RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|255764477|ref|YP_003065232.2| dephospho-CoA kinase
[Candidatus Liberibacter asiaticus str. psy62]
         (199 letters)



>gnl|CDD|30195 cd02022, DPCK, Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24)
           catalyzes the phosphorylation of dephosphocoenzyme A
           (dCoA) to yield CoA, which is the final step in CoA
           biosynthesis..
          Length = 179

 Score =  154 bits (390), Expect = 2e-38
 Identities = 70/181 (38%), Positives = 107/181 (59%), Gaps = 6/181 (3%)

Query: 3   IIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHY--EAVDIIKKTFPRSI--QNN 58
           IIGLTG IG+GK+TVA+ LK+  IPVI +D I  ++Y     A+  I + F   I  ++ 
Sbjct: 1   IIGLTGGIGSGKSTVAKLLKELGIPVIDADKIAHEVYEPGGPALQAIVEAFGPDILLEDG 60

Query: 59  KVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKRK 118
           ++++ +L  I+   P K + LE I HP++R   ++ L +   R EK+V  D PLLFE   
Sbjct: 61  ELDRKKLGEIVFADPEKRKKLEAITHPLIRKEIEEQLAE--ARKEKVVVLDIPLLFETGL 118

Query: 119 EYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGTIE 178
           E L D V+VV    E Q ER++ R   +EE     ++ QM  ++K +RAD+VI+  G++E
Sbjct: 119 EKLVDRVIVVDAPPEIQIERLMKRDGLSEEEAEARIASQMPLEEKRARADFVIDNSGSLE 178

Query: 179 A 179
            
Sbjct: 179 E 179


>gnl|CDD|30586 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
          Length = 201

 Score =  135 bits (340), Expect = 1e-32
 Identities = 68/199 (34%), Positives = 112/199 (56%), Gaps = 7/199 (3%)

Query: 1   MLIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLY--HYEAVDIIKKTFPRSI--Q 56
           MLIIGLTG IG+GK+TVA+ L +   PVI +DD+  ++     EA+  I + F   I  +
Sbjct: 2   MLIIGLTGGIGSGKSTVAKILAELGFPVIDADDVAREVVEPGGEALQEIAERFGLEILDE 61

Query: 57  NNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEK 116
           +  +++ +L   +   P     LEKI+HP++R   K ++          V  + PLLFE 
Sbjct: 62  DGGLDRRKLREKVFNDPEARLKLEKILHPLIRAEIKVVIDGAR---SPYVVLEIPLLFEA 118

Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGT 176
             E  FD V+VV    E + ER++ R    EE+    L+ Q + ++K++ AD VI+ +G+
Sbjct: 119 GGEKYFDKVIVVYAPPEIRLERLMKRDGLDEEDAEARLASQRDLEEKLALADVVIDNDGS 178

Query: 177 IEAIEKETQKMLKYILKIN 195
           IE + ++ +K+LK +L + 
Sbjct: 179 IENLLEQIEKLLKELLGLV 197


>gnl|CDD|144640 pfam01121, CoaE, Dephospho-CoA kinase.  This family catalyses the
           phosphorylation of the 3'-hydroxyl group of
           dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This
           enzyme uses ATP in its reaction.
          Length = 179

 Score =  121 bits (305), Expect = 2e-28
 Identities = 52/180 (28%), Positives = 91/180 (50%), Gaps = 7/180 (3%)

Query: 2   LIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYH--YEAVDIIKKTFPRSI--QN 57
           LI+GLTG IG+GK+TVA       +P++ +D I  ++      A+  I   F   I   +
Sbjct: 1   LIVGLTGGIGSGKSTVANLFADLGVPIVDADVIARQVVEPGSPALAAIVDHFGPDILLAD 60

Query: 58  NKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKR 117
            ++++  L  ++   P + + L  I+HP++R    K L  L+      V  D PLLFE  
Sbjct: 61  GQLDRRALRELVFSDPEEKQWLNAILHPLIRREMFKQLAQLT---SPYVLLDVPLLFESG 117

Query: 118 KEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGTI 177
              L   V+VV    E Q ER++ R   + E    I++ Q + +++++ AD V++ +  +
Sbjct: 118 LTKLCHRVLVVDAPVELQVERLMQRDGLSREQVQAIIAAQASREERLALADDVLDNDSGL 177


>gnl|CDD|38430 KOG3220, KOG3220, KOG3220, Similar to bacterial dephospho-CoA
           kinase [Coenzyme transport and metabolism].
          Length = 225

 Score =  119 bits (300), Expect = 5e-28
 Identities = 68/198 (34%), Positives = 106/198 (53%), Gaps = 4/198 (2%)

Query: 1   MLIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYH--YEAVDIIKKTFPRSI--Q 56
           MLI+GLTG I TGK+TV++  K   IPVI +D +  ++      A   I + F   I  +
Sbjct: 1   MLIVGLTGGIATGKSTVSQVFKALGIPVIDADVVAREVVEPGTPAYRRIVEAFGTEILLE 60

Query: 57  NNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEK 116
           + ++N+  L   +   P K + L KI HP +R    K +  L  RG +++  D PLLFE 
Sbjct: 61  DGEINRKVLGKRVFSDPKKRQALNKITHPAIRKEMFKEILKLLLRGYRVIVLDIPLLFEA 120

Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGT 176
           +   +    VVVTC  E Q ER++ R + +EE+    L  QM  + K   AD VI+  G+
Sbjct: 121 KLLKICHKTVVVTCDEELQLERLVERDELSEEDAENRLQSQMPLEKKCELADVVIDNNGS 180

Query: 177 IEAIEKETQKMLKYILKI 194
           +E + ++ +K+L  + K 
Sbjct: 181 LEDLYEQVEKVLALLQKS 198


>gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
          AMP kinases) [Nucleotide transport and metabolism].
          Length = 180

 Score = 36.4 bits (84), Expect = 0.005
 Identities = 15/48 (31%), Positives = 28/48 (58%)

Query: 3  IIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKT 50
          +I +TG+ G GKTTV + L++    VI  +++  +   Y   D ++K+
Sbjct: 2  LIAITGTPGVGKTTVCKLLRELGYKVIELNELAKENGLYTEYDELRKS 49


>gnl|CDD|38518 KOG3308, KOG3308, KOG3308, Uncharacterized protein of the uridine
           kinase family [Nucleotide transport and metabolism].
          Length = 225

 Score = 33.8 bits (77), Expect = 0.029
 Identities = 33/202 (16%), Positives = 76/202 (37%), Gaps = 16/202 (7%)

Query: 2   LIIGLTGSIGTGKTTVAEFLKK--EKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNK 59
           LI+G++G   +GKTT+A+ L +      +I  DD       Y+  + I+  +      + 
Sbjct: 5   LIVGISGCTNSGKTTLAKSLHRFFPGCSLIHQDDF------YKPENEIEVDYNNIDNWDL 58

Query: 60  VNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGE------KIVFFDTPLL 113
           +    +   L+K    L+           +         + + +       IV  D  ++
Sbjct: 59  LESLDMEKFLEKIATWLDSRHNAPEAREHLVSYANFEHYAQQFQIKAYKNHIVIIDGFMI 118

Query: 114 FE-KRKEYLFDAVVVVTCSFETQRERVLSRKKH-TEENFLFILSKQMNEKDKISRADYVI 171
           +  K +  LFD ++++T  +ET + R  +R  +  ++   F      + +     A    
Sbjct: 119 YNYKPQVDLFDRIIMLTLDYETCKRRREARTYYPPDDTGYFDPVVWPHYEKNFEEARDRS 178

Query: 172 NTEGTIEAIEKETQKMLKYILK 193
             +      +   +K+   + +
Sbjct: 179 RHDSLFLNGDVSEEKLDDKVNE 200


>gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and
          metabolism].
          Length = 218

 Score = 32.1 bits (73), Expect = 0.11
 Identities = 20/35 (57%), Positives = 23/35 (65%), Gaps = 4/35 (11%)

Query: 3  IIGLTGSIGTGKTTVA----EFLKKEKIPVISSDD 33
          IIG+ G  G+GKTTVA    E L  EK+ VIS DD
Sbjct: 10 IIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDD 44


>gnl|CDD|30196 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
          also known as uridine kinase or uridine-cytidine kinase
          (UCK), catalyzes the reversible phosphoryl transfer
          from ATP to uridine or cytidine to yield UMP or CMP. In
          the primidine nucleotide-salvage pathway, this enzyme
          combined with nucleoside diphosphate kinases further
          phosphorylates UMP and CMP to form UTP and CTP. This
          kinase also catalyzes the phosphorylation of several
          cytotoxic ribonucleoside analogs such as
          5-flurrouridine and cyclopentenyl-cytidine..
          Length = 198

 Score = 31.7 bits (72), Expect = 0.15
 Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 4/34 (11%)

Query: 3  IIGLTGSIGTGKTTVA----EFLKKEKIPVISSD 32
          IIG+ G  G+GKTTVA    E L   K+ +IS D
Sbjct: 1  IIGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQD 34


>gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular
          activities (AAA).  AAA family proteins often perform
          chaperone-like functions that assist in the assembly,
          operation, or disassembly of protein complexes.
          Length = 131

 Score = 30.3 bits (69), Expect = 0.42
 Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 4/49 (8%)

Query: 6  LTGSIGTGKTTVAEFLKKE-KIPV--ISSDDIVDKLYHYEAVDIIKKTF 51
          L G  GTGKTT+A+ + KE   P   IS  ++V K Y  E+   +++ F
Sbjct: 3  LYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-YVGESEKRLRELF 50


>gnl|CDD|31270 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
          Length = 283

 Score = 29.8 bits (67), Expect = 0.45
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 2   LIIGLTGSIGTGKTTVAEFLKK 23
            IIG+ GS+  GK+T A  L+ 
Sbjct: 83  FIIGIAGSVAVGKSTTARILQA 104


>gnl|CDD|31617 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and
           metabolism].
          Length = 216

 Score = 29.8 bits (67), Expect = 0.53
 Identities = 32/161 (19%), Positives = 61/161 (37%), Gaps = 20/161 (12%)

Query: 1   MLIIGLTGSIGTGKTTVAEFLKKE-KIPVIS----SDDIVDKLYHYEAVDIIKKTFPRSI 55
            ++I + G IG GK+T+A+ L +     V       +  +D  Y     D  +  F   +
Sbjct: 4   AMVIVIEGMIGAGKSTLAQALAEHLGFKVFYELVEDNPFLDLFYE----DPERYAFL--L 57

Query: 56  QNNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFE 115
           Q   +   R   I +    K  IL++ +     +  K      +    +  ++D   L++
Sbjct: 58  QIYFLLN-RFKKIKKALSDKNNILDRSIFEDYFLFAKLNFAKGTLSPSEFKYYDD--LYD 114

Query: 116 KRKEYLF------DAVVVVTCSFETQRERVLSRKKHTEENF 150
              E L       D ++ +  S ET   R+  R +  E + 
Sbjct: 115 NMLEELPYLPGRPDLLIYLDASLETLLRRIAKRGRPFEIDN 155


>gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
          expression and maturation of urease and hydrogenase
          [Posttranslational modification, protein turnover,
          chaperones / Transcription].
          Length = 202

 Score = 29.4 bits (66), Expect = 0.60
 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 5/37 (13%)

Query: 1  MLIIGLTGSIGTGKT-----TVAEFLKKEKIPVISSD 32
          ML IG+ G  G+GKT     T+     + KI VI+ D
Sbjct: 13 MLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGD 49


>gnl|CDD|33714 COG3932, COG3932, Uncharacterized ABC-type transport system,
           permease components [General function prediction only].
          Length = 209

 Score = 29.4 bits (66), Expect = 0.66
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 52  PRSIQNNKVNKARLLGILQKSPAKLEILEKIVHPMVR 88
           PR I +  + + +L G L+     ++ LE I  P +R
Sbjct: 86  PRKILDKTIKRRKLQGTLRAGKPWVKRLEAIARPRLR 122


>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. 
          Length = 168

 Score = 29.5 bits (67), Expect = 0.67
 Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 4/29 (13%)

Query: 4  IGLTGSIGTGKTT----VAEFLKKEKIPV 28
          I +TG  G GKTT    V E LK E + V
Sbjct: 2  IFITGPPGVGKTTLVKKVIELLKSEGVKV 30


>gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and
           metabolism].
          Length = 172

 Score = 29.4 bits (66), Expect = 0.68
 Identities = 46/197 (23%), Positives = 77/197 (39%), Gaps = 45/197 (22%)

Query: 4   IGLTGSIGTGKTTVAEFLKKE-KIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVNK 62
           I L G +G GK+T+   L K   +P I +D              I+K    SI       
Sbjct: 5   IVLIGFMGAGKSTIGRALAKALNLPFIDTD------------QEIEKRTGMSIA------ 46

Query: 63  ARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDT---PLLFEKRKE 119
                         EI E+      R  E ++L +L      ++   T    +L E+ + 
Sbjct: 47  --------------EIFEEEGEEGFRRLETEVLKELLEEDNAVI--ATGGGAVLSEENRN 90

Query: 120 YLFDAVVVV--TCSFETQRERVLSRKKH---TEENFLFILSKQMNEKDKISR--ADYVIN 172
            L    +VV     FET  ER+   +K      E+    L + + E+  + R  AD++I+
Sbjct: 91  LLKKRGIVVYLDAPFETLYERLQRDRKRPLLQTEDPREELEELLEERQPLYREVADFIID 150

Query: 173 TEGTIEAIEKETQKMLK 189
           T+   E + +E  + L+
Sbjct: 151 TDDRSEEVVEEILEALE 167


>gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
           shikimate pathway, a seven-step biosynthetic pathway
           which converts erythrose-4-phosphate to chorismic acid,
           found in bacteria, fungi and plants. Chorismic acid is a
           important intermediate in the synthesis of aromatic
           compounds, such as aromatic amino acids, p-aminobenzoic
           acid, folate and ubiquinone. Shikimate kinase catalyses
           the phosphorylation of the 3-hydroxyl group of shikimic
           acid using ATP..
          Length = 154

 Score = 29.4 bits (66), Expect = 0.74
 Identities = 40/181 (22%), Positives = 68/181 (37%), Gaps = 40/181 (22%)

Query: 3   IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVN 61
            I L G +G GKTTV   L K   +P +  D            ++I++    SI      
Sbjct: 1   NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD------------ELIEQRAGMSIP----- 43

Query: 62  KARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFD--TPLLFEKRKE 119
                          EI  +      R  E+++L  L  +   ++       L  E R+ 
Sbjct: 44  ---------------EIFAEEGEEGFRELEREVLLLLLTKENAVIATGGGAVLREENRRL 88

Query: 120 YLFDAVVV-VTCSFETQRERVLSRKKH--TEENFLFILSKQMNEKDKISR--ADYVINTE 174
            L + +VV +  S E   ER+   K     ++     L + + E++ + R  AD  I+T+
Sbjct: 89  LLENGIVVWLDASPEELLERLARDKTRPLLQDEDPERLRELLEEREPLYREVADLTIDTD 148

Query: 175 G 175
            
Sbjct: 149 E 149


>gnl|CDD|109538 pfam00485, PRK, Phosphoribulokinase / Uridine kinase family.  In
          Arabidopsis the region carries two binding domains, a
          phosphoribosylpyrophosphate-binding domain and, at the
          very C-terminus, a uracil-binding domain.
          Length = 196

 Score = 29.3 bits (66), Expect = 0.74
 Identities = 12/17 (70%), Positives = 13/17 (76%)

Query: 3  IIGLTGSIGTGKTTVAE 19
          IIG+ GS G GKTTVA 
Sbjct: 1  IIGVAGSSGAGKTTVAR 17


>gnl|CDD|73295 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
          superfamily consisting of multiple families of enzymes
          that share structural similarity and are functionally
          related to the catalysis of the reversible phosphate
          group transfer from nucleoside triphosphates to
          nucleosides/nucleotides, nucleoside monophosphates, or
          sugars. Members of this family play a wide variety of
          essential roles in nucleotide metabolism, the
          biosynthesis of coenzymes and aromatic compounds, as
          well as the metabolism of sugar and sulfate..
          Length = 69

 Score = 29.1 bits (65), Expect = 0.87
 Identities = 11/22 (50%), Positives = 17/22 (77%)

Query: 3  IIGLTGSIGTGKTTVAEFLKKE 24
          II +TG  G+GK+TVA+ L ++
Sbjct: 1  IIAITGGSGSGKSTVAKKLAEQ 22


>gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
           involved in the metabolism of nicotinamide adenine
           dinucleotide (NAD+). This enzyme catalyzes the
           phosphorylation of nicotinamide riboside (NR) to form
           nicotinamide mononucleotide (NMN). It defines the NR
           salvage pathway of NAD+ biosynthesis in addition to the
           pathways through nicotinic acid mononucleotide (NaMN).
           This enzyme can also phosphorylate the anticancer drug
           tiazofurin, which is an analog of nicotinamide
           riboside..
          Length = 187

 Score = 29.1 bits (65), Expect = 0.91
 Identities = 30/156 (19%), Positives = 59/156 (37%), Gaps = 19/156 (12%)

Query: 3   IIGLTGSIGTGKTTVAEFLKK--EKIPVISSDD----------IVDKLYHYEAVD-IIKK 49
           I+G++G   +GKTT+A+ L++      VI  DD            +    ++ ++ +  +
Sbjct: 1   IVGISGVTNSGKTTLAKLLQRILPNCCVIHQDDFFKPEDEIPVDENGFKQWDVLEALDME 60

Query: 50  TFPRSIQNNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGE-KIVFF 108
               ++      +        +S       EK    +     ++   DL    +  I+  
Sbjct: 61  AMMSTLDY--WRETGHFPKFLRSHGNENDPEK--EFIEDAQIEETKADLLGAEDLHILIV 116

Query: 109 DTPLLFE-KRKEYLFDAVVVVTCSFETQRERVLSRK 143
           D  LL+  K    LFD    +   +ET + R  +R 
Sbjct: 117 DGFLLYNYKPLVDLFDIRYFLRVPYETCKRRREART 152


>gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
          transfer from ATP to gluconate. The resulting product
          gluconate-6-phoshate is an important precursor of
          gluconate metabolism. GntK acts as a dimmer composed of
          two identical subunits..
          Length = 150

 Score = 28.7 bits (64), Expect = 1.00
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 3  IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDI 34
          II + G  G+GK+TV + L ++   P I  DD+
Sbjct: 1  IIVVMGVSGSGKSTVGKALAERLGAPFIDGDDL 33



 Score = 26.4 bits (58), Expect = 5.3
 Identities = 9/37 (24%), Positives = 12/37 (32%)

Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFI 153
            K       VVV CS   +  R + R         F+
Sbjct: 66  AKLASAGEGVVVACSALKRIYRDILRGGAANPRVRFV 102


>gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
          phosphoryl transfer from adenosine triphosphates (ATP)
          to adenosine monophosphates (AMP) and to yield
          adenosine diphosphates (ADP). This enzyme is required
          for the biosynthesis of ADP and is essential for
          homeostasis of adenosine phosphates..
          Length = 194

 Score = 28.7 bits (64), Expect = 1.0
 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 3  IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDIVDK 37
           I L G  G+GK T AE L KK  +P IS+ D++ +
Sbjct: 1  RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLRE 36


>gnl|CDD|30198 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the
          phosphorylation of pantothenic acid to form
          4'-phosphopantothenic, which is the first of five steps
          in coenzyme A (CoA) biosynthetic pathway. The reaction
          carried out by this enzyme is a key regulatory point in
          CoA biosynthesis..
          Length = 220

 Score = 28.7 bits (64), Expect = 1.1
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 9/61 (14%)

Query: 3  IIGLTGSIGTGKTTVAEFLK--------KEKIPVISSDDIVDKLYHYEAVDII-KKTFPR 53
          IIG+ GS+  GK+T A  L+           + +I++D  +          ++ +K FP 
Sbjct: 1  IIGIAGSVAVGKSTTARVLQALLSRWPDHPNVELITTDGFLYPNKELIERGLMDRKGFPE 60

Query: 54 S 54
          S
Sbjct: 61 S 61


>gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear
           protein involved oxidative stress response [Nucleotide
           transport and metabolism].
          Length = 176

 Score = 28.7 bits (64), Expect = 1.2
 Identities = 34/140 (24%), Positives = 52/140 (37%), Gaps = 37/140 (26%)

Query: 4   IGLTGSIGTGKTTVAEFLKKE-KIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVNK 62
           I +TG+ GTGK+T+AE L ++  +  I   D+V +   YE  D   K          +++
Sbjct: 10  ILVTGTPGTGKSTLAERLAEKTGLEYIEISDLVKENNLYEGYDEEYKCH-------ILDE 62

Query: 63  ARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKRKEYLF 122
            ++L                            L  L   G  IV +     F    E  F
Sbjct: 63  DKVL--------------------------DELEPLMIEGGNIVDYHGCDFF---PERWF 93

Query: 123 DAVVVVTCSFETQRERVLSR 142
           D VVV+        +R+ SR
Sbjct: 94  DLVVVLRTPNSVLYDRLKSR 113


>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
          transport and metabolism].
          Length = 178

 Score = 28.7 bits (64), Expect = 1.2
 Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 4/34 (11%)

Query: 2  LIIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDI 34
          LI+G  G+   GK+T+A+ L KK  +P + + DI
Sbjct: 4  LILGPPGA---GKSTLAKKLAKKLGLPHLDTGDI 34


>gnl|CDD|73011 cd03252, ABCC_Hemolysin, The ABC-transporter hemolysin B is a
          central component of the secretion machinery that
          translocates the toxin, hemolysin A, in a
          Sec-independent fashion across both membranes of E.
          coli.  The hemolysin A (HlyA) transport machinery is
          composed of the ATP-binding cassette (ABC) transporter
          HlyB located in the inner membrane, hemolysin D (HlyD),
          also anchored in the inner membrane, and TolC, which
          resides in the outer membrane.  HlyD apparently forms a
          continuous channel that bridges the entire periplasm,
          interacting with TolC and HlyB.  This arrangement
          prevents the appearance of periplasmic intermediates of
          HlyA during substrate transport.  Little is known about
          the molecular details of HlyA transport, but it is
          evident that ATP-hydrolysis by the ABC-transporter HlyB
          is a necessary source of energy..
          Length = 237

 Score = 28.3 bits (63), Expect = 1.3
 Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 10/66 (15%)

Query: 3  IIGLTGSIGTGKTTVAEFLKKEKIP-----VISSDDI--VDKLYHYEAVDIIKKT---FP 52
          ++G+ G  G+GK+T+ + +++  +P     ++   D+   D  +    V ++ +    F 
Sbjct: 30 VVGIVGRSGSGKSTLTKLIQRFYVPENGRVLVDGHDLALADPAWLRRQVGVVLQENVLFN 89

Query: 53 RSIQNN 58
          RSI++N
Sbjct: 90 RSIRDN 95


>gnl|CDD|110029 pfam00998, RdRP_3, Viral RNA dependent RNA polymerase.  This family
           includes viral RNA dependent RNA polymerase enzymes from
           hepatitis C virus and various plant viruses.
          Length = 485

 Score = 28.3 bits (64), Expect = 1.4
 Identities = 20/98 (20%), Positives = 28/98 (28%), Gaps = 20/98 (20%)

Query: 14  KTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKT--FPRSIQNNKVNKARLLGILQK 71
           K  V         PV   D I+      E ++I  K    PR I              Q 
Sbjct: 101 KIYVKALESLAVKPVQRRDAILKTFVKAEKINITAKPDPAPRVI--------------QP 146

Query: 72  SPAKLEILEKIVHPMVRMHEKKILHDL-SCRGEKIVFF 108
            P +   +E      +R  EK +   +    G   V  
Sbjct: 147 RPPRY-NVE--PGRYLRPCEKMLYKAIDKAFGGPTVLK 181


>gnl|CDD|146562 pfam03990, DUF348, Domain of unknown function (DUF348).  This
          domain normally occurs as tandem repeats; however it is
          found as a single copy in the S. cerevisiae DNA-binding
          nuclear protein YCR593. This protein is involved in
          sporulation part of the SET3C complex, which is
          required to repress early/middle sporulation genes
          during meiosis. The bacterial proteins are likely to be
          involved in a cell wall function as they are found in
          conjunction with the pfam07501 domain, which is
          involved in various cell surface processes.
          Length = 43

 Score = 28.2 bits (64), Expect = 1.5
 Identities = 7/30 (23%), Positives = 15/30 (50%)

Query: 5  GLTGSIGTGKTTVAEFLKKEKIPVISSDDI 34
          G   ++ T  +TV + L++  I +   D +
Sbjct: 8  GKEKTVWTTASTVGDLLEEAGITLGEEDKV 37


>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
          Length = 287

 Score = 27.8 bits (62), Expect = 2.0
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 10/39 (25%)

Query: 7   TGSIGTGKTTVA----------EFLKKEKIPVISSDDIV 35
           TGS GTGKTTVA           ++KK  +  ++ DD+V
Sbjct: 65  TGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDLV 103


>gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
          metabolism].
          Length = 179

 Score = 27.9 bits (62), Expect = 2.1
 Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 2  LIIGLTGSIGTGKTTVAEFLKKE-KIPVISSDDI 34
          ++I ++G  G+GKTTVA  L +   + ++S+  I
Sbjct: 1  MVITISGLPGSGKTTVARELAEHLGLKLVSAGTI 34


>gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like)
          small GTPases.  Arf proteins are activators 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.  Members of the Arf family are
          regulators of vesicle formation in intracellular
          traffic that interact reversibly with membranes of the
          secretory and endocytic compartments in a GTP-dependent
          manner.  They depart from other small GTP-binding
          proteins by a unique structural device, interswitch
          toggle, that implements front-back communication from
          N-terminus to the nucleotide binding site.  Arf-like
          (Arl) proteins are close relatives of the Arf, but only
          Arl1 has been shown to function in membrane traffic
          like the Arf proteins.  Arl2 has an unrelated function
          in the folding of native tubulin, and Arl4 may function
          in the nucleus.  Most other Arf family proteins are so
          far relatively poorly characterized.  Thus, despite
          their significant sequence homologies, Arf family
          proteins may regulate unrelated functions.
          Length = 158

 Score = 27.9 bits (63), Expect = 2.1
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 15/54 (27%)

Query: 2  LIIGLTGSIGTGKTTVAEFLKKEK----IPVISSDDIVDKLYHYEAVDIIKKTF 51
          LI+GL G+   GKTT+   LK  +    IP I         ++ E V+    +F
Sbjct: 3  LILGLDGA---GKTTILYKLKLGEVVTTIPTIG--------FNVETVEYKNVSF 45


>gnl|CDD|33963 COG4240, COG4240, Predicted kinase [General function prediction
           only].
          Length = 300

 Score = 27.7 bits (61), Expect = 2.3
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 9/59 (15%)

Query: 2   LIIGLTGSIGTGKTTVAEFLKK-------EKIPVISSDDIVDKLYHYEAVDIIKKTFPR 53
           LI+G++G  G+GK+T++  + +       E+   +S DD+   L H + + + ++  P 
Sbjct: 51  LIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLDDLY--LTHADRLRLARQVNPL 107


>gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
           envelope biogenesis, outer membrane].
          Length = 451

 Score = 27.6 bits (61), Expect = 2.3
 Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 3   IIGLTGSIGTGKTTVAEFLK 22
           +I +TGS   GKTT  E L 
Sbjct: 105 VIAITGS--NGKTTTKEMLA 122


>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
          of proteins which share a common ATP-binding domain.
          Functionally, proteins in this superfamily use the
          energy from hydrolysis of NTP to transfer electron or
          ion..
          Length = 99

 Score = 27.8 bits (61), Expect = 2.4
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 4/37 (10%)

Query: 3  IIGLTGSIGTGKTTV----AEFLKKEKIPVISSDDIV 35
          +I +TG  G GKTT+    A  L K    V+  DD V
Sbjct: 1  VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLIDDYV 37


>gnl|CDD|147298 pfam05041, Pecanex_C, Pecanex protein (C-terminus).  This family
           consists of C terminal region of the pecanex protein
           homologues. The pecanex protein is a maternal-effect
           neurogenic gene found in Drosophila.
          Length = 232

 Score = 27.5 bits (61), Expect = 2.6
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 73  PAKLEILEKIVHPMVRMHEKKILHD-LSCRGEKIVFFDTPLLFEKRKEY 120
            A +++L K+V P VRM   K+  D  +C  E   + +  +L++  +EY
Sbjct: 64  FADMDLLHKVVAPAVRM-SLKLHQDHFTCPDE---YDEPAVLYDAIQEY 108


>gnl|CDD|111395 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain.  This
          domain is found in HypB, a hydrogenase expression /
          formation protein, and UreG a urease accessory protein.
          Both these proteins contain a P-loop nucleotide binding
          motif. HypB has GTPase activity and is a guanine
          nucleotide binding protein. It is not known whether
          UreG binds GTP or some other nucleotide. Both enzymes
          are involved in nickel binding. HypB can store nickel
          and is required for nickel dependent hydrogenase
          expression. UreG is required for functional
          incorporation of the urease nickel metallocenter. GTP
          hydrolysis may required by these proteins for nickel
          incorporation into other nickel proteins. This family
          of domains also contains P47K, a Pseudomonas
          chlororaphis protein needed for nitrile hydratase
          expression, and the cobW gene product, which may be
          involved in cobalamin biosynthesis in Pseudomonas
          denitrificans.
          Length = 174

 Score = 27.6 bits (62), Expect = 2.6
 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 2  LIIGLTGSIGTGKTT-----VAEFLKKEKIPVI 29
           +  LTG +G+GKTT     + +  +  KI VI
Sbjct: 1  PVTVLTGFLGSGKTTLLEHLLRDNREGLKIAVI 33


>gnl|CDD|72981 cd03222, ABC_RNaseL_inhibitor, The ABC ATPase RNase L inhibitor
           (RLI) is a key enzyme in ribosomal biogenesis, formation
           of translation preinitiation complexes, and assembly of
           HIV capsids.  RLI's are not transport proteins, and thus
           cluster with a group of soluble proteins that lack the
           transmembrane components commonly found in other members
           of the family.  Structurally, RLI's have an N-terminal
           Fe-S domain and two nucleotide-binding domains, which
           are arranged to form two composite active sites in their
           interface cleft.  RLI is one of the most conserved
           enzymes between archaea and eukaryotes with a sequence
           identity more than 48%.  The high degree of evolutionary
           conservation suggests that RLI performs a central role
           in archaeal and eukaryotic physiology..
          Length = 177

 Score = 27.3 bits (60), Expect = 2.9
 Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 9/107 (8%)

Query: 3   IIGLTGSIGTGKTTVAEFLKKEKIPVISSD--DIVDKLYHYEAVDIIKKTFPRSIQNNKV 60
           +IG+ G  GTGKTT  + L  + IP   +D  D +  +Y  + +D+      R      +
Sbjct: 27  VIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAAL 86

Query: 61  NKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVF 107
            +     +  +  A L+I +       R++  + +  LS  G+K   
Sbjct: 87  LRNATFYLFDEPSAYLDIEQ-------RLNAARAIRRLSEEGKKTAL 126


>gnl|CDD|37321 KOG2110, KOG2110, KOG2110, Uncharacterized conserved protein,
           contains WD40 repeats [Function unknown].
          Length = 391

 Score = 27.2 bits (60), Expect = 3.0
 Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 4   IGLTGSIGTGKTTVAEFLKKEKIPVISS--DDIVDKLYHYE-AVDIIKKTFPRSIQNNKV 60
                S  T   ++ E L    +  I S       K+ H++    I +  FP SI   ++
Sbjct: 36  FEKCFSKDTEGVSIVEMLFSSSLVAIVSIKQPRKLKVVHFKKKTTICEIFFPTSILAVRM 95

Query: 61  NKARLLGILQKS 72
           N+ RL+  L++S
Sbjct: 96  NRKRLVVCLEES 107


>gnl|CDD|109594 pfam00543, P-II, Nitrogen regulatory protein P-II.  P-II
          modulates the activity of glutamine synthetase.
          Length = 102

 Score = 27.1 bits (61), Expect = 3.1
 Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 5/39 (12%)

Query: 13 GKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKTF 51
          G     EFL K KI ++  D+ VD     E V+ I K  
Sbjct: 45 GAEYYVEFLPKVKIEIVVPDEDVD-----EVVEAIIKAA 78


>gnl|CDD|112137 pfam03308, ArgK, ArgK protein.  The ArgK protein acts as an
          ATPase enzyme and as a kinase, and phosphorylates
          periplasmic binding proteins involved in the LAO
          (lysine, arginine, ornithine)/AO transport systems.
          Length = 267

 Score = 26.9 bits (60), Expect = 3.4
 Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 6/37 (16%)

Query: 2  LIIGLTGSIGTGKTTVAEFLKKE------KIPVISSD 32
            +G+TG  G GK+T+ E L  E      ++ V++ D
Sbjct: 30 HRVGITGVPGAGKSTLIEALGMELRRRGHRVAVLAVD 66


>gnl|CDD|48516 cd02967, mauD, Methylamine utilization (mau) D family; mauD protein
           is the translation product of the mauD gene found in
           methylotrophic bacteria, which are able to use
           methylamine as a sole carbon source and a nitrogen
           source. mauD is an essential accessory protein for the
           biosynthesis of methylamine dehydrogenase (MADH), the
           enzyme that catalyzes the oxidation of methylamine and
           other primary amines. MADH possesses an alpha2beta2
           subunit structure; the alpha subunit is also referred to
           as the large subunit. Each beta (small) subunit contains
           a tryptophan tryptophylquinone (TTQ) prosthetic group.
           Accessory proteins are essential for the proper
           transport of MADH to the periplasm, TTQ synthesis and
           the formation of several structural disulfide bonds.
           Bacterial mutants containing an insertion on the mauD
           gene were unable to grow on methylamine as a sole carbon
           source, were found to lack the MADH small subunit and
           had decreased amounts of the MADH large subunit..
          Length = 114

 Score = 27.2 bits (60), Expect = 3.5
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 123 DAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADY--VINTEGTIEA 179
           D + VV  S   + E     KKH  E F ++LS ++    ++S+  Y  +++  G I A
Sbjct: 52  DWLDVVLASDGEKAEHQRFLKKHGLEAFPYVLSAELGMAYQVSKLPYAVLLDEAGVIAA 110


>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is
          unkown. The protein sequences are similar to the ArgK
          protein in E. coli. ArgK protein is a membrane ATPase
          which is required for transporting arginine, ornithine
          and lysine into the cells by the arginine and ornithine
          (AO system) and lysine, arginine and ornithine (LAO)
          transport systems..
          Length = 148

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 6/36 (16%)

Query: 3  IIGLTGSIGTGKTTVAEFL------KKEKIPVISSD 32
          +IG+TG  G GK+T+ + L      + +++ V++ D
Sbjct: 1  VIGITGVPGAGKSTLIDALITALRARGKRVAVLAID 36


>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
          related GTPases of G3E family [Amino acid transport and
          metabolism].
          Length = 323

 Score = 26.8 bits (59), Expect = 3.8
 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 6/37 (16%)

Query: 2  LIIGLTGSIGTGKTTVAEFLKKE------KIPVISSD 32
           +IG+TG  G GK+T+ E L +E      ++ V++ D
Sbjct: 52 HVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVD 88


>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the
          form of molybdenum cofactor (Moco) which is associated
          with the metabolism of nitrogen, carbon and sulfur by
          redox active enzymes. In E. coli, the synthesis of Moco
          involves genes from several loci: moa, mob, mod, moe
          and mog. The mob locus contains mobA and mobB genes.
          MobB catalyzes the attachment of the guanine
          dinucleotide to molybdopterin..
          Length = 159

 Score = 26.7 bits (59), Expect = 3.9
 Identities = 11/21 (52%), Positives = 14/21 (66%)

Query: 1  MLIIGLTGSIGTGKTTVAEFL 21
          M +IG  G  G+GKTT+ E L
Sbjct: 1  MKVIGFVGYSGSGKTTLLEKL 21


>gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
           [General function prediction only].
          Length = 591

 Score = 26.7 bits (59), Expect = 4.5
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 3   IIGLTGSIGTGKTTVAEFLKKEKIPVISSDD 33
           ++G+ G  G GK+T  + L  E  P +   +
Sbjct: 102 VVGILGPNGIGKSTALKILAGELKPNLGRYE 132


>gnl|CDD|30199 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in
          the Benson-Calvin cycle in chloroplasts or
          photosynthetic prokaryotes. This enzyme catalyzes the
          phosphorylation of D-ribulose 5-phosphate to form
          D-ribulose 1, 5-biphosphate, using ATP and NADPH
          produced by the primary reactions of photosynthesis..
          Length = 273

 Score = 26.8 bits (59), Expect = 4.6
 Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 9/42 (21%)

Query: 3  IIGLTGSIGTGKTT----VAEFLKKEKIPVISSDDIVDKLYH 40
          IIG+ G  G GK+T    +      + + VI  DD     YH
Sbjct: 1  IIGVAGDSGCGKSTFLRRLTSLFGSDLVTVICLDD-----YH 37


>gnl|CDD|146552 pfam03975, CheD, CheD.  This chemotaxis protein stimulates
          methylation of MCP proteins.
          Length = 105

 Score = 26.7 bits (60), Expect = 4.9
 Identities = 8/14 (57%), Positives = 12/14 (85%)

Query: 19 EFLKKEKIPVISSD 32
          E+LKKE IP+++ D
Sbjct: 64 EYLKKEGIPIVAED 77


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
          nucleotide-binding domain (P-loop) near the N-terminus,
          participates in the maturation of the nickel center of
          carbon monoxide dehydrogenase (CODH). CODH from
          Rhodospirillum rubrum catalyzes the reversible
          oxidation of CO to CO2. CODH contains a
          nickel-iron-sulfur cluster (C-center) and an
          iron-sulfur cluster (B-center). CO oxidation occurs at
          the C-center. Three accessory proteins encoded by
          cooCTJ genes are involved in nickel incorporation into
          a nickel site. CooC functions as a nickel insertase
          that mobilizes nickel to apoCODH using energy released
          from ATP hydrolysis. CooC is a homodimer and has NTPase
          activities. Mutation at the P-loop abolishs its
          function..
          Length = 116

 Score = 26.3 bits (58), Expect = 5.4
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 8/44 (18%)

Query: 3  IIGLTGSIGTGKTTV----AEFLKKEKIPVISSD----DIVDKL 38
           I +TG  G GKTT+    A +L ++  PV++ D    D+ ++L
Sbjct: 1  KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPDDLPERL 44


>gnl|CDD|33845 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
          transport and metabolism].
          Length = 261

 Score = 26.5 bits (58), Expect = 5.7
 Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 8/66 (12%)

Query: 1  MLIIGLTGSIGTGKTTVAEFLKKE------KIPVISSDDIVDKLYHYEAVDIIKKTFPRS 54
          M +I LTG  G+GKTT A+ L KE      ++  +  D +      ++    I K   R 
Sbjct: 1  MPLIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLR--GILWDESLPILKEVYRE 58

Query: 55 IQNNKV 60
               V
Sbjct: 59 SFLKSV 64


>gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 744

 Score = 26.5 bits (58), Expect = 5.8
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 5/50 (10%)

Query: 6   LTGSIGTGKTTVAEFLKKEK----IPVISSDDIVDKLYHYEAVDIIKKTF 51
           L G  G+GKT +A  +        + +IS +D++  L        IKK F
Sbjct: 543 LEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIG-LSESAKCAHIKKIF 591


>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
          cellular Activities) superfamily represents an ancient
          group of ATPases belonging to the ASCE (for additional
          strand, catalytic E) division of the P-loop NTPase
          fold. The ASCE division also includes ABC, RecA-like,
          VirD4-like, PilT-like, and SF1/2 helicases. Members of
          the AAA+ ATPases function as molecular chaperons,
          ATPase subunits of proteases, helicases, or
          nucleic-acid stimulated ATPases. The AAA+ proteins
          contain several distinct features in addition to the
          conserved alpha-beta-alpha core domain structure and
          the Walker A and B motifs of the P-loop NTPases..
          Length = 151

 Score = 26.3 bits (58), Expect = 6.0
 Identities = 10/19 (52%), Positives = 12/19 (63%)

Query: 6  LTGSIGTGKTTVAEFLKKE 24
          L G  GTGKTT+A  +  E
Sbjct: 24 LYGPPGTGKTTLARAIANE 42


>gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
          protein [Coenzyme metabolism].
          Length = 161

 Score = 26.1 bits (57), Expect = 6.3
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 1  MLIIGLTGSIGTGKTTVAE 19
          M I+G+ G   +GKTT+ E
Sbjct: 2  MKILGIVGYKNSGKTTLIE 20


>gnl|CDD|38729 KOG3520, KOG3520, KOG3520, Predicted guanine nucleotide exchange
           factor [Signal transduction mechanisms].
          Length = 1167

 Score = 26.1 bits (57), Expect = 6.3
 Identities = 22/117 (18%), Positives = 48/117 (41%), Gaps = 15/117 (12%)

Query: 57  NNKVNKARLLGILQKSPAKLEILEKIVHPMVR--MHEKKILHD--LSCRGEK-------I 105
                K RL  I ++  AK     K      +  +  +K++HD  L+ +  +       +
Sbjct: 582 KEAEKKQRLEEIQRRLDAKSLSKYKNGEEFRKLDLTRRKLIHDGPLTWKTARGKTKDVHV 641

Query: 106 VFFDTPLLF--EKRKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNE 160
           +     L+   EK ++Y+F ++   +     Q+  ++ R+  T+E   F++S     
Sbjct: 642 LLLTDILVLLQEKDQKYIFKSLDKKSPVISLQK--LIVREVATDEKAFFLISMSDQG 696


>gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
          phosphorylation of deoxyribonucleosides to yield
          corresponding monophosphates (dNMPs). This family
          consists of various deoxynucleoside kinases including
          deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
          2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
          2.7.1.21) kinases. They are key enzymes in the salvage
          of deoxyribonucleosides originating from extra- or
          intracellular breakdown of DNA..
          Length = 193

 Score = 26.0 bits (57), Expect = 6.8
 Identities = 9/23 (39%), Positives = 16/23 (69%)

Query: 3  IIGLTGSIGTGKTTVAEFLKKEK 25
          +I + G+IG GK+T+A+ L +  
Sbjct: 1  VIVVEGNIGAGKSTLAKELAEHL 23


>gnl|CDD|48440 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S
           proteasome, multisubunit proteolytic complex, is the
           central enzyme of nonlysosomal protein degradation in
           both the cytosol and nucleus. It is composed of 28
           subunits arranged as four homoheptameric rings that
           stack on top of one another forming an elongated
           alpha-beta-beta-alpha cylinder with a central cavity.
           The proteasome alpha and beta subunits are members of
           the N-terminal nucleophile (Ntn)-hydrolase superfamily.
           Their N-terminal threonine residues are exposed as a
           nucleophile in peptide bond hydrolysis. Mammals have 7
           different alpha and 10 different beta proteasome subunit
           genes while archaea have one of each..
          Length = 209

 Score = 26.2 bits (58), Expect = 6.8
 Identities = 8/52 (15%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 9   SIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKV 60
           +IG G      FL+K     ++ ++ +       A+  +K+      +   +
Sbjct: 158 AIGKGSQEAKTFLEKRYKKDLTLEEAIK-----LALKALKEVLEEDKKAKNI 204


>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
          Translocation is mediated by EF-G (also called
          translocase).  The structure of EF-G closely resembles
          that of the complex between EF-Tu and tRNA.  This is an
          example of molecular mimicry; a protein domain evolved
          so that it mimics the shape of a tRNA molecule.  EF-G
          in the GTP form binds to the ribosome, primarily
          through the interaction of its EF-Tu-like domain with
          the 50S subunit.  The binding of EF-G to the ribosome
          in this manner stimulates the GTPase activity of EF-G. 
          On GTP hydrolysis, EF-G undergoes a conformational
          change that forces its arm deeper into the A site on
          the 30S subunit.  To accommodate this domain, the
          peptidyl-tRNA in the A site moves to the P site,
          carrying the mRNA and the deacylated tRNA with it.  The
          ribosome may be prepared for these rearrangements by
          the initial binding of EF-G as well.  The dissociation
          of EF-G leaves the ribosome ready to accept the next
          aminoacyl-tRNA into the A site.  This group contains
          only bacterial members.
          Length = 268

 Score = 26.0 bits (58), Expect = 7.9
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 4  IGLTGSIGTGKTTVAE 19
          I L G  G+GKTT+AE
Sbjct: 2  IALVGHSGSGKTTLAE 17


>gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4.
           Glycoside hydrolases cleave glycosidic bonds to release
           smaller sugars from oligo- or polysaccharides. Some
           bacteria simultaneously translocate and phosphorylate
           disaccharides via the phosphoenolpyruvate-dependent
           phosphotransferase system (PEP-PTS). After
           translocation, these phospho-disaccharides may be
           hydrolyzed by GH4 glycoside hydrolases. Other organisms
           (such as archaea and Thermotoga maritima) lack the
           PEP-PTS system, but have several enzymes normally
           associated with the PEP-PTS operon. GH4 family members
           include 6-phospho-beta-glucosidases,
           6-phospho-alpha-glucosidases,
           alpha-glucosidases/alpha-glucuronidases (only from
           Thermotoga), and alpha-galactosidases. They require two
           cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+),
           for activity. Some also require reducing conditions. GH4
           glycoside hydrolases are part of the NAD(P)-binding
           Rossmann fold superfamily, which includes a wide variety
           of protein families including the NAD(P)-binding domains
           of alcohol dehydrogenases, tyrosine-dependent
           oxidoreductases, glyceraldehyde-3-phosphate
           dehydrogenases, formate/glycerate dehydrogenases,
           siroheme synthases, 6-phosphogluconate dehydrogenases,
           aminoacid dehydrogenases, repressor rex, and NAD-binding
           potassium channel domains, among others.
          Length = 425

 Score = 25.9 bits (57), Expect = 8.4
 Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 23/100 (23%)

Query: 93  KILHDLSCRGEKIVFFDTPLLFEKRKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLF 152
           K   +L     ++  +D     E+R + +                +    +   +  F  
Sbjct: 22  KTPEEL--PISEVTLYDID---EERLDIILTIA------------KRYVEEVGADIKFE- 63

Query: 153 ILSKQMNEKDKISRADYVINT--EGTIEAIEKETQKMLKY 190
              K M+ +D I  AD+VIN    G +   EK+ Q  LKY
Sbjct: 64  ---KTMDLEDAIIDADFVINQFRVGGLTYREKDEQIPLKY 100


>gnl|CDD|32202 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
          and metabolism].
          Length = 189

 Score = 25.6 bits (56), Expect = 9.2
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 1  MLIIGLTGSIGTGKTTVAEFLKKE--KIPVISSDDI 34
            ++ +TG  G GKTTV +   KE  K  +++  D+
Sbjct: 4  RKVVVITGVPGVGKTTVLKIALKELVKHKIVNYGDL 39


>gnl|CDD|144174 pfam00481, PP2C, Protein phosphatase 2C.  Protein phosphatase 2C is
           a Mn++ or Mg++ dependent protein serine/threonine
           phosphatase.
          Length = 253

 Score = 25.8 bits (57), Expect = 9.3
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 15  TTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIK----KTFPRSIQNNKVNKAR 64
            T  +  + ++  +++SD + D L   E VDI++       P       V++A 
Sbjct: 192 VTSHKITESDEFLILASDGLWDVLSDQEVVDIVRSELSDGDPMEAAEKLVDEAI 245


>gnl|CDD|176519 cd08577, PI-PLCc_GDPD_SF_unchar3, Uncharacterized hypothetical
           proteins similar to the catalytic domains of
           Phosphoinositide-specific phospholipaseand
           Glycerophosphodiester phosphodiesterases.  This
           subfamily corresponds to a group of uncharacterized
           hypothetical proteins similar to the catalytic domains
           of Phosphoinositide-specific phospholipase C (PI-PLC),
           and glycerophosphodiester phosphodiesterases (GP-GDE),
           and also sphingomyelinases D (SMases D) and similar
           proteins. They hydrolyze the 3'-5' phosphodiester bonds
           in different substrates, utilizing a similar mechanism
           of general base and acid catalysis involving two
           conserved histidine residues.
          Length = 228

 Score = 25.7 bits (57), Expect = 9.3
 Identities = 8/31 (25%), Positives = 13/31 (41%)

Query: 106 VFFDTPLLFEKRKEYLFDAVVVVTCSFETQR 136
           +FFD  L  +   E L     +++ SF    
Sbjct: 141 IFFDGRLDEDLPDEQLARLSPMISASFAKFS 171


>gnl|CDD|33383 COG3583, COG3583, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 309

 Score = 25.7 bits (56), Expect = 9.6
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 5   GLTGSIGTGKTTVAEFLKKEKIPVISSDDIV 35
           G   ++ T  TTVA+ LK EKIP+  SD + 
Sbjct: 160 GKVRTVWTTATTVADLLKAEKIPLGKSDRVN 190


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.319    0.136    0.371 

Gapped
Lambda     K      H
   0.267   0.0731    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,331,093
Number of extensions: 123650
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 708
Number of HSP's successfully gapped: 127
Length of query: 199
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,340,536
Effective search space: 477458960
Effective search space used: 477458960
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: 55 (25.0 bits)