Sbjct: 304 VIRYKLPVHYVSTGQKV 320


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

 Score = 53.8 bits (129), Expect = 6e-08
 Identities = 53/187 (28%), Positives = 91/187 (48%), Gaps = 15/187 (8%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSD--AGLKVMLAAGDTFRSAAIDQLKIWADRTSADFV 170
           VI +VG  G GKTT I KL+++ +   A   V L   DT R    +QL  +  +      
Sbjct: 352 VIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLG--IA 409

Query: 171 CSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAP 230
             E  S  + L  +  ++ +  K+  ++IDTAG    +  L A +   +R  +++     
Sbjct: 410 VHEADSAESLL--DLLERLRDYKL--VLIDTAGMGQRDRALAAQL-NWLRAARQV----- 459

Query: 231 HSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLG 290
            + L VL A    + L +V    A A   G+++TK+D T R G  + +VV H++P+ ++ 
Sbjct: 460 -TSLLVLPANAHFSDLDEVVRRFAHAKPQGVVLTKLDETGRFGSALSVVVDHQMPITWVT 518

Query: 291 VGEGIND 297
            G+ + D
Sbjct: 519 DGQRVPD 525


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

 Score = 50.3 bits (120), Expect = 6e-07
 Identities = 64/301 (21%), Positives = 124/301 (41%), Gaps = 33/301 (10%)

Query: 4   QKVASESLSWIRKLTKGFASTSLKLKEGITDIISSRRLDDGVREELEDLLIRSDIGVAVA 63
           Q +  E  S I  + K   S   +L     +I      +     ++ED+L  +D   +  
Sbjct: 75  QSIKKEENSSIEDVLKEVKSLKNELAHKKEEI------NHPTILKIEDILRENDFSESYI 128

Query: 64  QKIVEELLTKRYAKDVS-VQRVLYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGV 122
           + I E +  +    D+    +V   V   I K +   S     +   +  V ++VG  GV
Sbjct: 129 KDINEFIKKEFSLSDLDDYDKVRDSVIIYIAKTIK-CSGSIIDNL--KKRVFILVGPTGV 185

Query: 123 GKTTVIGKLSKKMS----DAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDA 178
           GKTT I KL+        D  L + +   D +R  A  Q++ + D         E     
Sbjct: 186 GKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIE----- 240

Query: 179 AALAYEAFKQ--AQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQV 236
              +++  K+   Q+K  D++++DT G+   + + +A + +++    R            
Sbjct: 241 ---SFKDLKEEITQSKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGR-----DAEFHLA 292

Query: 237 LDATTGQNALRQVEMFHAVA--GTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGEG 294
           + +TT  + ++  E+FH  +      +I TK+D T   G LI ++   +  V ++  G+ 
Sbjct: 293 VSSTTKTSDVK--EIFHQFSPFSYKTVIFTKLDETTCVGNLISLIYEMRKEVSYVTDGQI 350

Query: 295 I 295
           +
Sbjct: 351 V 351


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

 Score = 43.4 bits (102), Expect = 8e-05
 Identities = 46/183 (25%), Positives = 82/183 (44%), Gaps = 14/183 (7%)

Query: 113 VILVVGVNGVGKTTVIGKLSKK--MSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFV 170
           V  ++G  GVGKTT   KL+ +  +     KV L   D++R    +QL+I+  +     V
Sbjct: 193 VYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYG-KLLGVSV 251

Query: 171 CSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAP 230
            S        L     +        +++IDT G    + +L     + I +L +      
Sbjct: 252 RSIKDIADLQLMLHELRGKH-----MVLIDTVGMSQRDQML----AEQIAMLSQCGTQVK 302

Query: 231 HSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLG 290
           H  L +L+AT+  + L +V   +   G  G I+TK+D  A  G  +  V+  K+ ++++ 
Sbjct: 303 H--LLLLNATSSGDTLDEVISAYQGHGIHGCIITKVDEAASLGIALDAVIRRKLVLHYVT 360

Query: 291 VGE 293
            G+
Sbjct: 361 NGQ 363


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

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 57/193 (29%), Positives = 89/193 (46%), Gaps = 44/193 (22%)

Query: 117 VGVNGVGKTTVIGKLSKK--MSDAGLKVMLAAGDTFRSAAIDQLKIW---------ADRT 165
           +G  GVGKTT   KL+ +  M     KV L   D++R    +QL+I+         A + 
Sbjct: 262 MGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVK- 320

Query: 166 SADFVCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAG-----RLHNNSILM-AGIGKMI 219
                      DAA L   A  + + K + VLI DT G     R+ +  I M  G G  +
Sbjct: 321 -----------DAADLRL-ALSELRNKHI-VLI-DTIGMSQRDRMVSEQIAMLHGAGAPV 366

Query: 220 RVLKRLDPHAPHSVLQVLDATTGQNALRQVEMFHAVAGTTGLIMTKMDGTARGGGLIPIV 279
              KRL          +L+AT+  + L +V   +   G  G I+TK+D  A  GG + +V
Sbjct: 367 ---KRL---------LLLNATSHGDTLNEVVQAYRGPGLAGCILTKLDEAASLGGALDVV 414

Query: 280 VTHKIPVYFLGVG 292
           + +K+P++++  G
Sbjct: 415 IRYKLPLHYVSNG 427


>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase.  Mutations have
           also been found that do not phosphorylate the
           periplasmic binding proteins, yet still allow transport.
           The ATPase activity of this protein seems to be
           necessary, however.
          Length = 300

 Score = 36.7 bits (85), Expect = 0.008
 Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 21/135 (15%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGD---TFRSAAIDQLKIWADRTS 166
             H + + G  G GK+T++  L  ++   GLKV + A D    F   +I   +    R +
Sbjct: 33  NAHRVGITGTPGAGKSTLLEALGMELRRRGLKVAVIAVDPSSPFTGGSILGDRTRMQRLA 92

Query: 167 AD---FV----CSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAG---------RLHNNSI 210
            D   F+            +    E      A   DV+I++T G          + +  +
Sbjct: 93  TDPGAFIRSMPTRGHLGGLSQATRELILLLDAAGYDVIIVETVGVGQSEVDIANMADTFV 152

Query: 211 L--MAGIGKMIRVLK 223
           +  + G G  ++ +K
Sbjct: 153 VVTIPGTGDDLQGIK 167


>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK).  Important residue
           (active site in E.coli) is residue 100 of the seed
           alignment.
          Length = 184

 Score = 35.9 bits (83), Expect = 0.012
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 109 HRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151
           HR  VI + G++G GK+T+   L KK+   G +V +  GD  R
Sbjct: 16  HRGVVIWLTGLSGSGKSTIANALEKKLESKGYRVYVLDGDNVR 58


>gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional.
          Length = 188

 Score = 34.9 bits (81), Expect = 0.026
 Identities = 13/27 (48%), Positives = 19/27 (70%)

Query: 111 PHVILVVGVNGVGKTTVIGKLSKKMSD 137
             V++V GV GVGKTTV+ K  +K+ +
Sbjct: 2   MKVVVVTGVPGVGKTTVLNKALEKLKE 28


>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
          Length = 446

 Score = 34.3 bits (80), Expect = 0.049
 Identities = 24/92 (26%), Positives = 52/92 (56%), Gaps = 14/92 (15%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSAD---- 168
           V+L+ G  G+GK+T++ +++ +++ AG KV+  +G+   SA+  Q+K+ A+R        
Sbjct: 82  VVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGE--ESAS--QIKLRAERLGLPSDNL 137

Query: 169 FVCSEIGSDAAALAYEAFKQAQAKKVDVLIID 200
           ++ +E   +A           + +K D+++ID
Sbjct: 138 YLLAETNLEA------ILATIEEEKPDLVVID 163


>gnl|CDD|179661 PRK03846, PRK03846, adenylylsulfate kinase; Provisional.
          Length = 198

 Score = 34.1 bits (79), Expect = 0.052
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 109 HRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151
           H+  V+   G++G GK+TV G L + + + G+   L  GD  R
Sbjct: 22  HKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLDGDNVR 64



 Score = 26.8 bits (60), Expect = 6.7
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 128 IGKLSKKMSDAGLKVMLA 145
           +G+++K M DAGL V+ A
Sbjct: 85  VGEVAKLMVDAGLVVLTA 102


>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.  Members
           of this protein are L-seryl-tRNA(Sec) kinase. This
           enzyme is part of a two-step pathway in Eukaryota and
           Archaea for performing selenocysteine biosynthesis by
           changing serine misacylated on selenocysteine-tRNA to
           selenocysteine. This enzyme performs the first step,
           phosphorylation of the OH group of the serine side
           chain. This family represents archaeal proteins with
           this activity.
          Length = 249

 Score = 34.0 bits (78), Expect = 0.056
 Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 4/49 (8%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIW 161
           +I++ G+ GVGK+T   +L+KK+S+  + V++   D  R    +   +W
Sbjct: 1   LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIR----ESFPVW 45


>gnl|CDD|179813 PRK04296, PRK04296, thymidine kinase; Provisional.
          Length = 190

 Score = 33.9 bits (79), Expect = 0.062
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 18/86 (20%)

Query: 123 GKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALA 182
           GK+T + + +    + G+KV++         AID      DR     V S IG    A+ 
Sbjct: 14  GKSTELLQRAYNYEERGMKVLVF------KPAID------DRYGEGKVVSRIGLSREAIP 61

Query: 183 YE------AFKQAQAKKVDVLIIDTA 202
                      + + +K+D ++ID A
Sbjct: 62  VSSDTDIFELIEEEGEKIDCVLIDEA 87


>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC.  This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 1042

 Score = 32.6 bits (74), Expect = 0.15
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 8/67 (11%)

Query: 91  LIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVI--------GKLSKKMSDAGLKV 142
           L  K           DF+    + L+ G  G GKTT++        GKL ++        
Sbjct: 6   LTLKNFGSYKGTHTIDFTALGPIFLICGKTGAGKTTLLDAITYALYGKLPRRSEVIRSLN 65

Query: 143 MLAAGDT 149
            L A  +
Sbjct: 66  SLYAAPS 72


>gnl|CDD|168091 PRK05541, PRK05541, adenylylsulfate kinase; Provisional.
          Length = 176

 Score = 32.3 bits (74), Expect = 0.18
 Identities = 13/46 (28%), Positives = 21/46 (45%)

Query: 106 DFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151
                 +VI + G+ G GKTT+   L +++      V+   GD  R
Sbjct: 2   QMKPNGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDGDELR 47


>gnl|CDD|132060 TIGR03015, pepcterm_ATPase, putative secretion ATPase, PEP-CTERM
           locus subfamily.  Members of this protein are marked as
           probable ATPases by the nucleotide binding P-loop motif
           GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of
           helicases, and extensive homology to ATPases of
           MSHA-type pilus systems and to GspA proteins associated
           with type II protein secretion systems.
          Length = 269

 Score = 32.0 bits (73), Expect = 0.24
 Identities = 37/102 (36%), Positives = 48/102 (47%), Gaps = 10/102 (9%)

Query: 108 SHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSA 167
           S R   IL+ G  G GKTT+I  L K+  D   +V+ A     R  A D L++ A     
Sbjct: 40  SQREGFILITGEVGAGKTTLIRNLLKR-LDQE-RVVAAKLVNTRVDAEDLLRMVAA---- 93

Query: 168 DFVCSEIGSDAAAL--AYEAF--KQAQAKKVDVLIIDTAGRL 205
           DF     G D AAL    E F  +Q  A K  +L++D A  L
Sbjct: 94  DFGLETEGRDKAALLRELEDFLIEQFAAGKRALLVVDEAQNL 135


>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
          Length = 175

 Score = 31.9 bits (73), Expect = 0.24
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151
            +   G++G GKTT+   L++K+ +AG  V +  GD  R
Sbjct: 6   TVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDGDAVR 44


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

 Score = 31.4 bits (72), Expect = 0.28
 Identities = 12/29 (41%), Positives = 20/29 (68%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           I + G  GVGKTT++ K+++ + + G KV
Sbjct: 3   IGITGPPGVGKTTLVLKIAELLKEEGYKV 31


>gnl|CDD|134018 PHA02518, PHA02518, ParA-like protein; Provisional.
          Length = 211

 Score = 31.4 bits (71), Expect = 0.33
 Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 13/87 (14%)

Query: 121 GVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSAD---FVCSEIGSD 177
           G GKTTV   L+  +   G KV+L   D   S+       WA+             +G  
Sbjct: 11  GAGKTTVATNLASWLHADGHKVLLVDLDPQGSST-----DWAEAREEGEPLIPVVRMGKS 65

Query: 178 AAALAYEAFKQAQAKKVDVLIIDTAGR 204
             A   +      A   D +++D A +
Sbjct: 66  IRADLPK-----VASGYDYVVVDGAPQ 87


>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
          Length = 180

 Score = 31.3 bits (72), Expect = 0.37
 Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 4/42 (9%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAA 154
           +I + G  G GKTTV   L++K+   GLK  ++AG+ FR  A
Sbjct: 2   IITISGPPGSGKTTVARLLAEKL---GLK-HVSAGEIFRELA 39


>gnl|CDD|182885 PRK10991, fucI, L-fucose isomerase; Provisional.
          Length = 588

 Score = 31.1 bits (71), Expect = 0.40
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 29 KEGITDIISSRRLDDGVREELEDLLIRSDIGVAVAQKIVEELLTKRYAKDVSVQRVLYD 87
          K GI   I  RR+  GVRE LE+  +  ++  A A  I E L   R+A    V+ V+ D
Sbjct: 6  KIGIRPTIDGRRM--GVRESLEEQTM--NMAKATAALITENL---RHACGEPVECVIAD 57


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

 Score = 31.0 bits (71), Expect = 0.48
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 109 HRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
            RP  +L+ G  G GKTT + K+ +++ +  +KV
Sbjct: 53  SRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKV 86


>gnl|CDD|172962 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
           dinucleotide biosynthesis protein MobA/MobB;
           Provisional.
          Length = 366

 Score = 30.5 bits (69), Expect = 0.53
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 96  LMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           L  L    +   +  P ++ VVG +G GKTT++ KL  ++   G ++
Sbjct: 190 LEQLRAIPDGTTTGAPPLLGVVGYSGTGKTTLLEKLIPELIARGYRI 236


>gnl|CDD|114590 pfam05872, DUF853, Bacterial protein of unknown function (DUF853). 
           This family consists of several bacterial proteins of
           unknown function. One member from Brucella melitensis is
           thought to be an ATPase.
          Length = 504

 Score = 30.5 bits (69), Expect = 0.59
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 115 LVVGVNGVGKTTVIGKLSKKMSDAGLKVMLA 145
           L+ G  G GKT  +  L++  SDAG+ V LA
Sbjct: 25  LIAGATGTGKTVTLQVLAESFSDAGVPVFLA 55


>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase.  Function:
           phosphorylation of DTMP to form DTDP in both de novo and
           salvage pathways of DTTP synthesis. Catalytic activity:
           ATP + thymidine 5'-phosphate = ADP + thymidine
           5'-diphosphate.
          Length = 195

 Score = 30.4 bits (69), Expect = 0.63
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVML 144
           I++ G++G GKTT    L K + + G  V+ 
Sbjct: 6   IVIEGIDGAGKTTQANLLKKLLQENGYDVLF 36


>gnl|CDD|184709 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
           biosynthesis protein MobB/FeS domain-containing protein
           protein; Provisional.
          Length = 229

 Score = 30.3 bits (69), Expect = 0.70
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
            I V+G    GKTT+I K+ K + + G +V
Sbjct: 3   AIGVIGFKDSGKTTLIEKILKNLKERGYRV 32


>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase.  This model
           includes the yeast LYS21 gene which carries out the
           first step of the alpha-aminoadipate (AAA) lysine
           biosynthesis pathway. A related pathway is found in
           Thermus thermophilus. This enzyme is closely related to
           2-isopropylmalate synthase (LeuA) and citramalate
           synthase (CimA), both of which are present in the
           euryarchaeota. Some archaea have a separate homocitrate
           synthase (AksA) which also synthesizes longer
           homocitrate analogs.
          Length = 344

 Score = 30.1 bits (68), Expect = 0.73
 Identities = 36/171 (21%), Positives = 52/171 (30%), Gaps = 58/171 (33%)

Query: 136 SDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQAKKVD 195
             AGL+V  +A DTFRS         AD  S        G D   +A             
Sbjct: 120 KSAGLEVRFSAEDTFRSE-------LADLLSIYETVGVFGVDRVGIA------------- 159

Query: 196 VLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHAPHSVLQVLDATTGQNALRQVEMFHAV 255
               DT G+          + ++IR + R+ P                         HA 
Sbjct: 160 ----DTVGKAA-----PRQVYELIRTVVRVVPGVDIE-------------------LHAH 191

Query: 256 AGTTGLIMTKMDGTARGGGLIPIVVTHKIPVYFLGVGE--GINDLEPFVAK 304
             T   +    +    G  ++   V        LG+GE  GI  L   +A+
Sbjct: 192 NDTGCAVANAYNAIEGGATIVDTTV--------LGIGERNGITPLGGILAR 234


>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
           subunit 1/adenylylsulfate kinase protein; Provisional.
          Length = 632

 Score = 30.3 bits (69), Expect = 0.74
 Identities = 11/45 (24%), Positives = 21/45 (46%)

Query: 107 FSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFR 151
              +P  +   G++G GK+T+   + +++   G    L  GD  R
Sbjct: 456 KGQKPATVWFTGLSGSGKSTIANLVERRLHALGRHTYLLDGDNVR 500


>gnl|CDD|179089 PRK00698, tmk, thymidylate kinase; Validated.
          Length = 205

 Score = 30.2 bits (69), Expect = 0.74
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 118 GVNGVGKTTVIGKLSKKMSDAGLKVML 144
           G++G GK+T I  L + +   G  V+ 
Sbjct: 10  GIDGAGKSTQIELLKELLEQQGRDVVF 36


>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
          Length = 182

 Score = 29.8 bits (67), Expect = 0.85
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 95  MLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
           M + LS  F   F  +   IL+VG++  GKTT++ KL
Sbjct: 1   MGLWLSSAFKSLFGKKEVRILMVGLDAAGKTTILYKL 37


>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
          Length = 181

 Score = 29.9 bits (67), Expect = 0.87
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 95  MLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
           M +  +K F+  F+ +   IL+VG++  GKTT++ KL
Sbjct: 1   MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKL 37


>gnl|CDD|183453 PRK12338, PRK12338, hypothetical protein; Provisional.
          Length = 319

 Score = 30.1 bits (68), Expect = 0.87
 Identities = 9/27 (33%), Positives = 21/27 (77%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKKMS 136
           +P+VIL+   +G+GK+T+  +L++ ++
Sbjct: 3   KPYVILIGSASGIGKSTIASELARTLN 29


>gnl|CDD|148565 pfam07015, VirC1, VirC1 protein.  This family consists of several
           bacterial VirC1 proteins. In Agrobacterium tumefaciens,
           a cis-active 24-base-pair sequence adjacent to the right
           border of the T-DNA, called overdrive, stimulates tumour
           formation by increasing the level of T-DNA processing.
           It is thought that the virC operon which enhances T-DNA
           processing probably does so because the VirC1 protein
           interacts with overdrive. It has now been shown that the
           virC1 gene product binds to overdrive but not to the
           right border of T-DNA.
          Length = 231

 Score = 29.8 bits (67), Expect = 1.0
 Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 121 GVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSA-DFVCSEIGSDAA 179
           G GKTT +  L   ++  G +V L   D  R   + + +  A R    D  C    +D  
Sbjct: 12  GAGKTTALMGLCSALASDGKRVALFEADENRP--LTKWRENALRKGTWDPACEIFNADEL 69

Query: 180 ALAYEAFKQAQAKKVDVLIIDTAGRLH--NNSIL 211
            L  +A++ A+    D  + DT G     NN+I+
Sbjct: 70  PLLEQAYEHAEGSGFDYALADTHGGSSELNNTII 103


>gnl|CDD|181310 PRK08233, PRK08233, hypothetical protein; Provisional.
          Length = 182

 Score = 29.3 bits (66), Expect = 1.3
 Identities = 9/28 (32%), Positives = 18/28 (64%)

Query: 111 PHVILVVGVNGVGKTTVIGKLSKKMSDA 138
             +I +  V+G GKTT+  +L+ K+ ++
Sbjct: 3   TKIITIAAVSGGGKTTLTERLTHKLKNS 30


>gnl|CDD|163008 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
           This protein contains domains distinctive of a single
           strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
           well as a helicase domain (central region, homologous to
           the corresponding region of the F-type relaxase TraI,
           TIGR02760). This protein likely fills the same role as
           TraI(F), nicking (at the oriT site) and unwinding the
           coiled plasmid prior to conjugative transfer.
          Length = 744

 Score = 29.0 bits (65), Expect = 1.7
 Identities = 33/112 (29%), Positives = 49/112 (43%), Gaps = 27/112 (24%)

Query: 116 VVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIG 175
           VVG  G GK+T++    +    AG +V+ AA       A + L+            +E G
Sbjct: 373 VVGRAGTGKSTMLKAAREAWEAAGYRVIGAA---LSGKAAEGLQ------------AESG 417

Query: 176 SDAAALAYEAFKQAQAKKV----DVLIIDTAGRLHNNSILMAGIGKMIRVLK 223
            ++  LA   +  A  + +    DVL+ID AG        M G  +M RVLK
Sbjct: 418 IESRTLASLEYAWANGRDLLSDKDVLVIDEAG--------MVGSRQMARVLK 461


>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
          Length = 282

 Score = 29.0 bits (65), Expect = 1.9
 Identities = 11/32 (34%), Positives = 20/32 (62%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKVML 144
           +I++ G+ G GK+T    L+  +S  G++V L
Sbjct: 5   LIIIEGLPGFGKSTTAKMLNDILSQNGIEVEL 36


>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
           factor.  Ras homologues involved in vesicular transport.
           Activator of phospholipase D isoforms. Unlike Ras
           proteins they lack cysteine residues at their C-termini
           and therefore are unlikely to be prenylated. ARFs are
           N-terminally myristoylated. Contains ATP/GTP-binding
           motif (P-loop).
          Length = 175

 Score = 28.7 bits (64), Expect = 1.9
 Identities = 13/33 (39%), Positives = 22/33 (66%)

Query: 99  LSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
           + K F+  F ++   IL+VG++  GKTT++ KL
Sbjct: 1   MGKLFSKLFGNKEMRILMVGLDAAGKTTILYKL 33


>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 = 28.4 bits (64), Expect = 2.4
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADRTS 166
            V+LV G  G GK+ +  +L+  +S+  +  +    DT       +  I    TS
Sbjct: 1   GVLLV-GPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTS 54


>gnl|CDD|185651 PTZ00472, PTZ00472, serine carboxypeptidase (CBP1); Provisional.
          Length = 462

 Score = 28.2 bits (63), Expect = 2.6
 Identities = 22/115 (19%), Positives = 37/115 (32%), Gaps = 46/115 (40%)

Query: 76  AKDVSVQRVLYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKM 135
            K  + Q    +V+ +     M   K FN+                             +
Sbjct: 329 VKPATWQSCNMEVNLMFEMDWM---KNFNYTVPG-------------------------L 360

Query: 136 SDAGLKVMLAAGDTFRSAAIDQLKIWADRTSADFVCSEIGSDAAALAYEAFKQAQ 190
            + G++VM+ AGD                   DF+C+ IG+ A  LA +    A+
Sbjct: 361 LEDGVRVMIYAGDM------------------DFICNWIGNKAWTLALQWPGNAE 397


>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.
            Members of this protein family have two copies of the
           ABC transporter ATP-binding cassette, but are found
           outside the common ABC transporter operon structure that
           features integral membrane permease proteins and
           substrate-binding proteins encoded next to the
           ATP-binding cassette (ABC domain) protein. The member
           protein ChvD from Agrobacterium tumefaciens was
           identified as both a candidate to interact with VirB8,
           based on yeast two-hybrid analysis, and as an apparent
           regulator of VirG. The general function of this protein
           family is unknown.
          Length = 552

 Score = 28.4 bits (64), Expect = 2.7
 Identities = 56/235 (23%), Positives = 93/235 (39%), Gaps = 62/235 (26%)

Query: 4   QKVASESLSWIRKLTKGFASTSLKLKEGITDIISSRRLDDGVREELEDLLIRSDIGVAVA 63
           QK     L W+R   K   + S   K  +       R ++ + +E +     ++I +   
Sbjct: 265 QKALKRELEWVRSSPKARQAKS---KARLA------RYEELLSQEFQKRNETAEIYIPPG 315

Query: 64  Q----KIVE-ELLTKRYAKDVSVQRVLYDVSELIHKMLMPLSKPFNWDFSHRPHVIL-VV 117
                K++E E L+K +       ++L D                +  F   P  I+ V+
Sbjct: 316 PRLGDKVIEAENLSKGFGD-----KLLID----------------DLSFKLPPGGIVGVI 354

Query: 118 GVNGVGKTTVIGKLSKKMS-DAG-LKVMLAAGDTFRSAAIDQLK--IWADRTSADFVCSE 173
           G NG GK+T+   ++ +   D+G +K+    G+T + A +DQ +  +  ++T    V  E
Sbjct: 355 GPNGAGKSTLFRMITGQEQPDSGTIKI----GETVKLAYVDQSRDALDPNKT----VWEE 406

Query: 174 I--GSDAAAL--------AYEA---FK-QAQAKKVDVLIIDTAGRLHNNSILMAG 214
           I  G D   L        AY     FK   Q KKV  L      R+H    L +G
Sbjct: 407 ISGGLDIIQLGKREVPSRAYVGRFNFKGSDQQKKVGQLSGGERNRVHLAKTLKSG 461


>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
          Length = 590

 Score = 28.2 bits (64), Expect = 3.0
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 109 HRPHVILVVGVNGVGKTTVI 128
           +   VI +VG NG+GKTT  
Sbjct: 363 YEGEVIGIVGPNGIGKTTFA 382



 Score = 27.5 bits (62), Expect = 4.3
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 113 VILVVGVNGVGKTTVIGKLS 132
           V  ++G NG+GKTT +  LS
Sbjct: 101 VTGILGPNGIGKTTAVKILS 120


>gnl|CDD|163345 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
           YlqF.  Members of this protein family are GTP-binding
           proteins involved in ribosome biogenesis, including the
           essential YlqF protein of Bacillus subtilis, which is an
           essential protein. They are related to Era, EngA, and
           other GTPases of ribosome biogenesis, but are circularly
           permuted. This family is not universal, and is not
           present in Escherichia coli, and so is not as well
           studied as some other GTPases. This model is built for
           bacterial members.
          Length = 276

 Score = 28.2 bits (64), Expect = 3.1
 Identities = 11/25 (44%), Positives = 18/25 (72%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKK 134
           RP   ++VG+  VGK+T+I +L+ K
Sbjct: 117 RPIRAMIVGIPNVGKSTLINRLAGK 141


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

 Score = 27.8 bits (62), Expect = 3.7
 Identities = 8/30 (26%), Positives = 20/30 (66%)

Query: 102 PFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
           P+ ++   +P ++++ G +GVGK  V+ ++
Sbjct: 4   PWLFNKPAKPLLVVISGPSGVGKDAVLARM 33


>gnl|CDD|149480 pfam08433, KTI12, Chromatin associated protein KTI12.  This is a
           family of chromatin associated proteins which interact
           with the Elongator complex, a component of the
           elongating form of RNA polymerase II. The Elongator
           complex has histone acetyltransferase activity.
          Length = 266

 Score = 28.0 bits (63), Expect = 3.7
 Identities = 9/29 (31%), Positives = 17/29 (58%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           I++ G+   GK+T   +L+K + + G  V
Sbjct: 2   IILTGLPSSGKSTRAKELAKYLEEKGYDV 30


>gnl|CDD|184198 PRK13638, cbiO, cobalt transporter ATP-binding subunit;
           Provisional.
          Length = 271

 Score = 27.7 bits (61), Expect = 3.8
 Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 98  PLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLS 132
           P+ K  N DFS  P V  +VG NG GK+T+   LS
Sbjct: 15  PVLKGLNLDFSLSP-VTGLVGANGCGKSTLFMNLS 48


>gnl|CDD|161745 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
           protein MobB.  This molybdenum cofactor biosynthesis
           enzyme is similar to the urease accessory protein UreG
           and to the hydrogenase accessory protein HypB, both GTP
           hydrolases involved in loading nickel into the
           metallocenters of their respective target enzymes.
          Length = 155

 Score = 27.7 bits (62), Expect = 4.1
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           V+ +VG    GKTT+I +L K +   G +V
Sbjct: 1   VLQIVGPKNSGKTTLIERLVKALKARGYRV 30


>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 = 27.8 bits (62), Expect = 4.2
 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 5/41 (12%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAA 154
            +++GV G GK+T+   L+ ++    ++     GD    AA
Sbjct: 1   FVLMGVAGSGKSTIASALAHRLGAKFIE-----GDDLHPAA 36


>gnl|CDD|183324 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
           Reviewed.
          Length = 556

 Score = 27.8 bits (63), Expect = 4.3
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 16/49 (32%)

Query: 116 VVGVNGVGKTTVIGKLSKKM------SDAG-LKVMLAAGDTFRSAAIDQ 157
           ++G NG GK+T+      KM       D+G +K+    G+T + A +DQ
Sbjct: 355 IIGPNGAGKSTLF-----KMITGQEQPDSGTIKI----GETVKLAYVDQ 394


>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
          Length = 180

 Score = 27.8 bits (62), Expect = 4.4
 Identities = 11/23 (47%), Positives = 16/23 (69%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKM 135
           +I + G  GVGKTTV   L++K+
Sbjct: 2   IIAITGTPGVGKTTVSKLLAEKL 24


>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
          Length = 279

 Score = 27.4 bits (61), Expect = 4.4
 Identities = 9/35 (25%), Positives = 20/35 (57%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGD 148
               G  G+GK+T +  ++  ++++G KV++   D
Sbjct: 4   FCFYGKGGIGKSTTVCNIAAALAESGKKVLVVGCD 38


>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 = 27.6 bits (62), Expect = 4.5
 Identities = 10/30 (33%), Positives = 16/30 (53%)

Query: 110 RPHVILVVGVNGVGKTTVIGKLSKKMSDAG 139
           RP  + + G  G GKT V   + K++ +A 
Sbjct: 39  RPSNVFIYGKTGTGKTAVTKYVMKELEEAA 68


>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24.  This family is based
           on the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 637

 Score = 27.6 bits (61), Expect = 4.5
 Identities = 13/61 (21%), Positives = 31/61 (50%), Gaps = 10/61 (16%)

Query: 76  AKDVSV-QRVLYDVSELIHKMLMPLSKPFNWDFSHRPHVILVVGVNGVGKTTVIGKLSKK 134
             +++V ++ + +V   +   ++  +         R  ++L+ G +G GK+T I  LSK+
Sbjct: 83  QHELAVHKKKIEEVETWLKAQVLENAP-------KR--ILLITGPSGCGKSTTIKILSKE 133

Query: 135 M 135
           +
Sbjct: 134 L 134


>gnl|CDD|130080 TIGR01007, eps_fam, capsular exopolysaccharide family.  This model
           describes the capsular exopolysaccharide proteins in
           bacteria. The exopolysaccharide gene cluster consists of
           several genes which encode a number of proteins which
           regulate the exoploysaccharide biosynthesis(EPS).
           Atleast 13 genes espA to espM in streptococcus species
           seem to direct the EPS proteins and all of which share
           high homology. Functional roles were characterized by
           gene disruption experiments which resulted in
           exopolysaccharide-deficient phenotypes.
          Length = 204

 Score = 27.4 bits (61), Expect = 4.9
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 113 VILVVGVN-GVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRS 152
           V+L+  V  G GK+T    ++   + AG K +L  GD   S
Sbjct: 19  VLLITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNS 59


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

 Score = 27.4 bits (61), Expect = 5.0
 Identities = 11/16 (68%), Positives = 13/16 (81%)

Query: 111 PHVILVVGVNGVGKTT 126
           P  IL+VG +GVGKTT
Sbjct: 35  PQSILLVGASGVGKTT 50


>gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA.  The gene protuct codes
           for a probable ATP-dependent protease involved in both
           DNA repair and degradation of proteins, peptides,
           glycopeptides. Also known as sms. Residues 11-28 of the
           SEED alignment contain a putative Zn binding domain.
           Residues 110-117 of the seed contain a putative ATP
           binding site both documented in Haemophilus and in
           Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
           178:5045-5048(1996)).
          Length = 454

 Score = 27.5 bits (61), Expect = 5.2
 Identities = 28/131 (21%), Positives = 56/131 (42%), Gaps = 30/131 (22%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLKIWADR----TSADF 169
           IL+ G  G+GK+T++ +++ +++   +KV+  +G+     ++ Q+K+ A R        +
Sbjct: 97  ILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE----ESLQQIKMRAIRLGLPEPNLY 152

Query: 170 VCSEIGSDAAALAYEAFKQAQAKKVDVLIIDTAGRLHNNSILMAGIGKMIRVLKRLDPHA 229
           V SE   +            + +     +ID+   L++  I                  A
Sbjct: 153 VLSETNWEQICAN------IEEENPQACVIDSIQTLYSPDI----------------SSA 190

Query: 230 PHSVLQVLDAT 240
           P SV QV + T
Sbjct: 191 PGSVSQVRECT 201


>gnl|CDD|180730 PRK06851, PRK06851, hypothetical protein; Provisional.
          Length = 367

 Score = 27.2 bits (61), Expect = 5.4
 Identities = 8/31 (25%), Positives = 18/31 (58%)

Query: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
            + ++ G  G GK+T++ K+ ++  + G  V
Sbjct: 31  RIFILKGGPGTGKSTLMKKIGEEFLEKGYDV 61


>gnl|CDD|184707 PRK14491, PRK14491, putative bifunctional molybdopterin-guanine
           dinucleotide biosynthesis protein MobB/MoeA;
           Provisional.
          Length = 597

 Score = 27.3 bits (61), Expect = 5.5
 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 106 DFSHRPHVIL--VVGVNGVGKTTVIGKLSKKMSDAGLKV 142
            F++   + L      +G GKTT++ +L  +++  GL++
Sbjct: 3   PFTNPLSIPLLGFCAYSGTGKTTLLEQLIPELNQRGLRL 41


>gnl|CDD|184708 PRK14493, PRK14493, putative bifunctional molybdopterin-guanine
           dinucleotide biosynthesis protein MobB/MoaE;
           Provisional.
          Length = 274

 Score = 27.3 bits (61), Expect = 5.8
 Identities = 10/28 (35%), Positives = 17/28 (60%)

Query: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAG 139
            V+ +VG    GKTT++ +L  ++S  G
Sbjct: 2   KVLSIVGYKATGKTTLVERLVDRLSGRG 29


>gnl|CDD|179620 PRK03642, PRK03642, putative periplasmic esterase; Provisional.
          Length = 432

 Score = 27.1 bits (60), Expect = 6.2
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 54  IRSDIGVAVAQKIVEELLTKRYAKDVSVQRVLYDVSELIHKMLMPLSKPF 103
           I SD+   +   IVE +  +    D  V+  +Y    L H +  PL K F
Sbjct: 202 IYSDVDYMLLGFIVESITGQPL--DRYVEESIYRPLGLTHTVFNPLQKGF 249


>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
          Length = 675

 Score = 27.2 bits (61), Expect = 6.3
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 4/40 (10%)

Query: 94  KMLMPLS--KPFNWDFSHRPHVILVVGVNGVGKTTVIGKL 131
             L P    K F    S +P  +++ G  GVGKT+ + KL
Sbjct: 162 ASLQPDVQLKIFEAWISRKP--VVLTGGTGVGKTSQVPKL 199


>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
           protein; Provisional.
          Length = 265

 Score = 27.3 bits (60), Expect = 6.4
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGLKVML 144
           H   ++G NG GK+T++  LS+ M+ A   V L
Sbjct: 34  HFTAIIGPNGCGKSTLLRTLSRLMTPAHGHVWL 66


>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
          Length = 365

 Score = 27.1 bits (61), Expect = 6.9
 Identities = 10/22 (45%), Positives = 17/22 (77%)

Query: 116 VVGVNGVGKTTVIGKLSKKMSD 137
           VVGV  VGK+T+I ++ K+++ 
Sbjct: 165 VVGVTNVGKSTLINRIIKEITG 186


>gnl|CDD|180114 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
          Length = 209

 Score = 27.0 bits (61), Expect = 7.4
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 106 DFSHRPHVILVVGVNGVGKTTV 127
               +P +I + G +G GKTTV
Sbjct: 1   MMMKKPIIIGIAGGSGSGKTTV 22


>gnl|CDD|184738 PRK14551, rnhB, ribonuclease HII; Provisional.
          Length = 212

 Score = 27.0 bits (60), Expect = 7.5
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 4/44 (9%)

Query: 28 LKEGITDIISSRRLDDGVREEL-EDLLIRSDIGVAVAQKIVEEL 70
          L +GI D   S+RL    REEL  +L     I V VA+     +
Sbjct: 29 LPDGIDD---SKRLSPERREELAAELREDDAIAVGVAEIPPARI 69


>gnl|CDD|180593 PRK06500, PRK06500, short chain dehydrogenase; Provisional.
          Length = 249

 Score = 26.8 bits (60), Expect = 7.6
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 20 GFASTSLKLKEGITDIISSRRLD--DGVREEL--EDLLIRSDIGVAVAQKIVEELLTKRY 75
          G  +    L EG    I+ R     +  R EL    L+IR+D G   AQK + + L + +
Sbjct: 19 GLETARQFLAEGARVAITGRDPASLEAARAELGESALVIRADAGDVAAQKALAQALAEAF 78

Query: 76 AK 77
           +
Sbjct: 79 GR 80


>gnl|CDD|172477 PRK13974, PRK13974, thymidylate kinase; Provisional.
          Length = 212

 Score = 26.9 bits (60), Expect = 8.0
 Identities = 13/29 (44%), Positives = 19/29 (65%)

Query: 112 HVILVVGVNGVGKTTVIGKLSKKMSDAGL 140
             I++ G++G GKTT I  LSK +  +GL
Sbjct: 4   KFIVLEGIDGCGKTTQIDHLSKWLPSSGL 32


>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 = 26.7 bits (59), Expect = 8.1
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 111 PHVILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           P  IL++G  GVGKT +  +L+K  +   +KV
Sbjct: 47  PKNILMIGPTGVGKTEIARRLAKLANAPFIKV 78


>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
          Length = 273

 Score = 26.9 bits (59), Expect = 8.1
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 114 ILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGD 148
           I + G  G+GK+T    L+  +S  G K++L   D
Sbjct: 4   IAIYGKGGIGKSTTTQNLTAALSTMGNKILLVGCD 38


>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 = 26.7 bits (60), Expect = 8.9
 Identities = 8/30 (26%), Positives = 19/30 (63%)

Query: 113 VILVVGVNGVGKTTVIGKLSKKMSDAGLKV 142
           +I++ G +GVGK+T++  L ++  +    +
Sbjct: 3   LIVISGPSGVGKSTLVKALLEEDPNLKFSI 32


>gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional.
          Length = 718

 Score = 26.4 bits (58), Expect = 9.3
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 10/53 (18%)

Query: 103 FNWDFSHRPHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAI 155
           F  D   R   I +VG NG+GK+T++  +S ++         ++G  FRSA +
Sbjct: 530 FGIDLDSR---IAMVGPNGIGKSTILKLISGELQP-------SSGTVFRSAKV 572


>gnl|CDD|183545 PRK12472, PRK12472, hypothetical protein; Provisional.
          Length = 508

 Score = 26.4 bits (58), Expect = 9.4
 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 18/89 (20%)

Query: 132 SKKMSDAGLKVMLAAGDTFRSAAIDQLKIWAD--RTSADFVCSEIGS------------- 176
           +K  +DA LK    A     +A  D+ K  A+  +  A    +E  +             
Sbjct: 233 AKARADAELK---RADKALAAAKTDEAKARAEERQQKAAQQAAEAATQLDTAKADAEAKR 289

Query: 177 DAAALAYEAFKQAQAKKVDVLIIDTAGRL 205
            AAA   EA K A AKK +     T  +L
Sbjct: 290 AAAAATKEAAKAAAAKKAETAKAATDAKL 318


  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
   0.320    0.136    0.383 

Gapped
Lambda     K      H
   0.267   0.0715    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,211,237
Number of extensions: 346015
Number of successful extensions: 1229
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1196
Number of HSP's successfully gapped: 138
Length of query: 321
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 228
Effective length of database: 3,984,929
Effective search space: 908563812
Effective search space used: 908563812
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: 57 (25.8 bits)