RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780873|ref|YP_003065286.1| aspartate kinase [Candidatus
Liberibacter asiaticus str. psy62]
         (411 letters)



>gnl|CDD|30873 COG0527, LysC, Aspartokinases [Amino acid transport and
           metabolism].
          Length = 447

 Score =  381 bits (980), Expect = e-106
 Identities = 179/457 (39%), Positives = 252/457 (55%), Gaps = 58/457 (12%)

Query: 1   MARIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTS- 59
           M  IV KFGGTSVA+ + I   A  VK + + G +V +VVSAM G TD L  L     S 
Sbjct: 1   MRLIVQKFGGTSVADAERILRVADIVKEDSEEGVKVVVVVSAMGGVTDLLVALAEGAESG 60

Query: 60  --------------------------------------------IDNARERDVVISTGEQ 75
                                                         + RERD ++S GE+
Sbjct: 61  RDAVAEQRHRDIASELILDPFIAARLAEVIAEFKKVLLGIALLGEVSPRERDELLSLGER 120

Query: 76  VSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVD-EKKIVTHLKKKQVVVIT 134
           +S+ L+  AL +LG+ A SL G Q  I TDS HG ARI   D E++++  L++ +V V+ 
Sbjct: 121 LSAALLAAALNALGVDARSLDGRQAGIATDSNHGNARILDEDSERRLLRLLEEGKVPVVA 180

Query: 135 GFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKK 194
           GFQG++ D   TTLGRGGSD SA A+AAA+ AD  +I+TDV G+YT DPRI P A L+ +
Sbjct: 181 GFQGINEDGETTTLGRGGSDYSAAALAAALGADEVEIWTDVDGVYTADPRIVPDARLLPE 240

Query: 195 ISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLICSGEDIMEK 254
           IS+EE LE++ LGAKV+  R+VE AM   + L ++++F      +  GTLI   E   ++
Sbjct: 241 ISYEEALELAYLGAKVLHPRAVEPAMRSGIPLRIKNTFNP----DAPGTLIT-AETESDE 295

Query: 255 KVITGIAYTKDEAQISLRRLRDHP--GISASIFSPLAEAHINIDMIIQNVSEDGQYVDIT 312
            V+ GIA   + A I++     +   G +A +F  LAEA IN+D+I Q++SE      I+
Sbjct: 296 PVVKGIALDDNVALITVSGPGMNGMVGFAARVFGILAEAGINVDLITQSISEVS----IS 351

Query: 313 FTTPSSSLEKALAVLSDNKENIGYDVIQHEDNLVKISAIGIGMQSYAGVASAFFLCLAEK 372
           FT P S   +AL  L + K       ++ E+ L  +S +G GM+S  GVA+  F  LAE+
Sbjct: 352 FTVPESDAPRALRALLEEKLE-LLAEVEVEEGLALVSIVGAGMRSNPGVAARIFQALAEE 410

Query: 373 GINIKAITTSEIKISVLIDSAYTELAVRSLHSCYGLD 409
            INI  I++SEI IS ++D    E AVR+LH  + L 
Sbjct: 411 NINIIMISSSEISISFVVDEKDAEKAVRALHEAFFLG 447


>gnl|CDD|58612 cd04246, AAK_AK-DapG-like, AAK_AK-DapG-like: Amino Acid Kinase
           Superfamily (AAK), AK-DapG-like; this CD includes the
           N-terminal catalytic aspartokinase (AK) domain of the
           diaminopimelate-sensitive aspartokinase isoenzyme AKI
           (DapG), a monofunctional enzymes found in Bacilli
           (Bacillus subtilis 168), Clostridia, and Actinobacteria
           bacterial species, as well as, the catalytic AK domain
           of the lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis 168, the lysine plus
           threonine-sensitive aspartokinase of Corynebacterium
           glutamicum, and related isoenzymes. In Bacillus
           subtilis, the regulation of the diaminopimelate-lysine
           biosynthetic pathway involves dual control by
           diaminopimelate and lysine, effected through separate
           diaminopimelate- and lysine-sensitive aspartokinase
           isoenzymes. The role of the AKI isoenzyme is most likely
           to provide a constant level of aspartyl-beta-phosphate
           for the biosynthesis of diaminopimelate for
           peptidoglycan synthesis and dipicolinate during
           sporulation. The B. subtilis 168 AKII is induced by
           methionine, and repressed and inhibited by lysine. In
           Corynebacterium glutamicum and other various
           Gram-positive bacteria, the DAP-lysine pathway is
           feedback regulated by the concerted action of lysine and
           threonine. Also included in this CD are the
           aspartokinases of the extreme thermophile, Thermus
           thermophilus HB27, the Gram-negative obligate
           methylotroph, Methylophilus methylotrophus AS1, and
           those single aspartokinase isoenzyme types found in
           Pseudomonas, C. glutamicum, and Amycolatopsis
           lactamdurans. The B. subtilis AKI is tetrameric
           consisting of two alpha and two beta subunits; the alpha
           (43 kD) and beta (17 kD) subunit formed by two in-phase
           overlapping genes. The alpha subunit contains the AK
           catalytic domain and two ACT domains. The beta subunit
           contains two ACT domains. The B. subtilis 168 AKII
           aspartokinase is also described as tetrameric consisting
           of two alpha and two beta subunits. Some archeal
           aspartokinases in this group lack recognizable ACT
           domains..
          Length = 239

 Score =  327 bits (840), Expect = 4e-90
 Identities = 136/244 (55%), Positives = 179/244 (73%), Gaps = 5/244 (2%)

Query: 3   RIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDN 62
            IV KFGGTSVA+I+ I+  A  +K+ V +G +V +VVSAM G TD L  L ++V+   +
Sbjct: 1   IIVQKFGGTSVADIERIKRVAERIKKAVKKGYQVVVVVSAMGGTTDELIGLAKEVSPRPS 60

Query: 63  ARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIV 122
            RE D+++STGEQ+S+ L+ +AL  LGI+AISL GWQ  I+TD  HG ARI  +D K+I+
Sbjct: 61  PRELDMLLSTGEQISAALLAMALNRLGIKAISLTGWQAGILTDDHHGNARIIDIDPKRIL 120

Query: 123 THLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTD 182
             L++  VVV+ GFQG++ D  +TTLGRGGSDT+AVA+AAA+KADRC+IYTDV G+YT D
Sbjct: 121 EALEEGDVVVVAGFQGVNEDGEITTLGRGGSDTTAVALAAALKADRCEIYTDVDGVYTAD 180

Query: 183 PRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLG 242
           PRI PKA  +  IS++EMLEM+SLGAKV+  RSVELA  Y + L VRSSF ++      G
Sbjct: 181 PRIVPKARKLDVISYDEMLEMASLGAKVLHPRSVELAKKYNVPLRVRSSFSEN-----PG 235

Query: 243 TLIC 246
           TLI 
Sbjct: 236 TLIT 239


>gnl|CDD|58627 cd04261, AAK_AKii-LysC-BS, AAK_AKii-LysC-BS: Amino Acid Kinase
           Superfamily (AAK), AKii; this CD includes the N-terminal
           catalytic aspartokinase (AK) domain of the
           lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis 168, and the lysine plus
           threonine-sensitive aspartokinase of Corynebacterium
           glutamicum, and related sequences. In B. subtilis 168,
           the regulation of the diaminopimelate (Dap)-lysine
           biosynthetic pathway involves dual control by Dap and
           lysine, effected through separate Dap- and
           lysine-sensitive aspartokinase isoenzymes. The B.
           subtilis 168 AKII is induced by methionine, and
           repressed and inhibited by lysine. Although
           Corynebacterium glutamicum is known to contain a single
           aspartokinase isoenzyme type, both the succinylase and
           dehydrogenase variant pathways of DAP-lysine synthesis
           operate simultaneously in this organism. In this
           organism and other various Gram-positive bacteria, the
           DAP-lysine pathway is feedback regulated by the
           concerted action of lysine and theronine. Also included
           in this CD are the aspartokinases of the extreme
           thermophile, Thermus thermophilus HB27, the
           Gram-negative obligate methylotroph, Methylophilus
           methylotrophus AS1, and those single aspartokinases
           found in Pseudomons, C. glutamicum, and Amycolatopsis
           lactamdurans. B. subtilis 168 AKII, and the C.
           glutamicum, Streptomyces clavuligerus and A.
           lactamdurans aspartokinases are described as tetramers
           consisting of two alpha and two beta subunits; the alpha
           (44 kD) and beta (18 kD) subunits formed by two in-phase
           overlapping polypeptides..
          Length = 239

 Score =  326 bits (838), Expect = 5e-90
 Identities = 135/244 (55%), Positives = 174/244 (71%), Gaps = 5/244 (2%)

Query: 3   RIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDN 62
            IV KFGGTSVA+I+ I+  A  +K+   +G +V +VVSAM G TD L EL ++++    
Sbjct: 1   LIVQKFGGTSVASIERIKRVAERIKKRKKKGNQVVVVVSAMGGTTDELIELAKEISPRPP 60

Query: 63  ARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIV 122
           ARE DV++STGEQVS  L+ +AL  LGI+AISL GWQ  I+TD  HG ARI  +D  +I 
Sbjct: 61  ARELDVLLSTGEQVSIALLAMALNRLGIKAISLTGWQAGILTDGHHGKARIIDIDPDRIR 120

Query: 123 THLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTD 182
             L++  VV++ GFQG++ D  +TTLGRGGSDTSAVA+AAA+ ADRC+IYTDV G+YT D
Sbjct: 121 ELLEEGDVVIVAGFQGINEDGDITTLGRGGSDTSAVALAAALGADRCEIYTDVDGVYTAD 180

Query: 183 PRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLG 242
           PRI PKA  + +IS++EMLEM+SLGAKV+  RSVELA  Y + L V SSF +       G
Sbjct: 181 PRIVPKARKLDEISYDEMLEMASLGAKVLHPRSVELAKKYGVPLRVLSSFSEEP-----G 235

Query: 243 TLIC 246
           TLI 
Sbjct: 236 TLIT 239


>gnl|CDD|58600 cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK),
           Aspartokinase (AK); this CD includes the N-terminal
           catalytic domain of aspartokinase
           (4-L-aspartate-4-phosphotransferase;). AK is the first
           enzyme in the biosynthetic pathway of the aspartate
           family of amino acids (lysine, threonine, methionine,
           and isoleucine) and the bacterial cell wall component,
           meso-diaminopimelate. It also catalyzes the conversion
           of aspartate and ATP to aspartylphosphate and ADP. One
           mechanism for the regulation of this pathway is by the
           production of several isoenzymes of aspartokinase with
           different repressors and allosteric inhibitors. Pairs of
           ACT domains are proposed to specifically bind amino
           acids leading to allosteric regulation of the enzyme. In
           Escherichia coli, three different aspartokinase
           isoenzymes are regulated specifically by lysine,
           methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII
           (MetL) are bifunctional enzymes that consist of an
           N-terminal AK and a C-terminal homoserine dehydrogenase
           (HSDH). ThrA and MetL are involved in threonine and
           methionine biosynthesis, respectively. The third
           isoenzyme, AKIII (LysC), is monofunctional and is
           involved in lysine synthesis. The three Bacillus
           subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII
           (YclM), are feedback-inhibited by meso-diaminopimelate,
           lysine, and lysine plus threonine, respectively. The E.
           coli lysine-sensitive AK is described as a homodimer,
           whereas, the B. subtilis lysine-sensitive AK is
           described as a heterodimeric complex of alpha- and beta-
           subunits that are formed from two in-frame overlapping
           genes. A single AK enzyme type has been described in
           Pseudomonas, Amycolatopsis, and Corynebacterium. The
           fungal aspartate pathway is regulated at the AK step,
           with L-Thr being an allosteric inhibitor of the
           Saccharomyces cerevisiae AK (Hom3). At least two
           distinct AK isoenzymes can occur in higher plants, one
           is a monofunctional lysine-sensitive isoenzyme, which is
           involved in the overall regulation of the pathway and
           can be synergistically inhibited by
           S-adenosylmethionine. The other isoenzyme is a
           bifunctional, threonine-sensitive AK-HSDH protein. Also
           included in this CD is the catalytic domain of the
           Methylomicrobium alcaliphilum ectoine AK, the first
           enzyme of the ectoine biosynthetic pathway, found in
           this bacterium, and several other
           halophilic/halotolerant bacteria..
          Length = 227

 Score =  248 bits (635), Expect = 2e-66
 Identities = 105/245 (42%), Positives = 145/245 (59%), Gaps = 19/245 (7%)

Query: 3   RIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDN 62
            +V KFGGTSVA+ + I+  A  +K     G  V +VVSAM G TD L EL         
Sbjct: 1   MVVQKFGGTSVASAERIKRVADIIKAYEK-GNRVVVVVSAMGGVTDLLIELAL------- 52

Query: 63  ARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIV 122
                 ++S GE++S+ L+  AL+  GI+A SL   Q  I TD  HG ARI  +  +++ 
Sbjct: 53  ------LLSFGERLSARLLAAALRDRGIKARSLDARQAGITTDDNHGAARIIEISYERLK 106

Query: 123 THLKKKQ-VVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTT 181
             L +   V V+TGF G + D  +TTLGRGGSD SA A+AAA+ AD  +I+TDV GIYT 
Sbjct: 107 ELLAEIGKVPVVTGFIGRNEDGEITTLGRGGSDYSAAALAAALGADEVEIWTDVDGIYTA 166

Query: 182 DPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQL 241
           DPRI P+A L+ +IS++E LE++  GAKV+  R+VE A    + + V+++F         
Sbjct: 167 DPRIVPEARLIPEISYDEALELAYFGAKVLHPRAVEPARKANIPIRVKNTFNPEAP---- 222

Query: 242 GTLIC 246
           GTLI 
Sbjct: 223 GTLIT 227


>gnl|CDD|58626 cd04260, AAK_AKi-DapG-BS, AAK_AKi-DapG-BS: Amino Acid Kinase
           Superfamily (AAK), AKi-DapG; this CD includes the
           N-terminal catalytic aspartokinase (AK) domain of  the
           diaminopimelate-sensitive aspartokinase isoenzyme AKI
           (DapG), a monofunctional class enzyme found in Bacilli
           (Bacillus subtilis 168), Clostridia, and Actinobacteria
           bacterial species.  In Bacillus subtilis, the regulation
           of the diaminopimelate-lysine biosynthetic pathway
           involves dual control by diaminopimelate and lysine,
           effected through separate diaminopimelate- and
           lysine-sensitive aspartokinase isoenzymes. AKI activity
           is invariant during the exponential and stationary
           phases of growth and is not altered by addition of amino
           acids to the growth medium. The role of this isoenzyme
           is most likely to provide a constant level of
           aspartyl-beta-phosphate for the biosynthesis of
           diaminopimelate for peptidoglycan synthesis and
           dipicolinate during sporulation. The B. subtilis AKI is
           tetrameric consisting of two alpha and two beta
           subunits; the alpha (43 kD) and beta (17 kD) subunit
           formed by two in-phase overlapping genes. The alpha
           subunit contains the AK catalytic domain and two ACT
           domains. The beta subunit contains two ACT domains..
          Length = 244

 Score =  214 bits (546), Expect = 3e-56
 Identities = 105/247 (42%), Positives = 158/247 (63%), Gaps = 10/247 (4%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAM--SGE---TDRLAELCRQVT 58
           IV KFGGTSV+  +     A  VK+ VD G +  +VVSAM   G+   TD L  L     
Sbjct: 2   IVQKFGGTSVSTKERREQVAKKVKQAVDEGYKPVVVVSAMGRKGDPYATDTLINLVYAEN 61

Query: 59  SIDNARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDE 118
           S  + RE D+++S GE +S+ ++   L++ G++A++L G Q  I+TD  +  A+I +V+ 
Sbjct: 62  SDISPRELDLLMSCGEIISAVVLTSTLRAQGLKAVALTGAQAGILTDDNYSNAKIIKVNP 121

Query: 119 KKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGI 178
           KKI++ LK+  VVV+ GFQG++ D  VTTLGRGGSDT+A A+ AA+ A+  +IYTDV GI
Sbjct: 122 KKILSALKEGDVVVVAGFQGVTEDGEVTTLGRGGSDTTAAALGAALNAEYVEIYTDVDGI 181

Query: 179 YTTDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQ 238
            T DPR+ P A ++  +S+ E+ +M+  GAKV+  R+VE+AM   + + +RS+  ++   
Sbjct: 182 MTADPRVVPNARILDVVSYNEVFQMAHQGAKVIHPRAVEIAMQANIPIRIRSTMSEN--- 238

Query: 239 EQLGTLI 245
              GTLI
Sbjct: 239 --PGTLI 243


>gnl|CDD|58609 cd04243, AAK_AK-HSDH-like, AAK_AK-HSDH-like: Amino Acid Kinase
           Superfamily (AAK), AK-HSDH-like; this family includes
           the N-terminal catalytic domain of aspartokinase (AK) of
           the bifunctional enzyme AK- homoserine dehydrogenase
           (HSDH). These aspartokinases are found in such bacteria
           as E. coli (AKI-HSDHI, ThrA  and  AKII-HSDHII, MetL) and
           in higher plants (Z. mays AK-HSDH). AK and HSDH are the
           first and third enzymes in the biosynthetic pathway of
           the aspartate family of amino acids. AK catalyzes the
           phosphorylation of Asp to P-aspartyl phosphate. HSDH
           catalyzes the NADPH-dependent conversion of Asp
           3-semialdehyde to homoserine. ThrA and MetL are involved
           in threonine and methionine biosynthesis, respectively.
           In E. coli, ThrA is subject to allosteric regulation by
           the end product L-threonine and the native enzyme is
           reported to be tetrameric. As with bacteria, plant AK
           and HSDH are feedback inhibited by pathway end products.
           Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
           Arabidopsis AK-HSDH is an alanine-activated,
           threonine-sensitive enzyme whose ACT domains, located
           C-terminal to the AK catalytic domain, were shown to be
           involved in allosteric activation. Also included in this
           CD is the catalytic domain of the aspartokinase (AK) of
           the lysine-sensitive aspartokinase isoenzyme AKIII, a
           monofunctional class enzyme (LysC) found in some
           bacteria such as E. coli. In E. coli, LysC is reported
           to be a homodimer of 50 kD subunits. Also included in
           this CD is  the catalytic domain of aspartokinase (AK)
           of the bifunctional enzyme AK - DAP decarboxylase
           (DapDC) found in some bacteria. DapDC, which is the lysA
           gene product, catalyzes the decarboxylation of DAP to
           lysine..
          Length = 293

 Score =  162 bits (412), Expect = 1e-40
 Identities = 90/297 (30%), Positives = 139/297 (46%), Gaps = 59/297 (19%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEV-------------AMVVSAMSGET--- 47
            V+KFGGTSVA+ + IR  A  +K        V             A+   A SG+    
Sbjct: 2   KVLKFGGTSVASAERIRRVADIIKSRASSPVLVVVSALGGVTNRLVALAELAASGDDAQA 61

Query: 48  ----------------------------------DRLAELCRQVTSIDNA--RERDVVIS 71
                                             +RL +L   +  +     + R  V+S
Sbjct: 62  IVLQEIRERHLDLIKELLSGESAAELLAALDSLLERLKDLLEGIRLLGELSDKTRAEVLS 121

Query: 72  TGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIVTHL--KKKQ 129
            GE +SS LM   LQ  G+ A  L   ++ ++TD     A +     K+ +  L  +  +
Sbjct: 122 FGELLSSRLMSAYLQEQGLPAAWLDAREL-LLTDDGFLNAVVDLKLSKERLAQLLAEHGK 180

Query: 130 VVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKA 189
           VVV  GF   + D   TTLGRGGSD SA  +AA + A+  +I+TDV G+YT DPR  P A
Sbjct: 181 VVVTQGFIASNEDGETTTLGRGGSDYSAALLAALLDAEEVEIWTDVDGVYTADPRKVPDA 240

Query: 190 HLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLIC 246
            L+K++S++E +E++  GAKV+  R+++ A+   + +F++++F      E  GTLI 
Sbjct: 241 RLLKELSYDEAMELAYFGAKVLHPRTIQPAIRKNIPIFIKNTFN----PEAPGTLIS 293


>gnl|CDD|58610 cd04244, AAK_AK-LysC-like, AAK_AK-LysC-like: Amino Acid Kinase
           Superfamily (AAK), AK-LysC-like; this CD includes the
           N-terminal catalytic aspartokinase (AK) domain of the
           lysine-sensitive AK isoenzyme found in higher plants.
           The lysine-sensitive AK isoenzyme is a monofunctional
           protein. It is involved in the overall regulation of the
           aspartate pathway and can be synergistically inhibited
           by S-adenosylmethionine. Also included in this CD is an
           uncharacterized LysC-like AK found in Euryarchaeota and
           some bacteria. AK catalyzes the conversion of aspartate
           and ATP to aspartylphosphate and ADP..
          Length = 298

 Score =  158 bits (401), Expect = 3e-39
 Identities = 101/302 (33%), Positives = 144/302 (47%), Gaps = 64/302 (21%)

Query: 3   RIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDN 62
           R+VMKFGGTSV + + IR  A  V      G EV +VVSAM G TDRL        S   
Sbjct: 1   RLVMKFGGTSVGSAERIRHVADLVGTY-AEGHEVVVVVSAMGGVTDRLLLAAEAAVSGRI 59

Query: 63  ARERDVV------------------------------ISTGEQVSSGLMVL--------- 83
           A  +D +                              +   E++  G+  L         
Sbjct: 60  AGVKDFIEILRLRHIKAAKEAISDEEIAEVESIIDSLLEELEKLLYGIAYLGELTPRSRD 119

Query: 84  ----------------ALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIVTHL-- 125
                           AL+SLGI+A +L G +  I+TD   G AR      +++   L  
Sbjct: 120 YIVSFGERLSAPIFSAALRSLGIKARALDGGEAGIITDDNFGNARPLPATYERVRKRLLP 179

Query: 126 --KKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDP 183
             +  ++ V+TGF G + D ++TTLGRGGSD SA  I AA+ AD   I+ DV G+ T DP
Sbjct: 180 MLEDGKIPVVTGFIGATEDGAITTLGRGGSDYSATIIGAALDADEIWIWKDVDGVMTADP 239

Query: 184 RIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGT 243
           RI P+A  + ++S+ E +E++  GAKV+  R+VE AM   + + V+++F      E  GT
Sbjct: 240 RIVPEARTIPRLSYAEAMELAYFGAKVLHPRTVEPAMEKGIPVRVKNTFN----PEAPGT 295

Query: 244 LI 245
           LI
Sbjct: 296 LI 297


>gnl|CDD|58599 cd02115, AAK, Amino Acid Kinases (AAK) superfamily, catalytic
           domain; present in such enzymes like N-acetylglutamate
           kinase (NAGK), carbamate kinase (CK), aspartokinase
           (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK).
           The AAK superfamily includes kinases that phosphorylate
           a variety of amino acid substrates. These kinases
           catalyze the formation of phosphoric anhydrides,
           generally with a carboxylate, and use ATP as the source
           of the phosphoryl group; are involved in amino acid
           biosynthesis. Some of these kinases control the process
           via allosteric feed-back inhibition..
          Length = 248

 Score =  154 bits (390), Expect = 4e-38
 Identities = 72/234 (30%), Positives = 126/234 (53%), Gaps = 5/234 (2%)

Query: 5   VMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSID--- 61
           V+KFGG+SV++ + +R+ A  + +    G  V +V  A    TD L      +       
Sbjct: 1   VIKFGGSSVSSEERLRNLARILVKLASEGGRVVVVHGAGPQITDELLAHGELLGYARGLR 60

Query: 62  -NARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKK 120
              RE D + + GE +S+ L+  AL+  GI+A+ L   Q    + +   + +I +V   +
Sbjct: 61  ITDRETDALAAMGEGMSNLLIAAALEQHGIKAVPLDLTQAGFASPNQGHVGKITKVSTDR 120

Query: 121 IVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYT 180
           + + L+   + +++GF G        TLGRGGSD++A  +AAA+KADR  I TDV G+YT
Sbjct: 121 LKSLLENGILPILSGFGGTDEK-ETGTLGRGGSDSTAALLAAALKADRLVILTDVDGVYT 179

Query: 181 TDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFED 234
            DPR  P A L+ ++++EE  E++  GA V++ ++ + A    + + + ++   
Sbjct: 180 ADPRKVPDAKLLSELTYEEAAELAYAGAMVLKPKAADPAARAGIPVRIANTENP 233


>gnl|CDD|58624 cd04258, AAK_AKiii-LysC-EC, AAK_AKiii-LysC-EC: Amino Acid Kinase
           Superfamily (AAK), AKiii-LysC-EC: this CD includes the
           N-terminal catalytic aspartokinase (AK) domain of the
           lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is
           a monofunctional class enzyme (LysC) found in some
           bacteria such as E. coli. Aspartokinase is the first
           enzyme in the aspartate metabolic pathway and catalyzes
           the conversion of aspartate and ATP to aspartylphosphate
           and ADP. In E. coli, LysC is reported to be a homodimer
           of 50 kD subunits..
          Length = 292

 Score =  153 bits (387), Expect = 1e-37
 Identities = 95/299 (31%), Positives = 129/299 (43%), Gaps = 64/299 (21%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELC--------- 54
           +V KFGGTSVA+   +   A  VK +        +VVSA +G T+ L  L          
Sbjct: 2   VVAKFGGTSVADYAAMLRCAAIVKSDASVR---LVVVSASAGVTNLLVALADAAESGEEI 58

Query: 55  --------------------RQVTSIDNARER-----------------------DVVIS 71
                                    +    E                        D ++S
Sbjct: 59  ESIPQLHEIRAIHFAILNRLGAPEELRAKLEELLEELTQLAEGAALLGELSPASRDELLS 118

Query: 72  TGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMAR----ICRVDEKKIVTHLKK 127
            GE++SS L   AL+  G+ A       + + TDS  G A            K++  L  
Sbjct: 119 FGERMSSLLFSEALREQGVPAEWFDVRTV-LRTDSRFGRAAPDLNALAELAAKLLKPLLA 177

Query: 128 KQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEP 187
             VVV  GF G +     TTLGRGGSD SA  +A A+ A+   I+TDV GIYTTDPRI P
Sbjct: 178 GTVVVTQGFIGSTEKGRTTTLGRGGSDYSAALLAEALHAEELQIWTDVAGIYTTDPRICP 237

Query: 188 KAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLIC 246
            A  +K+ISF E  EM++ GAKV+   ++  A+   + +FV SS +     E  GTLI 
Sbjct: 238 AARAIKEISFAEAAEMATFGAKVLHPATLLPAIRKNIPVFVGSSKD----PEAGGTLIT 292


>gnl|CDD|58623 cd04257, AAK_AK-HSDH, AAK_AK-HSDH: Amino Acid Kinase Superfamily
           (AAK), AK-HSDH; this CD includes the N-terminal
           catalytic domain of aspartokinase (AK) of the
           bifunctional enzyme AK - homoserine dehydrogenase
           (HSDH). These aspartokinases are found in bacteria (E.
           coli AKI-HSDHI, ThrA  and E. coli AKII-HSDHII, MetL) and
           higher plants (Z. mays AK-HSDH). AK and HSDH are the
           first and third enzymes in the biosynthetic pathway of
           the aspartate family of amino acids. AK catalyzes the
           phosphorylation of Asp to P-aspartyl phosphate. HSDH
           catalyzes the NADPH-dependent conversion of Asp
           3-semialdehyde to homoserine. ThrA and MetL are involved
           in threonine and methionine biosynthesis, respectively.
           In E. coli, ThrA is subject to allosteric regulation by
           the end product L-threonine and the native enzyme is
           reported to be tetrameric. As with bacteria, plant AK
           and HSDH are feedback inhibited by pathway end products.
           Maize AK-HSDH is a Thr-sensitive 180-kD enzyme.
           Arabidopsis AK-HSDH is an alanine-activated,
           threonine-sensitive enzyme whose ACT domains, located
           C-terminal to the AK catalytic domain, were shown to be
           involved in allosteric activation..
          Length = 294

 Score =  143 bits (362), Expect = 8e-35
 Identities = 80/297 (26%), Positives = 134/297 (45%), Gaps = 60/297 (20%)

Query: 5   VMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDNAR 64
           V+KFGGTS+AN + IR  A  +     + Q VA+VVSA    TD L EL    +S D+A 
Sbjct: 3   VLKFGGTSLANAERIRRVADIILNAAKQEQ-VAVVVSAPGKVTDLLLELAELASSGDDAY 61

Query: 65  ER--DVVISTGEQVSSGLMVLALQSLGIQAIS---------LQG---------------- 97
           E     + S    + + L+     +  + A+          L+G                
Sbjct: 62  EDILQELESKHLDLITELLSGDAAAELLSALGNDLEELKDLLEGIYLLGELPDSIRAKVL 121

Query: 98  -----WQIPIMTDSLHGMA-RICRVDEKKIVT----HLK------------------KKQ 129
                    +++  L+        +D ++++     +L                     +
Sbjct: 122 SFGERLSARLLSALLNQQGLDAAWIDARELIVTDGGYLNAVVDIELSKERIKAWFSSNGK 181

Query: 130 VVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKA 189
           V+V+TGF   +     TTLGR GSD SA  +AA + AD+ +I+TDV G+Y+ DPR    A
Sbjct: 182 VIVVTGFIASNPQGETTTLGRNGSDYSAAILAALLDADQVEIWTDVDGVYSADPRKVKDA 241

Query: 190 HLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLIC 246
            L+  +S++E +E+S  GAKV+  ++++      + + ++++F      E  GTLI 
Sbjct: 242 RLLPSLSYQEAMELSYFGAKVLHPKTIQPVAKKNIPILIKNTF----NPEAPGTLIS 294


>gnl|CDD|144336 pfam00696, AA_kinase, Amino acid kinase family.  This family
           includes kinases that phosphorylate a variety of amino
           acid substrates, as well as uridylate kinase and
           carbamate kinase. This family includes: Aspartokinase
           EC:2.7.2.4. Acetylglutamate kinase EC:2.7.2.8. Glutamate
           5-kinase EC:2.7.2.11. Uridylate kinase EC:2.7.4.-.
           Carbamate kinase EC:2.7.2.2.
          Length = 230

 Score =  142 bits (360), Expect = 1e-34
 Identities = 76/236 (32%), Positives = 116/236 (49%), Gaps = 15/236 (6%)

Query: 3   RIVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDN 62
           RIV+K GG+S+ + D I+  A  +    + G +V  VVS   G TD+L         I  
Sbjct: 2   RIVIKLGGSSLTDEDAIKRIAEEIALLSELGIKVV-VVSGGGGFTDKLLAAYGIAEKIGL 60

Query: 63  ARERDVVISTGEQVSSGLM---VLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEK 119
                      E   +GL+   V A + LG +A++L       ++D   G  R+   D +
Sbjct: 61  RVTAGATGLIIEAALAGLLDIVVSAGERLGARAVALL------LSDGGIGAVRLDANDTE 114

Query: 120 KIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIY 179
            I   L++  V VITGF G +     TTLGRG SDT A  +A A+ AD+  I TDV G+Y
Sbjct: 115 AIKELLEEGVVPVITGFGGENDTGETTTLGRGSSDTLAALLAEALGADKLIILTDVDGVY 174

Query: 180 TTDPRIEPKAHLMKKISFEEMLEMS-----SLGAKVMQVRSVELAMLYKMCLFVRS 230
           T DPR  P A L+ ++S++E  E+      + G KV    +++ A    + + + +
Sbjct: 175 TADPRKVPDAKLIPELSYDEAEELLAAGDGTGGMKVKDPAALKAARRGGIPVVIVN 230


>gnl|CDD|35677 KOG0456, KOG0456, KOG0456, Aspartate kinase [Amino acid transport
           and metabolism].
          Length = 559

 Score =  138 bits (349), Expect = 3e-33
 Identities = 122/474 (25%), Positives = 200/474 (42%), Gaps = 95/474 (20%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTS---- 59
            VMKFGG+SV + +  R   + V       +   +V+SAMS  T+ L     +       
Sbjct: 81  CVMKFGGSSVGSAE--RMIEVAVLILYFPDERPVVVLSAMSKTTNALLTAGEKAVCCGVA 138

Query: 60  ---------------IDNARE--------------------------------RDVVIST 72
                          I  A E                                RD ++S 
Sbjct: 139 NVESIEELSIIKELHIRTAHELIVDPAVIAKLLEGLEQLLKGIAMMKELTLRTRDYLVSF 198

Query: 73  GEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARI-----CRVDEKKIVTHLKK 127
           GE +S+      L  +G +A     ++I  +T        I       V +       K+
Sbjct: 199 GECLSTRFFAAYLNDIGHKARQYDAFEIGFITTDDFTNDDILEATYPAVSKLLSGDWAKE 258

Query: 128 KQVVVITGFQG-LSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIE 186
             V V+TGF G      ++TTLGRGGSD +A  I  A+  D   ++ DV G+ T DPRI 
Sbjct: 259 NAVPVVTGFLGKGWPTGALTTLGRGGSDLTATTIGKALGLDEIQVWKDVDGVLTCDPRIY 318

Query: 187 PKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLIC 246
           P A L+  ++F+E  E++  GA+V+   S+  A   ++ + V++S+         GT+I 
Sbjct: 319 PGARLVPYLTFDEAAELAYFGAQVLHPFSMRPAREGRIPVRVKNSYNPTAP----GTVIT 374

Query: 247 SGEDIMEKKVITGIAYTKDEAQI---SLRRLRDHPGISASIFSPLAEAHINIDMIIQNVS 303
              D M K  +T I   ++   +   S R L  H G  A +F+   +  I++D++    S
Sbjct: 375 PDRD-MSKAGLTSIVLKRNVTMLDIASTRMLGQH-GFLAKVFTIFEKLGISVDVV--ATS 430

Query: 304 EDGQYVDITFTTPSSSLEKALAVLSDNKENIGYDVIQHEDNLVKISAIGI---------- 353
           E    V I+ T   S L        D++E I  ++ Q  + L KI+ + +          
Sbjct: 431 E----VSISLTLDPSKL--------DSRELIQGELDQAVEELEKIAVVDLLKGRSIISLI 478

Query: 354 -GMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSLHS 404
             +Q+ +G+    F  LAE GIN++ I+   S++ IS +++    E  V++LH 
Sbjct: 479 GNVQNSSGILERMFCVLAENGINVQMISQGASKVNISCIVNEKEAEKCVQALHK 532


>gnl|CDD|58625 cd04259, AAK_AK-DapDC, AAK_AK-DapDC: Amino Acid Kinase Superfamily
           (AAK), AK-DapDC; this CD includes the N-terminal
           catalytic aspartokinase (AK) domain of the bifunctional
           enzyme AK - DAP decarboxylase (DapDC) found in some
           bacteria. Aspartokinase is the first enzyme in the
           aspartate metabolic pathway, catalyzes the conversion of
           aspartate and ATP to aspartylphosphate and ADP. DapDC,
           which is the lysA gene product, catalyzes the
           decarboxylation of DAP to lysine..
          Length = 295

 Score =  111 bits (278), Expect = 4e-25
 Identities = 79/297 (26%), Positives = 136/297 (45%), Gaps = 59/297 (19%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSID-- 61
           +V+KFGGTSV++     + A   ++ ++ G +  +V SA+SG +++L  L  Q    +  
Sbjct: 2   VVLKFGGTSVSSRARWDTIAKLAQKHLNTGGQPLIVCSALSGISNKLEALIDQALLDEHH 61

Query: 62  ------NARERDV---------------------------------------VISTGEQV 76
                  +R  ++                                       V++ GE +
Sbjct: 62  SLFNAIQSRHLNLAEQLEVDADALLANDLAQLQRWLTGISLLKQASPRTRAEVLALGELM 121

Query: 77  SSGLMVLALQSLGIQAISLQGWQIPIMTDSLHG------MARICR-VDEKKIVTHLKKKQ 129
           S+ L    L++ G++   L   ++   T +L G       AR      +  +   L    
Sbjct: 122 STRLGAAYLEAQGLKVKWLDARELLTATPTLGGETMNYLSARCESEYADALLQKRLADGA 181

Query: 130 VVVIT-GFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPK 188
            ++IT GF   +       LGRGGSDTSA   AA ++A RC+I+TDV G++T +P   P 
Sbjct: 182 QLIITQGFIARNAHGETVLLGRGGSDTSAAYFAAKLQAARCEIWTDVPGLFTANPHEVPH 241

Query: 189 AHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFEDHGQQEQLGTLI 245
           A L+K++ ++E  E++++GAKV+  R +  A    + + VRS+     + E  GTLI
Sbjct: 242 ARLLKRLDYDEAQEIATMGAKVLHPRCIPPARRANIPMVVRSTE----RPELSGTLI 294


>gnl|CDD|153185 cd04913, ACT_AKii-LysC-BS-like_1, ACT domains of the
           lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis (BS) strain 168 and related proteins. 
           This CD includes the N-terminal of the two ACT domains
           of the lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis (BS) strain 168, and the lysine plus
           threonine-sensitive aspartokinase of Corynebacterium
           glutamicum, and related sequences. In B. subtilis 168,
           the regulation of the diaminopimelate (Dap)-lysine
           biosynthetic pathway involves dual control by Dap and
           lysine, effected through separate Dap- and
           lysine-sensitive aspartokinase isoenzymes. The B.
           subtilis 168 AKII is induced by methionine and repressed
           and inhibited by lysine. Although Corynebacterium
           glutamicum is known to contain a single aspartokinase,
           both the succinylase and dehydrogenase variant pathways
           of DAP-lysine synthesis operate simultaneously in this
           organism. In corynebacteria and other various
           Gram-positive bacteria, the DAP-lysine pathway is
           feedback regulated by the concerted action of lysine and
           threonine. Conserved residues in the ACT domains have
           been shown to be involved in this concerted feedback
           inhibition. Also included in this CD are the
           aspartokinases of the extreme thermophile, Thermus
           thermophilus HB27, the Gram-negative obligate
           methylotroph, Methylophilus methylotrophus AS1, and
           those single aspartokinases found in Pseudomonas
           aeruginosa, C. glutamicum, and Amycolatopsis
           lactamdurans. B. subtilis 168 AKII, and the C.
           glutamicum, Streptomyces clavuligerus and A.
           lactamdurans aspartokinases are described as tetramers
           consisting of two alpha and two beta subunits; the alpha
           (44 kD) and beta (18 kD) subunits formed by two in-phase
           overlapping polypeptides. This CD includes the first ACT
           domain C-terminal to the AK catalytic domain of the
           alpha subunit and the first ACT domain of the beta
           subunit that lacks the AK catalytic domain. Unlike the
           C. glutamicum AK beta subunit, which is involved in
           feedback regulation, the B. subtilis AKII beta subunit
           is not. Cyanobacteria aspartokinases are unique to this
           CD and they have a unique domain architecture with two
           tandem pairs of ACT domains, C-terminal to the catalytic
           AK domain. In this CD, the first and third cyanobacteria
           AK ACT domains are present. Members of this CD belong to
           the superfamily of ACT regulatory domains.
          Length = 75

 Score =  100 bits (251), Expect = 8e-22
 Identities = 40/76 (52%), Positives = 57/76 (75%), Gaps = 1/76 (1%)

Query: 266 EAQISLRRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALA 325
           +A+I+LR + D PG++A IF  LAEA+IN+DMI+QNVS DG   DI+FT P S L+KALA
Sbjct: 1   QAKITLRGVPDKPGVAAKIFGALAEANINVDMIVQNVSRDG-TTDISFTVPKSDLKKALA 59

Query: 326 VLSDNKENIGYDVIQH 341
           VL   K+ +G + +++
Sbjct: 60  VLEKLKKELGAEEVEY 75


>gnl|CDD|58611 cd04245, AAK_AKiii-YclM-BS, AAK_AKiii-YclM-BS: Amino Acid Kinase
           Superfamily (AAK), AKiii-YclM-BS; this CD includes the
           N-terminal catalytic aspartokinase (AK) domain of the
           lysine plus threonine-sensitive aspartokinase isoenzyme
           AKIII, a monofunctional class enzyme found in Bacilli
           (Bacillus subtilis YclM) and Clostridia species.
           Aspartokinase is the first enzyme in the aspartate
           metabolic pathway and catalyzes the conversion of
           aspartate and ATP to aspartylphosphate and ADP. In
           Bacillus subtilis (BS), YclM is reported to be a single
           polypeptide of 50 kD. The Bacillus subtilis 168 AKIII is
           induced by lysine and repressed by threonine, and it is
           synergistically inhibited by lysine and threonine..
          Length = 288

 Score = 97.3 bits (242), Expect = 7e-21
 Identities = 51/186 (27%), Positives = 84/186 (45%), Gaps = 3/186 (1%)

Query: 30  VDRGQEVAMVVSAMSGETDRLAELCRQV---TSIDNARERDVVISTGEQVSSGLMVLALQ 86
           VDR  E+A  +       + +AE+   +      +     D + + GE +++ LM   L 
Sbjct: 73  VDRYAEIADELGLPMSILEEIAEILENLANLDYANPDYLLDALKARGEYLNAQLMAAYLN 132

Query: 87  SLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIVTHLKKKQVVVITGFQGLSHDNSVT 146
             GI A  +      ++     G A+I     +KI       + +VI GF G S +  + 
Sbjct: 133 YQGIDARYVIPKDAGLVVTDEPGNAQILPESYQKIKKLRDSDEKLVIPGFYGYSKNGDIK 192

Query: 147 TLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLEMSSL 206
           T  RGGSD +   +A   +AD  + +TDV GIY  +PRI      + ++++ EM E+S  
Sbjct: 193 TFSRGGSDITGAILARGFQADLYENFTDVDGIYAANPRIVANPKPISEMTYREMRELSYA 252

Query: 207 GAKVMQ 212
           G  V  
Sbjct: 253 GFSVFH 258


>gnl|CDD|153208 cd04936, ACT_AKii-LysC-BS-like_2, ACT domains of the
           lysine-sensitive, aspartokinase (AK) isoenzyme AKII of
           Bacillus subtilis (BS) strain 168 and related domains.
           This CD includes the C-terminal of the two ACT domains
           of the lysine-sensitive, aspartokinase (AK) isoenzyme
           AKII of Bacillus subtilis (BS) strain 168, and the
           lysine plus threonine-sensitive aspartokinase of
           Corynebacterium glutamicum, and related sequences. In B.
           subtilis strain 168, the regulation of the
           diaminopimelate (Dap)-lysine biosynthetic pathway
           involves dual control by Dap and lysine, effected
           through separate Dap- and lysine-sensitive AK
           isoenzymes. The B. subtilis strain 168 AKII is induced
           by methionine and repressed and inhibited by lysine.
           Although C. glutamicum is known to contain a single AK,
           both the succinylase and dehydrogenase variant pathways
           of DAP-lysine synthesis operate simultaneously in this
           organism. In corynebacteria and other various
           Gram-positive bacteria, the DAP-lysine pathway is
           feedback regulated by the concerted action of lysine and
           threonine. Conserved residues in the ACT domains have
           been shown to be involved in this concerted feedback
           inhibition. Also included in this CD are the AKs of the
           extreme thermophile, Thermus thermophilus HB27, the
           Gram-negative obligate methylotroph, Methylophilus
           methylotrophus AS1, and those single AKs found in
           Pseudomons, C. glutamicum, and Amycolatopsis
           lactamdurans. B. subtilis strain 168 AKII, and the C.
           glutamicum, Streptomyces clavuligerus and A.
           lactamdurans AKs are described as tetramers consisting
           of two alpha and two beta subunits; the alpha (44 kD)
           and beta (18 kD) subunits formed by two in-phase
           overlapping polypeptides. This CD includes the second
           ACT domain C-terminal to the AK catalytic domain of the
           alpha subunit and the second ACT domain of the beta
           subunit that lacks the AK catalytic domain. Unlike the
           C. glutamicum AK beta subunit, which is involved in
           feedback regulation, the B. subtilis AKII beta subunit
           is not. Cyanobacteria AKs are unique to this CD and they
           have a unique domain architecture with two tandem pairs
           of ACT domains, C-terminal to the catalytic AK domain.
           In this CD, the second and fourth cyanobacteria AK ACT
           domains are present. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 63

 Score = 88.0 bits (219), Expect = 4e-18
 Identities = 35/62 (56%), Positives = 44/62 (70%)

Query: 347 KISAIGIGMQSYAGVASAFFLCLAEKGINIKAITTSEIKISVLIDSAYTELAVRSLHSCY 406
           K+S +G GM+S+ GVA+  F  LAE GINI+ I+TSEIKIS LID    E AVR+LH  +
Sbjct: 2   KVSIVGAGMRSHPGVAAKMFEALAEAGINIEMISTSEIKISCLIDEDDAEKAVRALHEAF 61

Query: 407 GL 408
            L
Sbjct: 62  EL 63



 Score = 40.6 bits (96), Expect = 7e-04
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 6/56 (10%)

Query: 274 LRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSD 329
           +R HPG++A +F  LAEA INI+MI  + SE    + I+        EKA+  L +
Sbjct: 10  MRSHPGVAAKMFEALAEAGINIEMI--STSE----IKISCLIDEDDAEKAVRALHE 59


>gnl|CDD|153195 cd04923, ACT_AK-LysC-DapG-like_2, ACT domains of the
           lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis (BS) strain 168 and related domains.
           This CD includes the C-terminal of the two ACT domains
           of the lysine-sensitive aspartokinase isoenzyme AKII of
           Bacillus subtilis (BS) strain 168, and the lysine plus
           threonine-sensitive aspartokinase of Corynebacterium
           glutamicum, as well as, the second and fourth, of four,
           ACT domains present in cyanobacteria AK. Also included
           are the C-terminal of the two ACT domains of the
           diaminopimelate-sensitive aspartokinase isoenzyme AKI
           found in Bacilli (B. subtilis strain 168), Clostridia,
           and Actinobacteria bacterial species. Members of this CD
           belong to the superfamily of ACT regulatory domains.
          Length = 63

 Score = 85.3 bits (212), Expect = 3e-17
 Identities = 34/62 (54%), Positives = 44/62 (70%)

Query: 347 KISAIGIGMQSYAGVASAFFLCLAEKGINIKAITTSEIKISVLIDSAYTELAVRSLHSCY 406
           K+S +G GM+S+ GVA+  F  LAE GINI+ I+TSEIKIS L+D    E AVR+LH  +
Sbjct: 2   KVSIVGAGMRSHPGVAAKMFKALAEAGINIEMISTSEIKISCLVDEDDAEKAVRALHEAF 61

Query: 407 GL 408
            L
Sbjct: 62  EL 63



 Score = 39.4 bits (93), Expect = 0.002
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 8/65 (12%)

Query: 267 AQISLR--RLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKAL 324
           A++S+    +R HPG++A +F  LAEA INI+MI  + SE    + I+        EKA+
Sbjct: 1   AKVSIVGAGMRSHPGVAAKMFKALAEAGINIEMI--STSE----IKISCLVDEDDAEKAV 54

Query: 325 AVLSD 329
             L +
Sbjct: 55  RALHE 59


>gnl|CDD|153163 cd04891, ACT_AK-LysC-DapG-like_1, ACT domains of the
           lysine-sensitive aspartokinase isoenzyme AKII and
           related proteins.  This CD includes the N-terminal of
           the two ACT domains of the lysine-sensitive
           aspartokinase isoenzyme AKII of Bacillus subtilis (BS)
           strain 168, and the lysine plus threonine-sensitive
           aspartokinase of Corynebacterium glutamicum, as well as,
           the first and third, of four, ACT domains present in
           cyanobacteria AK. Also included are the N-terminal of
           the two ACT domains of the diaminopimelate-sensitive
           aspartokinase isoenzyme AKI found in Bacilli (Bacillus
           subtilis strain 168), Clostridia, and Actinobacteria
           bacterial species. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 61

 Score = 84.5 bits (210), Expect = 4e-17
 Identities = 35/61 (57%), Positives = 47/61 (77%), Gaps = 1/61 (1%)

Query: 267 AQISLRRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAV 326
           AQ++++ + D PG++A IFS LAEA IN+DMI+Q+VS  G   DI+FT P S LEKALA+
Sbjct: 1   AQVTIKGVPDKPGVAAKIFSALAEAGINVDMIVQSVSRGG-TTDISFTVPKSDLEKALAI 59

Query: 327 L 327
           L
Sbjct: 60  L 60


>gnl|CDD|58613 cd04247, AAK_AK-Hom3, AAK_AK-Hom3: Amino Acid Kinase Superfamily
           (AAK), AK-Hom3; this CD includes the N-terminal
           catalytic domain of the aspartokinase HOM3, a
           monofunctional class enzyme found in Saccharomyces
           cerevisiae and other related AK domains. Aspartokinase,
           the first enzyme in the aspartate metabolic pathway,
           catalyzes the conversion of aspartate and ATP to
           aspartylphosphate and ADP, and in fungi, is responsible
           for the production of threonine, isoleucine and
           methionine. S. cerevisiae has a single aspartokinase
           isoenzyme type, which is regulated by feedback,
           allosteric inhibition by L-threonine. Recent studies
           show that the allosteric transition triggered by binding
           of threonine to AK involves a large change in the
           conformation of the native hexameric enzyme that is
           converted to an inactive one of different shape and
           substantially smaller hydrodynamic size..
          Length = 306

 Score = 80.0 bits (197), Expect = 1e-15
 Identities = 55/208 (26%), Positives = 100/208 (48%), Gaps = 18/208 (8%)

Query: 16  IDCIRSAALH-VKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSID--NARERDVVIST 72
           ++ IRS  L   ++ +   +  A +   ++ E + L +       +   + R +D+VIST
Sbjct: 72  VEDIRSDHLAAARKFIKNPELQAELEEEINKECELLRKYLEAAKILSEISPRTKDLVIST 131

Query: 73  GEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEK---KIVTHLKKK- 128
           GE++S   M   L+  G+ A      +   ++  +     I  +D+    ++   L +K 
Sbjct: 132 GEKLSCRFMAAVLRDRGVDA------EYVDLSHIVDLDFSIEALDQTFYDELAQVLGEKI 185

Query: 129 -----QVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDP 183
                +V V+TGF G      ++ +GRG +D  A   A  + AD   I+ +V GI+T DP
Sbjct: 186 TACENRVPVVTGFFGNVPGGLLSQIGRGYTDLCAALCAVGLNADELQIWKEVDGIFTADP 245

Query: 184 RIEPKAHLMKKISFEEMLEMSSLGAKVM 211
           R  P A L+  I+ EE  E++  G++V+
Sbjct: 246 RKVPTARLLPSITPEEAAELTYYGSEVI 273



 Score = 35.7 bits (82), Expect = 0.026
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 4  IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDNA 63
          +V KFGGTSV       + A  + +   +G +VA+V SA S  T       R + + D A
Sbjct: 3  VVQKFGGTSVGKF--PDNIADDIVKAYLKGNKVAVVCSARSTGTKAEGTTNRLLQAADEA 60


>gnl|CDD|58605 cd04239, AAK_UMPK-like, AAK_UMPK-like: UMP kinase (UMPK)-like, the
           microbial/chloroplast uridine monophosphate kinase
           (uridylate kinase) enzyme that catalyzes UMP
           phosphorylation and plays a key role in pyrimidine
           nucleotide biosynthesis. Regulation of this process is
           via feed-back control and via gene repression of
           carbamoyl phosphate synthetase (the first enzyme of the
           pyrimidine biosynthesis pathway). The UMP kinases of E.
           coli (Ec) and Pyrococcus furiosus (Pf) are known to
           function as homohexamers, with GTP and UTP being
           allosteric effectors. Like other related enzymes
           (carbamate kinase, aspartokinase, and N-acetylglutamate
           kinase) the E. coli and most bacterial UMPKs have a
           conserved, N-terminal, lysine residue proposed to
           function in the catalysis of the phosphoryl group
           transfer, whereas most archaeal UMPKs appear to lack
           this residue and the Pyrococcus furiosus structure has
           an additional Mg ion bound to the ATP molecule which is
           proposed to function as the catalysis instead. Also
           included in this CD are the alpha and beta subunits of
           the Mo storage protein (MosA and MosB) characterized as
           an alpha4-beta4 octamer containing an ATP-dependent,
           polynuclear molybdenum-oxide cluster. These and related 
           sequences in this CD are members of the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 229

 Score = 72.5 bits (178), Expect = 2e-13
 Identities = 67/255 (26%), Positives = 110/255 (43%), Gaps = 39/255 (15%)

Query: 3   RIVMKFGGTSVA------NIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQ 56
           RIV+K  G ++A      + + ++  A  +K  VD G EVA+VV    G   R       
Sbjct: 1   RIVLKLSGEALAGEGGGIDPEVLKEIAREIKEVVDLGVEVAIVVGG--GNIAR------- 51

Query: 57  VTSIDNARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARIC-R 115
              I  AR       T + +  G++   + +L +Q  +L+   +     S   M  +   
Sbjct: 52  -GYIAAARGMPRA--TADYI--GMLATVMNALALQD-ALEKLGVKTRVMSAIPMQGVAEP 105

Query: 116 VDEKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDV 175
              ++ + HL+K ++V+  G  G       TT      DT+A   A  I AD     T+V
Sbjct: 106 YIRRRAIRHLEKGRIVIFGGGTGNPG---FTT------DTAAALRAEEIGADVLLKATNV 156

Query: 176 CGIYTTDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFV-----RS 230
            G+Y  DP+  P A    +IS++E+L+    G KVM   ++ L    K+ + V       
Sbjct: 157 DGVYDADPKKNPDAKKYDRISYDELLKK---GLKVMDATALTLCRRNKIPIIVFNGLKPG 213

Query: 231 SFEDHGQQEQLGTLI 245
           +     + E +GTLI
Sbjct: 214 NLLRALKGEHVGTLI 228


>gnl|CDD|153164 cd04892, ACT_AK-like_2, ACT domains C-terminal to the catalytic
           domain of aspartokinase (AK;
           4-L-aspartate-4-phosphotransferase).  This CD includes
           the second of two ACT domains C-terminal to the
           catalytic domain of aspartokinase (AK;
           4-L-aspartate-4-phosphotransferase). The exception in
           this group, is the inclusion of the first ACT domain of
           the bifunctional  aspartokinase - homoserine
           dehydrogenase-like enzyme group
           (ACT_AKi-HSDH-ThrA-like_1) which includes the
           monofunctional,  threonine-sensitive, aspartokinase
           found  in Methanococcus jannaschii and other related
           archaeal species. AK catalyzes the conversion of
           aspartate and ATP to aspartylphosphate and ADP. AK is
           the first enzyme in the pathway of the biosynthesis of
           the aspartate family of amino acids (lysine, threonine,
           methionine, and isoleucine) and the bacterial cell wall
           component, meso-diaminopimelate. One mechanism for the
           regulation of this pathway is by the production of
           several isoenzymes of AK with different repressors and
           allosteric inhibitors. Pairs of ACT domains are proposed
           to specifically bind amino acids leading to allosteric
           regulation of the enzyme. In Escherichia coli (EC),
           three different AK isoenzymes are regulated specifically
           by lysine, methionine, and threonine. AK-HSDHI (ThrA)
           and AK-HSDHII (MetL) are bifunctional enzymes that
           consist of an N-terminal AK and a C-terminal homoserine
           dehydrogenase (HSDH). ThrA and MetL are involved in
           threonine and methionine biosynthesis, respectively. The
           third isoenzyme, AKIII (LysC), is monofunctional and is
           involved in lysine synthesis. The three Bacillus
           subtilis (BS) isoenzymes, AKI (DapG), AKII (LysC), and
           AKIII (YclM), are feedback inhibited by
           meso-diaminopimelate, lysine, and lysine plus threonine,
           respectively. The E. coli lysine-sensitive AK is
           described as a homodimer, whereas, the B. subtilis
           lysine-sensitive AK is described as is a heterodimeric
           complex of alpha- and beta- subunits that are formed
           from two in-frame overlapping genes. A single AK enzyme
           type has been described in Pseudomonas, Amycolatopsis,
           and Corynebacterium, and apparently, unique to
           cyanobacteria, are AKs with two tandem pairs of ACT
           domains, C-terminal to the catalytic domain. The fungal
           aspartate pathway is regulated at the AK step, with
           L-Thr being an allosteric inhibitor of the Saccharomyces
           cerevisiae AK (Hom3). At least two distinct AK
           isoenzymes can occur in higher plants, a monofunctional
           lysine-sensitive isoenzyme, which is involved in the
           overall regulation of the pathway and can be
           synergistically inhibited by S-adenosylmethionine. The
           other isoenzyme is a bifunctional, threonine-sensitive
           AK-HSDH protein. Also included in this CD are the ACT
           domains of the Methylomicrobium alcaliphilum AK; the
           first enzyme of the ectoine biosynthetic pathway found
           in this bacterium and several other
           halophilic/halotolerant bacteria. Members of this CD
           belong to the superfamily of ACT regulatory domains.
          Length = 65

 Score = 65.6 bits (161), Expect = 2e-11
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 347 KISAIGIGMQSYAGVASAFFLCLAEKGINIKAITT--SEIKISVLIDSAYTELAVRSLHS 404
            +S +G GM+   GVA+  F  LAE GINI  I+   SE+ IS ++D    + AV++LH 
Sbjct: 2   LVSVVGAGMRGTPGVAARIFSALAEAGINIIMISQGSSEVNISFVVDEDDADKAVKALHE 61

Query: 405 CYGL 408
            + L
Sbjct: 62  EFFL 65



 Score = 47.5 bits (114), Expect = 6e-06
 Identities = 25/58 (43%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 272 RRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSD 329
             +R  PG++A IFS LAEA INI MI Q  SE    V+I+F       +KA+  L +
Sbjct: 8   AGMRGTPGVAARIFSALAEAGINIIMISQGSSE----VNISFVVDEDDADKAVKALHE 61


>gnl|CDD|58620 cd04254, AAK_UMPK-PyrH-Ec, UMP kinase (UMPK)-Ec, the
           microbial/chloroplast uridine monophosphate kinase
           (uridylate kinase) enzyme that catalyzes UMP
           phosphorylation and plays a key role in pyrimidine
           nucleotide biosynthesis; regulation of this process is
           via feed-back control and via gene repression of
           carbamoyl phosphate synthetase (the first enzyme of the
           pyrimidine biosynthesis pathway). The UMP kinase of E.
           coli (Ec) is known to function as a homohexamer, with
           GTP and UTP being allosteric effectors. Like other
           related enzymes (carbamate kinase, aspartokinase, and
           N-acetylglutamate kinase) the E. coli and most bacterial
           and chloroplast UMPKs (this CD) have a conserved,
           N-terminal, lysine residue proposed to function in the
           catalysis of the phosphoryl group transfer, whereas most
           archaeal UMPKs appear to lack this residue and the
           Pyrococcus furiosus structure has an additional Mg ion
           bound to the ATP molecule which is proposed to function
           as the catalysis instead. Members of this CD belong to
           the Amino Acid Kinase Superfamily (AAK)..
          Length = 231

 Score = 65.5 bits (160), Expect = 2e-11
 Identities = 61/256 (23%), Positives = 108/256 (42%), Gaps = 40/256 (15%)

Query: 3   RIVMKFGGTSVA-------NIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCR 55
           R+++K  G ++A       + + +   A  +K  VD G EVA+VV            + R
Sbjct: 2   RVLLKLSGEALAGENGFGIDPEVLNRIAREIKEVVDLGVEVAIVVGG--------GNIFR 53

Query: 56  QVTSIDNARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARIC- 114
             ++ +   +R    +T + +  G++   + +L +Q  +L+   +     S   M  +  
Sbjct: 54  GASAAEAGMDR----ATADYM--GMLATVINALALQD-ALESLGVKTRVMSAIPMQGVAE 106

Query: 115 RVDEKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTD 174
               ++ + HL+K +VV+  G  G       TT      DT+A   A  I AD     T 
Sbjct: 107 PYIRRRAIRHLEKGRVVIFAGGTGNPF---FTT------DTAAALRAIEINADVILKATK 157

Query: 175 VCGIYTTDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFVRSSFED 234
           V G+Y  DP+  P A     ++++E+L     G KVM   +  L     + + V +  E 
Sbjct: 158 VDGVYDADPKKNPNAKRYDHLTYDEVLSK---GLKVMDATAFTLCRDNNLPIVVFNINEP 214

Query: 235 HG-----QQEQLGTLI 245
                  + E +GTLI
Sbjct: 215 GNLLKAVKGEGVGTLI 230


>gnl|CDD|153140 cd04868, ACT_AK-like, ACT domains C-terminal to the catalytic
           domain of aspartokinase (AK;
           4-L-aspartate-4-phosphotransferase).  This CD includes
           each of two ACT domains C-terminal to the catalytic
           domain of aspartokinase (AK;
           4-L-aspartate-4-phosphotransferase). Typically, AK
           consists of two ACT domains in a tandem repeat, but the
           second ACT domain is inserted within the first,
           resulting in, what is normally the terminal beta strand
           of ACT2, formed from a region N-terminal of ACT1. AK
           catalyzes the conversion of aspartate and ATP to
           aspartylphosphate and ADP. Aspartokinase is the first
           enzyme in the pathway of the biosynthesis of the
           aspartate family of amino acids (lysine, threonine,
           methionine, and isoleucine) and the bacterial cell wall
           component, meso-diaminopimelate. One mechanism for the
           regulation of this pathway is by the production of
           several isoenzymes of aspartokinase with different
           repressors and allosteric inhibitors. Pairs of ACT
           domains are proposed to specifically bind amino acids
           leading to allosteric regulation of the enzyme. In
           Escherichia coli (EC), three different aspartokinase
           isoenzymes are regulated specifically by lysine,
           methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII
           (MetL) are bifunctional enzymes that consist of an
           N-terminal AK and a C-terminal homoserine dehydrogenase
           (HSDH). ThrA and MetL are involved in threonine and
           methionine biosynthesis, respectively. The third
           isoenzyme, AKIII (LysC), is monofunctional and is
           involved in lysine synthesis. The three Bacillus
           subtilis (BS) isoenzymes, AKI (DapG), AKII (LysC), and
           AKIII (YclM), are feedback inhibited by
           meso-diaminopimelate, lysine, and lysine plus threonine,
           respectively. The E. coli lysine-sensitive AK is
           described as a homodimer, whereas, the B. subtilis
           lysine-sensitive AK is described as is a heterodimeric
           complex of alpha- and beta- subunits that are formed
           from two in-frame overlapping genes. A single AK enzyme
           type has been described in Pseudomonas, Amycolatopsis,
           and Corynebacterium, and apparently, unique to
           cyanobacteria, are aspartokinases with two tandem pairs
           of ACT domains, C-terminal to the catalytic domain. The
           fungal aspartate pathway is regulated at the AK step,
           with L-Thr being an allosteric inhibitor of the
           Saccharomyces cerevisiae AK (Hom3). At least two
           distinct AK isoenzymes can occur in higher plants, a
           monofunctional lysine-sensitive isoenzyme, which is
           involved in the overall regulation of the pathway and
           can be synergistically inhibited by
           S-adenosylmethionine. The other isoenzyme is a
           bifunctional, threonine-sensitive AK-HSDH protein. Also
           included in this AK family CD are the ACT domains of the
           Methylomicrobium alcaliphilum AK; the first enzyme of
           the ectoine biosynthetic pathway found in this bacterium
           and several other halophilic/halotolerant bacteria.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 60

 Score = 61.0 bits (149), Expect = 6e-10
 Identities = 31/63 (49%), Positives = 42/63 (66%), Gaps = 6/63 (9%)

Query: 267 AQISLR--RLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKAL 324
           A++S+    +R  PG++A IFS LAEA IN+DMI Q+ SE    V+I+FT   S LEKA+
Sbjct: 1   AKVSIVGVGMRGTPGVAAKIFSALAEAGINVDMISQSESE----VNISFTVDESDLEKAV 56

Query: 325 AVL 327
             L
Sbjct: 57  KAL 59



 Score = 52.5 bits (127), Expect = 2e-07
 Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 2/59 (3%)

Query: 347 KISAIGIGMQSYAGVASAFFLCLAEKGINIKAITTS--EIKISVLIDSAYTELAVRSLH 403
           K+S +G+GM+   GVA+  F  LAE GIN+  I+ S  E+ IS  +D +  E AV++LH
Sbjct: 2   KVSIVGVGMRGTPGVAAKIFSALAEAGINVDMISQSESEVNISFTVDESDLEKAVKALH 60


>gnl|CDD|30874 COG0528, PyrH, Uridylate kinase [Nucleotide transport and
           metabolism].
          Length = 238

 Score = 60.2 bits (146), Expect = 1e-09
 Identities = 59/260 (22%), Positives = 110/260 (42%), Gaps = 41/260 (15%)

Query: 1   MARIVMKFGGTSVA-------NIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAEL 53
             RI++K  G ++A       + + +   A  +K  VD G EVA+VV            +
Sbjct: 5   YMRILLKLSGEALAGEQGFGIDPEVLDRIANEIKELVDLGVEVAVVVGG--------GNI 56

Query: 54  CRQVTSIDNARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARI 113
            R         +R     T + +  G++   + +L +Q  +L+   +     S   M ++
Sbjct: 57  ARGYIGAAAGMDR----VTADYM--GMLATVMNALALQD-ALERLGVDTRVQSAIAMPQV 109

Query: 114 C-RVDEKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIY 172
                 ++ + HL+K +VV+  G  G       TT      DT+A   A  I+AD     
Sbjct: 110 AEPYSRREAIRHLEKGRVVIFGGGTGNPG---FTT------DTAAALRAEEIEADVLLKA 160

Query: 173 T-DVCGIYTTDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQVRSVELAMLYKMCLFV--- 228
           T  V G+Y  DP+ +P A     ++++E+L++     KVM   +  LA    + + V   
Sbjct: 161 TNKVDGVYDADPKKDPDAKKYDTLTYDEVLKIGL---KVMDPTAFSLARDNGIPIIVFNI 217

Query: 229 --RSSFEDHGQQEQLGTLIC 246
               + +   + E++GT++ 
Sbjct: 218 NKPGNLKRALKGEEVGTIVE 237


>gnl|CDD|58621 cd04255, AAK_UMPK-MosAB, AAK_UMPK-MosAB: This CD includes the alpha
           and beta subunits of the Mo storage protein (MosA and
           MosB) which are related to uridine monophosphate kinase
           (UMPK) enzymes that catalyze the phosphorylation of UMP
           by ATP, yielding UDP, and playing a key role in
           pyrimidine nucleotide biosynthesis. The Mo storage
           protein from the nitrogen-fixing bacterium, Azotobacter
           vinelandii, is characterized as an alpha4-beta4 octamer
           containing a polynuclear molybdenum-oxide cluster which
           is ATP-dependent to bind Mo and pH-dependent to release
           Mo. These and related bacterial sequences in this CD are
           members of the Amino Acid Kinase Superfamily (AAK)..
          Length = 262

 Score = 52.6 bits (126), Expect = 2e-07
 Identities = 38/154 (24%), Positives = 62/154 (40%), Gaps = 14/154 (9%)

Query: 62  NARERDVVISTGEQVSS----------GLMVLALQSLGIQAISLQGWQIPIMTDSLHGMA 111
              E  ++I TG    +          G+    L  LG  ++S Q  ++     + HG +
Sbjct: 60  LRPEHKLLILTGGGTRARHVYSIGLDLGMPTGVLAKLG-ASVSEQNAEMLATLLAKHGGS 118

Query: 112 RICRVDEKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGR---GGSDTSAVAIAAAIKADR 168
           ++   D  ++ T LK  +  VI+G             GR     +D  A  +A  I A  
Sbjct: 119 KVGHGDLLQLPTFLKAGRAPVISGMPPYGLWEHPAEEGRIPPHRTDVGAFLLAEVIGARN 178

Query: 169 CDIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLE 202
                D  G+YT DP+   KA  + +IS  E+L+
Sbjct: 179 LIFVKDEDGLYTADPKKNKKAEFIPEISAAELLK 212


>gnl|CDD|153194 cd04922, ACT_AKi-HSDH-ThrA_2, ACT domains of the bifunctional
           enzyme aspartokinase (AK) - homoserine dehydrogenase
           (HSDH).  This CD includes the second  of two ACT domains
           of the bifunctional enzyme aspartokinase (AK) -
           homoserine dehydrogenase (HSDH). The ACT domains are
           positioned between the N-terminal catalytic domain of AK
           and the C-terminal HSDH domain found in bacteria
           (Escherichia coli (EC) ThrA) and higher plants (Zea mays
           AK-HSDH). AK and HSDH are the first and third enzymes in
           the biosynthetic pathway of the aspartate family of
           amino acids. AK catalyzes the phosphorylation of Asp to
           P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent
           conversion of Asp 3-semialdehyde to homoserine. HSDH is
           the first committed reaction in the branch of the
           pathway that leads to Thr and Met. In E. coli, ThrA is
           subject to allosteric regulation by the end product
           L-threonine and the native enzyme is reported to be
           tetrameric. As with bacteria, plant AK and HSDH are
           feedback inhibited by pathway end products. Maize
           AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis
           AK-HSDH is an alanine-activated, threonine-sensitive
           enzyme whose ACT domains were shown to be involved in
           allosteric activation. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 66

 Score = 48.1 bits (115), Expect = 4e-06
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 348 ISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSLHS 404
           ++ +G GM    GVA+ FF  LA+  +NI+AI   +SE  IS +ID      A+R++H 
Sbjct: 4   LALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGSSERNISAVIDEDDATKALRAVHE 62



 Score = 36.9 bits (86), Expect = 0.010
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 273 RLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSDN 330
            +   PG++A+ FS LA+A++NI  I Q  SE     +I+         KAL  + + 
Sbjct: 10  GMAGTPGVAATFFSALAKANVNIRAIAQGSSE----RNISAVIDEDDATKALRAVHER 63


>gnl|CDD|145157 pfam01842, ACT, ACT domain.  This family of domains generally have
           a regulatory role. ACT domains are linked to a wide
           range of metabolic enzymes that are regulated by amino
           acid concentration. Pairs of ACT domains bind
           specifically to a particular amino acid leading to
           regulation of the linked enzyme. The ACT domain is found
           in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95,
           which is inhibited by serine. Aspartokinase EC:2.7.2.4,
           which is regulated by lysine. Acetolactate synthase
           small regulatory subunit, which is inhibited by valine.
           Phenylalanine-4-hydroxylase EC:1.14.16.1, which is
           regulated by phenylalanine. Prephenate dehydrogenase
           EC:4.2.1.51. formyltetrahydrofolate deformylase
           EC:3.5.1.10, which is activated by methionine and
           inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5.
          Length = 66

 Score = 47.3 bits (113), Expect = 8e-06
 Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 273 RLRDHPGISASIFSPLAEAHINIDMIIQNVSED-GQYVDITFTTPSSSLEKALAVLSD 329
            + D PG+ A +F  LA+  INI+ I Q+ S D    V I        LE AL  L  
Sbjct: 6   GVPDRPGLLARVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEALKK 63



 Score = 27.3 bits (61), Expect = 7.2
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 349 SAIGIGMQSYAGVASAFFLCLAEKGINIKAITTS-------EIKISVLIDSAYTELAVRS 401
           + + +G+    G+ +  F  LA++GINI++I+ S        + I V++D    E A+ +
Sbjct: 1   TVLEVGVPDRPGLLARVFGALADRGINIESISQSTSGDKAGIVFIVVVVDEEDLEAALEA 60

Query: 402 LHS 404
           L  
Sbjct: 61  LKK 63


>gnl|CDD|153196 cd04924, ACT_AK-Arch_2, ACT domains of a monofunctional
           aspartokinase found mostly in Archaea species
           (ACT_AK-Arch_2).  Included in this CD is the second of
           two ACT domains of a monofunctional aspartokinase found
           mostly in Archaea species (ACT_AK-Arch_2). The first or
           N-terminal ACT domain of these proteins cluster with the
           ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which
           includes the threonine-sensitive archaeal Methanococcus
           jannaschii aspartokinase ACT 1 domain. Members of this
           CD belong to the superfamily of ACT regulatory domains.
          Length = 66

 Score = 47.1 bits (112), Expect = 9e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 348 ISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSLHSC 405
           ++ +G GM+   GVA   F  L + GIN+  I+  +SE  IS ++       AV+++H  
Sbjct: 4   VAVVGSGMRGTPGVAGRVFGALGKAGINVIMISQGSSEYNISFVVAEDDGWAAVKAVHDE 63

Query: 406 YGL 408
           +GL
Sbjct: 64  FGL 66



 Score = 32.9 bits (75), Expect = 0.18
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 274 LRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSD 329
           +R  PG++  +F  L +A IN+ MI Q  SE     +I+F         A+  + D
Sbjct: 11  MRGTPGVAGRVFGALGKAGINVIMISQGSSE----YNISFVVAEDDGWAAVKAVHD 62


>gnl|CDD|153139 cd02116, ACT, ACT domains are commonly involved in specifically
           binding an amino acid or other small ligand leading to
           regulation of the enzyme.  Members of this CD belong to
           the superfamily of ACT regulatory domains. Pairs of ACT
           domains are commonly involved in specifically binding an
           amino acid or other small ligand leading to regulation
           of the enzyme. The ACT domain has been detected in a
           number of diverse proteins; some of these proteins are
           involved in amino acid and purine biosynthesis,
           phenylalanine hydroxylation, regulation of bacterial
           metabolism and transcription, and many remain to be
           characterized. ACT domain-containing enzymes involved in
           amino acid and purine synthesis are in many cases
           allosteric enzymes with complex regulation enforced by
           the binding of ligands. The ACT domain is commonly
           involved in the binding of a small regulatory molecule,
           such as the amino acids L-Ser and L-Phe in the case of
           D-3-phosphoglycerate dehydrogenase and the bifunctional
           chorismate mutase-prephenate dehydratase enzyme
           (P-protein), respectively. Aspartokinases typically
           consist of two C-terminal ACT domains in a tandem
           repeat, but  the second ACT domain is inserted within
           the first, resulting in, what is normally the terminal
           beta strand of ACT2, formed from a region N-terminal of
           ACT1. ACT domain repeats have been shown to have
           nonequivalent ligand-binding sites with complex
           regulatory patterns such as those seen in the
           bifunctional enzyme, aspartokinase-homoserine
           dehydrogenase (ThrA). In other enzymes, such as
           phenylalanine hydroxylases, the ACT domain appears to
           function as a flexible small module providing allosteric
           regulation via transmission of conformational changes,
           these conformational changes are not necessarily
           initiated by regulatory ligand binding at the ACT domain
           itself. ACT domains are present either singularly, N- or
           C-terminal, or in pairs present C-terminal or between
           two catalytic domains. Unique to cyanobacteria are four
           ACT domains C-terminal to an aspartokinase domain. A few
           proteins are composed almost entirely of ACT domain
           repeats as seen in the four ACT domain protein, the ACR
           protein, found in higher plants; and the two ACT domain
           protein, the glycine cleavage system transcriptional
           repressor (GcvR) protein, found in some bacteria. Also
           seen are single ACT domain proteins similar to the
           Streptococcus pneumoniae ACT domain protein
           (uncharacterized pdb structure 1ZPV) found in both
           bacteria and archaea. Purportedly, the ACT domain is an
           evolutionarily mobile ligand binding regulatory module
           that has been fused to different enzymes at various
           times.
          Length = 60

 Score = 45.7 bits (109), Expect = 2e-05
 Identities = 24/56 (42%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 273 RLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSS-LEKALAVL 327
              D PG+ A + S LAEA INI  I Q  S DG   DI         LEK L  L
Sbjct: 4   SGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVVDGDGDLEKLLEAL 59


>gnl|CDD|58619 cd04253, AAK_UMPK-PyrH-Pf, AAK_UMPK-PyrH-Pf: UMP kinase (UMPK)-Pf,
           the mostly archaeal uridine monophosphate kinase
           (uridylate kinase) enzymes that catalyze UMP
           phosphorylation and play a key role in pyrimidine
           nucleotide biosynthesis; regulation of this process is
           via feed-back control and via gene repression of
           carbamoyl phosphate synthetase (the first enzyme of the
           pyrimidine biosynthesis pathway). The UMP kinase of
           Pyrococcus furiosus (Pf) is known to function as a
           homohexamer, with GTP and UTP being allosteric
           effectors. Like other related enzymes (carbamate kinase,
           aspartokinase, and N-acetylglutamate kinase) the E. coli
           and most bacterial UMPKs have a conserved, N-terminal,
           lysine residue proposed to function in the catalysis of
           the phosphoryl group transfer, whereas most archaeal
           UMPKs (this CD) appear to lack this residue and the
           Pyrococcus furiosus structure has an additional Mg ion
           bound to the ATP molecule which is proposed to function
           as the catalysis instead. Members of this CD belong to
           the Amino Acid Kinase Superfamily (AAK)..
          Length = 221

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 49/207 (23%), Positives = 87/207 (42%), Gaps = 42/207 (20%)

Query: 3   RIVMKFGGTSVA---NIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTS 59
           RIV+  GG+ +A   + D I+  A +V R++  G +VA+VV    G   R          
Sbjct: 1   RIVISLGGSVLAPEKDADFIKEYA-NVLRKISDGHKVAVVVGG--GRLAR--------EY 49

Query: 60  IDNARERDVVISTGEQVSSGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEK 119
           I  AR+    +   E          L  +GI A  L      ++  +L           +
Sbjct: 50  ISVARK----LGASEAF--------LDEIGIMATRLNAR---LLIAALGDAYPPVPTSYE 94

Query: 120 KIVTHLKKKQVVVITGFQ-GLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGI 178
           + +  +   ++VV+ G + G S            +D  A  +A  + AD     T+V G+
Sbjct: 95  EALEAMFTGKIVVMGGTEPGQS------------TDAVAALLAERLGADLLINATNVDGV 142

Query: 179 YTTDPRIEPKAHLMKKISFEEMLEMSS 205
           Y+ DPR +P A    ++S +E++++  
Sbjct: 143 YSKDPRKDPDAKKFDRLSADELIDIVG 169


>gnl|CDD|153193 cd04921, ACT_AKi-HSDH-ThrA-like_1, ACT domains of the bifunctional
           enzyme aspartokinase (AK) - homoserine dehydrogenase
           (HSDH).  This CD includes the first of two ACT domains
           of the bifunctional enzyme aspartokinase (AK) -
           homoserine dehydrogenase (HSDH). The ACT domains are
           positioned between the N-terminal catalytic domain of AK
           and the C-terminal HSDH domain found in bacteria
           (Escherichia coli (EC) ThrA) and higher plants (Zea mays
           AK-HSDH). AK and HSDH are the first and third enzymes in
           the biosynthetic pathway of the aspartate family of
           amino acids. AK catalyzes the phosphorylation of Asp to
           P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent
           conversion of Asp 3-semialdehyde to homoserine. HSDH is
           the first committed reaction in the branch of the
           pathway that leads to Thr and Met. In E. coli, ThrA is
           subject to allosteric regulation by the end product
           L-threonine and the native enzyme is reported to be
           tetrameric. As with bacteria, plant AK and HSDH are
           feedback inhibited by pathway end products. Maize
           AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis
           AK-HSDH is an alanine-activated, threonine-sensitive
           enzyme whose ACT domains were shown to be involved in
           allosteric activation. Also included in this CD is the
           first of two ACT domains of a tetrameric,
           monofunctional, threonine-sensitive, AK found in
           Methanococcus jannaschii and other related archaeal
           species. Members of this CD belong to the superfamily of
           ACT regulatory domains.
          Length = 80

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 269 ISLRRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVL 327
           I    +   PGI+A IFS LA A IN+ +I Q  SE      I+F    S  +KAL  L
Sbjct: 6   IEGTGMVGVPGIAARIFSALARAGINVILISQASSEHS----ISFVVDESDADKALEAL 60



 Score = 39.5 bits (93), Expect = 0.002
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 345 LVKISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSL 402
           L+ I   G GM    G+A+  F  LA  GIN+  I+  +SE  IS ++D +  + A+ +L
Sbjct: 3   LINIE--GTGMVGVPGIAARIFSALARAGINVILISQASSEHSISFVVDESDADKALEAL 60

Query: 403 HSCYGLDVQ 411
              + L+++
Sbjct: 61  EEEFALEIK 69


>gnl|CDD|153188 cd04916, ACT_AKiii-YclM-BS_2, ACT domains located C-terminal to the
           catalytic domain of the lysine plus threonine-sensitive
           aspartokinase isoenzyme AKIII.  This CD includes the
           second of two ACT domains located C-terminal to the
           catalytic domain of the lysine plus threonine-sensitive
           aspartokinase isoenzyme AKIII, a monofunctional class
           enzyme found in Bacilli (Bacillus subtilis (BS) YclM)
           and Clostridia species. Aspartokinase is the first
           enzyme in the aspartate metabolic pathway and catalyzes
           the conversion of aspartate and ATP to aspartylphosphate
           and ADP. B. subtilis YclM is reported to be a single
           polypeptide of 50 kD. AKIII from B. subtilis strain 168
           is induced by lysine and repressed by threonine and it
           is synergistically inhibited by lysine and threonine.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 66

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 272 RRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVL 327
             +++  G+SA   + LA+A INI MI Q  SE    + I     +   +KA+  +
Sbjct: 9   EGMKNTVGVSARATAALAKAGINIRMINQGSSE----ISIMIGVHNEDADKAVKAI 60



 Score = 37.2 bits (87), Expect = 0.008
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 348 ISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSLHS 404
           I  +G GM++  GV++     LA+ GINI+ I   +SEI I + + +   + AV++++ 
Sbjct: 4   IMVVGEGMKNTVGVSARATAALAKAGINIRMINQGSSEISIMIGVHNEDADKAVKAIYE 62


>gnl|CDD|153191 cd04919, ACT_AK-Hom3_2, ACT domains located C-terminal to the
           catalytic domain of the aspartokinase (AK) HOM3.  This
           CD includes the second of two ACT domains located
           C-terminal to the catalytic domain of the aspartokinase
           (AK) HOM3, a monofunctional class enzyme found in
           Saccharomyces cerevisiae, and other related ACT domains.
           AK is the first enzyme in the aspartate metabolic
           pathway, catalyzes the conversion of aspartate and ATP
           to aspartylphosphate and ADP, and in fungi, is
           responsible for the production of threonine, isoleucine
           and methionine. S. cerevisiae has a single AK, which is
           regulated by feedback, allosteric inhibition by
           L-threonine. Recent studies shown that the allosteric
           transition triggered by binding of threonine to AK
           involves a large change in the conformation of the
           native hexameric enzyme that is converted to an inactive
           one of different shape and substantially smaller
           hydrodynamic size. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 66

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 348 ISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSLH 403
           +S +G  M++  G+A   F  LA+  INI+ I+   SEI IS +ID      A+  +H
Sbjct: 4   LSLVGKHMKNMIGIAGRMFTTLADHRINIEMISQGASEINISCVIDEKDAVKALNIIH 61



 Score = 35.2 bits (81), Expect = 0.034
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 4/56 (7%)

Query: 272 RRLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVL 327
           + +++  GI+  +F+ LA+  INI+MI Q  SE    ++I+         KAL ++
Sbjct: 9   KHMKNMIGIAGRMFTTLADHRINIEMISQGASE----INISCVIDEKDAVKALNII 60


>gnl|CDD|58608 cd04242, AAK_G5K_ProB, AAK_G5K_ProB: Glutamate-5-kinase (G5K)
           catalyzes glutamate-dependent ATP cleavage; G5K
           transfers the terminal phosphoryl group of ATP to the
           gamma-carboxyl group of glutamate, in the first and
           controlling step of proline (and, in mammals, ornithine)
           biosynthesis. G5K is subject to feedback allosteric
           inhibition by proline or ornithine. In microorganisms
           and plants, proline plays an important role as an
           osmoprotectant and, in mammals, ornithine biosynthesis
           is crucial for proper ammonia detoxification, since a
           G5K mutation has been shown to cause human
           hyperammonaemia. Microbial G5K generally consists of two
           domains: a catalytic G5K domain and one PUA (pseudo
           uridine synthases and archaeosine-specific
           transglycosylases) domain, and some lack the PUA domain.
           G5K requires free Mg for activity, it is tetrameric, and
           it aggregates to higher forms in a proline-dependent
           way. G5K lacking the PUA domain remains tetrameric,
           active, and proline-inhibitable, but the Mg requirement
           and the proline-triggered aggregation are greatly
           diminished and abolished, respectively, and more proline
           is needed for inhibition. Although plant and animal G5Ks
           are part of a bifunctional polypeptide, delta
           1-pyrroline-5-carboxylate synthetase (P5CS), composed of
           an N-terminal G5K (ProB) and a C-terminal glutamyl 5-
           phosphate reductase (G5PR; ProA); bacterial and yeast
           G5Ks are monofunctional single-polypeptide enzymes. In
           this CD, all three domain architectures are present:
           G5K, G5K+PUA, and G5K+G5PR..
          Length = 251

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 14/45 (31%), Positives = 25/45 (55%)

Query: 151 GGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKI 195
           G +D  +  +A  + AD   + +DV G+Y  +PR  P A L+ ++
Sbjct: 142 GDNDRLSALVAGLVNADLLILLSDVDGLYDKNPRENPDAKLIPEV 186


>gnl|CDD|153153 cd04881, ACT_HSDH-Hom, ACT_HSDH_Hom CD includes the C-terminal ACT
           domain of the NAD(P)H-dependent, homoserine
           dehydrogenase (HSDH) and related domains.  The
           ACT_HSDH_Hom CD includes the C-terminal ACT domain of
           the NAD(P)H-dependent, homoserine dehydrogenase (HSDH)
           encoded by the hom gene of Bacillus subtilis and other
           related sequences. HSDH reduces aspartate semi-aldehyde
           to the amino acid homoserine, one that is required for
           the biosynthesis of Met, Thr, and Ile from Asp. Neither
           the enzyme nor the aspartate pathway is found in the
           animal kingdom. This mostly bacterial HSDH group has a
           C-terminal ACT domain and is believed to be involved in
           enzyme regulation. A C-terminal deletion in the
           Corynebacterium glutamicum HSDH abolished allosteric
           inhibition by L-threonine. Members of this CD belong to
           the superfamily of ACT regulatory domains.
          Length = 79

 Score = 38.7 bits (91), Expect = 0.003
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 275 RDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVD---ITFTTPSSSLEKALAVLSDNK 331
           +D PG+ A I   LAE  I+I+ +IQ  ++ G+      +T  T  ++L  ALA +    
Sbjct: 8   KDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTHETSEAALNAALAEIEALD 67

Query: 332 ENIGYDVI 339
              G   +
Sbjct: 68  AVQGVPSV 75


>gnl|CDD|30894 COG0548, ArgB, Acetylglutamate kinase [Amino acid transport and
           metabolism].
          Length = 265

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 48/214 (22%), Positives = 84/214 (39%), Gaps = 22/214 (10%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTSIDNA 63
           IV+K GG+++ + + + + A  +      G    +V        + LA+L  +   +   
Sbjct: 5   IVIKLGGSAMEDENLLEAFASDIALLKSVGIRPVVVHGGGPQIDEMLAKLGIEPEFVKGL 64

Query: 64  RERD-VVISTGEQVSSGLM----VLALQSLGIQAISLQG---------WQIPIMTDSLHG 109
           R  D   +   E V  G +    V  L   G QA+ L G                  L  
Sbjct: 65  RVTDAETLEVVEMVLGGTVNKEIVARLSKHGGQAVGLSGVDGNLVTAKKLDVDDGVDLGY 124

Query: 110 MARICRVDEKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRC 169
           +  I +V+ + I   L    + VI     +  D     +    +DT+A A+AAA+KA++ 
Sbjct: 125 VGEIRKVNPELIERLLDNGAIPVIAPI-AVDEDGETLNVN---ADTAAGALAAALKAEKL 180

Query: 170 DIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLEM 203
            + TDV G+            L+ ++  EE  E+
Sbjct: 181 ILLTDVPGVLDDK----GDPSLISELDAEEAEEL 210


>gnl|CDD|30612 COG0263, ProB, Glutamate 5-kinase [Amino acid transport and
           metabolism].
          Length = 369

 Score = 37.9 bits (88), Expect = 0.005
 Identities = 14/53 (26%), Positives = 28/53 (52%)

Query: 144 SVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKIS 196
           +   +  G +DT +  +A  + AD   + +D+ G+Y  +PR  P A L+ ++ 
Sbjct: 142 ATEEIKFGDNDTLSALVAILVGADLLVLLSDIDGLYDANPRTNPDAKLIPEVE 194


>gnl|CDD|153209 cd04937, ACT_AKi-DapG-BS_2, ACT domains of the
           diaminopimelate-sensitive aspartokinase (AK) isoenzyme
           AKI.  This CD includes the C-terminal of the two ACT
           domains of the diaminopimelate-sensitive aspartokinase
           (AK) isoenzyme AKI, a monofunctional class enzyme found
           in Bacilli (Bacillus subtilis (BS) strain 168),
           Clostridia, and Actinobacteria bacterial species. In B.
           subtilis, the regulation of the diaminopimelate-lysine
           biosynthetic pathway involves dual control by
           diaminopimelate and lysine, effected through separate
           diaminopimelate- and lysine-sensitive AK isoenzymes. AKI
           activity is invariant during the exponential and
           stationary phases of growth and is not altered by
           addition of amino acids to the growth medium. The role
           of this isoenzyme is most likely to provide a constant
           level of aspartyl-beta-phosphate for the biosynthesis of
           diaminopimelate for peptidoglycan synthesis and
           dipicolinate during sporulation. The BS AKI is
           tetrameric consisting of two alpha and two beta
           subunits; the alpha (43 kD) and beta (17 kD) subunit
           formed by two in-phase overlapping genes. The alpha
           subunit contains the AK catalytic domain and two ACT
           domains. The beta subunit contains two ACT domains.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 64

 Score = 37.4 bits (87), Expect = 0.007
 Identities = 18/64 (28%), Positives = 30/64 (46%)

Query: 345 LVKISAIGIGMQSYAGVASAFFLCLAEKGINIKAITTSEIKISVLIDSAYTELAVRSLHS 404
             K++ IG  ++   GV +     L+++GI I     S   IS L+     + AV +LH 
Sbjct: 1   CAKVTIIGSRIRGVPGVMAKIVGALSKEGIEILQTADSHTTISCLVSEDDVKEAVNALHE 60

Query: 405 CYGL 408
            + L
Sbjct: 61  AFEL 64


>gnl|CDD|58617 cd04251, AAK_NAGK-UC, AAK_NAGK-UC: N-Acetyl-L-glutamate kinase -
           uncharacterized (NAGK-UC). This domain is similar to
           Escherichia coli and Pseudomonas aeruginosa NAGKs which
           catalyze the phosphorylation of the gamma-COOH group of
           N-acetyl-L-glutamate (NAG) by ATP in the second step of
           microbial arginine biosynthesis. These uncharacterized
           domain sequences are found in some bacteria (Deinococci
           and Chloroflexi) and archea and belong to the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 257

 Score = 37.2 bits (86), Expect = 0.009
 Identities = 50/206 (24%), Positives = 83/206 (40%), Gaps = 30/206 (14%)

Query: 4   IVMKFGGTSVANIDCIRSAALHVKREVDRGQEVAMVVSAMSGETDRLAELC----RQVTS 59
           IV+K GG+ V+++D +         ++    E  +VV       +   +      + VTS
Sbjct: 1   IVVKIGGSVVSDLDKVID-------DIANFGERLIVVHGGGNYVNEYLKRLGVEPKFVTS 53

Query: 60  IDNARERDVVISTGE--QVSSGLM----VLALQSLGIQAISLQGWQIPIMTDSLHGMARI 113
               R R     T E   +  GL+    V  L SLG++A+ L G    ++      + R+
Sbjct: 54  PSGIRSRYTDKETLEVFVMVMGLINKKIVARLHSLGVKAVGLTGLDGRLLEAKRKEIVRV 113

Query: 114 CRVDEKKIVT-----HLKKKQVVVITGFQGLSHDNSVTTLGRGG--------SDTSAVAI 160
                K I+       ++K    +I       +   V+ +             D +A AI
Sbjct: 114 NERGRKMIIRGGYTGKVEKVNSDLIEALLDAGYLPVVSPVAYSEEGEPLNVDGDRAAAAI 173

Query: 161 AAAIKADRCDIYTDVCGIYTTDPRIE 186
           AAA+KA+R  + TDV G+Y     IE
Sbjct: 174 AAALKAERLILLTDVEGLYLDGRVIE 199


>gnl|CDD|58604 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase
           (NAGK)-like . Included in this CD are the Escherichia
           coli and Pseudomonas aeruginosa type NAGKs which
           catalyze the phosphorylation of N-acetyl-L-glutamate
           (NAG) by ATP in the second step of arginine biosynthesis
           found in bacteria and photosynthetic organisms using
           either the acetylated, noncyclic (NC), or
           non-acetylated, cyclic (C) route of ornithine
           biosynthesis. Also included in this CD is a distinct
           group of uncharacterized (UC) bacterial and archeal
           NAGKs. Members of this CD belong to the Amino Acid
           Kinase Superfamily (AAK)..
          Length = 256

 Score = 35.9 bits (83), Expect = 0.022
 Identities = 31/118 (26%), Positives = 51/118 (43%), Gaps = 16/118 (13%)

Query: 74  EQVSSGL----MVLALQSLGIQAISLQGW--------QIPIMTDSLHGMARICRVDEKKI 121
           E V +G     +V  L   G +A+ L G         +       L  +  +  V+ + +
Sbjct: 72  EMVLAGKVNKELVSLLNRAGGKAVGLSGKDGGLIKAEKKEEKDIDLGFVGEVTEVNPELL 131

Query: 122 VTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIY 179
            T L+   + VI     ++ D    T      DT+A AIAAA+KA++  + TDV G+ 
Sbjct: 132 ETLLEAGYIPVIAP---IAVDEDGETYNVNA-DTAAGAIAAALKAEKLILLTDVPGVL 185


>gnl|CDD|31796 COG1608, COG1608, Predicted archaeal kinase [General function
           prediction only].
          Length = 252

 Score = 35.3 bits (81), Expect = 0.031
 Identities = 51/207 (24%), Positives = 82/207 (39%), Gaps = 15/207 (7%)

Query: 4   IVMKFGGTSVANID---CIRSAAL-HVKREVDRGQEVAMVVSAMSGETDRLAELCRQVTS 59
           I++K GG+ + + D    +R   L  + RE+  G+   ++V    G     A     +  
Sbjct: 3   IILKLGGSVITDKDKPRTVREDRLRRIAREISNGKPEKLIVVHGGGSFGHPAAKEFGLEG 62

Query: 60  IDNARERDVVISTGEQVS--SGLMVLALQSLGIQAISLQGWQIPIMTDSLHGMARICRVD 117
           + N         T   +   + ++V AL   G++A+S+     PI         RI    
Sbjct: 63  LKNYLSPLGFSLTHLAMLELNSIVVDALLDAGVRAVSVV----PI--SFSTFNGRILYTY 116

Query: 118 EKKIVTHLKKKQVVVITGFQGLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCG 177
            + I   L+K  V V+ G      DN    +     D   + +A  +K DR    TDV G
Sbjct: 117 LEAIKDALEKGFVPVLYGDVVPDDDNGYEIIS---GDDIVLHLAKELKPDRVIFLTDVDG 173

Query: 178 IYTTDPRIEPKAHLMKKISFEEMLEMS 204
           +Y  DP   P A L+ +I     L  S
Sbjct: 174 VYDRDPGKVPDARLLSEIEGRVALGGS 200


>gnl|CDD|153144 cd04872, ACT_1ZPV, ACT domain proteins similar to the yet
           uncharacterized Streptococcus pneumoniae ACT domain
           protein.  This CD, ACT_1ZPV, includes those single ACT
           domain proteins similar to the yet uncharacterized
           Streptococcus pneumoniae ACT domain protein (pdb
           structure 1ZPV). Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 88

 Score = 34.5 bits (80), Expect = 0.055
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 275 RDHPGISASIFSPLAEAHINIDMIIQNVSEDG----QYVDITFTTPSSSLEKALAVLSDN 330
           +D  GI A + + LAE ++NI  I Q + +        VDI  +  +    +    L + 
Sbjct: 9   KDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI--SESNLDFAELQEELEEL 66

Query: 331 KENIGYDV-IQHED 343
            + +G  + IQHED
Sbjct: 67  GKELGVKIRIQHED 80


>gnl|CDD|58616 cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase -
           cyclic (NAGK-C) catalyzes the phosphorylation of the
           gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in
           the second step of arginine biosynthesis found in some
           bacteria and photosynthetic organisms using the
           non-acetylated, cyclic route of ornithine biosynthesis.
           In this pathway, glutamate is first N-acetylated and
           then phosphorylated by NAGK to give phosphoryl NAG,
           which is converted to NAG-ornithine. There are two
           variants of this pathway. In one, typified by the
           pathway in Thermotoga maritima and Pseudomonas
           aeruginosa, the acetyl group is recycled by reversible
           transacetylation from acetylornithine to glutamate. The
           phosphorylation of NAG by NAGK is feedback inhibited by
           arginine. In photosynthetic organisms, NAGK is the
           target of the nitrogen-signaling protein PII. Hexameric
           formation of NAGK domains appears to be essential to
           both arginine inhibition and NAGK-PII complex formation.
           NAGK-C are members of the Amino Acid Kinase Superfamily
           (AAK)..
          Length = 279

 Score = 34.3 bits (79), Expect = 0.057
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query: 154 DTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLEM 203
           DT+A AIAAA+KA++  + TDV G+            L+ +IS +E  E+
Sbjct: 180 DTAAGAIAAALKAEKLILLTDVAGVLD---DPNDPGSLISEISLKEAEEL 226


>gnl|CDD|153186 cd04914, ACT_AKi-DapG-BS_1, ACT domains of the
           diaminopimelate-sensitive aspartokinase (AK) isoenzyme
           AKI.  This CD includes the N-terminal of the two ACT
           domains of the diaminopimelate-sensitive aspartokinase
           (AK) isoenzyme AKI, a monofunctional class enzyme found
           in Bacilli (Bacillus subtilis (BS) strain 168),
           Clostridia, and Actinobacteria, bacterial species. In B.
           subtilis, the regulation of the diaminopimelate-lysine
           biosynthetic pathway involves dual control by
           diaminopimelate and lysine, effected through separate
           diaminopimelate- and lysine-sensitive aspartokinase
           isoenzymes. AKI activity is invariant during the
           exponential and stationary phases of growth and is not
           altered by addition of amino acids to the growth medium.
           The role of this isoenzyme is most likely to provide a
           constant level of aspartyl-beta-phosphate for the
           biosynthesis of diaminopimelate for peptidoglycan
           synthesis and dipicolinate during sporulation. The B.
           subtilis AKI is tetrameric consisting of two alpha and
           two beta subunits; the alpha (43 kD) and beta (17 kD)
           subunit formed by two in-phase overlapping genes. The
           alpha subunit contains the AK catalytic domain and two
           ACT domains. The beta subunit contains two ACT domains.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 67

 Score = 33.8 bits (78), Expect = 0.090
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)

Query: 284 IFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSDNKENIGYD 337
           +F  LA A I++D+I  NVS +     + FT      EKA+ +L    E +G D
Sbjct: 19  VFKALANAGISVDLI--NVSPEE----VIFTVDGEVAEKAVDIL----EKMGLD 62


>gnl|CDD|153189 cd04917, ACT_AKiii-LysC-EC_2, ACT domains located C-terminal to the
           catalytic domain of the lysine-sensitive aspartokinase
           isoenzyme AKIII.  This CD includes the second of two ACT
           domains located C-terminal to the catalytic domain of
           the lysine-sensitive aspartokinase isoenzyme AKIII, a
           monofunctional class enzyme found in bacteria
           (Escherichia coli (EC) LysC). Aspartokinase is the first
           enzyme in the aspartate metabolic pathway and catalyzes
           the conversion of aspartate and ATP to aspartylphosphate
           and ADP. The E. coli AKIII (LysC) binds two feedback
           allosteric inhibitor lysine molecules at the dimer
           interface located between the ACT1 domain of two
           subunits. The second ACT domain (ACT2), this CD, is not
           involved in the binding of heterotrophic effectors.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 64

 Score = 33.3 bits (77), Expect = 0.14
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 345 LVKISAIGIGMQSYAGVASAFFLCLAEKGINIKAIT--TSEIKISVLIDSAYTELAVRSL 402
           L  ++ IG  +   AGV    F  L +  IN++ I    S   +  L+     +  V+ L
Sbjct: 1   LALVALIGNDISETAGVEKRIFDALED--INVRMICYGASNHNLCFLVKEEDKDEVVQRL 58

Query: 403 HSC 405
           HS 
Sbjct: 59  HSR 61


>gnl|CDD|153181 cd04909, ACT_PDH-BS, C-terminal ACT domain of the monofunctional,
           NAD dependent, prephenate dehydrogenase (PDH).  The
           C-terminal ACT domain of the monofunctional, NAD
           dependent, prephenate dehydrogenase (PDH) enzyme that
           catalyzes the formation of 4-hydroxyphenylpyruvate from
           prephenate, found in Bacillus subtilis (BS) and other
           Firmicutes, Deinococci, and Bacteroidetes. PDH is the
           first enzyme in the aromatic amino acid pathway specific
           for the biosynthesis of tyrosine. This enzyme is
           feedback-inhibited by tyrosine in B. subtilis and other
           microorganisms. Both phenylalanine and tryptophan have
           been shown to be inhibitors of this activity in B.
           subtilis. Bifunctional  chorismate mutase-PDH (TyrA)
           enzymes such as those seen in Escherichia coli  do not
           contain an ACT domain. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 69

 Score = 31.0 bits (71), Expect = 0.54
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 276 DHPGISASIFSPLAEAHINI-DMIIQNVSED-GQYVDITFTTPSSSLEKALAVLSD 329
           D PG+ A +   L +A I+I ++ I  + E  G  + I+F T     E+A  +L +
Sbjct: 10  DEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQ-EDRERAKEILKE 64


>gnl|CDD|33623 COG3830, COG3830, ACT domain-containing protein [Signal
           transduction mechanisms].
          Length = 90

 Score = 30.9 bits (70), Expect = 0.58
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 276 DHPGISASIFSPLAEAHINIDMIIQNVSED----GQYVDITFTTPSSSLEKALAVLSDNK 331
           D  GI A++   LAE  +NI  I Q V +        VDI+      +  +    L+   
Sbjct: 12  DRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVDISKEVVDFAALRDE--LAAEG 69

Query: 332 ENIGYDV-IQHED 343
           + +G DV +Q ED
Sbjct: 70  KKLGVDVRVQRED 82


>gnl|CDD|58607 cd04241, AAK_FomA-like, AAK_FomA-like: This CD includes a
           fosfomycin biosynthetic gene product, FomA, and similar
           proteins found in a wide range of organisms. Together,
           the fomA and fomB genes in the fosfomycin biosynthetic
           gene cluster of Streptomyces wedmorensis confer
           high-level fosfomycin resistance. FomA and FomB proteins
           converted fosfomycin to fosfomycin monophosphate and
           fosfomycin diphosphate in the presence of ATP and a
           magnesium ion, indicating that FomA and FomB catalyzed
           phosphorylations of fosfomycin and fosfomycin
           monophosphate, respectively. FomA and related  sequences
           in this CD are members of the Amino Acid Kinase
           Superfamily (AAK)..
          Length = 252

 Score = 31.0 bits (70), Expect = 0.59
 Identities = 32/124 (25%), Positives = 51/124 (41%), Gaps = 11/124 (8%)

Query: 84  ALQSLGIQAISLQGWQIPIMTDSLHGMARICRVDEKKIVTHLKKKQVVVITGFQGLSHDN 143
           AL   G+ A+S+      +  +      RI   D + I   L +  V V+ G   L    
Sbjct: 88  ALLEAGVPAVSVPPSSFFVTENG-----RIVSFDLEVIKELLDRGFVPVLHGDVVLDEGG 142

Query: 144 SVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLEM 203
            +T L     D   V +A A+K +R    TDV G+Y   P   P A L+ +I    + ++
Sbjct: 143 GITILS---GDDIVVELAKALKPERVIFLTDVDGVYDKPP---PDAKLIPEIDVGSLEDI 196

Query: 204 SSLG 207
            +  
Sbjct: 197 LAAL 200


>gnl|CDD|32237 COG2054, COG2054, Uncharacterized archaeal kinase related to
           aspartokinases, uridylate kinases [General function
           prediction only].
          Length = 212

 Score = 30.7 bits (69), Expect = 0.66
 Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 153 SDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKISFEEMLEMSSLGAKVMQ 212
           SD+ +V IAA   A      TDV GIY  D    PK  L+++I   ++      G   + 
Sbjct: 118 SDSISVWIAAKAGATEVVKATDVDGIYEED----PKGKLVREIRASDLKT----GETSVD 169

Query: 213 VRSVELAMLYKMCLFV 228
               +L + YKM   V
Sbjct: 170 PYLPKLLVKYKMNCRV 185


>gnl|CDD|153161 cd04889, ACT_PDH-BS-like, C-terminal ACT domain of the
           monofunctional, NAD dependent, prephenate dehydrogenase
           (PDH) enzyme that catalyzes the formation of
           4-hydroxyphenylpyruvate from prephenate.  Included in
           this CD is the C-terminal ACT domain of the
           monofunctional, NAD dependent, prephenate dehydrogenase
           (PDH) enzyme that catalyzes the formation of
           4-hydroxyphenylpyruvate from prephenate, found in
           Bacillus subtilis (BS) and other Firmicutes, Deinococci,
           and Bacteroidetes. PDH is the first enzyme in the
           aromatic amino acid pathway specific for the
           biosynthesis of tyrosine. This enzyme is feedback
           inhibited by tyrosine in B. subtilis and other
           microorganisms. Both phenylalanine and tryptophan have
           been shown to be inhibitors of this activity in B.
           subtilis. Bifunctional  chorismate mutase-PDH (TyrA)
           enzymes such as those seen in Escherichia coli do not
           contain an ACT domain. Also included in this CD is the
           N-terminal ACT domain of a novel protein composed almost
           entirely of two tandem ACT domains as seen in the
           uncharacterized structure (pdb 2F06) of the Bt0572
           protein from Bacteroides thetaiotaomicron and related
           ACT domains. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 56

 Score = 30.6 bits (70), Expect = 0.83
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 276 DHPGISASIFSPLAEAHINI-DMIIQNVSEDGQYVDITFTTPSSSLEKALAVLS 328
           + PG  A +   LAEA INI  + I     +   + + F+ P    E+A  VL 
Sbjct: 7   NKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFSDP----ERAKEVLK 56


>gnl|CDD|39088 KOG3885, KOG3885, KOG3885, Fibroblast growth factor [Signal
           transduction mechanisms].
          Length = 155

 Score = 30.6 bits (69), Expect = 0.84
 Identities = 7/34 (20%), Positives = 18/34 (52%)

Query: 340 QHEDNLVKISAIGIGMQSYAGVASAFFLCLAEKG 373
             +  + +I  + +G+ +  GV S  +L + ++G
Sbjct: 54  SDQHTIFEIITVAVGVVAIKGVESELYLAMNKEG 87


>gnl|CDD|58606 cd04240, AAK_UC, AAK_UC: Uncharacterized (UC) amino acid
           kinase-like proteins found mainly in archaea and a few
           bacteria. Sequences in this CD are members of the Amino
           Acid Kinase (AAK) superfamily..
          Length = 203

 Score = 29.9 bits (67), Expect = 1.2
 Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 12/69 (17%)

Query: 138 GLSHDNSVTTLGRGGSDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLMKKISF 197
            L H   VT      SD+ A  +A  + A R  I TDV GIY      E    L+ +I+ 
Sbjct: 107 PLPHSWEVT------SDSIAAWLAKKLGAKRLVIVTDVDGIY------EKDGKLVNEIAA 154

Query: 198 EEMLEMSSL 206
            E+L  +S+
Sbjct: 155 AELLGETSV 163


>gnl|CDD|153207 cd04935, ACT_AKiii-DAPDC_1, ACT domains of a bifunctional AKIII
           (LysC)-like aspartokinase/meso-diaminopimelate
           decarboxylase (DAPDC) bacterial protein.  This CD
           includes the first of two ACT domains of a bifunctional
           AKIII (LysC)-like aspartokinase/meso-diaminopimelate
           decarboxylase (DAPDC) bacterial protein. Aspartokinase
           (AK) is the first enzyme in the aspartate metabolic
           pathway and catalyzes the conversion of aspartate and
           ATP to aspartylphosphate and ADP. The lysA gene encodes
           the enzyme DAPDC, a pyridoxal-5'-phosphate
           (PLP)-dependent enzyme which catalyzes the final step in
           the lysine biosynthetic pathway converting
           meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT
           domains are positioned centrally with the AK catalytic
           domain N-terminal and the DAPDC domains C-terminal.
           Members of this CD belong to the superfamily of ACT
           regulatory domains.
          Length = 75

 Score = 29.4 bits (66), Expect = 1.7
 Identities = 11/44 (25%), Positives = 23/44 (52%)

Query: 348 ISAIGIGMQSYAGVASAFFLCLAEKGINIKAITTSEIKISVLID 391
           +S   +GM    G  +  F    + G+++  ++TSE  ++V +D
Sbjct: 4   VSMETLGMWQQVGFLADVFAPFKKHGVSVDLVSTSETNVTVSLD 47


>gnl|CDD|28940 cd00058, FGF, Acidic and basic fibroblast growth factor family;
           FGFs are mitogens, which stimulate growth or
           differentiation of cells of mesodermal or
           neuroectodermal origin. The family plays essential roles
           in patterning and differentiation during vertebrate
           embryogenesis, and has neurotrophic activities. FGFs
           have a high affinity for heparan sulfate proteoglycans
           and require heparan sulfate to activate one of four cell
           surface FGF receptors. Upon binding to FGF, the
           receptors dimerize and their intracellular tyrosine
           kinase domains become active. FGFs have internal
           pseudo-threefold symmetry (beta-trefoil topology)..
          Length = 123

 Score = 29.0 bits (65), Expect = 2.3
 Identities = 10/32 (31%), Positives = 19/32 (59%)

Query: 342 EDNLVKISAIGIGMQSYAGVASAFFLCLAEKG 373
              +++  A+ +G+ S  GVAS  +LC+ + G
Sbjct: 28  SYTILERIAVAVGVVSIKGVASCRYLCMNKCG 59


>gnl|CDD|30789 COG0440, IlvH, Acetolactate synthase, small (regulatory) subunit
           [Amino acid transport and metabolism].
          Length = 163

 Score = 29.0 bits (65), Expect = 2.3
 Identities = 19/100 (19%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 274 LRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTT-----PSSSLEKALAVLS 328
           + + PG+ + +    +    NI+ +    +E      IT            + K L  L 
Sbjct: 11  VENEPGVLSRVTGLFSRRGYNIESLTVGPTETPGLSRITIVVSGDEQVLEQIIKQLNKLI 70

Query: 329 DN---KENIGYDVIQHEDNLVKISAIGIGMQSYAGVASAF 365
           D     +      ++ E  L+K+SA G      A +   F
Sbjct: 71  DVLKVLDLTSEPHVERELALIKVSAEGSERGEIARITEIF 110


>gnl|CDD|153158 cd04886, ACT_ThrD-II-like, C-terminal ACT domain of biodegradative
           (catabolic) threonine dehydratase II (ThrD-II) and other
           related ACT domains.  This CD includes the C-terminal
           ACT domain of biodegradative (catabolic) threonine
           dehydratase II (ThrD-II) and other related ACT domains.
           The Escherichia coli tdcB gene product, ThrD-II,
           anaerobically catalyzes the pyridoxal
           phosphate-dependent dehydration of L-threonine and
           L-serine to ammonia and to alpha-ketobutyrate and
           pyruvate, respectively. Tetrameric ThrD-II is subject to
           allosteric activation by AMP, inhibition by alpha-keto
           acids, and catabolite inactivation by several
           metabolites of glycolysis and the citric acid cycle.
           Also included in  this CD are  N-terminal ACT domains
           present in smaller (~170 a.a.) archaeal proteins of
           unknown function. Members of this CD belong to the
           superfamily of ACT regulatory domains.
          Length = 73

 Score = 28.7 bits (65), Expect = 2.9
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 10/74 (13%)

Query: 273 RLRDHPGISASIFSPLAEAHINIDMIIQN-----VSEDGQYVDITFTTPSSS-LEKALAV 326
            L D PG  A + + +AEA  NI  +  +     +      V++T  T  +  +E+ +A 
Sbjct: 4   ELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETRGAEHIEEIIAA 63

Query: 327 LSDNKENIGYDVIQ 340
           L +     GYDV +
Sbjct: 64  LREA----GYDVRR 73


>gnl|CDD|153377 cd07365, MhpB_like, Subunit B of the Class III Extradiol
           ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate
           1,2-dioxygenase (MhpB), which catalyzes the oxidization
           and subsequent ring-opening of
           2,3-dihydroxyphenylpropionate.
           2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB)
           catalyzes the oxidization and subsequent ring-opening of
           2,3-dihydroxyphenylpropionate, yielding the product
           2-hydroxy-6-oxo-nona-2,4-diene 1,9-dicarboxylate.  It is
           an essential enzyme in the beta-phenylpropionic
           degradation pathway, in which beta-phenylpropionic is
           first hydrolyzed to produce
           2,3-dihydroxyphenylpropionate. The enzyme is a member of
           the class III extradiol dioxygenase family, a group of
           enzymes which use a non-heme Fe(II) to cleave aromatic
           rings between a hydroxylated carbon and an adjacent
           non-hydroxylated carbon. LigAB-like class III enzymes
           are usually composed of two subunits, designated A and
           B, which form a tetramer composed of two copies of each
           subunit. This model represents the catalytic subunit, B.
           MhpB is likely to be a tetramer.
          Length = 310

 Score = 28.4 bits (64), Expect = 3.4
 Identities = 30/91 (32%), Positives = 39/91 (42%), Gaps = 15/91 (16%)

Query: 67  DVVISTGEQVSSGLMVLALQSL--GIQAISLQGWQIPIMTDS----LHGMARICRVDEKK 120
           DV IS   QV  G     L+ L  G+    +    IPI  +S    L  M R   + E  
Sbjct: 104 DVAISHRMQVDHG-FTQPLEELFGGLDRYPV----IPIFVNSVAPPLAPMRRARALGEA- 157

Query: 121 IVTHLKK--KQVVVITGFQGLSHDNSVTTLG 149
           +   L K  K+V+ + G  GLSHD  V  L 
Sbjct: 158 VGRFLAKLDKRVLFL-GSGGLSHDPPVPQLA 187


>gnl|CDD|36369 KOG1154, KOG1154, KOG1154, Gamma-glutamyl kinase [Amino acid
           transport and metabolism].
          Length = 285

 Score = 28.4 bits (63), Expect = 3.7
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 153 SDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEP 187
           +D+ A  +AA IKAD   + +DV G+YT  P  +P
Sbjct: 169 NDSLAAILAAEIKADLLILLSDVDGLYTGPPDADP 203


>gnl|CDD|33403 COG3603, COG3603, Uncharacterized conserved protein [Function
           unknown].
          Length = 128

 Score = 28.0 bits (62), Expect = 4.6
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 11/63 (17%)

Query: 276 DHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSDNKENIG 335
              GI AS+  PL++  I    I    + D  ++ +        LEKA+  L    E  G
Sbjct: 75  GLTGILASVSQPLSDNGIG---IFAVSTYDTDHILVR----EEDLEKAVKAL----EEAG 123

Query: 336 YDV 338
           ++V
Sbjct: 124 HEV 126


>gnl|CDD|153184 cd04912, ACT_AKiii-LysC-EC-like_1, ACT domains located C-terminal
           to the catalytic domain of  the lysine-sensitive
           aspartokinase isoenzyme AKIII.  This CD includes the
           first of two ACT domains located C-terminal to the
           catalytic domain of  the lysine-sensitive aspartokinase
           isoenzyme AKIII, a monofunctional class enzyme found in
           bacteria (Escherichia coli (EC) LysC) and plants, (Zea
           mays Ask1, Ask2, and Arabidopsis thaliana AK1).
           Aspartokinase is the first enzyme in the aspartate
           metabolic pathway and catalyzes the conversion of
           aspartate and ATP to aspartylphosphate and ADP. Like the
           A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has
           two bound feedback allosteric inhibitor lysine molecules
           at the dimer interface located between the ACT1 domain
           of two subunits. The lysine-sensitive plant isoenzyme is
           synergistically inhibited by S-adenosylmethionine. A
           homolog of this group appears to be the Saccharomyces
           cerevisiae AK (Hom3) which clusters with this group as
           well. Members of this CD belong to the superfamily of
           ACT regulatory domains.
          Length = 75

 Score = 27.6 bits (62), Expect = 5.9
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 365 FFLCLAEKGINIKAITTSEIKISVLIDSAYTELAVRSLHSC 405
            F   A+ G+++  I+TSE+ +S+ +D          L + 
Sbjct: 21  VFEIFAKHGLSVDLISTSEVSVSLTLDPTKNLSDQLLLDAL 61


>gnl|CDD|36403 KOG1189, KOG1189, KOG1189, Global transcriptional regulator, cell
           division control protein [Amino acid transport and
           metabolism].
          Length = 960

 Score = 27.4 bits (60), Expect = 7.3
 Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 284 IFSPLAEAHIN-IDMIIQNVSEDGQYVDITFTTPSSSLEK 322
           IF      HI+ I    QNV  D  Y+ I F TP S   K
Sbjct: 498 IFGIPVPFHISTIKNASQNVEGDYTYLRINFNTPGSPGGK 537


>gnl|CDD|153154 cd04882, ACT_Bt0572_2, C-terminal ACT domain of a novel protein
           composed of just two ACT domains.  Included in this CD
           is the C-terminal ACT domain of a novel protein composed
           of just two ACT domains, as seen in the yet
           uncharacterized structure (pdb 2F06) of the Bt0572
           protein from Bacteroides thetaiotaomicron and related
           proteins. Members of this CD belong to the superfamily
           of ACT regulatory domains.
          Length = 65

 Score = 27.2 bits (61), Expect = 8.7
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 273 RLRDHPGISASIFSPLAEAHINIDMIIQNVSEDGQYVDITFTTPSSSLEKALAVLSDNK 331
            + D PG    I   L+E  INI+ +   V + G    + F T    +EKA+ VL +  
Sbjct: 5   EVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRT--EDIEKAIEVLQERG 61


>gnl|CDD|58622 cd04256, AAK_P5CS_ProBA, AAK_P5CS_ProBA: Glutamate-5-kinase (G5K)
           domain of the bifunctional delta
           1-pyrroline-5-carboxylate synthetase (P5CS), composed of
           an N-terminal G5K (ProB) and a C-terminal glutamyl 5-
           phosphate reductase (G5PR, ProA), the first and second
           enzyme catalyzing proline (and, in mammals, ornithine)
           biosynthesis. G5K transfers the terminal phosphoryl
           group of ATP to the gamma-carboxyl group of glutamate,
           and is subject to feedback allosteric inhibition by
           proline or ornithine. In plants, proline plays an
           important role as an osmoprotectant and, in mammals,
           ornithine biosynthesis is crucial for proper ammonia
           detoxification, since a G5K mutation has been shown to
           cause human hyperammonaemia..
          Length = 284

 Score = 27.2 bits (60), Expect = 9.4
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 153 SDTSAVAIAAAIKADRCDIYTDVCGIYTTDPRIEPKAHLM 192
           +D+ A  +A  +KAD   + +DV G+Y   P     A L+
Sbjct: 180 NDSLAARLAVELKADLLILLSDVDGLYDGPPG-SDDAKLI 218


  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    0.133    0.367 

Gapped
Lambda     K      H
   0.267   0.0708    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,471,944
Number of extensions: 228458
Number of successful extensions: 748
Number of sequences better than 10.0: 1
Number of HSP's gapped: 703
Number of HSP's successfully gapped: 96
Length of query: 411
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 315
Effective length of database: 4,189,273
Effective search space: 1319620995
Effective search space used: 1319620995
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)