RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780999|ref|YP_003065412.1| NAD synthetase [Candidatus
Liberibacter asiaticus str. psy62]
         (562 letters)



>gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT,
           glutaminase) domain of glutamine-dependent NAD
           synthetases (class 7 and 8 nitrilases).
           Glutamine-dependent NAD synthetases are bifunctional
           enzymes, which have an N-terminal GAT domain and a
           C-terminal NAD+ synthetase domain. The GAT domain is a
           glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to
           L-glutamate and ammonia. The ammonia is used by the NAD+
           synthetase domain in the ATP-dependent amidation of
           nicotinic acid adenine dinucleotide. Glutamine
           aminotransferases are categorized depending on their
           active site residues into different unrelated classes.
           This class of GAT domain belongs to a larger nitrilase
           superfamily comprised of nitrile- or amide-hydrolyzing
           enzymes and amide-condensing enzymes, which depend on a
           Glu-Lys-Cys catalytic triad. This superfamily has been
           classified in the literature based on global and
           structure based sequence analysis into thirteen
           different enzyme classes (referred to as 1-13), this
           subgroup corresponds to classes 7 and 8. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
           Mycobacterium tuberculosis glutamine-dependent NAD+
           synthetase forms a homooctamer.
          Length = 261

 Score =  299 bits (769), Expect = 1e-81
 Identities = 97/233 (41%), Positives = 138/233 (59%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           +IA+AQLNP VGD+ GN  K   A  EA  QG DL++F EL ++GYPPEDL+ +  F++A
Sbjct: 1   RIALAQLNPTVGDLEGNAEKILEAIREAKAQGADLVVFPELSLTGYPPEDLLLRPDFLEA 60

Query: 66  CSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYSEFHE 125
              A++ L + T D    +VVG P +    + N+  +L  G I+ V  K  LPNY  F E
Sbjct: 61  AEEALEELAAATADLDIAVVVGLPLRHDGKLYNAAAVLQNGKILGVVPKQLLPNYGVFDE 120

Query: 126 KRTFISGYSNDPIVFRDIRLGILICEDIWKNSNICKHLKKQGAEFLFSLNASPYYHNKLK 185
           KR F  G   D + F+ +R+G+ ICED+W        L   GA+ + +L+ASP++  K  
Sbjct: 121 KRYFTPGDKPDVLFFKGLRIGVEICEDLWVPDPPSAELALAGADLILNLSASPFHLGKQD 180

Query: 186 KRHEIVTGQISHVHLPIIYVNQVGGQDELIFDGASFCFDGQQQLAFQMKHFSE 238
            R E+V+ + +   LP +YVNQVGGQD+L+FDG SF  D   +L  +   F E
Sbjct: 181 YRRELVSSRSARTGLPYVYVNQVGGQDDLVFDGGSFIADNDGELLAEAPRFEE 233


>gnl|CDD|30166 cd00553, NAD_synthase, NAD+ synthase is a homodimer, which
           catalyzes the final step in de novo nicotinamide adenine
           dinucleotide (NAD+) biosynthesis, an amide transfer from
           either ammonia or glutamine to nicotinic acid adenine
           dinucleotide (NaAD). The conversion of NaAD to NAD+
           occurs via an NAD-adenylate intermediate and requires
           ATP and Mg2+. The intemediate is subsequently cleaved
           into NAD+ and AMP. In many prokaryotes, such as E. coli
           , NAD synthetase consists of a single domain and is
           strictly ammonia dependent. In contrast, eukaryotes and
           other prokaryotes have an additional N-terminal
           amidohydrolase domain that prefer glutamine,
           Interestingly, NAD+ synthases in these prokaryotes, can
           also utilize ammonia as an amide source ..
          Length = 248

 Score =  270 bits (692), Expect = 8e-73
 Identities = 106/262 (40%), Positives = 151/262 (57%), Gaps = 16/262 (6%)

Query: 270 QEEEADYNACVLSLRDYVQKNNFHKVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYK 329
           ++ E   NA VL LRDY++K+ F  V++GLSGGIDSAL AA+AV ALG+ENV  + +P +
Sbjct: 1   EDLEEIINALVLFLRDYLRKSGFKGVVLGLSGGIDSALVAALAVRALGRENVLALFMPSR 60

Query: 330 YTSPQSLEDAAACAKALGCKYDVLPIHDLVNHFFSLMSQFLQEEPSGIVAENIQSRIRGN 389
           Y+S ++ EDA   A+ALG ++  + I   V  F +L+ +    E   +   NIQ+R+R  
Sbjct: 61  YSSEETREDAKELAEALGIEHVNIDIDPAVEAFLALLGESGGSELEDLALGNIQARLRMV 120

Query: 390 ILMALSNHSKAMLLTTSNKSEISVGYGTLYGDMSGGFNPLKDLYKTQVFQLASWRNSHGI 449
           IL AL+N    ++L T NKSE+ +GY T YGD +   NP+ DLYKTQV +LA +      
Sbjct: 121 ILYALANKLGGLVLGTGNKSELLLGYFTKYGDGAADINPIGDLYKTQVRELARYLG---- 176

Query: 450 TSGLGPLTEVIPPSILEKSPSAELRPHQTDQESLP-PYPILDDIIKRIVENEES-FINND 507
                     +P SI++K PSAEL P QTD++ L  PY  LD  +   +E          
Sbjct: 177 ----------VPESIIDKPPSAELWPGQTDEDELGMPYEELDQFLYLRLEGGLGPEEILA 226

Query: 508 QEYNDETVRYVEHLLYGSEYKR 529
               +E V+ V  L   +E+KR
Sbjct: 227 PGIIEEVVKRVFRLYKKNEHKR 248


>gnl|CDD|145596 pfam02540, NAD_synthase, NAD synthase.  NAD synthase (EC:6.3.5.1)
           is involved in the de novo synthesis of NAD and is
           induced by stress factors such as heat shock and glucose
           limitation.
          Length = 243

 Score =  263 bits (674), Expect = 1e-70
 Identities = 104/260 (40%), Positives = 146/260 (56%), Gaps = 21/260 (8%)

Query: 276 YNACVLSLRDYVQKNNFHKVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQS 335
               V  LRDYVQK+    V++GLSGGIDSA+ A +AV ALGKENV  +++P   +S + 
Sbjct: 2   IERLVDFLRDYVQKSGAKGVVLGLSGGIDSAVVAYLAVKALGKENVLALIMPSINSSEED 61

Query: 336 LEDAAACAKALGCKYDVLPIHDLVNHFFSLMSQFLQEEPSGIVAENIQSRIRGNILMALS 395
           ++DA A A+ LG  Y  + I  +V  F  L     Q     +   N+++RIR  IL A +
Sbjct: 62  VQDALALAENLGINYKTIDIKPIVRAFSQL----FQPAKDDLAKGNLKARIRMIILYAHA 117

Query: 396 NHSKAMLLTTSNKSEISVGYGTLYGDMSGGFNPLKDLYKTQVFQLASWRNSHGITSGLGP 455
           N    ++L T NKSE+++GY T YGD +    P+ DLYKTQV++LA   N          
Sbjct: 118 NKFNRLVLGTGNKSELALGYFTKYGDGACDIAPIGDLYKTQVYELAKRLN---------- 167

Query: 456 LTEVIPPSILEKSPSAELRPHQTDQESLP-PYPILDDIIKRIVENEESF--INNDQEYND 512
               +P  I++K PSA+L P QTD++ L   Y  LD I+K ++E + S   I  D     
Sbjct: 168 ----VPERIIKKPPSADLWPGQTDEDELGITYDELDQILKGLIEKKLSPEEIIGDLGLPA 223

Query: 513 ETVRYVEHLLYGSEYKRRQA 532
           E V  VE+L+  SE+KRR  
Sbjct: 224 EVVERVENLIQKSEHKRRLP 243


>gnl|CDD|30520 COG0171, NadE, NAD synthase [Coenzyme metabolism].
          Length = 268

 Score =  254 bits (649), Expect = 7e-68
 Identities = 117/287 (40%), Positives = 157/287 (54%), Gaps = 31/287 (10%)

Query: 270 QEEEADYNACVLSLRDYVQKNNFHKVIIGLSGGIDSALCAAIAVDALGK----ENVQTIM 325
            + E + N  V  LRDY++K  F  V++GLSGGIDSAL  A+AV ALGK    ENV  + 
Sbjct: 3   IDLEEEINRLVDFLRDYLKKAGFKGVVLGLSGGIDSALVLALAVRALGKGDSKENVLAVR 62

Query: 326 LPYKYTSPQSLEDAAACAKALGCKYDVLPIHDLVNHFFS-LMSQFLQEEPSGIVAENIQS 384
           LPY YT     EDA   A+ALG  Y  + I   V+ F   L+  FL      +   NI++
Sbjct: 63  LPYGYTVQADEEDAQDLAEALGIDYKEINIKPAVDAFLKKLLKLFLGIYLEDLALGNIKA 122

Query: 385 RIRGNILMALSNHSKAMLLTTSNKSEISVGYGTLYGDMSGGFNPLKDLYKTQVFQLASWR 444
           R+R  IL A++N    ++L T NKSE+++GY T YGD +   NP+ DLYKTQV+ LA   
Sbjct: 123 RLRMVILYAIANKLGGLVLGTGNKSELALGYFTKYGDGAVDINPIADLYKTQVYALARHL 182

Query: 445 NSHGITSGLGPLTEVIPPSILEKSPSAELRPH---QTDQESLP-PYPILDDIIKRIVENE 500
                          IP  IL+K P+A+L P    QTD+  L  PY  LDDI+  ++EN 
Sbjct: 183 G--------------IPEEILKKPPTADLWPDEPGQTDEAELGMPYEELDDILYGLLENG 228

Query: 501 ESFINNDQEYNDETVRYVEHLLYGSEYKRRQAPVGTKITAKSFGRDR 547
           +       E ++E V+ +E L   SE+KRR  P+G KIT   F    
Sbjct: 229 Q-------EISEELVKKIERLYKKSEHKRR-LPIGPKITPWKFLSFG 267


>gnl|CDD|30737 COG0388, COG0388, Predicted amidohydrolase [General function
           prediction only].
          Length = 274

 Score =  159 bits (403), Expect = 2e-39
 Identities = 63/246 (25%), Positives = 110/246 (44%), Gaps = 5/246 (2%)

Query: 3   KKLKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPED-LVFKKS 61
             +++A AQ+ P  GD A N+A+  R   EA  +G DL++F ELF++GYP ED L  +++
Sbjct: 1   SMMRVAAAQMAPKAGDPAENLARILRLIREAAARGADLVVFPELFLTGYPCEDDLFLEEA 60

Query: 62  FIQACSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYS 121
             +A    ++ L +   +GG  IV G   + ++   N+ +I   G I+    K++L +  
Sbjct: 61  AAEAGEETLEFLAALAEEGGVIIVGGPLPEREKLYNNAALIDPDGEILGKYRKLHLFDA- 119

Query: 122 EFHEKRTFISG-YSNDPIVFRDIRLGILICEDIWKNSNICKHLKKQGAEFLFSLNASPYY 180
            + E+R F  G            ++G+LIC D+       + L   GAE L    A P  
Sbjct: 120 FYEERRFFTPGDEGVVVFETDGGKIGLLICYDLRFPELARRLLALGGAELLLVPAAWP-A 178

Query: 181 HNKLKKRHEIVTGQISHVHLPIIYVNQVGGQDE-LIFDGASFCFDGQQQLAFQMKHFSEQ 239
              L     ++  +     + ++  N+ G     L F G S   D   ++  +     E 
Sbjct: 179 ERGLDHWEVLLRARAIENQVYVLAANRAGFDGAGLEFCGHSAIIDPDGEVLAEAGEEEEG 238

Query: 240 NFMTEW 245
             + + 
Sbjct: 239 VLLADI 244


>gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes. 
           This superfamily (also known as the C-N hydrolase
           superfamily) contains hydrolases that break
           carbon-nitrogen bonds; it includes nitrilases, cyanide
           dihydratases, aliphatic amidases, N-terminal amidases,
           beta-ureidopropionases, biotinidases, pantotheinase,
           N-carbamyl-D-amino acid amidohydrolases, the glutaminase
           domain of glutamine-dependent NAD+ synthetase,
           apolipoprotein N-acyltransferases, and
           N-carbamoylputrescine amidohydrolases, among others.
           These enzymes depend on a Glu-Lys-Cys catalytic triad,
           and work through a thiol acylenzyme intermediate.
           Members of this superfamily generally form homomeric
           complexes, the basic building block of which is a
           homodimer. These oligomers include dimers, tetramers,
           hexamers, octamers, tetradecamers, octadecamers, as well
           as variable length helical arrangements and
           homo-oligomeric spirals. These proteins have roles in
           vitamin and co-enzyme metabolism, in detoxifying small
           molecules, in the synthesis of signaling molecules, and
           in the post-translational modification of proteins. They
           are used industrially, as biocatalysts in the fine
           chemical and pharmaceutical industry, in cyanide
           remediation, and in the treatment of toxic effluent.
           This superfamily has been classified previously in the
           literature, based on global and structure-based sequence
           analysis, into thirteen different enzyme classes
           (referred to as 1-13). This hierarchy includes those
           thirteen classes and a few additional subfamilies. A
           putative distant relative, the plasmid-borne TraB
           family, has not been included in the hierarchy.
          Length = 253

 Score =  124 bits (314), Expect = 5e-29
 Identities = 65/220 (29%), Positives = 106/220 (48%), Gaps = 14/220 (6%)

Query: 7   IAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQAC 66
           IA  QL P +GD+  N+AKA R  +EA  QG DLI+  ELF++GY  E         +  
Sbjct: 1   IAAVQLAPKIGDVEANLAKALRLIKEAAEQGADLIVLPELFLTGYSFESAKEDLDLAEEL 60

Query: 67  SS-AIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDA-GNIIAVRDKINLPNYSEFH 124
               ++ L     + G  IV G   +D + + N+ V++D  G II    KI+L +   F 
Sbjct: 61  DGPTLEALAELAKELGIYIVAGIAEKDGDKLYNTAVVIDPDGEIIGKYRKIHLFD---FG 117

Query: 125 EKRTFISGYSNDPIVF--RDIRLGILICEDIWKNSNICKHLKKQGAEFLFSLNASPYYHN 182
           E+R F  G  ++  VF     ++G+LIC D+     + + L  +GA+ +    A P    
Sbjct: 118 ERRYFSPG--DEFPVFDTPGGKIGLLICYDLR-FPELARELALKGADIILVPAAWPTARR 174

Query: 183 KLKKRHEIVTGQISHVH-LPIIYVNQVGGQDELIFDGASF 221
              +  E++    +  + + ++  N+VG +  L F G S 
Sbjct: 175 ---EHWELLLRARAIENGVYVVAANRVGEEGGLEFAGGSM 211


>gnl|CDD|143610 cd07586, nitrilase_8, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 269

 Score =  114 bits (287), Expect = 8e-26
 Identities = 69/228 (30%), Positives = 110/228 (48%), Gaps = 22/228 (9%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           ++AIAQ++PV+GD+  N+ K     E A  +G DL++F EL ++GY   DLV++ + + A
Sbjct: 1   RVAIAQIDPVLGDVEENLEKHLEIIETARERGADLVVFPELSLTGYNLGDLVYEVA-MHA 59

Query: 66  CSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVL-NSVVILDAGNIIAVRDKINLPNYSEFH 124
               +  L      GG  +V GF  + ++G   NS   L+ G ++ V  K+ LP Y  F 
Sbjct: 60  DDPRLQALAE--ASGGICVVFGFVEEGRDGRFYNSAAYLEDGRVVHVHRKVYLPTYGLFE 117

Query: 125 EKRTFISGYSNDPI-VF--RDIRLGILICEDIWKNSNICKH-LKKQGAEFLFSLNASPYY 180
           E R F  G     +  F  R  R G+LICED W  S    + L   GA+ +F    SP  
Sbjct: 118 EGRYFAPG---SHLRAFDTRFGRAGVLICEDAWHPSLP--YLLALDGADVIFIPANSPA- 171

Query: 181 HNKLKKRHEIVTG--QISHVH-----LPIIYVNQVGGQDELIFDGASF 221
              +    +       +   +     + +++ N+VG +D + F G S 
Sbjct: 172 -RGVGGDFDNEENWETLLKFYAMMNGVYVVFANRVGVEDGVYFWGGSR 218


>gnl|CDD|144405 pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase.  This family
           contains hydrolases that break carbon-nitrogen bonds.
           The family includes: Nitrilase EC:3.5.5.1, Aliphatic
           amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12,
           Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related
           proteins generally have a conserved E-K-C catalytic
           triad, and are multimeric alpha-beta-beta-alpha sandwich
           proteins.
          Length = 172

 Score =  103 bits (260), Expect = 1e-22
 Identities = 54/175 (30%), Positives = 86/175 (49%), Gaps = 5/175 (2%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           ++A+ QL P   D+  N+ K     EEA RQG DLI+F ELFI GY      + +     
Sbjct: 1   RVALVQLPPSAFDLEANLQKLLELIEEAARQGADLIVFPELFIPGYAHGAAEYLELAEAI 60

Query: 66  CSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDA-GNIIAVRDKINLPNYSEFH 124
               +  L +     G  +V G P +D  G+ N++V++D  G ++    K +L  + E+ 
Sbjct: 61  PGEVLQALSALARKNGITVVAGIPERDGGGLYNTLVLIDPDGELLGKYRKRHLVPFGEWV 120

Query: 125 EKRTFISGYSNDPIVFRDI-RLGILICEDIWKNSNICKHLKKQGAEFLFSLNASP 178
           E+  F  G +  P+    + +LG+LIC +I     + + L  +GAE L   N S 
Sbjct: 121 ERPLFGPGGATFPVFDTPVGKLGLLICYEIR-FPELARMLALKGAEILA--NPSA 172


>gnl|CDD|143600 cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and
           related proteins (putative class 13 nitrilases).
           Pseudomonas sp. MCI3434 R-amidase hydrolyzes
           (R,S)-piperazine-2-tert-butylcarboxamide to form
           (R)-piperazine-2-carboxylic acid. It does so with strict
           R-stereoselectively. Its preferred substrates are
           carboxamide compounds which have the amino or imino
           group connected to their beta- or gamma-carbon. This
           subgroup belongs to a larger nitrilase superfamily
           comprised of nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. This superfamily has been classified in
           the literature based on global and structure based
           sequence analysis into thirteen different enzyme classes
           (referred to as 1-13), class 13 represents proteins that
           at the time were difficult to place in a distinct
           similarity group. It has been suggested that this
           subgroup represents a new class. Members of the
           nitrilase superfamily generally form homomeric
           complexes, the basic building block of which is a
           homodimer. Native R-amidase however appears to be a
           monomer.
          Length = 254

 Score =  102 bits (256), Expect = 3e-22
 Identities = 59/228 (25%), Positives = 102/228 (44%), Gaps = 32/228 (14%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           ++A+ Q     GD+A N+A+   A   A   G DL++F ELF++GY   D V + +  + 
Sbjct: 1   RLALYQGPARDGDVAANLARLDEAAARAAAAGADLLVFPELFLTGYNIGDAVARLA--EP 58

Query: 66  CS-SAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDA-GNIIAVRDKINLPNYSEF 123
               A+  L++     G  IVVG+P +    V N+ V++D  G ++A   K +L   S  
Sbjct: 59  ADGPALQALRAIARRHGIAIVVGYPERAGGAVYNAAVLIDEDGTVLANYRKTHLFGDS-- 116

Query: 124 HEKRTFISGYSNDPIVFRDIRLGILICEDIWKNSNICKHLKKQGAEFLF--SLNASPYYH 181
            E+  F  G     +  R +R+G+LIC D+ +   + + L   GA+ +   +    PY  
Sbjct: 117 -ERAAFTPGDRFPVVELRGLRVGLLICYDV-EFPELVRALALAGADLVLVPTALMEPYGF 174

Query: 182 NKLKKRHEIVTGQISHV---------HLPIIYVNQVGGQDELIFDGAS 220
                        ++            + + Y N+ G +D L + G S
Sbjct: 175 -------------VARTLVPARAFENQIFVAYANRCGAEDGLTYVGLS 209


>gnl|CDD|37514 KOG2303, KOG2303, KOG2303, Predicted NAD synthase, contains CN
           hydrolase domain [Coenzyme transport and metabolism,
           General function prediction only].
          Length = 706

 Score = 85.8 bits (212), Expect = 3e-17
 Identities = 130/605 (21%), Positives = 209/605 (34%), Gaps = 136/605 (22%)

Query: 1   MLKKLKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFK- 59
           M +K+ +A   LN    D  GN+ +  ++ EEA  +G    L  EL I+GY  ED   + 
Sbjct: 1   MGRKVTVATCTLNQWALDFEGNMQRILKSIEEAKARGARYRLGPELEITGYGCEDHFLES 60

Query: 60  KSFIQACSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPN 119
            + + +     + ++S          +G P   +    N  V+     I+ +R K+ L N
Sbjct: 61  DTLLHSWEMLAELVESPVTQDIL-CDIGMPVMHRNVRYNCRVLFLNRKILLIRPKMWLAN 119

Query: 120 YSEFHEKRTFIS-------------------------GYSNDPIVFRDIRLGILICEDIW 154
              + E R F                            + +  +   D  +G  ICE++W
Sbjct: 120 DGNYRESRWFTPWTRPRVTEEYQLPRMIQKHTGQETVPFGDAVLQTWDTCIGSEICEELW 179

Query: 155 KNSNICKHLKKQGAEFLFSLNASPYYH--NKLKKRHEIVTGQISHVHLPIIYVNQVGGQ- 211
              +    +   G E +   NAS  +H   KL  R +++    S      +Y NQ G   
Sbjct: 180 TPRSPHIDMALDGVEII--TNASGSHHELRKLNTRVDLILNATSKCGGVYLYANQRGCDG 237

Query: 212 DELIFDGASFCFDGQQQLAFQMKHFSEQNF------------------------------ 241
           D L +DG +        LA Q   FS  +                               
Sbjct: 238 DRLYYDGCAMIAMNGSVLA-QGSQFSLDDVEVVTATVDLEDVRSYRASISSRGLQASRAV 296

Query: 242 -MTEWHYDQQLSQWN--YMSDDSASTMYIPLQEEEADYN-ACVLSLRDYVQKNNFHKVII 297
                H D +LSQ      +            EEE     AC   L DY++++      +
Sbjct: 297 KYPRIHVDFELSQHFDLLATPTEPIEWKYHSPEEEIALGPACW--LWDYLRRSGQAGFFL 354

Query: 298 GLSGGIDSALCAAIA-------VDALGKENVQ---------------------------- 322
            LSGG+DS+  AAI          A+   + Q                            
Sbjct: 355 PLSGGVDSSATAAIVYSMCRQVCKAVQSGDEQVLADVRRIVNDISYTPTDPADLCNRILY 414

Query: 323 TIMLPYKYTSPQSLEDAAACAKALGCKYDVLPIHDLVNHFFSLMSQFLQEEPS------- 375
           T  +  + +S ++   A   A  +G  +  L I   V+   SL +    + P        
Sbjct: 415 TCYMGSENSSKETRRRAKELANQIGSYHIDLNIDTAVSAVLSLFNLVTGKTPRFKSHGGS 474

Query: 376 ---GIVAENIQSRIR-------GNILMALSNHSKAML-LTTSNKSEISVGYGTLYGDMSG 424
               +  +NIQ+RIR         +L+ +      +L L ++N  E   GY T Y   S 
Sbjct: 475 NRENLALQNIQARIRMVLAYLFAQLLLWVRGRPGGLLVLGSANVDESLRGYLTKYDCSSA 534

Query: 425 GFNPLKDLYKTQVFQLASWRNSHGITSGLGPLTEVIPPSILEKSPSAELRP------HQT 478
             NP+  + KT + +   +        GL  L       IL+  P+AEL P       QT
Sbjct: 535 DINPIGGISKTDLRRFLQYAKEK---FGLPALQS-----ILDAPPTAELEPLTDGDYSQT 586

Query: 479 DQESL 483
           D+  +
Sbjct: 587 DEADM 591


>gnl|CDD|143604 cd07580, nitrilase_2, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 268

 Score = 82.8 bits (205), Expect = 2e-16
 Identities = 49/175 (28%), Positives = 77/175 (44%), Gaps = 20/175 (11%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           ++A  Q +P VGD+  N+A++     EA   G +L++  EL  +GY     VF +S  +A
Sbjct: 1   RVACVQFDPRVGDLDANLARSIELIREAADAGANLVVLPELANTGY-----VF-ESRDEA 54

Query: 66  CSSA--------IDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINL 117
            + A                 + G  IV GF  +D + + NS V++    +I    K +L
Sbjct: 55  FALAEEVPDGASTRAWAELAAELGLYIVAGFAERDGDRLYNSAVLVGPDGVIGTYRKAHL 114

Query: 118 PNYSEFHEKRTFISGYSNDPIVFRDI-RLGILICEDIWKNSNICKHLKKQGAEFL 171
            N     EK  F  G    P+      R+G+ IC D W      + L  QGA+ +
Sbjct: 115 WN----EEKLLFEPGDLGLPVFDTPFGRIGVAICYDGW-FPETFRLLALQGADIV 164


>gnl|CDD|143607 cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 253

 Score = 77.2 bits (191), Expect = 1e-14
 Identities = 49/175 (28%), Positives = 78/175 (44%), Gaps = 19/175 (10%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           KIA+ QL+ V GD   NI +     EEA   G DLI+  E++ +GY  +DL   +   + 
Sbjct: 1   KIALIQLDIVWGDPEANIERVESLIEEAAAAGADLIVLPEMWNTGYFLDDL--YELADED 58

Query: 66  CSSAIDTLKSDTHDGGAGIVVG-FPRQDQEGVLNSVVILDA-GNIIAVRDKINLPNYSEF 123
               +  L       G  IV G    ++   + N+  ++D  G +IA   KI+L      
Sbjct: 59  GGETVSFLSELAKKHGVNIVAGSVAEKEGGKLYNTAYVIDPDGELIATYRKIHLFGLMG- 117

Query: 124 HEKRTFISGYSNDPIVFR--DIRLGILICEDI----WKNSNICKHLKKQGAEFLF 172
            E +   +G  ++  VF     ++G+ IC D+           + L  +GAE LF
Sbjct: 118 -EDKYLTAG--DELEVFELDGGKVGLFICYDLRFPEL-----FRKLALEGAEILF 164


>gnl|CDD|143608 cd07584, nitrilase_6, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 258

 Score = 72.4 bits (178), Expect = 3e-13
 Identities = 64/224 (28%), Positives = 106/224 (47%), Gaps = 20/224 (8%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKK-SFIQ 64
           K+A+ Q++ V+GD+  N+ KA    +EA  +G DLI F EL  +GY P+ L  K     +
Sbjct: 1   KVALIQMDSVLGDVKANLKKAAELCKEAAAEGADLICFPELATTGYRPDLLGPKLWELSE 60

Query: 65  ACSSAIDTLKSD-THDGGAGIVVGF-PRQDQEGVL-NSVVILDA-GNIIAVRDKINLPNY 120
                   L S+   + G  IV GF  +    G + NS V++D  G  + V  KI+L  +
Sbjct: 61  PIDGPTVRLFSELAKELGVYIVCGFVEKGGVPGKVYNSAVVIDPEGESLGVYRKIHL--W 118

Query: 121 SEFHEKRTFISGYSNDPIVFRDI-RLGILICEDIWKNSNICKHLKKQGAEFLFSLNASPY 179
               EK+ F  G    P+      ++G++IC D+     + + L  +GAE +F  +A   
Sbjct: 119 GL--EKQYFREGEQY-PVFDTPFGKIGVMICYDM-GFPEVARILTLKGAEVIFCPSA--- 171

Query: 180 YHNKLKKRHEIVTGQIS---HVHLPIIYVNQVGGQDELIFDGAS 220
           +  +     +I     +    V +    VN+VG + +L+  G S
Sbjct: 172 WREQDADIWDINLPARALENTVFV--AAVNRVGNEGDLVLFGKS 213


>gnl|CDD|143609 cd07585, nitrilase_7, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 261

 Score = 72.0 bits (177), Expect = 4e-13
 Identities = 55/232 (23%), Positives = 90/232 (38%), Gaps = 30/232 (12%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           +IA+ Q    VGD A N+A   R   +A  QG +L+ F E+ I+GY     + +++ +  
Sbjct: 1   RIALVQFEARVGDKARNLAVIARWTRKAAAQGAELVCFPEMCITGYTHVRALSREAEVPD 60

Query: 66  CSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYSEFHE 125
              +   L       G  I+ G   +  +   N+ ++     ++    K++L       E
Sbjct: 61  -GPSTQALSDLARRYGLTILAGLIEKAGDRPYNTYLVCLPDGLVHRYRKLHLFR----RE 115

Query: 126 KRTFISGYSNDPIVF--RDIRLGILICED--IWKNSNICKHLKKQGAEFLFSLNASPYYH 181
                +G  ++  VF    +R GILIC D    +N          GAE LF+ +A+P   
Sbjct: 116 HPYIAAG--DEYPVFATPGVRFGILICYDNHFPENVRAT---ALLGAEILFAPHATP--G 168

Query: 182 NKLKKRHEIVTGQISHVHLP---------IIYVNQVGGQDELIFDGASFCFD 224
               K  E          LP         +   N VG     +F G +   D
Sbjct: 169 TTSPKGREWW-----MRWLPARAYDNGVFVAACNGVGRDGGEVFPGGAMILD 215


>gnl|CDD|143601 cd07577, Ph0642_like, Pyrococcus horikoshii Ph0642 and related
           proteins, members of the nitrilase superfamily (putative
           class 13 nitrilases).  Uncharacterized subgroup of the
           nitrilase superfamily. This superfamily is comprised of
           nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. Pyrococcus horikoshii Ph0642 is a
           hypothetical protein belonging to this subgroup. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           This subgroup was classified as belonging to class 13,
           which represents proteins that at the time were
           difficult to place in a distinct similarity group.
           Members of this superfamily generally form homomeric
           complexes, the basic building block of which is a
           homodimer.
          Length = 259

 Score = 67.3 bits (165), Expect = 1e-11
 Identities = 46/159 (28%), Positives = 67/159 (42%), Gaps = 25/159 (15%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           K+   Q NP  G++  N+ K             DLI+  ELF +GY      F  S  + 
Sbjct: 1   KVGYVQFNPKFGEVEKNLKKVESL---IKGVEADLIVLPELFNTGY-----AFT-SKEEV 51

Query: 66  CSSA--------IDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINL 117
            S A           L+    + GA IV G P +D +   NS V++     I +  K +L
Sbjct: 52  ASLAESIPDGPTTRFLQELARETGAYIVAGLPERDGDKFYNSAVVVGPEGYIGIYRKTHL 111

Query: 118 PNYSEFHEKRTFISGYSNDPIVFR--DIRLGILICEDIW 154
                F+E++ F         VF   DIR+G++IC D W
Sbjct: 112 -----FYEEKLFFEPGDTGFRVFDIGDIRIGVMICFD-W 144


>gnl|CDD|143605 cd07581, nitrilase_3, Uncharacterized subgroup of the nitrilase
           superfamily (putative class 13 nitrilases).  The
           nitrilase superfamily is comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13).
           Class 13 represents proteins that at the time were
           difficult to place in a distinct similarity group; this
           subgroup represents either a new class or one that was
           included previously in class 13. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer.
          Length = 255

 Score = 66.8 bits (164), Expect = 1e-11
 Identities = 45/158 (28%), Positives = 68/158 (43%), Gaps = 19/158 (12%)

Query: 7   IAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKS----- 61
           +A+AQ     GD   N+ K RR   EA   G DL++F E  ++ +      + +      
Sbjct: 1   VALAQFA-SSGDKEENLEKVRRLLAEAAAAGADLVVFPEYTMARFGDGLDDYARVAEPLD 59

Query: 62  --FIQACSSAIDTLKSDTHDGGAGIVVGFPRQDQEG-VLN-SVVILDAGNIIAVRDKINL 117
             F+ A       L     + G  +V G      +G V N  VV+   G IIAV  KI+L
Sbjct: 60  GPFVSA-------LARLARELGITVVAGMFEPAGDGRVYNTLVVVGPDGEIIAVYRKIHL 112

Query: 118 PNYSEFHEKRTFISGYSNDPIVFR--DIRLGILICEDI 153
            +   F E  T   G    P+VF    +++G+  C D+
Sbjct: 113 YDAFGFRESDTVAPGDELPPVVFVVGGVKVGLATCYDL 150


>gnl|CDD|143588 cd07564, nitrilases_CHs, Nitrilases, cyanide hydratase (CH)s, and
           similar proteins (class 1 nitrilases).  Nitrilases
           (nitrile aminohydrolases, EC:3.5.5.1) hydrolyze nitriles
           (RCN) to ammonia and the corresponding carboxylic acid.
           Most nitrilases prefer aromatic nitriles, some prefer
           arylacetonitriles and others aliphatic nitriles. This
           group includes the nitrilase cyanide dihydratase (CDH),
           which hydrolyzes inorganic cyanide (HCN) to produce
           formate. It also includes cyanide hydratase (CH), which
           hydrolyzes HCN to formamide. This group includes four
           Arabidopsis thaliana nitrilases (Ath)NIT1-4. AthNIT1-3
           have a strong substrate preference for
           phenylpropionitrile (PPN) and other nitriles which may
           originate from the breakdown of glucosinolates. The
           product of PPN hydrolysis, phenylacetic acid has auxin
           activity. AthNIT1-3 can also convert indoacetonitrile to
           indole-3-acetic acid (IAA, auxin), but with a lower
           affinity and velocity. From their expression patterns,
           it has been speculated that NIT3 may produce IAA during
           the early stages of germination, and that NIT3 may
           produce IAA during embryo development and maturation.
           AthNIT4 has a strong substrate specificity for the
           nitrile, beta-cyano-L-alanine (Ala(CN)), an intermediate
           of cyanide detoxification. AthNIT4 has both a nitrilase
           activity and a nitrile hydratase (NHase) activity, which
           generate aspartic acid and asparagine respectively from
           Ala(CN). NHase catalyzes the hydration of nitriles to
           their corresponding amides. This subgroup belongs to a
           larger nitrilase superfamily comprised of belong to a
           larger nitrilase superfamily comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13),
           this subgroup corresponds to class 1.
          Length = 297

 Score = 63.7 bits (156), Expect = 1e-10
 Identities = 44/169 (26%), Positives = 71/169 (42%), Gaps = 22/169 (13%)

Query: 5   LKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYP--------PEDL 56
           +K+A  Q  PV  D+A  + KA R  EEA   G  L++F E FI GYP         E  
Sbjct: 1   VKVAAVQAAPVFLDLAATVEKACRLIEEAAANGAQLVVFPEAFIPGYPYWIWFGAPAEGR 60

Query: 57  VFKKSFIQAC----SSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDA-GNIIAV 111
                + +         ++ L     + G  +V+G   +D   + N+ +++D  G ++  
Sbjct: 61  ELFARYYENSVEVDGPELERLAEAARENGIYVVLGVSERDGGTLYNTQLLIDPDGELLGK 120

Query: 112 RDKINLPNYSEFHEKRTFISGYSNDPIVF--RDIRLGILICEDIWKNSN 158
             K+  P +    E+  +  G  +   V      RLG LIC   W+N  
Sbjct: 121 HRKL-KPTH---AERLVWGQGDGSGLRVVDTPIGRLGALIC---WENYM 162


>gnl|CDD|36024 KOG0806, KOG0806, KOG0806, Carbon-nitrogen hydrolase [Amino acid
           transport and metabolism].
          Length = 298

 Score = 61.1 bits (148), Expect = 8e-10
 Identities = 39/170 (22%), Positives = 59/170 (34%), Gaps = 22/170 (12%)

Query: 2   LKKLKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKS 61
           L     A+  L   +  +  NI    +A +EA +QG  +I+F E  + GY      F +S
Sbjct: 11  LPNATEALVSLEEALLLMNENIDILEKAVKEAAKQGAKIIVFPEDGLYGY-----NFTES 65

Query: 62  FIQACSSAIDTLKSDTHDGGAG---------IVVGFPRQDQEG--VLNSVVILDA-GNII 109
           F        D    D    G           I+ G   ++  G  + NS       G+ +
Sbjct: 66  FYPYLEDIPDPGCRDPSRQGLSEVAERLSCYIIGGSIEEEALGDKLYNSCADSSCPGDGL 125

Query: 110 AVRDKINL-----PNYSEFHEKRTFISGYSNDPIVFRDIRLGILICEDIW 154
           A   K +L     P    + E      G     +     + GI IC DI 
Sbjct: 126 AKYRKNHLFDTDGPGVIRYRESHLLSPGDQFTVVDTSYGKFGIFICFDIR 175


>gnl|CDD|143596 cd07572, nit, Nit1, Nit 2, and related proteins, and the Nit1-like
           domain of NitFhit (class 10 nitrilases).  This subgroup
           includes mammalian Nit1 and Nit2, the Nit1-like domain
           of the invertebrate NitFhit, and various uncharacterized
           bacterial and archaeal Nit-like proteins. Nit1 and Nit2
           are candidate tumor suppressor proteins. In NitFhit, the
           Nit1-like domain is encoded as a fusion protein with the
           non-homologous tumor suppressor, fragile histidine triad
           (Fhit). Mammalian Nit1 and Fhit may affect distinct
           signal pathways, and both may participate in DNA
           damage-induced apoptosis. Nit1 is a negative regulator
           in T cells. Overexpression of Nit2 in HeLa cells leads
           to a suppression of cell growth through cell cycle
           arrest in G2. These Nit proteins and the Nit1-like
           domain of NitFhit belong to a larger nitrilase
           superfamily comprised of nitrile- or amide-hydrolyzing
           enzymes and amide-condensing enzymes, which depend on a
           Glu-Lys-Cys catalytic triad. This superfamily has been
           classified in the literature based on global and
           structure based sequence analysis into thirteen
           different enzyme classes (referred to as 1-13), this
           subgroup corresponds to class 10.
          Length = 265

 Score = 60.5 bits (148), Expect = 1e-09
 Identities = 43/179 (24%), Positives = 78/179 (43%), Gaps = 17/179 (9%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQA 65
           ++A+ Q+     D   N+A+A+   EEA  QG  L++  E F      +      +  + 
Sbjct: 1   RVALIQMT-STADKEANLARAKELIEEAAAQGAKLVVLPECFNYPGGTDAFKLALAEEEG 59

Query: 66  CSSAIDTLKSDTHDGGAGIVVG-FPRQDQEG--VLN-SVVILDAGNIIAVRDKI-----N 116
               +  L     + G  +V G  P +D +   V N S+V    G ++A   KI     +
Sbjct: 60  DGPTLQALSELAKEHGIWLVGGSIPERDDDDGKVYNTSLVFDPDGELVARYRKIHLFDVD 119

Query: 117 LPNYSEFHEKRTFISGYSNDPIVFRDI---RLGILICEDIWKNSNICKHLKKQGAEFLF 172
           +P    + E  T   G  ++ +V  D    ++G+ IC D+ +   + + L +QGA+ L 
Sbjct: 120 VPGGISYRESDTLTPG--DEVVVV-DTPFGKIGLGICYDL-RFPELARALARQGADILT 174


>gnl|CDD|31794 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
           [General function prediction only].
          Length = 269

 Score = 59.1 bits (143), Expect = 3e-09
 Identities = 24/81 (29%), Positives = 46/81 (56%), Gaps = 5/81 (6%)

Query: 283 LRDYVQKNNFHKVIIGLSGGIDSALCAAIAVDALGKENVQ-TIMLPYKYTSPQSLEDAAA 341
           L+  +++    KV++  SGG+DS+L A +A +ALG   V  T+  P  Y   + +E+A  
Sbjct: 10  LKKAIKE--KKKVVVAFSGGVDSSLLAKLAKEALGDNVVAVTVDSP--YIPRREIEEAKN 65

Query: 342 CAKALGCKYDVLPIHDLVNHF 362
            AK +G +++ + ++ +   F
Sbjct: 66  IAKEIGIRHEFIKMNRMDPEF 86


>gnl|CDD|143597 cd07573, CPA, N-carbamoylputrescine amidohydrolase (CPA) (class 11
           nitrilases).  CPA (EC 3.5.1.53, also known as
           N-carbamoylputrescine amidase and carbamoylputrescine
           hydrolase) converts N-carbamoylputrescine to putrescine,
           a step in polyamine biosynthesis in plants and bacteria.
           This subgroup includes Arabidopsis thaliana CPA, also
           known as nitrilase-like 1 (NLP1), and Pseudomonas
           aeruginosa AguB. This subgroup belongs to a larger
           nitrilase superfamily comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13),
           this subgroup corresponds to class 11. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer; P.
           aeruginosa AugB is a homohexamer, Arabidopsis thaliana
           NLP1 is a homooctomer.
          Length = 284

 Score = 53.3 bits (129), Expect = 2e-07
 Identities = 41/156 (26%), Positives = 71/156 (45%), Gaps = 7/156 (4%)

Query: 5   LKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDL---VFKKS 61
           + +A+ Q+     D   N+AKA     EA  QG  ++   ELF + Y  ++     F  +
Sbjct: 1   VTVALVQMA-CSEDPEANLAKAEELVREAAAQGAQIVCLQELFETPYFCQEEDEDYFDLA 59

Query: 62  FIQACSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVL-NSVVILDA-GNIIAVRDKINLPN 119
                       ++   + G  I V    +   G+  NS V++DA G+++ V  K+++P+
Sbjct: 60  EPPIPGPTTARFQALAKELGVVIPVSLFEKRGNGLYYNSAVVIDADGSLLGVYRKMHIPD 119

Query: 120 YSEFHEKRTFISGYSN-DPIVFRDIRLGILICEDIW 154
              ++EK  F  G +       R  R+G+LIC D W
Sbjct: 120 DPGYYEKFYFTPGDTGFKVFDTRYGRIGVLICWDQW 155


>gnl|CDD|143590 cd07566, ScNTA1_like, Saccharomyces cerevisiae N-terminal amidase
           NTA1, and related proteins (class 3 nitrilases).
           Saccharomyces cerevisiae NTA1 functions in the N-end
           rule protein degradation pathway. It specifically
           deaminates the N-terminal asparagine and glutamine
           residues of substrates of this pathway, to aspartate and
           glutamate respectively, these latter are the
           destabilizing residues. This subgroup belongs to a
           larger nitrilase superfamily comprised of nitrile- or
           amide-hydrolyzing enzymes and amide-condensing enzymes,
           which depend on a Glu-Lys-Cys catalytic triad. This
           superfamily has been classified in the literature based
           on global and structure based sequence analysis into
           thirteen different enzyme classes (referred to as 1-13),
           this subgroup corresponds to class 3.
          Length = 295

 Score = 51.6 bits (124), Expect = 7e-07
 Identities = 41/178 (23%), Positives = 70/178 (39%), Gaps = 38/178 (21%)

Query: 6   KIAIAQLNPVVGDIAGNIAKA----RRAREEANRQGMDLILFTELFISGY--------PP 53
           +IA  QLNP +G +  N+++A     + ++ A  +  D+++  EL ++GY         P
Sbjct: 1   RIACLQLNPQIGQVEENLSRAWELLDKTKKRAKLKKPDILVLPELALTGYNFHSLEHIKP 60

Query: 54  --EDLVFKKSFIQACSSAIDTLKSDTHDGGAGIVVGFPRQDQEG---VLNSVVILDA-GN 107
             E      SF  A   A    K + H     +V+G+P +  E    + NS +++D  G 
Sbjct: 61  YLEPTTSGPSFEWAREVA---KKFNCH-----VVIGYPEKVDESSPKLYNSALVVDPEGE 112

Query: 108 IIAVRDKINLPNYSE-----------FHEKRTFISGYSNDP-IVFRDIRLGILICEDI 153
           ++    K  L    E                 F      D   V   ++  I IC D+
Sbjct: 113 VVFNYRKSFLYYTDEEWGCEENPGGFQTFPLPFAKDDDFDGGSVDVTLKTSIGICMDL 170


>gnl|CDD|143603 cd07579, nitrilase_1_R2, Second nitrilase domain of an
           uncharacterized subgroup of the nitrilase superfamily
           (putative class 13 nitrilases).  Members of this
           subgroup have two nitrilase domains. This is the second
           of those two domains. The nitrilase superfamily is
           comprised of nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. This superfamily has been classified in
           the literature based on global and structure based
           sequence analysis into thirteen different enzyme classes
           (referred to as 1-13). Class 13 represents proteins that
           at the time were difficult to place in a distinct
           similarity group; this subgroup represents either a new
           class or one that was included previously in class 13.
           Members of this superfamily generally form homomeric
           complexes, the basic building block of which is a
           homodimer.
          Length = 279

 Score = 51.4 bits (123), Expect = 7e-07
 Identities = 41/151 (27%), Positives = 69/151 (45%), Gaps = 17/151 (11%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYP-PEDLVFKKSFIQ 64
           +IA+AQ  P   DIAGN+A   R   EA   G +L++F EL ++G   P       +   
Sbjct: 1   RIAVAQFAPT-PDIAGNLATIDRLAAEAKATGAELVVFPELALTGLDDPASEAESDT--- 56

Query: 65  ACSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYSEFH 124
               A+  L+         +V GF   D +G+ NS V++    ++    K +L       
Sbjct: 57  --GPAVSALRRLARRLRLYLVAGFAEADGDGLYNSAVLVGPEGLVGTYRKTHLIE----- 109

Query: 125 EKRTFISGYSNDPIVFRDI---RLGILICED 152
            +R++ +   +   V+ D+   R+G+LI  D
Sbjct: 110 PERSWATP-GDTWPVY-DLPLGRVGLLIGHD 138


>gnl|CDD|30177 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
           nucleotide alpha hydrolases superfamily. Adenine
           nucleotide alpha hydrolases superfamily  includes N type
           ATP PPases and ATP sulphurylases. It forms a
           apha/beta/apha fold which  binds to Adenosine group.
           This subfamily   of proteins probably binds ATP. This
           domain is about 200 amino acids long with a strongly
           conserved motif SGGKD at the N terminus..
          Length = 202

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 295 VIIGLSGGIDSALCAAIAVDALGKE-NVQTIMLPYKYTSPQSLEDAAACAKALGCKYDVL 353
           V +  SGG+DS L    AVDALG      T   P      + LE+A   AK +G +++V+
Sbjct: 1   VAVAFSGGVDSTLLLKAAVDALGDRVLAVTATSP--LFPRRELEEAKRLAKEIGIRHEVI 58

Query: 354 PIHDLVN 360
              +L +
Sbjct: 59  ETDELDD 65


>gnl|CDD|30948 COG0603, COG0603, Predicted PP-loop superfamily ATPase [General
           function prediction only].
          Length = 222

 Score = 45.6 bits (108), Expect = 4e-05
 Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAAACAKALGCKYDVL 353
           K ++ LSGG+DS  C A A        V  +   Y     + LE A   AK LG  + ++
Sbjct: 4   KAVVLLSGGLDSTTCLAWAKKE--GYEVHALTFDYGQRHRKELEAAKELAKKLGVPHHII 61

Query: 354 PI 355
            +
Sbjct: 62  DV 63


>gnl|CDD|143593 cd07569, DCase, N-carbamyl-D-amino acid amidohydrolase (DCase,
           class 6 nitrilases).  DCase hydrolyses
           N-carbamyl-D-amino acids to produce D-amino acids. It is
           an important biocatalyst in the pharmaceutical industry,
           producing useful D-amino acids for example in the
           preparation of beta-lactam antibiotics. This subgroup
           belongs to a larger nitrilase superfamily comprised of
           nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. This superfamily has been classified in
           the literature based on global and structure based
           sequence analysis into thirteen different enzyme classes
           (referred to as 1-13), this subgroup corresponds to
           class 6. Members of this superfamily generally form
           homomeric complexes, the basic building block of which
           is a homodimer. Agrobacterium radiobacter DCase forms a
           tetramer (dimer of dimers). Some DCases may form
           trimers.
          Length = 302

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 44/173 (25%), Positives = 72/173 (41%), Gaps = 24/173 (13%)

Query: 3   KKLKIAIAQLNPVVGDIAGNIAKARRAR--EEANRQGMDLILFTEL-----FISGYPPED 55
           +++ +A AQ+ P+          AR     EEA  +G  L++F EL     F   Y P++
Sbjct: 2   RQVILAAAQMGPIARAETRESVVARLIALLEEAASRGAQLVVFPELALTTFFPRWYFPDE 61

Query: 56  LVFKKSFIQAC-SSAIDTLKSDTHDGGAGIVVGFPRQDQEGVLN-----SVVILDAGNII 109
                 F     +     L     + G G  +G+    ++G +      S+++  +G I+
Sbjct: 62  AELDSFFETEMPNPETQPLFDRAKELGIGFYLGYAELTEDGGVKRRFNTSILVDKSGKIV 121

Query: 110 AVRDKINLPNYSEF-------H-EKRTFISGYSNDPIVFR--DIRLGILICED 152
               K++LP + E        H EKR F  G    P VFR     +G+ IC D
Sbjct: 122 GKYRKVHLPGHKEPEPYRPFQHLEKRYFEPGDLGFP-VFRVPGGIMGMCICND 173


>gnl|CDD|143602 cd07578, nitrilase_1_R1, First nitrilase domain of an
           uncharacterized subgroup of the nitrilase superfamily
           (putative class 13 nitrilases).  Members of this
           subgroup have two nitrilase domains. This is the first
           of those two domains. The nitrilase superfamily is
           comprised of nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. This superfamily has been classified in
           the literature based on global and structure based
           sequence analysis into thirteen different enzyme classes
           (referred to as 1-13). Class 13 represents proteins that
           at the time were difficult to place in a distinct
           similarity group; this subgroup represents either a new
           class or one that was included previously in class 13.
           Members of this superfamily generally form homomeric
           complexes, the basic building block of which is a
           homodimer.
          Length = 258

 Score = 45.2 bits (107), Expect = 4e-05
 Identities = 40/156 (25%), Positives = 61/156 (39%), Gaps = 14/156 (8%)

Query: 5   LKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYPPEDLVFKKSFIQ 64
            K A  Q  P +G+   NI +     EEA R G  LI+  E+  +GY   D      F++
Sbjct: 1   YKAAAIQFEPEMGEKERNIERLLALCEEAARAGARLIVTPEMATTGYCWYDRAEIAPFVE 60

Query: 65  ----ACSSAIDTLKSDTHDGGAGIVVGFPRQDQEGVL--NSVVILDAGNIIAVRDKINLP 118
                 ++    L  +       IVVG P  D    +  NS V++    +I    K    
Sbjct: 61  PIPGPTTARFAELAREHD---CYIVVGLPEVDSRSGIYYNSAVLIGPSGVIGRHRK---- 113

Query: 119 NYSEFHEKRTFISGYSNDPIVFRDI-RLGILICEDI 153
            +    E +    G     +   +I R+ +LIC DI
Sbjct: 114 THPYISEPKWAADGDLGHQVFDTEIGRIALLICMDI 149


>gnl|CDD|30178 cd01991, Asn_Synthase_B_C, The C-terminal domain of Asparagine
           Synthase B. This domain is always found associated
           n-terminal amidotransferase domain. Family members that
           contain this domain catalyse the conversion of aspartate
           to asparagine. Asparagine synthetase B  catalyzes the
           assembly of asparagine from aspartate, Mg(2+)ATP, and
           glutamine. The three-dimensional architecture of the
           N-terminal domain of asparagine synthetase B is similar
           to that observed for glutamine
           phosphoribosylpyrophosphate amidotransferase while the
           molecular motif of the C-domain is reminiscent to that
           observed for GMP synthetase ..
          Length = 269

 Score = 42.8 bits (100), Expect = 2e-04
 Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 7/99 (7%)

Query: 283 LRDYVQKNNFHKVIIG--LSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAA 340
           L D V++     V +G  LSGG+DS+L AA+A   L  E V+T  + + +      E A 
Sbjct: 4   LEDAVRRRLRSDVPVGVLLSGGLDSSLVAALA-ARLLPEPVKTFSIGFGFEGSDEREYAR 62

Query: 341 ACAKALGCKYDVLPI--HDLVNHFFSLMSQFLQEEPSGI 377
             A+ LG ++  +     DL+     ++  +  +EP   
Sbjct: 63  RVAEHLGTEHHEVEFTPADLLAALPDVI--WELDEPFAD 99


>gnl|CDD|36023 KOG0805, KOG0805, KOG0805, Carbon-nitrogen hydrolase [Amino acid
          transport and metabolism].
          Length = 337

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 4  KLKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGYP 52
           +++ I Q + V  D    + KA +   EA  +G +L+LF E FI GYP
Sbjct: 17 IVRVTIVQASTVYNDTPATLDKAEKYIVEAASKGAELVLFPEAFIGGYP 65


>gnl|CDD|30185 cd01998, tRNA_Me_trans, tRNA methyl transferase. This family
           represents
           tRNA(5-methylaminomethyl-2-thiouridine)-
           methyltransferase which is involved in the biosynthesis
           of the modified nucleoside
           5-methylaminomethyl-2-thiouridine present in the wobble
           position of some tRNAs. This family of enzyme only
           presents in bacteria and eukaryote. The  archaeal
           counterpart of this enzyme performs same function, but
           is completely unrelated in sequence..
          Length = 349

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 294 KVIIGLSGGIDSALCAAIA------VDALGKENVQTIMLPYKYTSPQSLEDAAACAKALG 347
           KV++ +SGG+DS++ AA+       V  +  +N           S + L+DA   A  LG
Sbjct: 1   KVVVAMSGGVDSSVAAALLKEQGYEVIGVFMKNWDEDDGKGGCCSEEDLKDARRVADQLG 60

Query: 348 CKYDVLPIHDLVNHFFS-LMSQFLQE 372
             + V+   +    ++  +   FL+E
Sbjct: 61  IPHYVV---NFEKEYWEKVFEPFLEE 83


>gnl|CDD|145938 pfam03054, tRNA_Me_trans, tRNA methyl transferase.  This family
           represents
           tRNA(5-methylaminomethyl-2-thiouridine)-
           methyltransferase which is involved in the biosynthesis
           of the modified nucleoside
           5-methylaminomethyl-2-thiouridine present in the wobble
           position of some tRNAs.
          Length = 354

 Score = 41.5 bits (98), Expect = 6e-04
 Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 13/88 (14%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKY--------TSPQSLEDAAACAKA 345
           KV++ +SGG+DS++ A +  +  G E +   M  +           S + L DA    + 
Sbjct: 2   KVVVAMSGGVDSSVAAYLLKEQ-GYEVIGVFMKNWDEEDEFGHGCCSEEDLADAQRVCEQ 60

Query: 346 LGCKYDVLPIHDLVNHFFSLM-SQFLQE 372
           LG    V+   +    ++  +   FL E
Sbjct: 61  LGIPLYVV---NFEKEYWEKVFEPFLDE 85


>gnl|CDD|30184 cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase.
           It contains two subdomains; the ATP pyrophosphatase
           domain which closes to the N-termial and the
           dimerization domain at C-terminal end. The ATP-PPase is
           a twisted, five-stranded parallel beta-sheet sandwiched
           between helical layers. It has a signature
           nucleotide-binding motif, or P-loop, at the end of the
           first-beta strand.The dimerization domain formed by the
           C-terminal 115 amino acid for prokaryotic proteins. It
           is adjacent to teh ATP-binding site of the ATP-PPase
           subdomain. The largest difference between the primary
           sequence of prokaryotic and eukaryotic GMP synthetase
           map to the dimerization domain.Eukaryotic GMP synthetase
           has several large insertions relative to prokaryotes..
          Length = 295

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKE 319
           KVI+ LSGG+DS + A +   A+G  
Sbjct: 1   KVILALSGGVDSTVAAVLLHKAIGDR 26


>gnl|CDD|73293 cd01995, ExsB, ExsB is a transcription regulator related protein.
           It is a subfamily of a Adenosine nucleotide binding
           superfamily of proteins. This protein family is
           represented by a single member in nearly every completed
           large (> 1000 genes) prokaryotic genome. In Rhizobium
           meliloti, a species in which the exo genes make
           succinoglycan, a symbiotically important
           exopolysaccharide, exsB is located nearby and affects
           succinoglycan levels, probably through polar effects on
           exsA expression or the same polycistronic mRNA. In
           Arthrobacter viscosus, the homologous gene is designated
           ALU1 and is associated with an aluminum tolerance
           phenotype. The function is unknown.
          Length = 169

 Score = 38.3 bits (89), Expect = 0.006
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAAACAKALG 347
           K ++ LSGG+DS  C A A    G E V  +   Y     +  E A   A+ LG
Sbjct: 1   KAVVLLSGGLDSTTCLAWAKKE-GYE-VHALSFDYGQRHAKEEEAAKLIAEKLG 52


>gnl|CDD|30865 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
           transport and metabolism].
          Length = 315

 Score = 37.8 bits (88), Expect = 0.008
 Identities = 13/25 (52%), Positives = 19/25 (76%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGK 318
           KVI+ LSGG+DS++ A +A  A+G 
Sbjct: 23  KVILALSGGVDSSVAAVLAHRAIGD 47


>gnl|CDD|30716 COG0367, AsnB, Asparagine synthase (glutamine-hydrolyzing) [Amino
           acid transport and metabolism].
          Length = 542

 Score = 36.6 bits (84), Expect = 0.021
 Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 4/84 (4%)

Query: 283 LRDYVQKNNFHKVIIG--LSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAA 340
           L D V++     V +G  LSGG+DS+L AAIA + LGKE   T  + ++ +     + A 
Sbjct: 219 LEDAVKRRLVADVPVGVFLSGGLDSSLIAAIAAEELGKEGKTTFTVGFEDSDSPDAKYAR 278

Query: 341 ACAKALGC--KYDVLPIHDLVNHF 362
           A AK LG      +L   +L+N  
Sbjct: 279 AVAKFLGTPHHEIILTNEELLNAL 302


>gnl|CDD|143598 cd07574, nitrilase_Rim1_like, Uncharacterized subgroup of the
           nitrilase superfamily; some members of this subgroup
           have an N-terminal RimI domain (class 12 nitrilases).
           Some members of this subgroup are implicated in
           post-translational modification, as they contain an
           N-terminal GCN5-related N-acetyltransferase (GNAT)
           protein RimI family domain. The nitrilase superfamily is
           comprised of nitrile- or amide-hydrolyzing enzymes and
           amide-condensing enzymes, which depend on a Glu-Lys-Cys
           catalytic triad. This superfamily has been classified in
           the literature based on global and structure based
           sequence analysis into thirteen different enzyme classes
           (referred to as 1-13), this subgroup corresponds to
           class 12. Members of this superfamily generally form
           homomeric complexes, the basic building block of which
           is a homodimer.
          Length = 280

 Score = 36.4 bits (85), Expect = 0.022
 Identities = 47/198 (23%), Positives = 77/198 (38%), Gaps = 32/198 (16%)

Query: 5   LKIAIAQLNPV--VGDIAGNIAKARRAREEANRQGMDLILFTELF---ISGYPPEDLVFK 59
           +++A AQ  P+          AK      EA   G DL++F E F   +    PE +   
Sbjct: 1   VRVAAAQY-PLRRYASFEEFAAKVEYWVAEAAGYGADLLVFPEYFTMELLSLLPEAIDGL 59

Query: 60  KSFIQACSSAIDTLKSDTHDG--------GAGIVVG-FPRQDQEGVLNSVVILDAGNIIA 110
              I+    A+  L  D            G  I+ G  P ++   + N   +      I 
Sbjct: 60  DEAIR----ALAALTPDYVALFSELARKYGINIIAGSMPVREDGRLYNRAYLFGPDGTIG 115

Query: 111 VRDKINL-PNYSEFHEKRTFISGYSNDPIVFRDI---RLGILICEDIWKNSNICKHLKKQ 166
            +DK+++ P    F  +   ISG  +   VF D    ++GILIC D  +   + + L + 
Sbjct: 116 HQDKLHMTP----FEREEWGISG-GDKLKVF-DTDLGKIGILICYDS-EFPELARALAEA 168

Query: 167 GAEFLF--SLNASPYYHN 182
           GA+ L   S   +   + 
Sbjct: 169 GADLLLVPSCTDTRAGYW 186


>gnl|CDD|30830 COG0482, TrmU, Predicted tRNA(5-methylaminomethyl-2-thiouridylate)
           methyltransferase, contains the PP-loop ATPase domain
           [Translation, ribosomal structure and biogenesis].
          Length = 356

 Score = 36.0 bits (83), Expect = 0.027
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 13/69 (18%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKY---------TSPQSLEDAAACAK 344
           KV++G+SGG+DS++ A +    L ++  + I L  K           S + L DA   A 
Sbjct: 5   KVLVGMSGGVDSSVAAYL----LKEQGYEVIGLFMKNWDEDGGGGCCSEEDLRDAERVAD 60

Query: 345 ALGCKYDVL 353
            LG    V+
Sbjct: 61  QLGIPLYVV 69


>gnl|CDD|143592 cd07568, ML_beta-AS_like, mammalian-like beta-alanine synthase
           (beta-AS) and similar proteins (class 5 nitrilases).
           This family includes mammalian-like beta-AS (EC 3.5.1.6,
           also known as beta-ureidopropionase or
           N-carbamoyl-beta-alanine amidohydrolase). This enzyme
           catalyzes the third and final step in the catabolic
           pyrimidine catabolic pathway responsible for the
           degradation of uracil and thymine, the hydrolysis of
           N-carbamyl-beta-alanine and
           N-carbamyl-beta-aminoisobutyrate to the beta-amino
           acids, beta-alanine and beta-aminoisobutyrate
           respectively. This family belongs to a larger nitrilase
           superfamily comprised of nitrile- or amide-hydrolyzing
           enzymes and amide-condensing enzymes, which depend on a
           Glu-Lys-Cys catalytic triad. This superfamily has been
           classified in the literature based on global and
           structure based sequence analysis into thirteen
           different enzyme classes (referred to as 1-13), this
           subgroup corresponds to class 5. Members of this
           superfamily generally form homomeric complexes, the
           basic building block of which is a homodimer. Beta-ASs
           from this subgroup are found in various oligomeric
           states, dimer (human), hexamer (calf liver), decamer
           (Arabidopsis and Zea mays), and in the case of
           Drosophila melanogaster beta-AS, as a homooctamer
           assembled as a left-handed helical turn, with the
           possibility of higher order oligomers formed by adding
           dimers at either end. Rat beta-AS changes its oligomeric
           state (hexamer, trimer, dodecamer) in response to
           allosteric effectors. Eukaryotic Saccharomyces kluyveri
           beta-AS belongs to a different superfamily.
          Length = 287

 Score = 35.5 bits (82), Expect = 0.036
 Identities = 32/154 (20%), Positives = 58/154 (37%), Gaps = 8/154 (5%)

Query: 6   KIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGY--PPEDLVFKKSFI 63
              I    P+       I K      EA   G  ++   E+F   Y    +D  + +   
Sbjct: 12  SNVIPTDAPIEKQKEAMIQKHVTMIREAAEAGAQIVCLQEIFYGPYFCAEQDTKWYEFAE 71

Query: 64  QACSSAIDTLKSD-THDGGAGIVVGFPRQDQEGVL-NSVVILDA-GNIIAVRDKINLPNY 120
           +  +       +    +    +++    ++Q G L N+  ++DA G  +    K ++P+ 
Sbjct: 72  EIPNGPTTKRFAALAKEYNMVLILPIYEKEQGGTLYNTAAVIDADGTYLGKYRKNHIPHV 131

Query: 121 SEFHEKRTFISGYSNDPIVF--RDIRLGILICED 152
             F EK  F  G    P VF     ++G+ IC D
Sbjct: 132 GGFWEKFYFRPGNLGYP-VFDTAFGKIGVYICYD 164


>gnl|CDD|30386 COG0037, MesJ, Predicted ATPase of the PP-loop superfamily
           implicated in cell cycle control [Cell division and
           chromosome partitioning].
          Length = 298

 Score = 34.8 bits (79), Expect = 0.058
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSP--QSLEDAAACAKALGCKYD 351
           K+++ +SGG DS     +  +   +  V+ + + +       Q  E      + LG    
Sbjct: 23  KILVAVSGGKDSLALLHLLKELGRRIEVEAVHVDHGLRGYSDQEAELVEKLCEKLGIPLI 82

Query: 352 V 352
           V
Sbjct: 83  V 83


>gnl|CDD|144363 pfam00733, Asn_synthase, Asparagine synthase.  This family is
           always found associated with pfam00310. Members of this
           family catalyse the conversion of aspartate to
           asparagine.
          Length = 195

 Score = 34.5 bits (80), Expect = 0.077
 Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAAACAKALGCK--YD 351
            V + LSGG+DS+L AA+A        ++T  + ++ +       A   A  LG      
Sbjct: 19  PVGVLLSGGLDSSLIAALA-ARQSSPPLKTFSVGFEGSDYDEAPYAELVADHLGTDHHEI 77

Query: 352 VLPIHDLVNHFFSLMSQFLQEEPSGI 377
           ++   +L++    ++     EEP G 
Sbjct: 78  IVTEEELLDALPEVIYHL--EEPFGD 101


>gnl|CDD|36835 KOG1622, KOG1622, KOG1622, GMP synthase [Nucleotide transport and
           metabolism].
          Length = 552

 Score = 34.2 bits (78), Expect = 0.10
 Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 11/129 (8%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAAACAKALGCKYDVL 353
           KV++ +SGG+DS +CAA+   ALG + V  I +   +      ++A    K L   Y  +
Sbjct: 232 KVLVAVSGGVDSTVCAALLRRALGPDRVHAIHVDNGF---MRKKEAEQVEKTL--VYLGI 286

Query: 354 PIHDLVNHFFSLMSQFLQEEPSGIVAENIQSRIRGNILMALSNHSKAMLLTTSNKSEISV 413
           PI             FL  +  G+     + +I G   + + +   + L     + E  +
Sbjct: 287 PI-----TVVDASETFLS-KLKGVTDPEEKRKIIGRTFIKVFDPVASELNKKHGEKESFL 340

Query: 414 GYGTLYGDM 422
             GTL  D+
Sbjct: 341 AQGTLRPDL 349


>gnl|CDD|35791 KOG0571, KOG0571, KOG0571, Asparagine synthase
           (glutamine-hydrolyzing) [Amino acid transport and
           metabolism].
          Length = 543

 Score = 32.6 bits (74), Expect = 0.28
 Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 8/86 (9%)

Query: 275 DYNACVLSLRDYVQKNNFHKVIIG--LSGGIDSALCAAIAVDALGKENVQTIMLPYKYT- 331
           DY A   +L   V+K     V  G  LSGG+DS+L A+IA   L K         + +  
Sbjct: 206 DYLALRHTLEKAVRKRLMTDVPFGVLLSGGLDSSLVASIAARELKKAQAARGSKLHSFAI 265

Query: 332 ----SPQSLEDAAACAKALGCKYDVL 353
               SP  L  A   A  +G  +   
Sbjct: 266 GLEDSP-DLLAARKVADFIGTIHHEH 290


>gnl|CDD|30179 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
           PP-loop faimly implicated in cell cycle control [Cell
           division and chromosome partitioning]. This is a
           subfamily of Adenine nucleotide alpha hydrolases
           superfamily.Adeninosine nucleotide alpha hydrolases
           superfamily  includes N type ATP PPases and ATP
           sulphurylases. It forms a apha/beta/apha fold which
           binds to Adenosine group.  This domain has  a strongly
           conserved motif SGGXD at the N terminus..
          Length = 185

 Score = 31.4 bits (71), Expect = 0.63
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 294 KVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKY-TSPQSLEDAAACAKALGCKYDV 352
           K+++ +SGG DS     +  +   +  ++ + +   +   P+S E+AA  A    C    
Sbjct: 1   KILVAVSGGPDSMALLHLLSELKPRLGLRLVAVHVDHGLRPESDEEAAFVADL--CAKLG 58

Query: 353 LPIHDLVNHF 362
           +P++ LV   
Sbjct: 59  IPLYILVVAL 68


>gnl|CDD|73292 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
           superfamily  including N type ATP PPases and ATP
           sulphurylases. The domain forms a apha/beta/apha fold
           which  binds to Adenosine group...
          Length = 103

 Score = 31.3 bits (70), Expect = 0.65
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 8/66 (12%)

Query: 295 VIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDA--------AACAKAL 346
           V++  SGG DS++ AA+      +    T+          + E A           AK  
Sbjct: 1   VLVAFSGGKDSSVAAALLKKLGYQVIAVTVDHGISPRLEDAKEIAKEAREEAAKRIAKEK 60

Query: 347 GCKYDV 352
           G +   
Sbjct: 61  GAETIA 66


>gnl|CDD|30183 cd01996, Alpha_ANH_like_III, This is a subfamily of Adenine
           nucleotide alpha hydrolases superfamily.Adeninosine
           nucleotide alpha hydrolases superfamily  includes N type
           ATP PPases and ATP sulphurylases. It forms a
           apha/beta/apha fold which  binds to Adenosine group.
           This subfamily   of proteins is predicted to  bind ATP.
           This domain has  a strongly conserved motif SGGKD at the
           N terminus..
          Length = 154

 Score = 29.5 bits (66), Expect = 2.4
 Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 295 VIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDA 339
            IIG+SGG DS+    +  +  G  N   + +   + S +++++ 
Sbjct: 4   CIIGVSGGKDSSYALYLLKEKYGL-NPLAVTVDNGFNSEEAVKNI 47


>gnl|CDD|36026 KOG0808, KOG0808, KOG0808, Carbon-nitrogen hydrolase [Amino acid
           transport and metabolism].
          Length = 387

 Score = 29.2 bits (65), Expect = 3.2
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 99  SVVILDAGNIIAVRDKINLPNYSEFHEKRTFISGYSNDPIVFRDI--RLGILIC 150
           +VVI + GN+I    K ++P   +F+E   ++ G    P VF  +  R+ + IC
Sbjct: 183 AVVISNNGNVIGKHRKNHIPRVGDFNESTYYMEGDLGHP-VFETVFGRIAVNIC 235


>gnl|CDD|33098 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
           production and conversion].
          Length = 356

 Score = 28.8 bits (64), Expect = 4.0
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 81  GAGIVVGFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYSEFHEKRT------FISGYS 134
           GAG+   FP         ++   DA     +  K+  P+ +E    +       F++ Y 
Sbjct: 37  GAGLRASFPDAAYVAAGATIGAADAVWQADIILKVRAPSAAEIALLKEGATLVSFLNPYQ 96

Query: 135 NDPIVFRDIRLGI 147
           ND +VF      +
Sbjct: 97  NDELVFALAIFVL 109


>gnl|CDD|143599 cd07575, Xc-1258_like, Xanthomonas campestris XC1258 and related
          proteins, members of the nitrilase superfamily
          (putative class 13 nitrilases).  Uncharacterized
          subgroup belonging to a larger nitrilase superfamily
          comprised of nitrile- or amide-hydrolyzing enzymes and
          amide-condensing enzymes, which depend on a Glu-Lys-Cys
          catalytic triad. This superfamily has been classified
          in the literature based on global and structure based
          sequence analysis into thirteen different enzyme
          classes (referred to as 1-13), class 13 represents
          proteins that at the time were difficult to place in a
          distinct similarity group; this subgroup either
          represents a new class or one that was included
          previously in class 13. Members of this superfamily
          generally form homomeric complexes, the basic building
          block of which is a homodimer. XC1258 is a
          homotetramer.
          Length = 252

 Score = 28.7 bits (65), Expect = 4.8
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 5  LKIAIAQLNPVVGDIAGNIAKARRAREEANRQGMDLILFTELFISGY 51
          LKIA+ Q + V  D   N+A      E+  ++  DLI+  E+F +G+
Sbjct: 1  LKIALIQTDLVWEDPEANLAHFEEKIEQL-KEKTDLIVLPEMFTTGF 46


>gnl|CDD|30168 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
           phosphosulphate (PAPS) reductase enzymes or PAPS
           sulphotransferase. PAPS reductase is part of the adenine
           nucleotide alpha hydrolases superfamily also including N
           type ATP PPases and ATP sulphurylases. A highly modified
           version of the P loop, the fingerprint peptide of
           mononucleotide-binding proteins, is present in the
           active site of the protein, which appears to be a
           positively charged cleft containing a number of
           conserved arginine and lysine residues. Although PAPS
           reductase has no ATPase activity, it shows a striking
           similarity to the structure of the ATP pyrophosphatase
           (ATP PPase) domain of GMP synthetase, indicating that
           both enzyme families have evolved from a common
           ancestral nucleotide-binding fold.   The enzyme uses
           thioredoxin as an electron donor for the reduction of
           PAPS to phospho-adenosine-phosphate (PAP) . It is also
           found in NodP nodulation protein P from Rhizobium
           meliloti which has ATP sulphurylase activity (sulphate
           adenylate transferase) ..
          Length = 173

 Score = 28.5 bits (63), Expect = 5.6
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 294 KVIIGLSGGIDSALCAAIAVDAL-GKENVQTIMLPYKYTSPQSLEDAAACAKALGCKYDV 352
            V++  SGG DS +   +A+ AL   + V  I L   Y  P++ E     A+  G    V
Sbjct: 1   NVVVSFSGGKDSTVLLHLALKALPELKPVPVIFLDTGYEFPETYEFVDRVAERYGLPLVV 60

Query: 353 L 353
           +
Sbjct: 61  V 61


>gnl|CDD|38016 KOG2805, KOG2805, KOG2805, tRNA
           (5-methylaminomethyl-2-thiouridylate)-methyltransferase
           [Translation, ribosomal structure and biogenesis].
          Length = 377

 Score = 28.4 bits (63), Expect = 6.0
 Identities = 7/20 (35%), Positives = 15/20 (75%)

Query: 292 FHKVIIGLSGGIDSALCAAI 311
             +V++ +SGG+DS++ A +
Sbjct: 5   PDRVVVAMSGGVDSSVAARL 24


>gnl|CDD|37406 KOG2195, KOG2195, KOG2195, Transferrin receptor and related
           proteins containing the protease-associated (PA) domain
           [Posttranslational modification, protein turnover,
           chaperones, Inorganic ion transport and metabolism,
           General function prediction only].
          Length = 702

 Score = 28.1 bits (62), Expect = 6.2
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 8/67 (11%)

Query: 487 PILDDIIKRIVENEESFINNDQEYNDETVRYVEHLLYGSEYKRRQAPVGTKITAKSFGRD 546
           P+L D+I+   ++  S    DQ         V  L  GS+Y       G  I +  F  +
Sbjct: 451 PLLTDLIEEAAKSVLSPDKGDQS------NRVLSLGGGSDYASFLQFAG--IPSVDFAFN 502

Query: 547 RLYPISN 553
           R YP  +
Sbjct: 503 RTYPFYH 509


>gnl|CDD|33750 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate
           sulfotransferase [General function prediction only].
          Length = 407

 Score = 28.0 bits (62), Expect = 7.7
 Identities = 13/65 (20%), Positives = 23/65 (35%)

Query: 290 NNFHKVIIGLSGGIDSALCAAIAVDALGKENVQTIMLPYKYTSPQSLEDAAACAKALGCK 349
           N F +V +  SGG DS L   +  +   +     I + +     Q         +     
Sbjct: 25  NTFPRVCVSFSGGKDSGLMLHLVAEVARENGRDKISVLFIDWEAQYSCTIDYVQEMRESY 84

Query: 350 YDVLP 354
           +DV+ 
Sbjct: 85  HDVIE 89


>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
           only].
          Length = 346

 Score = 27.9 bits (62), Expect = 8.1
 Identities = 10/63 (15%), Positives = 25/63 (39%)

Query: 87  GFPRQDQEGVLNSVVILDAGNIIAVRDKINLPNYSEFHEKRTFISGYSNDPIVFRDIRLG 146
           G+  ++Q  +L  +  L    I+ V +KI++ +  +  E    +     +  +      G
Sbjct: 262 GYSLEEQISLLEEIKELFKAPIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKG 321

Query: 147 ILI 149
             +
Sbjct: 322 CGL 324


>gnl|CDD|37983 KOG2772, KOG2772, KOG2772, Transaldolase [Carbohydrate transport
           and metabolism].
          Length = 337

 Score = 27.6 bits (61), Expect = 8.4
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 433 YKTQVFQLASWRNSHGITSGLGPLTEVIPPSILEKSPSAELRPHQTDQESLPPYPILDDI 492
           YKT V   AS+RN+  I +  G     I P++L +  ++         E    +  L D+
Sbjct: 230 YKTLVMA-ASFRNTGEIKNLAGVDYLTISPALLPQLVNS---TEDQPLELSASHAKLKDL 285

Query: 493 IKRIVENEESF---INNDQ 508
            K    +EE F   +N D 
Sbjct: 286 EKVSYSDEEGFRWDLNEDA 304


>gnl|CDD|36185 KOG0967, KOG0967, KOG0967, ATP-dependent DNA ligase I [Replication,
           recombination and repair].
          Length = 714

 Score = 27.6 bits (61), Expect = 8.6
 Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 3/35 (8%)

Query: 233 MKHFSEQNFMTEWHYDQQLSQWNYMSDDSASTMYI 267
           ++ F ++ F  E+ YD + +Q + + D    T+ I
Sbjct: 359 LERFQDKAFTCEYKYDGERAQIHKLED---GTVEI 390


>gnl|CDD|176269 cd08044, TAF5_NTD2, TAF5_NTD2 is the second conserved N-terminal
           region of TATA Binding Protein (TBP) Associated Factor 5
           (TAF5), involved in forming Transcription Factor IID
           (TFIID).  The TATA Binding Protein (TBP) Associated
           Factor 5 (TAF5) is one of several TAFs that bind TBP and
           are involved in forming Transcription Factor IID (TFIID)
           complex. TAF5 contains three domains, two conserved
           sequence motifs at the N-terminal and one at the
           C-terminal region. TFIID is one of seven General
           Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
           TFIIF, and TFIID) involved in accurate initiation of
           transcription by RNA polymerase II in eukaryotes. TFIID
           plays an important role in the recognition of promoter
           DNA and assembly of the preinitiation complex. TFIID
           complex is composed of the TBP and at least 13 TAFs.  In
           yeast and human cells, TAFs have been found as
           components of other complexes besides TFIID. TAF5 may
           play a major role in forming TFIID and its related
           complexes. TAFs from various species were originally
           named by their predicted molecular weight or their
           electrophoretic mobility in polyacrylamide gels. A new,
           unified nomenclature for the pol II TAFs has been
           suggested to show the relationship between TAF orthologs
           and paralogs. TAF5 has a paralog gene (TAF5L) which has
           a redundant function. Several hypotheses are proposed
           for TAFs functions such as serving as activator-binding
           sites, core-promoter recognition or a role in essential
           catalytic activity. C-terminus of TAF5 contains six WD40
           repeats that likely form a closed beta propeller
           structure and may be involved in protein-protein
           interaction. The first part of the TAF5 N-terminal
           (TAF5_NTD1) homodimerizes in the absence of other TAFs.
           The second conserved N-terminal part of TAF5 (TAF5_NTD2)
           has an alpha-helical domain. One study has shown that
           TAF5_NTD2 homodimerizes only at high concentration of
           calcium but not any other metals. No dimerization was
           observed in other structural studies of TAF_NTD2.
           Several TAFs interact via histone-fold (HFD) motifs; HFD
           is the interaction motif involved in heterodimerization
           of the core histones and their assembly into nucleosome
           octamer. However, TAF5 does not have a HFD motif.
          Length = 133

 Score = 27.5 bits (62), Expect = 9.7
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 8/62 (12%)

Query: 331 TSPQSLEDAAACAKALGCKYDVLPIHDLVNHFFSLMSQFLQEEPSG----IVAENIQSRI 386
           T+P+ L++          KY +     +    +SL+ +FL+         I+ E+I   +
Sbjct: 76  TTPEHLKENELAKLFRSNKYVI----RMSRDAYSLLLRFLESWGGSLLLKILNEHIDIDV 131

Query: 387 RG 388
           R 
Sbjct: 132 RD 133


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.319    0.136    0.398 

Gapped
Lambda     K      H
   0.267   0.0762    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,926,320
Number of extensions: 379631
Number of successful extensions: 956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 911
Number of HSP's successfully gapped: 59
Length of query: 562
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 463
Effective length of database: 4,124,446
Effective search space: 1909618498
Effective search space used: 1909618498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)