RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780831|ref|YP_003065244.1| hypothetical protein
CLIBASIA_03620 [Candidatus Liberibacter asiaticus str. psy62]
         (341 letters)



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

 Score =  267 bits (685), Expect = 3e-72
 Identities = 128/337 (37%), Positives = 197/337 (58%), Gaps = 5/337 (1%)

Query: 5   LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQ 64
           L+  +  +L     P  K+N+  ++ L  + ++ +T+++ + +P       + L+     
Sbjct: 13  LRAMVAGTLANFQHPTLKHNLTTLKALHHVALLDDTLHIELVMPFVWNSAFEELKEQCSA 72

Query: 65  IIQNIPTVKNAVVTLTENKNPPQQRNNL----NVKKFVAVASGKGGVGKSTTVVNIACAL 120
            +  I   K     L+ N    ++ NN      VK  +AV+SGKGGVGKS+T VN+A AL
Sbjct: 73  ELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALAL 132

Query: 121 KNKGKNVAILDADVYGPSIPKLLKISGKVEIS-DKKFLKPKENYGIKIMSMASLVDENVA 179
             +G  V ILDAD+YGPSIP +L    +   S D   + P   +G+   S+  LV ++ A
Sbjct: 133 AAEGAKVGILDADIYGPSIPTMLGAEDQRPTSPDGTHMAPIMAHGLATNSIGYLVTDDNA 192

Query: 180 MIWRGPMVQSAIMHMLHNVVWGQLDFLLIDMPPGTGDAHLTIAQKIPLSGVVIVSTPQDL 239
           M+WRGPM   A+M ML   +W  LD+L++DMPPGTGD  LT+AQ IP++G V+V+TPQD+
Sbjct: 193 MVWRGPMASKALMQMLQETLWPDLDYLVLDMPPGTGDIQLTLAQNIPVTGAVVVTTPQDI 252

Query: 240 ALIDVKRAISMYQKMNIPIIGMIENMSYFLASDTGKKYDLFGNGGARFEAEKIGIPFLES 299
           ALID K+ I M++K+ +P++G++ENMS  + S+ G    +FG GGA   AEK     L  
Sbjct: 253 ALIDAKKGIVMFEKVEVPVLGIVENMSMHICSNCGHHEPIFGTGGAEKLAEKYHTQLLGQ 312

Query: 300 VPFDMDVRVLSDLGIPIVVHNMNSATSEIYQEISDRI 336
           +P  + +R   D G P VV    S  + IY++++DR+
Sbjct: 313 MPLHISLREDLDRGTPTVVSRPESEFTAIYRQLADRV 349


>gnl|CDD|151135 pfam10609, ParA, ParA/MinD ATPase like.  This family contains
           ATPases involved in plasmid partitioning. It also
           contains the cytosolic Fe-S cluster assembling factor
           NBP35 which is required for biogenesis and export of
           both ribosomal subunits.
          Length = 81

 Score =  151 bits (384), Expect = 2e-37
 Identities = 50/81 (61%), Positives = 70/81 (86%)

Query: 203 LDFLLIDMPPGTGDAHLTIAQKIPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMI 262
           LD+L+IDMPPGTGD HLT+AQ +P+ G VIV+TPQD+AL+DV++AI M++K+N+PI+G++
Sbjct: 1   LDYLIIDMPPGTGDEHLTLAQSLPVDGAVIVTTPQDVALLDVRKAIDMFKKLNVPILGIV 60

Query: 263 ENMSYFLASDTGKKYDLFGNG 283
           ENMSYF+  D G+K  +FG G
Sbjct: 61  ENMSYFVCPDCGEKIYIFGKG 81


>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 = 84.8 bits (210), Expect = 3e-17
 Identities = 66/255 (25%), Positives = 115/255 (45%), Gaps = 43/255 (16%)

Query: 98  VAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLK-----------IS 146
           + +ASGKGG GK+T   N+  AL   GK V  LDAD+   ++  +L            ++
Sbjct: 3   ITIASGKGGTGKTTITANLGVALAKLGKKVLALDADITMANLELILGMEDKPVTLHDVLA 62

Query: 147 GKVEISDKKFLKPKENYGIKIMSMA-SLVDENVAMIWRGPMVQSAIMHMLHNVVWGQLDF 205
           G+ +I D  +  P   +G+K++    SL     A   +   V   I+           DF
Sbjct: 63  GEADIKDAIYEGP---FGVKVIPAGVSLEGLRKADPDKLEDVLKEIIDDT--------DF 111

Query: 206 LLIDMPPGTGD---AHLTIAQKIPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMI 262
           LLID P G        L  A ++     ++V  P+  ++ D  +   + +K+   I+G++
Sbjct: 112 LLIDAPAGLERDAVTALAAADEL-----LLVVNPEISSITDALKTKIVAEKLGTAILGVV 166

Query: 263 ENMSYFLASDTGKKYDLFGNGGARFEAEKI-GIPFLESVPFDMDVRVLSDLGIPIVVHNM 321
            N      ++ G++           E E I  +P L  VP D +VR  +  G P+V++N 
Sbjct: 167 LNRVTRDKTELGRE-----------EIETILEVPVLGVVPEDPEVRRAAAFGEPVVIYNP 215

Query: 322 NSATSEIYQEISDRI 336
           NS  ++ + E++  +
Sbjct: 216 NSPAAQAFMELAAEL 230


>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 = 67.4 bits (165), Expect = 5e-12
 Identities = 66/256 (25%), Positives = 116/256 (45%), Gaps = 34/256 (13%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLK----------- 144
           + + + SGKGGVGK+TT  N+  AL   GK V ++DAD+   ++  LL            
Sbjct: 2   RVIVITSGKGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDLLLGLENRIVYTLVD 61

Query: 145 -ISGKVEISDKKFLKPKENYGIKIMSMASLVDENVAMIWRGPMVQSAIMHMLHNVVWGQL 203
            + G+  +  +  +K K    + ++  +   D++         V    M  L N +  + 
Sbjct: 62  VVEGECRL-QQALIKDKRLKNLYLLPASQTRDKD--------AVTPEQMKKLVNELKEEF 112

Query: 204 DFLLIDMPPG--TGDAHLTIAQKIPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGM 261
           D+++ID P G  +G     +A   P    ++V+TP+  A+ D  R I + +   I  I +
Sbjct: 113 DYVIIDCPAGIESG-FRNAVA---PADEAIVVTTPEVSAVRDADRVIGLLEAKGIEKIHL 168

Query: 262 IENMSYFLASDTGKKYDLFGNGGARFEAEKIGIPFLESVPFDMDVRVLSDLGIPIVVHNM 321
           I N    L  +  KK D+          E + IP +  +P D  + V ++ G P+V+ N 
Sbjct: 169 IVNR---LRPEMVKKGDMLSVDDVL---EILSIPLIGVIPEDEAIIVSTNKGEPVVL-ND 221

Query: 322 NSATSEIYQEISDRIQ 337
            S   + ++ I+ RI 
Sbjct: 222 KSRAGKAFENIARRIL 237


>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 = 49.4 bits (118), Expect = 1e-06
 Identities = 47/189 (24%), Positives = 81/189 (42%), Gaps = 38/189 (20%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLK----------- 144
           K + + S K G GKSTT  NIA A    G    ++D D+    +    K           
Sbjct: 18  KVLLITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNSVMSGTFKSQNKITGLTNF 77

Query: 145 ISGKVEISDKKFLKPKENYGIKIMSMASLVDENVAMIWRGP-------MVQSAIMHMLHN 197
           +SG  ++SD           I   ++     EN+ +I  GP       ++QS+    L  
Sbjct: 78  LSGTTDLSD----------AICDTNI-----ENLFVITSGPVPPNPTELLQSSNFKTLIE 122

Query: 198 VVWGQLDFLLIDMPP-GT-GDAHLTIAQKIPLSGVVIVSTPQDLALIDVKRAISMYQKMN 255
            +    D+++ID PP GT  DA + IA+       ++V+   ++   DV++A    ++  
Sbjct: 123 TLRKYFDYIIIDTPPIGTVTDAAI-IARAC--DASILVTDAGEIKKRDVQKAKEQLEQTG 179

Query: 256 IPIIGMIEN 264
              +G++ N
Sbjct: 180 SNFLGVVLN 188


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

 Score = 44.8 bits (106), Expect = 3e-05
 Identities = 18/43 (41%), Positives = 24/43 (55%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPS 138
           K +AV + KGG GK+T   N+A  L   G  V ++D D  G S
Sbjct: 1   KIIAVLNQKGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSS 43


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

 Score = 43.2 bits (102), Expect = 1e-04
 Identities = 19/31 (61%), Positives = 22/31 (70%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           GKGG+GKSTTV NIA AL   GK V ++  D
Sbjct: 8   GKGGIGKSTTVCNIAAALAESGKKVLVVGCD 38


>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 = 42.7 bits (101), Expect = 1e-04
 Identities = 18/38 (47%), Positives = 24/38 (63%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           K +A+   KGGVGK+T   N+A ALK  G+ V  +D D
Sbjct: 2   KVIAIVGVKGGVGKTTLTANLASALKLLGEPVLAIDLD 39


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

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 18/39 (46%), Positives = 25/39 (64%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADV 134
           + + V SGKGGVGK+T+   IA  L  KGK   ++D D+
Sbjct: 3   RIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDI 41


>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 = 42.0 bits (99), Expect = 2e-04
 Identities = 18/37 (48%), Positives = 23/37 (62%)

Query: 97  FVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
            + V + KGG GKSTT V++A AL   G  VA +D D
Sbjct: 2   VIVVGNEKGGSGKSTTAVHVAVALLYLGARVATIDLD 38


>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 = 42.0 bits (99), Expect = 2e-04
 Identities = 19/31 (61%), Positives = 21/31 (67%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           GKGG+GKSTT  NIA AL   GK V I+  D
Sbjct: 7   GKGGIGKSTTTQNIAAALAEMGKKVMIVGCD 37


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

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNV 127
           GKGG+GKSTT  N++ A    GK V
Sbjct: 9   GKGGIGKSTTSSNLSAAFAKLGKKV 33


>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 = 40.6 bits (95), Expect = 6e-04
 Identities = 55/235 (23%), Positives = 103/235 (43%), Gaps = 51/235 (21%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD---------VYGPSIPKLLKISGKVEISD 153
           GKGG GKS T  N++  +   GK V  L  D           G S+P +++++ + +++ 
Sbjct: 7   GKGGSGKSFTTTNLSHMMAEMGKRVLQLGCDPKHDSTSLLFGGISLPTIIEVATEKKLAG 66

Query: 154 KKFLKPKENYGIKIMSMASLVDENVAMIWRGPMVQSA-----IMH---MLHNVVWGQ--L 203
           ++       +   IM+ +  V     M   GP V        I+H   +L  + +     
Sbjct: 67  EEVKVGDVCFKTTIMNGSGGV---YGMELGGPEVGRGCGGRGIIHGFDLLEKLGFHDWDF 123

Query: 204 DFLLIDMPPGTGDA-----HLTIAQKIPLSGVVIVSTPQDLALI----DVKRAISMYQKM 254
           DF+L+D     GD         +A+   L+  VIV    D   +    ++  A+  ++K+
Sbjct: 124 DFVLMDF---LGDVVCGGFATPLARS--LAEEVIVIGSNDRQSLYVANNICNAVEYFRKL 178

Query: 255 --NIPIIGMIENMSYFLASDTGKKYDLFGNGGARFEAEKIGIPFLESVPFDMDVR 307
              + ++G++ N           + D  G+G A+  A ++GIP L ++P D ++R
Sbjct: 179 GGRVGLLGLVVN-----------RDD--GSGEAQAFAREVGIPVLAAIPADEELR 220


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

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 16/38 (42%), Positives = 24/38 (63%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           K +   S KGG GK+T ++ +  AL + GK VA+ +AD
Sbjct: 2   KLLTFCSFKGGAGKTTALMGLCAALASDGKRVALFEAD 39


>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 = 39.6 bits (93), Expect = 0.001
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 79  LTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTVVNIACAL-KNKGKNVAILDADVYGP 137
           L  N     ++ N N+   + V S   G GKS T +N+A +L +   K V ++DAD+  P
Sbjct: 22  LLANAFSANRKKNNNL---IMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRP 78

Query: 138 SIPKLLKISGKVEISD 153
           S+ + L +  +  +SD
Sbjct: 79  SLHRTLGLEAEPGLSD 94


>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 = 39.4 bits (92), Expect = 0.001
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNV 127
           GKGG+GKSTT  N++ A    GK V
Sbjct: 7   GKGGIGKSTTSSNLSVAFAKLGKRV 31


>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 = 38.7 bits (90), Expect = 0.002
 Identities = 15/38 (39%), Positives = 24/38 (63%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           + +   S KGG GK+T ++ +  AL + GK VA+ +AD
Sbjct: 2   QLITFCSFKGGAGKTTALMGLCSALASDGKRVALFEAD 39


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

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 62  AQQIIQNIP-------TVKNAVVTLTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTVV 114
           A+++++ +P         +     L +      + + +  +  V    G  GVGK+TT+ 
Sbjct: 153 ARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLA 212

Query: 115 NIA--CALKNKGKNVAILDADVY 135
            +A    L++  K VA++  D Y
Sbjct: 213 KLAARFVLEHGNKKVALITTDTY 235


>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 = 37.5 bits (87), Expect = 0.005
 Identities = 39/177 (22%), Positives = 74/177 (41%), Gaps = 13/177 (7%)

Query: 95  KKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISGKVEISDK 154
           +K +AV S K G G S    N+A      G+   ++DA++  P   +  K+S +  +SD 
Sbjct: 103 RKALAVVSAKSGEGCSYIAANLAIVFSQLGEKTLLIDANLRDPVQHRNFKLSEQRGLSDI 162

Query: 155 KFLKPKENYGIKIMSMASLVDENVAMIWRGP-----MVQSAIMHMLHNVVWGQLDFLLID 209
              +        I  + +L + +V      P     ++       L N V G  D +++D
Sbjct: 163 LAGRSDLE---VITHIPALENLSVLPAGAIPPNPQELLARPAFTDLLNKVMGDYDVVIVD 219

Query: 210 MPPG--TGDAHLTIAQKIPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMIEN 264
            P    + DA + +A +    G +IVS   +  L ++         + + ++G + N
Sbjct: 220 TPSAEHSSDAQI-VATRA--RGTLIVSRVNETRLHELTSLKEHLSGVGVRVVGAVLN 273


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

 Score = 36.3 bits (84), Expect = 0.013
 Identities = 21/48 (43%), Positives = 27/48 (56%), Gaps = 7/48 (14%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAI---LDAD----VYGPSIPKLL 143
           GKGG+GKSTTV N+A A  N  + + I     AD    + G  IP +L
Sbjct: 9   GKGGIGKSTTVSNMAAAYSNDHRVLVIGCDPKADTTRTLCGKRIPTVL 56



 Score = 29.4 bits (66), Expect = 1.2
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 33  EIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTE 81
           E++IV +  Y+S+   + IA  ++ L+     II N   + N V  ++E
Sbjct: 141 EVYIVTSGEYMSLYAANNIARGIKKLKGKLGGIICNCRGIDNEVEIVSE 189


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

 Score = 35.4 bits (81), Expect = 0.021
 Identities = 17/41 (41%), Positives = 22/41 (53%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLL 143
           GKGG+GKSTT  N+  AL   G  + ++  D    S   LL
Sbjct: 8   GKGGIGKSTTTQNLTAALSTMGNKILLVGCDPKADSTRMLL 48


>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 = 35.0 bits (81), Expect = 0.031
 Identities = 18/48 (37%), Positives = 24/48 (50%)

Query: 98  VAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKI 145
           VAV  G+GG G ST    +A A    G    ++DAD +G  +  LL  
Sbjct: 96  VAVIGGRGGAGASTLAAALALAAARHGLRTLLVDADPWGGGLDLLLGA 143


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

 Score = 34.5 bits (80), Expect = 0.039
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 62  AQQIIQNIP--------TVKNAVVTLTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTV 113
           A+++++ +         T    ++ L  N  P +  + L     VA+  G  GVGK+TT+
Sbjct: 180 AEKLLKLLLEHMPPRERTAWRYLLELLANMIPVRVEDILKQGGVVALV-GPTGVGKTTTL 238

Query: 114 VNIA--CALKNKGKNVAILDADVY 135
             +A   AL    K VA++  D Y
Sbjct: 239 AKLAARYALLYGKKKVALITLDTY 262


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

 Score = 34.4 bits (79), Expect = 0.045
 Identities = 18/41 (43%), Positives = 21/41 (51%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLL 143
           GKGG+GKSTT  N    L   GK V ++  D    S   LL
Sbjct: 8   GKGGIGKSTTTQNTVAGLAEMGKKVMVVGCDPKADSTRLLL 48


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

 Score = 33.6 bits (77), Expect = 0.072
 Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 103 GKGGVGKSTTVVNIACALKN-KGKNVAILDAD 133
           GKGG+GKSTT  N A A+     K V I   D
Sbjct: 9   GKGGIGKSTTTQNTAAAMAYFHDKKVFIHGCD 40


>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 = 33.4 bits (77), Expect = 0.081
 Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 90  NNLNVKKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           N  NV  FV V     GVGK+TT+  +A  LK +GK+V +   D
Sbjct: 70  NKPNVILFVGV----NGVGKTTTIAKLANKLKKQGKSVLLAAGD 109


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

 Score = 33.4 bits (77), Expect = 0.088
 Identities = 16/41 (39%), Positives = 21/41 (51%)

Query: 95  KKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVY 135
           K  V V  G  G GK+TT+  +A  LK  G +V I   D +
Sbjct: 139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTF 179


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

 Score = 32.9 bits (75), Expect = 0.11
 Identities = 15/31 (48%), Positives = 19/31 (61%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           GKGG+GKSTT  N   AL   G+ + I+  D
Sbjct: 11  GKGGIGKSTTSQNTLAALVEMGQKILIVGCD 41


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

 Score = 32.6 bits (75), Expect = 0.15
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 102 SGKGGVGKSTTVVNIACALKNKGKNV 127
           +G  GVGK+T V+ IA  LK +G  V
Sbjct: 6   TGPPGVGKTTLVLKIAELLKEEGYKV 31


>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 = 32.0 bits (73), Expect = 0.21
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISG 147
           G  G GK+   + +A     +GK V  +D +  G S  +  +I+ 
Sbjct: 19  GPPGSGKTNICMILAVNAARQGKKVVYIDTE--GLSPERFKQIAE 61


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

 Score = 31.7 bits (73), Expect = 0.25
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 106 GVGKSTTVVNIACALKNKGKNVAILDADVYGP 137
           G GK+TT   +A   K KG  V ++ AD Y P
Sbjct: 105 GSGKTTTAAKLARYFKKKGLKVGLVAADTYRP 136


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

 Score = 31.9 bits (72), Expect = 0.25
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           GKGG+GKSTT  N   A+   G+ + I+  D
Sbjct: 13  GKGGIGKSTTSQNTLAAMAEMGQRILIVGCD 43


>gnl|CDD|165315 PHA03016, PHA03016, hypothetical protein; Provisional.
          Length = 441

 Score = 31.9 bits (72), Expect = 0.26
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 13  LKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTV 72
           L +L  P +K  I  ++  + IF++ N   +       I  Q+Q+L  +  +  + I  +
Sbjct: 233 LDILFTPDKKIEINNIEISNNIFLIDNKQNV-------INDQIQNLFHSFIKKHKIIKEI 285

Query: 73  KNAVVTLTENKNPPQQRNNLNVK 95
            N ++   + K+      N N+K
Sbjct: 286 NNFIILFNKYKDELSFNINQNLK 308


>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 = 31.1 bits (70), Expect = 0.42
 Identities = 39/210 (18%), Positives = 78/210 (37%), Gaps = 14/210 (6%)

Query: 78  TLTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGP 137
            L   +    +  ++   + V     +  +GKS    N A  + + GK   ++DAD    
Sbjct: 529 ELRVKEEAVAEAKSVAEPEVVETQRPRPVLGKSDIEANAAALIASGGKRALLIDADGRKA 588

Query: 138 SIPKLLKISGKVEISDKKFLKPKEN---YGIKIMSMASLVDENVAMIWRGP--MVQSAIM 192
           ++ ++L      E+S    L          +     ASL   +  +   G   ++ S  M
Sbjct: 589 ALSQIL---VAREVSGLLDLLAGLRSLLLDLTASGAASLPMLDSGLFPHGITELLASPAM 645

Query: 193 HMLHNVVWGQLDFLLIDMPPGTGDAHLTIAQKIPLSGVVIVSTPQDLALIDVKRA-ISMY 251
             L        D +++D+        +  A    L+ ++++ T  D  +++  RA     
Sbjct: 646 FSLVIHARLYSDCVVVDVGTADPVRDMRAAA--RLAIIMLLVTAYDRVVVECGRADAQGI 703

Query: 252 QKMNIPIIGMIENMSYFLASDTGKKYDLFG 281
            ++N  + G+  NM   L  +   KY   G
Sbjct: 704 SRLNGEVTGVFLNM---LDPNDEVKYIESG 730


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

 Score = 30.8 bits (69), Expect = 0.48
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 103 GKGGVGKSTTVVNIA--CALKNKGKNVAILDADVYGPSIPKLLKISGKV 149
           G  GVGK+TT   +A  C ++     VA+L  D Y     + L+I GK+
Sbjct: 144 GPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKI 192


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

 Score = 30.1 bits (68), Expect = 0.87
 Identities = 15/34 (44%), Positives = 18/34 (52%)

Query: 100 VASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           V  GKGGVGKS     IA    +KG+    +D D
Sbjct: 7   VLQGKGGVGKSFIAATIAQYKASKGQKPLCIDTD 40


>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 = 29.9 bits (68), Expect = 0.90
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 98  VAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           +AV + KGG GK+TT  ++A  L  +G  V  +D D
Sbjct: 107 IAVTNFKGGSGKTTTAAHLAQYLALRGYRVLAIDLD 142


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

 Score = 29.7 bits (66), Expect = 1.1
 Identities = 33/168 (19%), Positives = 72/168 (42%), Gaps = 10/168 (5%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVY-GPSIPKLLKISGKVEISDKKFLKPKE 161
           G+ GVGK+TT+V +   L  + + V  +  D +   ++ +    + K+++       P E
Sbjct: 213 GQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAE 272

Query: 162 -NYGIKIMSMASLVDEN-VAMIWRGPMVQSAIMHMLHNVVWGQLDFLLIDMPPGTGDAH- 218
               ++ M+  + VD   +  + R  + + ++  +         D        G   A  
Sbjct: 273 LEEAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSGMKSADV 332

Query: 219 LTIAQK---IPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMIE 263
           +TI  K   IP+ G +I    +   + D+    ++ Q+ N+P++ M +
Sbjct: 333 MTILPKLAEIPIDGFIITKMDETTRIGDL---YTVMQETNLPVLYMTD 377


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

 Score = 29.7 bits (68), Expect = 1.2
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 106 GVGKSTTVVNIACALKNKGKNVAILDAD 133
           GVGK+TT+  +A   K +GK V +   D
Sbjct: 124 GVGKTTTIGKLAHKYKAQGKKVLLAAGD 151


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

 Score = 29.6 bits (66), Expect = 1.2
 Identities = 13/36 (36%), Positives = 23/36 (63%)

Query: 98  VAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           + VA+ KGGV K++  V++A  L  KG  V +++ +
Sbjct: 109 IGVAAHKGGVYKTSVSVHLAQDLALKGLRVLLVEGN 144


>gnl|CDD|152384 pfam11949, DUF3466, Protein of unknown function (DUF3466).  This
           family of proteins are functionally uncharacterized.
           This protein is found in bacteria. Proteins in this
           family are typically between 564 to 612 amino acids in
           length.
          Length = 589

 Score = 29.3 bits (66), Expect = 1.3
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 4/59 (6%)

Query: 251 YQKMNIPIIGMIENM--SYFLASDTGKKYDLFGNGGARFEAEKI--GIPFLESVPFDMD 305
           Y+ + I  I +      +Y +A +   ++   G    +        G+ + E  PF  D
Sbjct: 25  YEIVEISDIDLGGTYESTYGVAINADGEFVGAGETRKKLSTGDADDGVSYREEGPFATD 83


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

 Score = 29.1 bits (65), Expect = 1.5
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 93  NVKKFVAVASGKGGVGKSTTVVNIAC----ALKNKGKNVAILDADVY 135
           N+KK V +  G  GVGK+TT+  +A        +K  N+ I+  D Y
Sbjct: 171 NLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNY 217


>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 = 29.2 bits (66), Expect = 1.6
 Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 60  SNAQQIIQNIPTVKNAVVTLTENKNPPQQRNNLNVKKFVAVASGKGGVGKSTTVVNIACA 119
           S  QQ I+    V   +V +   +N     N       V +  G  G GK+TT   +A  
Sbjct: 68  SPGQQFIK---IVHEELVAILGGEN--ASLNLAKKPPTVILMVGLQGSGKTTTCGKLAYY 122

Query: 120 LKNK-GKNVAILDADVYGPSIPKLLKISGK 148
           LK K GK V ++  D+Y P+  + LK+ G+
Sbjct: 123 LKKKQGKKVLLVACDLYRPAAIEQLKVLGQ 152


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

 Score = 29.0 bits (66), Expect = 1.7
 Identities = 11/24 (45%), Positives = 12/24 (50%)

Query: 106 GVGKSTTVVNIACALKNKGKNVAI 129
           G GKST  V +  AL   GK   I
Sbjct: 69  GEGKSTVTVGLGDALNKIGKKTVI 92


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

 Score = 29.1 bits (65), Expect = 1.8
 Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 103 GKGGVGKSTTVVNIA--CALKNKGKNVAILDADVYGPSIPKLLKISGKV 149
           G  GVGK+TT   +A    +++    VA+L  D Y     + L+I GK+
Sbjct: 198 GPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKL 246


>gnl|CDD|162148 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
           Toc86/159, G and M domains.  The long precursor of the
           86K protein originally described is proposed to have
           three domains. The N-terminal A-domain is acidic,
           repetitive, weakly conserved, readily removed by
           proteolysis during chloroplast isolation, and not
           required for protein translocation. The other domains
           are designated G (GTPase) and M (membrane anchor); this
           family includes most of the G domain and all of M.
          Length = 763

 Score = 28.8 bits (64), Expect = 2.0
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 16/75 (21%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISG-----KVEISDKKFL 157
           GK GVGKS T+ +I       G+     DA  +G     + +I G     K+ + D   L
Sbjct: 125 GKSGVGKSATINSIF------GEVKFSTDA--FGMGTTSVQEIEGLVQGVKIRVIDTPGL 176

Query: 158 KP---KENYGIKIMS 169
           K     ++   KI+S
Sbjct: 177 KSSASDQSKNEKILS 191


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

 Score = 28.9 bits (65), Expect = 2.0
 Identities = 13/31 (41%), Positives = 15/31 (48%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           G  G GK+T    +   LK K  NV  LD D
Sbjct: 14  GLAGSGKTTIAKALYERLKLKYSNVIYLDGD 44


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

 Score = 28.9 bits (64), Expect = 2.2
 Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 86  PQQRNNLNVKKFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           P +R + +++  +AV + KGG GK+TT  ++A  L  +G  V  +D D
Sbjct: 113 PHRRGSEHLQ-VIAVTNFKGGSGKTTTSAHLAQYLALQGYRVLAVDLD 159


>gnl|CDD|178630 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
           protein; Provisional.
          Length = 697

 Score = 28.7 bits (64), Expect = 2.2
 Identities = 20/69 (28%), Positives = 25/69 (36%), Gaps = 18/69 (26%)

Query: 146 SGKVEISDKKFLKPKENYGIKIMSM-----------ASLVDENVAMIWRGPMVQSAIMHM 194
           SG  E   + F    EN+ IK  +M             L+DE  AMI R P   +  M  
Sbjct: 439 SGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNM-- 496

Query: 195 LHNVVWGQL 203
                W  L
Sbjct: 497 -----WAAL 500


>gnl|CDD|181855 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
          Length = 332

 Score = 28.6 bits (65), Expect = 2.4
 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)

Query: 102 SGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPS 138
           +G  GVGKST +  +   L  +G  VA+L  D   PS
Sbjct: 62  TGVPGVGKSTFIEALGMHLIEQGHKVAVLAVD---PS 95


>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 = 28.5 bits (63), Expect = 2.6
 Identities = 10/31 (32%), Positives = 14/31 (45%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDAD 133
           G  G GK+T    +A  L   G  V  +D +
Sbjct: 9   GPPGSGKTTLARALARELGPPGGGVIYIDGE 39


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

 Score = 28.5 bits (65), Expect = 2.7
 Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 106 GVGKSTTVVNIACALKNK-GKNVAILDADVYGPSIPKLLKISGK 148
           G GK+TT   +A  LK K  K V ++ ADVY P+  + LK  G+
Sbjct: 110 GAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGE 153


>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
          family.  In the case of PUF60 (GP|6176532), in complex
          with p54, and in the presence of U2AF, facilitates
          association of U2 snRNP with pre-mRNA.
          Length = 612

 Score = 28.5 bits (63), Expect = 2.9
 Identities = 10/38 (26%), Positives = 14/38 (36%)

Query: 57 SLRSNAQQIIQNIPTVKNAVVTLTENKNPPQQRNNLNV 94
          S     Q +    P V   +  L +   PPQQ   + V
Sbjct: 1  SADIENQPVAAFRPAVSVPMPVLGDKWKPPQQTGEVKV 38


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

 Score = 28.4 bits (64), Expect = 2.9
 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 8/37 (21%)

Query: 102 SGKGGVGKSTTVVNIACA----LKNKGKNVAILDADV 134
           +G  G GK+T    IA A    L+  G  V +LD D 
Sbjct: 10  TGLSGAGKTT----IARALAEKLREAGYPVEVLDGDA 42


>gnl|CDD|182028 PRK09685, PRK09685, DNA-binding transcriptional activator FeaR;
           Provisional.
          Length = 302

 Score = 28.1 bits (63), Expect = 3.3
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 12/61 (19%)

Query: 215 GDAH-LTIAQK-----IPLSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMIENMSYF 268
            DAH  T+ Q      I      +     D+ LID  R  S+Y +      G+ E +S  
Sbjct: 68  DDAHFFTVFQLSGHAIIEQDDRQVQLAAGDITLIDASRPCSIYPQ------GLSEQISLL 121

Query: 269 L 269
           L
Sbjct: 122 L 122


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

 Score = 28.0 bits (63), Expect = 3.5
 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)

Query: 103 GKGGVGKSTTVVNIA--CALKNKGKNVAILDADVY 135
           G  GVGK+TT   +A  C +++    VA+L  D Y
Sbjct: 263 GPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSY 297


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

 Score = 28.0 bits (63), Expect = 3.8
 Identities = 9/23 (39%), Positives = 12/23 (52%)

Query: 108 GKSTTVVNIACALKNKGKNVAIL 130
           GK+T +  I   LK +G  VA  
Sbjct: 13  GKTTLIEKILKNLKERGYRVATA 35


>gnl|CDD|161995 TIGR00682, lpxK, tetraacyldisaccharide 4'-kinase.  Also called
           lipid-A 4'-kinase. This essential gene encodes an enzyme
           in the pathway of lipid A biosynthesis in Gram-negative
           organisms. A single copy of this protein is found in
           Gram-negative bacteria. PSI-BLAST converges on this set
           of apparent orthologs without identifying any other
           homologs.
          Length = 311

 Score = 27.8 bits (62), Expect = 4.1
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 105 GGVGKSTTVVNIACALKNKGKNVAIL 130
           GG GK+  VV +A  LK++G  V +L
Sbjct: 39  GGTGKTPVVVWLAELLKDRGLRVGVL 64


>gnl|CDD|161831 TIGR00345, arsA, arsenite-activated ATPase (arsA).  The N-terminal
           50 amino acids hits Pfam families NB-ARC and fer4_NifH.
           residues 4-11 of the seed alignment contain a potential
           ATP binding site. The function of the gene product is to
           catalyze the extrusion of the oxyanions arsenite,
           antimonite and arsenate for detoxification. Some members
           of this family contain a duplication so the model finds
           hits twice.
          Length = 284

 Score = 27.8 bits (62), Expect = 4.1
 Identities = 10/38 (26%), Positives = 19/38 (50%)

Query: 227 LSGVVIVSTPQDLALIDVKRAISMYQKMNIPIIGMIEN 264
            +  V+V  P+ ++L + +RA     K  I +  +I N
Sbjct: 189 RTSFVLVVIPEKMSLYESERAHKELAKYGIKVDAVIVN 226


>gnl|CDD|179218 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase; Validated.
          Length = 451

 Score = 27.8 bits (63), Expect = 4.2
 Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 3/30 (10%)

Query: 99  AVASGKGGVGKSTTVVNIACALKNKGKNVA 128
           A ASG    GK+T  + +  AL+ +G  V 
Sbjct: 10  APASG---SGKTTVTLGLMRALRRRGLRVQ 36


>gnl|CDD|182800 PRK10875, recD, exonuclease V subunit alpha; Provisional.
          Length = 615

 Score = 27.6 bits (62), Expect = 4.4
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 98  VAVASGKGGVGKSTTVVNIACAL 120
           ++V SG  G GK+TTV  +  AL
Sbjct: 169 ISVISGGPGTGKTTTVAKLLAAL 191


>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 = 27.8 bits (62), Expect = 4.4
 Identities = 16/39 (41%), Positives = 20/39 (51%)

Query: 102 SGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIP 140
           +G  GVGKST    +A  L  K  +V IL  D+   S P
Sbjct: 5   TGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIRESFP 43


>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 = 27.3 bits (61), Expect = 5.1
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 102 SGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISGKV 149
            G    GK+T +  +  ALK +G  VA +  D +   I K  K S + 
Sbjct: 5   VGPKNSGKTTLIERLVKALKARGYRVATIKHDHHDFDIDKNGKDSYRH 52


>gnl|CDD|149371 pfam08283, Gemini_AL1_M, Geminivirus rep protein central domain. 
          This is the cetral domain of the geminivirus rep
          proteins.
          Length = 106

 Score = 27.4 bits (61), Expect = 5.9
 Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)

Query: 42 YLSI---TVPHTIAHQLQSLRSNAQQIIQNIP 70
           LSI     P   A QL +L  NA ++  + P
Sbjct: 21 ALSIIKEEFPKDWALQLHNLEYNANRLFPDPP 52


>gnl|CDD|177806 PLN00412, PLN00412, NADP-dependent glyceraldehyde-3-phosphate
           dehydrogenase; Provisional.
          Length = 496

 Score = 27.4 bits (61), Expect = 6.1
 Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 201 GQLDFLLIDMPPGTGDAHLTIAQKIPLSGVVIVSTP 236
           G+  FL+ D  PG       +  KIPL GVV+   P
Sbjct: 133 GEGKFLVSDSFPGNERNKYCLTSKIPL-GVVLAIPP 167


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

 Score = 27.1 bits (60), Expect = 6.2
 Identities = 11/29 (37%), Positives = 20/29 (68%)

Query: 104 KGGVGKSTTVVNIACALKNKGKNVAILDA 132
           +GGVG ++    +A +L+  G+NV ++DA
Sbjct: 10  RGGVGTTSITAALAWSLQMLGENVLVIDA 38


>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
           protein; Provisional.
          Length = 388

 Score = 27.2 bits (61), Expect = 6.3
 Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 5/37 (13%)

Query: 96  KFVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDA 132
           KF  V  G G VG S     +A AL   G  VA+L  
Sbjct: 5   KFDVVVVGGGLVGAS-----LALALAQSGLRVALLAP 36


>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 = 27.0 bits (60), Expect = 6.8
 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)

Query: 102 SGKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIP 140
           +G  G GKST +  +   L+ +G  VA++  D   PS P
Sbjct: 40  TGTPGAGKSTLLEALGMELRRRGLKVAVIAVD---PSSP 75


>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 = 27.1 bits (60), Expect = 6.9
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 61  NAQQIIQNIPTVKNAVVTLTENKNPP--QQRNNLNVKKFVAVASGKGGVGKSTTVVNIAC 118
           N +++IQ+   V   +  L +        ++   NV  FV    G  G GK+TT   +A 
Sbjct: 69  NKRKMIQHA--VFKELCNLVDPGVEAFTPKKGKQNVIMFV----GLQGSGKTTTCTKLAY 122

Query: 119 ALKNKGKNVAILDADVY 135
             + KG    ++ AD +
Sbjct: 123 YYQRKGFKPCLVCADTF 139


>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
           Envelope Protein Translocase). 
          Length = 313

 Score = 26.8 bits (59), Expect = 8.1
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 93  NVKKFVAVASGKGGVGKSTTVVNI 116
           +V     +  GKGGVGKS+TV +I
Sbjct: 35  DVSSLTILVMGKGGVGKSSTVNSI 58


>gnl|CDD|148179 pfam06418, CTP_synth_N, CTP synthase N-terminus.  This family
           consists of the N-terminal region of the CTP synthase
           protein (EC:6.3.4.2). This family is found in
           conjunction with pfam00117 located in the C-terminal
           region of the protein. CTP synthase catalyses the
           synthesis of CTP from UTP by amination of the pyrimidine
           ring at the 4-position.
          Length = 275

 Score = 26.7 bits (60), Expect = 8.4
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)

Query: 96  KFVAVASGKGGV----GKSTTVVNIACALKNKGKNVAILDADVY 135
           K++ V    GGV    GK  T  ++   LK++G  V I   D Y
Sbjct: 2   KYIFVT---GGVVSSLGKGITAASLGRLLKSRGLKVTIQKIDPY 42


>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 = 26.7 bits (59), Expect = 8.8
 Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 9/53 (16%)

Query: 87  QQRNNLNVKK-FVAVASGKGGVGKSTTVVNIACA----LKNKGKNVAILDADV 134
            +R  LN  +  V   +G  G GKST    IA A    L++KG  V +LD D 
Sbjct: 8   DERQALNGHRGVVIWLTGLSGSGKST----IANALEKKLESKGYRVYVLDGDN 56


>gnl|CDD|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase
           N; Provisional.
          Length = 342

 Score = 26.5 bits (58), Expect = 9.3
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 8   QIVDS-LKVLSIPGEK-NNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQI 65
           +IVD  L+V  I G++  N+V M  + E    HN  Y ++    +I H   +    A++I
Sbjct: 137 EIVDQVLQVEKIVGDRATNVVFMG-MGEPM--HN--YFNVIRAASILHDPDAFNLGAKRI 191

Query: 66  IQNIPTVKNAVVTLTENKNP 85
             +   V N +    ENK P
Sbjct: 192 TISTSGVVNGIRRFIENKEP 211


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

 Score = 26.8 bits (60), Expect = 9.6
 Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 103 GKGGVGKSTTVVNIACALKNKGKNVAILDADVYGPSIPKLLKISGK-VEISDKKFL--KP 159
           G  G GK+   + +A      GK V  +D +  G S  +  +I+G+  E      +  +P
Sbjct: 30  GPPGSGKTNICLQLAVEAAKNGKKVIYIDTE--GLSPERFKQIAGEDFEELLSNIIIFEP 87

Query: 160 ---KENYGIKIMSMASLVDENVAMI 181
              +E     I     L  ENV +I
Sbjct: 88  SSFEEQSEA-IRKAEKLAKENVGLI 111


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.135    0.381 

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: 5,509,516
Number of extensions: 356879
Number of successful extensions: 925
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 101
Length of query: 341
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 247
Effective length of database: 3,963,321
Effective search space: 978940287
Effective search space used: 978940287
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 (21.7 bits)
S2: 57 (25.8 bits)