RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780806|ref|YP_003065219.1| chromosome partitioning
protein A [Candidatus Liberibacter asiaticus str. psy62]
         (265 letters)



>gnl|CDD|163271 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
           Members of this family are the RepA (or ParA) protein
           involved in replicon partitioning. All known examples
           occur in bacterial species with two or more replicons,
           on a plasmid or the smaller chromosome. Note that an
           apparent exception may be seen as a pseudomolecule from
           assembly of an incompletely sequenced genome. Members of
           this family belong to a larger family that also includes
           the enzyme cobyrinic acid a,c-diamide synthase, but
           assignment of that name to members of this family would
           be in error.
          Length = 387

 Score =  112 bits (283), Expect = 8e-26
 Identities = 68/244 (27%), Positives = 119/244 (48%), Gaps = 30/244 (12%)

Query: 8   IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIE----------L 57
           +I + N KGG GKTTTA +L+  LA  G  VL IDLDPQ + S   G +          L
Sbjct: 106 VIAVTNFKGGSGKTTTAAHLAQYLALRGYRVLAIDLDPQASLSALFGYQPEFDVGENETL 165

Query: 58  YDR-KYSSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIE------MILGGEKDRLF 110
           Y   +Y       E + +++I+ +T  P L ++P  ++L+  E      +  G   D +F
Sbjct: 166 YGAIRYDD-----ERRPLSEIIRKTYFPGLDLVPGNLELMEFEHETPRALSRGQGGDTIF 220

Query: 111 --RLDKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLE 168
             R+ +AL+ ++  D+  + +DCPP    LT++A+ AA  +L+ +  +   +  +SQ L 
Sbjct: 221 FARVGEALA-EVEDDYDVVVIDCPPQLGFLTLSALCAATGVLITVHPQMLDVMSMSQFLL 279

Query: 169 TVEEVRRTVNSA-----LDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVR 223
              ++   V  A      D    ++T ++  +    Q+V+ +R   G  V    + ++  
Sbjct: 280 MTGDLLGVVREAGGNLSYDFMRYLVTRYEPNDGPQAQMVAFLRSLFGDHVLTNPMLKSTA 339

Query: 224 ISEA 227
           IS+A
Sbjct: 340 ISDA 343


>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal.  This
           model represents the archaeal branch of the MinD family.
           MinD, a weak ATPase, works in bacteria with MinC as a
           generalized cell division inhibitor and, through
           interaction with MinE, prevents septum placement
           inappropriate sites. Often several members of this
           family are found in archaeal genomes, and the function
           is uncharacterized. More distantly related proteins
           include flagellar biosynthesis proteins and ParA
           chromosome partitioning proteins. The exact roles of the
           various archaeal MinD homologs are unknown.
          Length = 251

 Score =  107 bits (269), Expect = 3e-24
 Identities = 74/260 (28%), Positives = 128/260 (49%), Gaps = 24/260 (9%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDRKYSSY 65
           RIITIA+ KGG GKTT   NL  ALA +G+ VL +D D    N    LG+E  D+  + +
Sbjct: 1   RIITIASGKGGTGKTTITANLGVALAKLGKKVLALDADITMANLELILGME--DKPVTLH 58

Query: 66  DLLIEEKNINQILIQTAIPN-LSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDF 124
           D+L  E +I   + +   P  + +IP+ + L G+       K    +L+  L  ++  D 
Sbjct: 59  DVLAGEADIKDAIYEG--PFGVKVIPAGVSLEGL------RKADPDKLEDVLK-EIIDDT 109

Query: 125 SYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQ 184
            ++ +D P       + A+AAAD +L+ +  E  +   ++  L+T     +       I 
Sbjct: 110 DFLLIDAPAGLERDAVTALAAADELLLVVNPEISS---ITDALKTKIVAEK---LGTAIL 163

Query: 185 GIILTMFDS-RNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAG 243
           G++L      +  L ++ +  +   L   V   V+P +  +  A ++G+P +IY+     
Sbjct: 164 GVVLNRVTRDKTELGREEIETI---LEVPVL-GVVPEDPEVRRAAAFGEPVVIYNPNSPA 219

Query: 244 SQAYLKLASELIQQERHRKE 263
           +QA+++LA+EL   E   KE
Sbjct: 220 AQAFMELAAELAGIEYEPKE 239


>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
          Length = 405

 Score = 84.3 bits (208), Expect = 3e-17
 Identities = 59/240 (24%), Positives = 115/240 (47%), Gaps = 20/240 (8%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLG------IELYDR 60
           ++I + N KGG GKTTT+ +L+  LA  G  VL +DLDPQ + S  LG      +   + 
Sbjct: 122 QVIAVTNFKGGSGKTTTSAHLAQYLALQGYRVLAVDLDPQASLSALLGVLPETDVGANET 181

Query: 61  KYSSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIE------MILGGEKDRLF--RL 112
            Y++       + +  ++  T    L ++P  ++L+  E      +   G +D LF  R+
Sbjct: 182 LYAAIRYDDTRRPLRDVIRPTYFDGLHLVPGNLELMEFEHTTPKALSDKGTRDGLFFTRV 241

Query: 113 DKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEE 172
            +A   ++  D+  + +DCPP    LT++ + AA S+++ +  +   +  +SQ L    +
Sbjct: 242 AQAFD-EVADDYDVVVIDCPPQLGFLTLSGLCAATSMVITVHPQMLDIASMSQFLLMTRD 300

Query: 173 VRRTVNSA-----LDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEA 227
           +   V  A      D    +LT ++ +++   +V + +R      V    + ++  +S+A
Sbjct: 301 LLGVVKEAGGNLQYDFIRYLLTRYEPQDAPQTKVAALLRNMFEDHVLTNPMVKSAAVSDA 360


>gnl|CDD|131023 TIGR01968, minD_bact, septum site-determining protein MinD.  This
           model describes the bacterial and chloroplast form of
           MinD, a multifunctional cell division protein that
           guides correct placement of the septum. The homologous
           archaeal MinD proteins, with many archaeal genomes
           having two or more forms, are described by a separate
           model.
          Length = 261

 Score = 77.0 bits (190), Expect = 4e-15
 Identities = 77/261 (29%), Positives = 126/261 (48%), Gaps = 31/261 (11%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDR-KYSS 64
           R+I I + KGGVGKTTT  NL TALA +G+ V+LID D    N    LG+E  +R  Y+ 
Sbjct: 2   RVIVITSGKGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDLLLGLE--NRIVYTL 59

Query: 65  YDLLIEEKNINQILIQTA-IPNLSIIPSTMDLLGIEMILGGEKDRLFRLD-KALSVQLTS 122
            D++  E  + Q LI+   + NL ++P++            +KD +     K L  +L  
Sbjct: 60  VDVVEGECRLQQALIKDKRLKNLYLLPASQT---------RDKDAVTPEQMKKLVNELKE 110

Query: 123 DFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLL-----ETVEEVRRTV 177
           +F Y+ +DCP        NA+A AD  +V    E  A+    +++     + +E++   V
Sbjct: 111 EFDYVIIDCPAGIESGFRNAVAPADEAIVVTTPEVSAVRDADRVIGLLEAKGIEKIHLIV 170

Query: 178 NSALDIQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIY 237
           N       +   M    + LS   V DV + L   +   VIP +  I  + + G+P ++ 
Sbjct: 171 NR------LRPEMVKKGDMLS---VDDVLEILSIPLIG-VIPEDEAIIVSTNKGEPVVLN 220

Query: 238 DLKCAGSQAYLKLASELIQQE 258
           D K    +A+  +A  ++ +E
Sbjct: 221 D-KSRAGKAFENIARRILGEE 240


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

 Score = 76.8 bits (189), Expect = 5e-15
 Identities = 50/172 (29%), Positives = 76/172 (44%), Gaps = 46/172 (26%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYD 66
           +II + NQKGG GKTT A NL++ L A G  VLL+DLDPQG+++                
Sbjct: 1   KIIAVLNQKGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSSTD--------------- 45

Query: 67  LLIEEKNINQILIQTAIPNLSIIPS-TMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFS 125
              E +   + L    IP + +  S   DL                       ++ S + 
Sbjct: 46  -WAEAREEGEPL----IPVVRMGKSIRADLP----------------------KVASGYD 78

Query: 126 YIFLDCPPSFNLLTMNAMAAADSILVPLQCEFF---ALEGLSQLLETVEEVR 174
           Y+ +D  P  + L   A+  AD +L+P+Q   F   A   L +L++  +EV 
Sbjct: 79  YVVVDGAPQDSELARAALRIADMVLIPVQPSPFDIWAAPDLVELIKARQEVT 130


>gnl|CDD|184261 PRK13705, PRK13705, plasmid-partitioning protein SopA; Provisional.
          Length = 388

 Score = 75.8 bits (186), Expect = 1e-14
 Identities = 69/233 (29%), Positives = 110/233 (47%), Gaps = 30/233 (12%)

Query: 8   IITIANQKGGVGKTTTAINLSTALAAIGENVLLID-LDPQGNASTGLGIELYDRKYSSYD 66
           +I +A  KGGV KT+ +++L+  LA  G  VLL++  DPQG AS   G  + D    + D
Sbjct: 108 VIGVAAHKGGVYKTSVSVHLAQDLALKGLRVLLVEGNDPQGTASMYHGW-VPDLHIHAED 166

Query: 67  LLI-----EEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDR---------LFRL 112
            L+     E+ +    +  T  P L IIPS + L  IE  L G+ D          + RL
Sbjct: 167 TLLPFYLGEKDDATYAIKPTCWPGLDIIPSCLALHRIETELMGKFDEGKLPTDPHLMLRL 226

Query: 113 DKALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEE 172
             A+   +  D+  I +D  P+  + T+N + AAD ++VP   E F      Q  + + +
Sbjct: 227 --AIE-TVAHDYDVIVIDSAPNLGIGTINVVCAADVLIVPTPAELFDYTSALQFFDMLRD 283

Query: 173 VRRTVNSALDIQG------IILTMFDSRN-SLSQQVVSDVRKNLGGKVYNTVI 218
           + + V    D++G      I+LT + + N S S  +   +R   G  V   V+
Sbjct: 284 LLKNV----DLKGFEPDVRILLTKYSNSNGSQSPWMEEQIRDAWGSMVLKNVV 332


>gnl|CDD|117696 pfam09140, MipZ, ATPase MipZ.  MipZ is an ATPase that forms a
           complex with the chromosome partitioning protein ParB
           near the chromosomal origin of replication. It is
           responsible for the temporal and spatial regulation of
           FtsZ ring formation.
          Length = 261

 Score = 68.5 bits (168), Expect = 1e-12
 Identities = 60/233 (25%), Positives = 97/233 (41%), Gaps = 43/233 (18%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYD 66
            +I + N+KGG GK+TTA++++ AL  +G  V  IDLD +    T        R   +  
Sbjct: 1   HVIVVGNEKGGSGKSTTAVHVAVALLYLGARVATIDLDLRQRTLT--------RYIENRA 52

Query: 67  LLIEEKNINQILIQTAIPNLSIIPSTMDL-LGIEMILGGEKDRLFRLDKALSVQLTSDFS 125
              E   +        +P    +P  + L   +  +  GE     RL++A+   L  D  
Sbjct: 53  ATAERTGL-------DLP----VPKHLCLPDDVSEVFDGESADDARLEEAV-ADLEQDAD 100

Query: 126 YIFLDCPPSFNLLTMNAMAAADSILVPLQCEF-------------FALEGLSQLLETVEE 172
           +I +D P S + L+  A + AD+++ PL   F             F +   S   E V E
Sbjct: 101 FIVIDTPGSDSPLSRLAHSRADTLVTPLNDSFVDFDLLGQVDPETFKVTRPSFYAEMVWE 160

Query: 173 VRRTVNSA--LDIQGII----LTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIP 219
            R+    A    I  I+    L+  ++RN   ++ V D    L  +V   V P
Sbjct: 161 ARKKRAQADRAPIDWIVLRNRLSTLEARN---KRRVEDALNELSKRVGFRVAP 210


>gnl|CDD|107201 PHA02519, PHA02519, plasmid partition protein SopA; Reviewed.
          Length = 387

 Score = 66.2 bits (161), Expect = 9e-12
 Identities = 65/237 (27%), Positives = 105/237 (44%), Gaps = 26/237 (10%)

Query: 2   EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLID-LDPQGNASTGLGIELYDR 60
           ++K   ++ + + KGGV KT++A++ +  LA  G  VLLI+  DPQG AS   G  + D 
Sbjct: 102 DDKNPVVLAVMSHKGGVYKTSSAVHTAQWLALQGHRVLLIEGNDPQGTASMYHGY-VPDL 160

Query: 61  KYSSYDLLI-----EEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKA 115
              + D L+     E  N    +  T  P L IIPS + L  IE  L    D   +L   
Sbjct: 161 HIHADDTLLPFYLGERDNAEYAIKPTCWPGLDIIPSCLALHRIETDLMQYHDA-GKLPHP 219

Query: 116 LSVQLTS-------DFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLE 168
             + L +       ++  I +D  P+    T+N + AAD I+V    E F    + Q   
Sbjct: 220 PHLMLRAAIESVWDNYDIIVIDSAPNLGTGTINVVCAADVIVVATPAELFDYVSVLQFFT 279

Query: 169 TVEEVRRTVNSALDIQG------IILTMFDSRN-SLSQQVVSDVRKNLGGKVYNTVI 218
            + ++  TV    D+ G      ++LT +     + S+ +   +R   G  V   V+
Sbjct: 280 MLLDLLATV----DLGGFEPVVRLLLTKYSLTVGNQSRWMEEQIRNTWGSMVLRQVV 332


>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
          Length = 270

 Score = 58.4 bits (141), Expect = 2e-09
 Identities = 72/268 (26%), Positives = 125/268 (46%), Gaps = 32/268 (11%)

Query: 6   SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDRK--Y 62
           +RII + + KGGVGKTT++  ++T LA  G+  ++ID D    N    +G E   R+  Y
Sbjct: 2   ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCE---RRVVY 58

Query: 63  SSYDLLIEEKNINQILIQTA-IPNLSIIPSTMDLLGIEMILGGEKDRLFR--LDKALSVQ 119
              +++  +  +NQ LI+     NL I+P++            +KD L R  + K L   
Sbjct: 59  DFVNVIQGDATLNQALIKDKRTENLYILPASQTR---------DKDALTREGVAKVLDDL 109

Query: 120 LTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETV-EEVRRTVN 178
              DF +I  D P       + A+  AD  ++    E  ++    ++L  +  + RR  N
Sbjct: 110 KAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAEN 169

Query: 179 SALDI-QGIILTMFD----SRNSL--SQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYG 231
               I + ++LT ++    SR  +   + V+  +R  L G     VIP +  +  A + G
Sbjct: 170 GEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVG-----VIPEDQSVLRASNQG 224

Query: 232 KPAIIYDLKCAGSQAYLKLASELIQQER 259
           +P +I D++    +AY      L+ +ER
Sbjct: 225 EP-VILDIEADAGKAYADTVDRLLGEER 251


>gnl|CDD|163238 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein
          YhjQ.  Members of this family are the YhjQ protein,
          found immediately upsteam of bacterial cellulose
          synthase (bcs) genes in a broad range of bacteria,
          including both copies of the bcs locus in Klebsiella
          pneumoniae. In several species it is seen clearly as
          part of the bcs operon. It is identified as a probable
          component of the bacterial cellulose metabolic process
          not only by gene location, but also by partial
          phylogenetic profiling, or Haft-Selengut algorithm
          (PubMed:16930487), based on a bacterial cellulose
          biosynthesis genome property profile. Cellulose plays
          an important role in biofilm formation and structural
          integrity in some bacteria. Mutants in yhjQ in
          Escherichia coli, show altered morphology an growth,
          but the function of YhjQ has not yet been determined.
          Length = 246

 Score = 52.0 bits (125), Expect = 2e-07
 Identities = 24/40 (60%), Positives = 28/40 (70%)

Query: 8  IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG 47
          +I I   KGGVGKTT   NL++AL  +GE VL IDLDPQ 
Sbjct: 3  VIAIVGVKGGVGKTTLTANLASALKLLGEPVLAIDLDPQN 42



 Score = 36.2 bits (84), Expect = 0.009
 Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 4/129 (3%)

Query: 127 IFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGI 186
           + +D P   + +T  A+AAAD +LV +  +      L Q    +                
Sbjct: 118 VLIDVPRGPSPITRQALAAADLVLVVVNADAACYATLHQQALALFAGSGPRIGP----HF 173

Query: 187 ILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQA 246
           ++  FD    LS+ V + +R+ LG ++   VI R+  +SEA + G P + Y      +  
Sbjct: 174 LINQFDPARQLSRDVRAVLRQTLGSRLLPFVIHRDEAVSEALARGTPVLNYAPHSQAAHD 233

Query: 247 YLKLASELI 255
              LA  L+
Sbjct: 234 IRTLAGWLL 242


>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
          Length = 369

 Score = 47.3 bits (113), Expect = 4e-06
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 8   IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
           II +++ KGGVGK++TA+NL+ ALAA G  V ++D D
Sbjct: 109 IIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILDAD 145


>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 = 45.1 bits (107), Expect = 2e-05
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSY- 65
           +++ I + K G GK+TT+ N++ A A  G   LLID D +   S   G      K +   
Sbjct: 18  KVLLITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRN--SVMSGTFKSQNKITGLT 75

Query: 66  DLLIEEKNINQILIQTAIPNLSIIPS 91
           + L    +++  +  T I NL +I S
Sbjct: 76  NFLSGTTDLSDAICDTNIENLFVITS 101


>gnl|CDD|183881 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
          ATP-binding protein; Provisional.
          Length = 270

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 18/32 (56%), Positives = 24/32 (75%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
          KGG+GK+TT+ NLS A A +G+ VL I  DP+
Sbjct: 10 KGGIGKSTTSSNLSAAFAKLGKKVLQIGCDPK 41


>gnl|CDD|162661 TIGR02016, BchX, chlorophyllide reductase iron protein subunit X.
           This model represents the X subunit of the three-subunit
           enzyme, (bacterio)chlorophyllide reductase. This enzyme
           is responsible for the reduction of the chlorin B-ring
           and is closely related to the protochlorophyllide
           reductase complex which reduces the D-ring. Both of
           these complexes in turn are homologous to nitrogenase.
           This subunit is homologous to the nitrogenase component
           II, or "iron" protein.
          Length = 296

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 34/98 (34%), Positives = 50/98 (51%), Gaps = 5/98 (5%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL--GIEL--YDRKY 62
           RII I   KGG GK+ T  NLS  +A +G+ VL +  DP+ ++++ L  GI L       
Sbjct: 1   RIIAIYG-KGGSGKSFTTTNLSHMMAEMGKRVLQLGCDPKHDSTSLLFGGISLPTIIEVA 59

Query: 63  SSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEM 100
           +   L  EE  +  +  +T I N S     M+L G E+
Sbjct: 60  TEKKLAGEEVKVGDVCFKTTIMNGSGGVYGMELGGPEV 97


>gnl|CDD|130078 TIGR01005, eps_transp_fam, exopolysaccharide transport protein
           family.  The model describes the exopolysaccharide
           transport protein family in bacteria. The transport
           protein is part of a large genetic locus which is
           associated with exopolysaccharide (EPS) biosynthesis.
           Detailed molecular characterization and gene fusion
           analysis revealed atleast seven gene products are
           involved in the overall regulation, which among other
           things, include exopolysaccharide biosynthesis, property
           of conferring virulence and exopolysaccharide export.
          Length = 754

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 35/198 (17%), Positives = 71/198 (35%), Gaps = 25/198 (12%)

Query: 1   MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDR 60
               +  ++     +  +GK+    N +  +A+ G+  LLID D +  A + + +     
Sbjct: 541 KSVAEPEVVETQRPRPVLGKSDIEANAAALIASGGKRALLIDADGRKAALSQILVA--RE 598

Query: 61  KYSSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQL 120
                DLL   +++   L  +   +L ++ S +   GI  +L      +F    +L +  
Sbjct: 599 VSGLLDLLAGLRSLLLDLTASGAASLPMLDSGLFPHGITELLASP--AMF----SLVIHA 652

Query: 121 TSDFSYIFLDCPPSFNLLTMNAMAAAD--SILVPLQCEFFALEGLSQLLETVEEVRRTVN 178
                 + +D         +  M AA   +I++ L   +            VE  R    
Sbjct: 653 RLYSDCVVVDVGT---ADPVRDMRAAARLAIIMLLVTAY----DRV----VVECGRADAQ 701

Query: 179 S----ALDIQGIILTMFD 192
                  ++ G+ L M D
Sbjct: 702 GISRLNGEVTGVFLNMLD 719


>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
          reductase, iron-sulfur ATP-binding protein.  The BchL
          peptide (ChlL in chloroplast and cyanobacteria) is an
          ATP-binding iron-sulfur protein of the dark form
          protochlorophyllide reductase, an enzyme similar to
          nitrogenase. This subunit resembles the nitrogenase
          NifH subunit.
          Length = 268

 Score = 42.9 bits (101), Expect = 8e-05
 Identities = 18/36 (50%), Positives = 27/36 (75%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
          KGG+GK+TT+ NLS A A +G+ VL I  DP+ +++
Sbjct: 8  KGGIGKSTTSSNLSVAFAKLGKRVLQIGCDPKHDST 43


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

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 17/39 (43%), Positives = 28/39 (71%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL 53
          KGG+GK+TT  NL+ AL+ +G  +LL+  DP+ +++  L
Sbjct: 9  KGGIGKSTTTQNLTAALSTMGNKILLVGCDPKADSTRML 47


>gnl|CDD|132063 TIGR03018, pepcterm_TyrKin, exopolysaccharide/PEPCTERM locus
           tyrosine autokinase.  Members of this protein family are
           related to a known protein-tyrosine autokinase and to
           numerous homologs from exopolysaccharide biosynthesis
           region proteins, many of which are designated as chain
           length determinants. Most members of this family contain
           a short region, immediately C-terminal to the region
           modeled here, with an abundance of Tyr residues. These
           C-terminal tyrosine residues are likely to be
           autophosphorylation sites. Some members of this family
           are fusion proteins.
          Length = 207

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 16  GGVGKTTTAINLSTALAA-IGENVLLIDLD---PQGNASTGLGIELYDRKYSSYDLLIEE 71
            G GK+ TAINL+ +LA    + VLLID D   P       LG+E  +   S   LL   
Sbjct: 45  PGEGKSFTAINLAISLAQEYDKTVLLIDADLRRPS--LHRTLGLE-AEPGLSDC-LLDPV 100

Query: 72  KNINQILIQTAIPNLSIIPS 91
            ++  +L+ T I  LS++P+
Sbjct: 101 LDLADVLVPTNIGRLSLLPA 120


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

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 17/40 (42%), Positives = 27/40 (67%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLG 54
          KGG+GK+TT  N++ ALA  G+ VL++  DP+ + +  L 
Sbjct: 9  KGGIGKSTTVCNIAAALAESGKKVLVVGCDPKADCTRNLV 48



 Score = 30.5 bits (69), Expect = 0.43
 Identities = 28/117 (23%), Positives = 51/117 (43%), Gaps = 7/117 (5%)

Query: 143 MAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ-QV 201
              AD + +   C+  A+   + + + ++   +   SAL   GII   ++ R+ +    +
Sbjct: 139 KGLADDVYIVTTCDPMAIYAANNICKGIKRFAKRGKSALG--GII---YNGRSVIDAPDI 193

Query: 202 VSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQAYLKLASELIQQE 258
           V +  K +G  V    IP +  I+EA  YGK  I Y      S  + +LA  + +  
Sbjct: 194 VEEFAKKIGTNVIGK-IPMSNIITEAEIYGKTVIEYAPDSEISNIFRELAEAIYENN 249


>gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein.  This model describes
          nitrogenase (EC 1.18.6.1) iron protein, also called
          nitrogenase reductase or nitrogenase component II. This
          model includes molybdenum-iron nitrogenase reductase
          (nifH), vanadium-iron nitrogenase reductase (vnfH), and
          iron-iron nitrogenase reductase (anfH). The model
          excludes the homologous protein from the
          light-independent protochlorophyllide reductase.
          Length = 275

 Score = 39.7 bits (93), Expect = 8e-04
 Identities = 15/32 (46%), Positives = 25/32 (78%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
          KGG+GK+TT  N++ ALA +G+ V+++  DP+
Sbjct: 8  KGGIGKSTTTQNIAAALAEMGKKVMIVGCDPK 39



 Score = 30.8 bits (70), Expect = 0.35
 Identities = 24/114 (21%), Positives = 51/114 (44%), Gaps = 7/114 (6%)

Query: 146 ADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNS-LSQQVVSD 204
           A  I +    E  AL   + + + + +  ++    L   G+I    +SRN    ++++ +
Sbjct: 141 AQEIYIVTSGEMMALYAANNICKGILKYAKSGGVRLG--GLI---CNSRNVDDEKELIDE 195

Query: 205 VRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQAYLKLASELIQQE 258
             K LG ++ + V PR+  + +A       I YD +   +  Y +LA ++ +  
Sbjct: 196 FAKKLGTQLIHFV-PRSNIVQKAEIRKMTVIEYDPESEQANEYRELAKKIYENT 248


>gnl|CDD|183173 PRK11519, PRK11519, tyrosine kinase; Provisional.
          Length = 719

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 4/91 (4%)

Query: 1   MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYD 59
           M + ++ ++ +      +GKT    NL+  ++   + VLLID D  +G     LG    +
Sbjct: 521 MMQAQNNVLMMTGVSPSIGKTFVCANLAAVISQTNKRVLLIDCDMRKGYTHELLGTNNVN 580

Query: 60  RKYSSYDLLIEEKNINQILIQTAIPNLSIIP 90
                 D+LI + +I      T+I N  +IP
Sbjct: 581 ---GLSDILIGQGDITTAAKPTSIANFDLIP 608


>gnl|CDD|148269 pfam06564, YhjQ, YhjQ protein.  This family consists of several
          bacterial YhjQ proteins. The function of this family is
          unknown. However, the family does contain a P-loop
          sequence motif suggesting a nucleotide binding
          function.
          Length = 244

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 15/31 (48%), Positives = 20/31 (64%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDP 45
          +GGVG T+    L  AL  +GE+VL+ID  P
Sbjct: 10 RGGVGTTSLTAALGWALQQLGESVLVIDASP 40


>gnl|CDD|183908 PRK13236, PRK13236, nitrogenase reductase; Reviewed.
          Length = 296

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 17/50 (34%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 1  MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
          M ++  R I     KGG+GK+TT+ N   A+A +G+ +L++  DP+ +++
Sbjct: 1  MTDENIRQIAFYG-KGGIGKSTTSQNTLAAMAEMGQRILIVGCDPKADST 49


>gnl|CDD|182204 PRK10037, PRK10037, cell division protein; Provisional.
          Length = 250

 Score = 37.5 bits (87), Expect = 0.004
 Identities = 35/152 (23%), Positives = 61/152 (40%), Gaps = 17/152 (11%)

Query: 8   IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDL 67
           I+ +   +GGVG T+    L+ +L  +GENVL+ID  P         ++   R+  +  L
Sbjct: 3   ILGLQGVRGGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVDFTHRQGWARAL 62

Query: 68  LIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALS--------VQ 119
           L  +   +  L  T         S +DLL    +   E++        L         ++
Sbjct: 63  LDGQDWRDAGLRYT---------SQLDLLPFGQLSIEEQENPQHWQTRLGDICSALQQLK 113

Query: 120 LTSDFSYIFLDCPPSFNLLTMNAMAAADSILV 151
            +  + +I LD P   + LT   ++  D  L 
Sbjct: 114 ASGRYQWILLDLPRGASPLTRQLLSLCDHSLA 145


>gnl|CDD|183906 PRK13234, nifH, nitrogenase reductase; Reviewed.
          Length = 295

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 14/36 (38%), Positives = 26/36 (72%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
          KGG+GK+TT+ N   AL  +G+ +L++  DP+ +++
Sbjct: 12 KGGIGKSTTSQNTLAALVEMGQKILIVGCDPKADST 47


>gnl|CDD|183907 PRK13235, nifH, nitrogenase reductase; Reviewed.
          Length = 274

 Score = 35.9 bits (83), Expect = 0.012
 Identities = 14/36 (38%), Positives = 25/36 (69%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
          KGG+GK+TT  N    LA +G+ V+++  DP+ +++
Sbjct: 9  KGGIGKSTTTQNTVAGLAEMGKKVMVVGCDPKADST 44


>gnl|CDD|163527 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood
           CpaE-like protein.  Members of this protein family
           belong to the MinD/ParA family of P-loop NTPases, and in
           particular show homology to the CpaE family of pilus
           assembly proteins (see PubMed:12370432). Nearly all
           members are found, not only in a gene context consistent
           with pilus biogenesis or a pilus-like secretion
           apparatus, but also near a DEAD/DEAH-box helicase,
           suggesting an involvement in DNA transfer activity. The
           model describes a clade restricted to the
           Actinobacteria.
          Length = 322

 Score = 35.4 bits (82), Expect = 0.014
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 6   SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL 57
             ++ +   +GG G +T A  L+ A A  G   LL+D DP G      G++L
Sbjct: 93  GVVVAVIGGRGGAGASTLAAALALAAARHGLRTLLVDADPWGG-----GLDL 139


>gnl|CDD|139909 PRK13849, PRK13849, putative crown gall tumor protein VirC1;
          Provisional.
          Length = 231

 Score = 34.8 bits (80), Expect = 0.024
 Identities = 16/38 (42%), Positives = 24/38 (63%)

Query: 7  RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
          +++T  + KGG GKTT  + L  ALA+ G+ V L + D
Sbjct: 2  KLLTFCSFKGGAGKTTALMGLCAALASDGKRVALFEAD 39


>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 = 34.5 bits (79), Expect = 0.028
 Identities = 17/38 (44%), Positives = 25/38 (65%)

Query: 7  RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
          ++IT  + KGG GKTT  + L +ALA+ G+ V L + D
Sbjct: 2  QLITFCSFKGGAGKTTALMGLCSALASDGKRVALFEAD 39


>gnl|CDD|183904 PRK13231, PRK13231, nitrogenase reductase-like protein; Reviewed.
          Length = 264

 Score = 32.1 bits (73), Expect = 0.14
 Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL 53
          KGG+GK+TT  N++ A +     VL+I  DP+ + +  L
Sbjct: 10 KGGIGKSTTVSNMAAAYSN-DHRVLVIGCDPKADTTRTL 47


>gnl|CDD|184096 PRK13505, PRK13505, formate--tetrahydrofolate ligase;
          Provisional.
          Length = 557

 Score = 31.7 bits (73), Expect = 0.22
 Identities = 9/24 (37%), Positives = 14/24 (58%)

Query: 17 GVGKTTTAINLSTALAAIGENVLL 40
          G GK+T  + L  AL  IG+  ++
Sbjct: 69 GEGKSTVTVGLGDALNKIGKKTVI 92


>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
           kinase Etk; Provisional.
          Length = 726

 Score = 31.0 bits (70), Expect = 0.32
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 1   MEEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
           M E ++ I+ I       GKT  +  L+  +A   + VL ID D
Sbjct: 526 MMETENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFIDAD 569


>gnl|CDD|183905 PRK13233, nifH, nitrogenase reductase; Reviewed.
          Length = 275

 Score = 30.9 bits (70), Expect = 0.32
 Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 15 KGGVGKTTTAINLSTALAAI-GENVLLIDLDPQGNAS 50
          KGG+GK+TT  N + A+A    + V +   DP+ +++
Sbjct: 10 KGGIGKSTTTQNTAAAMAYFHDKKVFIHGCDPKADST 46


>gnl|CDD|179865 PRK04570, PRK04570, cell division protein ZipA; Provisional.
          Length = 243

 Score = 29.9 bits (67), Expect = 0.68
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 132 PPSFNLLTMNAM-AAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTM 190
           P SF++  +  M   A +  + L     AL+   ++L TV+ +      A  + G++L  
Sbjct: 155 PGSFDMANIREMQTPAIAFFLTLPAPMTALDAWEKMLPTVQRM------AELLDGVVLD- 207

Query: 191 FDSRNSLSQQVVSDVRKNL 209
            DSRN+L +Q ++ +R  L
Sbjct: 208 -DSRNALGRQRIAHIRDEL 225


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

 Score = 29.2 bits (66), Expect = 1.1
 Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLDP-QGNASTGLGIELYDR 60
          G GKTT A  L+  L   G  V ++D D  + N S GLG    DR
Sbjct: 14 GAGKTTIARALAEKLREAGYPVEVLDGDAVRTNLSKGLGFSKEDR 58


>gnl|CDD|179349 PRK01906, PRK01906, tetraacyldisaccharide 4'-kinase; Provisional.
          Length = 338

 Score = 29.0 bits (65), Expect = 1.3
 Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 8/42 (19%)

Query: 16  GGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL 57
           GG GKT T I L  AL A G         P G  S G G ++
Sbjct: 67  GGTGKTPTVIALVDALRAAG-------FTP-GVVSRGYGAKI 100


>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
          Length = 241

 Score = 28.9 bits (65), Expect = 1.5
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDP 45
          KGGVGK+  A  ++   A+ G+  L ID DP
Sbjct: 11 KGGVGKSFIAATIAQYKASKGQKPLCIDTDP 41


>gnl|CDD|184097 PRK13506, PRK13506, formate--tetrahydrofolate ligase;
          Provisional.
          Length = 578

 Score = 28.8 bits (65), Expect = 1.5
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 17 GVGKTTTAINLSTALAAIGENV 38
          G GKT T I L+  L A+G+ V
Sbjct: 68 GEGKTVTTIGLTQGLNALGQKV 89


>gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein
          RadB.  This family consists exclusively of archaeal
          RadB protein, a homolog of bacterial RecA (TIGR02012),
          eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
          archaeal RadA (TIGR02236).
          Length = 209

 Score = 28.2 bits (63), Expect = 2.0
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 7/50 (14%)

Query: 7  RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIE 56
            IT      G GKT   + L+   A  G+ V+ ID       + GL  E
Sbjct: 12 GTITQIYGPPGSGKTNICMILAVNAARQGKKVVYID-------TEGLSPE 54


>gnl|CDD|163455 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
           subfamily.  Members of this protein family are the
           putative conjugative coupling factor, TraD (or TraG),
           rather distantly related to the well-characterized TraD
           of the F plasmid. Members are associated with
           conjugative-transposon-like mobile genetic elements of
           the class that includes SXT, an antibiotic resistance
           transfer element in some Vibrio cholerae strains.
          Length = 634

 Score = 28.4 bits (64), Expect = 2.2
 Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 17  GVGKTTTAINLSTALAAIGENVLLIDLDPQGNA 49
           GVGKT  A  L T     G+ V  I +DP+G+A
Sbjct: 186 GVGKTRLAELLITQDIRRGDVV--IVIDPKGDA 216


>gnl|CDD|182150 PRK09928, PRK09928, choline transport protein BetT; Provisional.
          Length = 679

 Score = 28.1 bits (63), Expect = 2.4
 Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 133 PSFNLLTMNAMAAADSILVPLQCEFFAL-EGLSQLLETVEEVRRTVNSALDIQGIILTMF 191
           P F+LL+  AM  A  I + L   FF++ E ++Q ++  E   +T+ +A   Q ++ T+F
Sbjct: 91  PEFSLLSWAAMLFAAGIGIDLM--FFSVAEPVTQYMQPPEGAGQTIEAAR--QAMVWTLF 146


>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 = 2.5
 Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 11/70 (15%)

Query: 156 EFFALEGLSQLLETVEEVRRTVNS--ALDIQGIIL--------TMFD-SRNSLSQQVVSD 204
               LE +       + V   V    A+D  G+ L        TMF+  +N L   + + 
Sbjct: 107 NLMGLEHIEAAQAAGKPVIFLVPHGWAIDYAGLRLASQGLPMVTMFNNHKNPLFDWLWNR 166

Query: 205 VRKNLGGKVY 214
           VR   GG VY
Sbjct: 167 VRSRFGGHVY 176


>gnl|CDD|181591 PRK08945, PRK08945, putative oxoacyl-(acyl carrier protein)
           reductase; Provisional.
          Length = 247

 Score = 27.9 bits (63), Expect = 2.7
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)

Query: 226 EAPSYGKPAII-YDLKCAGSQAYLKLASELIQQ 257
           EA    +PAII  DL  A  Q Y +LA  + +Q
Sbjct: 57  EAAGGPQPAIIPLDLLTATPQNYQQLADTIEEQ 89


>gnl|CDD|167327 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
          Length = 887

 Score = 27.5 bits (61), Expect = 3.9
 Identities = 8/24 (33%), Positives = 12/24 (50%)

Query: 95  LLGIEMILGGEKDRLFRLDKALSV 118
           LL ++  L  E   LF L + + V
Sbjct: 576 LLAVDGALARETHALFALFEHIDV 599


>gnl|CDD|184501 PRK14093, PRK14093,
           UDP-N-acetylmuramoylalanyl-D-glutamyl-2,
           6-diaminopimelate--D-alanyl-D-alanine ligase;
           Provisional.
          Length = 479

 Score = 27.0 bits (60), Expect = 4.9
 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)

Query: 5   KSRIITIANQKGGVGKTTTAINLSTALAAIGE 36
           ++++I +    G VGKT+T   L   L A GE
Sbjct: 107 EAKVIAVT---GSVGKTSTKEALRGVLGAQGE 135


>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 = 27.0 bits (59), Expect = 5.0
 Identities = 12/28 (42%), Positives = 15/28 (53%)

Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLD 44
          G GKTT A  L+  L   G  V+ ID +
Sbjct: 12 GSGKTTLARALARELGPPGGGVIYIDGE 39


>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
          Provisional.
          Length = 225

 Score = 26.8 bits (60), Expect = 5.7
 Identities = 10/27 (37%), Positives = 14/27 (51%)

Query: 16 GGVGKTTTAINLSTALAAIGENVLLID 42
           G GKT   + L+   A  G+ V+ ID
Sbjct: 32 PGSGKTNICLQLAVEAAKNGKKVIYID 58


>gnl|CDD|132074 TIGR03029, EpsG, chain length determinant protein tyrosine kinase
           EpsG.  The proteins in this family are homologs of the
           EpsG protein found in Methylobacillus strain 12S and are
           generally found in operons with other Eps homologs. The
           protein is believed to function as the protein tyrosine
           kinase component of the chain length regulator (along
           with the transmembrane component EpsF).
          Length = 274

 Score = 26.7 bits (59), Expect = 6.1
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 7   RIITIANQKGGVGKTTTAINLSTALAAIGENVLLID 42
           + + + + K G G +  A NL+   + +GE  LLID
Sbjct: 104 KALAVVSAKSGEGCSYIAANLAIVFSQLGEKTLLID 139


>gnl|CDD|182515 PRK10522, PRK10522, multidrug transporter membrane
           component/ATP-binding component; Provisional.
          Length = 547

 Score = 26.5 bits (59), Expect = 6.9
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 74  INQILIQTAIPNLSIIPSTMDLLGIEMI 101
           INQ LI+TA  +L ++P  + LL + M 
Sbjct: 36  INQRLIETADTSLLVLPEFLGLLLLLMA 63


>gnl|CDD|178325 PLN02724, PLN02724, Molybdenum cofactor sulfurase.
          Length = 805

 Score = 26.4 bits (58), Expect = 7.0
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 14/74 (18%)

Query: 50  STGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRL 109
            TGL   LYDR++    L        +IL Q  +P + +I + +DL   ++++     R 
Sbjct: 543 ETGL---LYDREWMIQSL------TGEILTQKKVPEMCLITTFIDLESGKLVV-----RA 588

Query: 110 FRLDKALSVQLTSD 123
            R D  L + L SD
Sbjct: 589 PRCDHKLEIPLESD 602


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

 Score = 26.6 bits (60), Expect = 7.0
 Identities = 13/24 (54%), Positives = 15/24 (62%)

Query: 17  GVGKTTTAINLSTALAAIGENVLL 40
           GVGKTTT   L+    A G+ VLL
Sbjct: 124 GVGKTTTIGKLAHKYKAQGKKVLL 147


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

 Score = 26.4 bits (59), Expect = 7.5
 Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 3/34 (8%)

Query: 17 GVGKTTTAINLSTALAAIGENVLL---IDLDPQG 47
          GVGKTTTA  L+ AL   G +      IDL   G
Sbjct: 56 GVGKTTTARILARALNYEGPDGDGGPTIDLCGVG 89


>gnl|CDD|184403 PRK13929, PRK13929, rod-share determining protein MreBH;
           Provisional.
          Length = 335

 Score = 26.4 bits (58), Expect = 8.2
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 6/79 (7%)

Query: 64  SYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFR---LDKALS--- 117
            Y+LLI E+   Q+ ++     +   P TM++ G +++ G  K        +  A+    
Sbjct: 196 KYNLLIGERTAEQVKMEIGYALIEHEPETMEVRGRDLVTGLPKTITLESKEIQGAMRESL 255

Query: 118 VQLTSDFSYIFLDCPPSFN 136
           + +         DCPP  +
Sbjct: 256 LHILEAIRATLEDCPPELS 274


>gnl|CDD|179086 PRK00683, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
           synthetase; Provisional.
          Length = 418

 Score = 26.3 bits (58), Expect = 8.3
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 5/44 (11%)

Query: 3   EKKSRIITIANQKGGV-----GKTTTAINLSTALAAIGENVLLI 41
           EK    +    +K GV      K TT   +  AL A+G  V++I
Sbjct: 275 EKPPHRMEYLGEKDGVHYINDSKATTVSAVEKALLAVGNQVIVI 318


>gnl|CDD|185113 PRK15191, PRK15191, fimbrial protein BcfF; Provisional.
          Length = 172

 Score = 26.2 bits (57), Expect = 8.3
 Identities = 14/41 (34%), Positives = 23/41 (56%)

Query: 19  GKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYD 59
           G T + + +S + AA   N  L+ L    + ++G+GI LYD
Sbjct: 77  GSTASGVTVSFSGAADSRNTDLLALTAGESDASGIGIALYD 117


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

 Score = 26.2 bits (59), Expect = 8.7
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 175 RTVNSALDIQGIILTMFDS 193
           +  N AL + G+ILT  D 
Sbjct: 234 KAFNEALGLTGVILTKLDG 252


>gnl|CDD|161846 TIGR00379, cobB, cobyrinic acid a,c-diamide synthase.  This model
          describes cobyrinic acid a,c-diamide synthase, the cobB
          (cbiA in Salmonella) protein of cobalamin biosynthesis.
          It is responsible for the amidation of carboxylic
          groups at positions A and C of either cobyrinic acid or
          hydrogenobrynic acid. NH(2) groups are provided by
          glutamine and one molecule of ATP hydrogenolyzed for
          each amidation.
          Length = 449

 Score = 26.3 bits (58), Expect = 9.4
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 9  ITIANQKGGVGKTTTAINLSTALAAIGENV 38
          + IA    GVGKTT +  +  AL+     V
Sbjct: 2  VVIAGTSSGVGKTTISTGIMKALSRRKLRV 31


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.317    0.135    0.365 

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: 4,115,967
Number of extensions: 259528
Number of successful extensions: 694
Number of sequences better than 10.0: 1
Number of HSP's gapped: 680
Number of HSP's successfully gapped: 75
Length of query: 265
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 173
Effective length of database: 4,006,537
Effective search space: 693130901
Effective search space used: 693130901
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.4 bits)