RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781102|ref|YP_003065515.1|
UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase
[Candidatus Liberibacter asiaticus str. psy62]
         (497 letters)



>gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
           envelope biogenesis, outer membrane].
          Length = 475

 Score =  379 bits (974), Expect = e-105
 Identities = 188/472 (39%), Positives = 253/472 (53%), Gaps = 19/472 (4%)

Query: 32  EVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRSNTP 91
            ++ DSR ++ G +FVA  G K DGH FI  AIA GA A+VV     L +      +  P
Sbjct: 12  GLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDIKLAE------AGVP 65

Query: 92  ILVVDNTRKFLSLFASRLYGK--HPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGP 149
           ++VV  T   L+  A   YG       ++ VTGT+GK++  S + QI ++ G  +  IG 
Sbjct: 66  VIVVTGTNGKLTTLALAFYGLPSGKLKVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGT 125

Query: 150 TSTISSFAQDN--RLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIAG 207
                S        LTTP  + L   L  L  +G     +E SSHGL Q R++G+    G
Sbjct: 126 EGDELSPGILEPTGLTTPEALDLQNLLRDLLDRGAEIAVMEVSSHGLVQGRVEGVTFDVG 185

Query: 208 SFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRV 267
            FTNL RDH+DYH T + Y  AK  LFE  LP    A+I  DD +  +  +R  NA    
Sbjct: 186 VFTNLSRDHLDYHGTMEYYGAAKAVLFE-SLPHSGEAVINPDDGHGLDYKERLKNALGDY 244

Query: 268 LSVGYQGKFIHLKK--VCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAI 325
           ++ G   K   L    +    +         G   ++  PLPG F VYNAL A    +A+
Sbjct: 245 ITYGCDFKRPDLDYRGIEESSSGSDFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALAL 304

Query: 326 GIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGRII 385
           G+D   +L  LE L  VPGR E V  N  G  + VDYAH  + LE  L+ +R   +GR+I
Sbjct: 305 GVDLEDILAGLETLKPVPGRMELV--NIGGKLVIVDYAHNPDGLEKALRAVRLHAAGRLI 362

Query: 386 VVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSEDPEKIRAEIIHGIPG---FIEK 442
           VVFGCGGDRD+ KRP MG IA  LADI IVT DNPRSEDP  I A+I+ GI     +   
Sbjct: 363 VVFGCGGDRDKSKRPDMGAIAEQLADIVIVTSDNPRSEDPAVILADILAGIEAPEKYEII 422

Query: 443 GNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNGEKKMSVDCDIIREILG 494
            +R EAIR A+++  + DV+++AGKGHET  I+    K+   D +++RE L 
Sbjct: 423 EDREEAIRKALDLAKEGDVVLIAGKGHETYQIML-ELKRPFDDREVVREALL 473


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

 Score =  140 bits (354), Expect = 8e-34
 Identities = 92/366 (25%), Positives = 157/366 (42%), Gaps = 27/366 (7%)

Query: 27  ERKINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATI 86
              ++ VS DSR ++ G +FVA+ G + DGH FI QA+A GA A++V+            
Sbjct: 21  PVVVSGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAAGAAAVLVARPV------LPP 74

Query: 87  RSNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQ 146
                +L+V +T + L   A     K    ++A+TG++GK++    +  I    G     
Sbjct: 75  AIPLVVLLVLDTLEALGKLAKAYRQKFNAKVIAITGSNGKTTTKEMLAAILSTKGKVH-- 132

Query: 147 IGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVTHVSVEASSHGLDQHRLDGIKLIA 206
               +T  +F   N +  P  +     L   +      + +  +  G      +  +   
Sbjct: 133 ----ATPGNFN--NEIGLPLTL-----LRLPADTEYAVLEMGMNHPGEIAELSEIARPDI 181

Query: 207 GSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCR 266
              TN+G  H++   +++    AK  +    L  E  AI+ AD+   K    +  NA  +
Sbjct: 182 AVITNIGEAHLEGFGSREGIAEAKAEILAG-LRPEGIAILNADNPLLKNWAAKIGNA--K 238

Query: 267 VLSVG-YQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAI 325
           VLS G   G       +         T+ +EG + +F  PLPG   V NAL AA L + +
Sbjct: 239 VLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALALEL 298

Query: 326 GIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSN--SLEMILKNIRTITSGR 383
           G+D   +   L++L  V GR E +      G+  +D ++ +N  S+   L  +  +   +
Sbjct: 299 GLDLEEIAAGLKELKPVKGRLEVILL--ANGKTLIDDSYNANPDSMRAALDLLAALPGRK 356

Query: 384 IIVVFG 389
            I V G
Sbjct: 357 GIAVLG 362


>gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
           envelope biogenesis, outer membrane].
          Length = 448

 Score =  117 bits (294), Expect = 9e-27
 Identities = 90/367 (24%), Positives = 148/367 (40%), Gaps = 49/367 (13%)

Query: 102 LSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNR 161
           + LF  RL G+ P  I+A+TGT+GK++  S +  + + +GL +   G             
Sbjct: 100 IELFY-RLSGEAP--IVAITGTNGKTTTTSLIAHLLKAAGLDALLGG------------N 144

Query: 162 LTTPSPIYLAKALSYLSSQ-GVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYH 220
           + TP       AL  L          +E SS  L       ++       N+  DH+D H
Sbjct: 145 IGTP-------ALELLEQAEPADVYVLELSSFQL--ETTSSLRPEIAVILNISEDHLDRH 195

Query: 221 QTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLK 280
            + + Y  AK+R+ E    +   A+I ADDAY K +   A  A     S G         
Sbjct: 196 GSMENYAAAKLRILEG---QTEVAVINADDAYLKTLADEATKARVIWFSFGEPLADGDYI 252

Query: 281 KVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLH 340
               +  K +  +  +         LPG   + NAL A  L  A+G+    +LE L    
Sbjct: 253 YDGKLVFKGEKLLPAD------ELKLPGAHNLENALAALALARALGVPPEAILEALSSFT 306

Query: 341 VVPGRFEFVGTNSRGGRIYVDYAHTSN--SLEMILKNIRTITSGRIIVVFGCGGDRDQGK 398
            +P R EFVG     G ++++ +  +N  +    L        G +I++   GGD     
Sbjct: 307 GLPHRLEFVGEK--DGVLFINDSKATNVDATLAALSGFD----GPVILI--AGGDDKGAD 358

Query: 399 RPIMGKIALDLADIAIVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNK 458
              + +I   +    ++       ED EKI A +    P  +      EA++ A E+   
Sbjct: 359 FSPLAEILAKVIKKLVL-----IGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQP 413

Query: 459 QDVLVVA 465
            DV++++
Sbjct: 414 GDVVLLS 420


>gnl|CDD|31116 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
           biogenesis, outer membrane].
          Length = 459

 Score =  106 bits (265), Expect = 2e-23
 Identities = 93/421 (22%), Positives = 161/421 (38%), Gaps = 61/421 (14%)

Query: 67  GAEAIVVSSAYS--LQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVTGTS 124
            A+ +VVS+A      +  A +    P++          + A  +  +     +AV GT 
Sbjct: 66  DADVVVVSNAIKEDNPEIVAALERGIPVI------SRAEMLAELMRFRT---SIAVAGTH 116

Query: 125 GKSSVASFVQQICQRSGLS-SFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLSSQGVT 183
           GK++  S +  + + +GL  +F IG    + +F  + RL +    ++A+A          
Sbjct: 117 GKTTTTSMLAWVLEAAGLDPTFLIG--GILKNFGTNARLGS-GDYFVAEA---------- 163

Query: 184 HVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEELLPKESP 243
               E+ S  L  +    I       TN+  DH+DY+   +A   A    F   +P    
Sbjct: 164 ---DESDSSFLHYNPRVAI------VTNIEFDHLDYYGDLEAIKQA-FHHFVRNVPFYGR 213

Query: 244 AIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKF-IHLKKVCAIHNKQQVTISVEGKD-FD 301
           A++  DD   +E++ R       V++ G+  +     + +    +     +   G++  +
Sbjct: 214 AVVCGDDPNLRELLSRGCW--SPVVTYGFDDEADWRAENIRQDGSGTTFDVLFRGEELGE 271

Query: 302 FLFPLPGEFQVYNALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVD 361
              PLPG   V NAL A  +   +GID   + E L     V  RFE  G    G  +  D
Sbjct: 272 VKLPLPGRHNVLNALAAIAVARELGIDPEAIAEALASFQGVKRRFELKGE-VNGVTVIDD 330

Query: 362 YAHTSNSLEMILKNIRTIT--SGRIIVVFGCGGDRDQGKRPIMGK-------IALDLADI 412
           YAH    ++  L   R       RI+ VF       Q  R    +        AL  AD 
Sbjct: 331 YAHHPTEIKATLAAARQKVPGGKRIVAVF-------QPHRYSRTRDLLDDFAKALSDADE 383

Query: 413 AIVTDDNPRSEDPEKIRAEIIH-----GIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGK 467
            I+ D     E+P +              PG ++  +  + +    ++    DV++  G 
Sbjct: 384 VILLDVYAAGEEPIEGDVSSEDLAEKIRQPGHVDVPDLDDLVELLAKVAQPGDVILFMGA 443

Query: 468 G 468
           G
Sbjct: 444 G 444


>gnl|CDD|145824 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase
           domain.  This family contains a number of related ligase
           enzymes which have EC numbers 6.3.2.*. This family
           includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC,
           MurD, Mure and MurF catalyse consecutive steps in the
           synthesis of peptidoglycan. Peptidoglycan consists of a
           sheet of two sugar derivatives, with one of these
           N-acetylmuramic acid attaching to a small pentapeptide.
           The pentapeptide is is made of L-alanine, D-glutamic
           acid, Meso-diaminopimelic acid and D-alanyl alanine. The
           peptide moiety is synthesized by successively adding
           these amino acids to UDP-N-acetylmuramic acid. MurC
           transfers the L-alanine, MurD transfers the D-glutamate,
           MurE transfers the diaminopimelic acid, and MurF
           transfers the D-alanyl alanine. This family also
           includes Folylpolyglutamate synthase that transfers
           glutamate to folylpolyglutamate.
          Length = 87

 Score = 93.2 bits (232), Expect = 1e-19
 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 1/88 (1%)

Query: 342 VPGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGRIIVVFGCGGDRDQGKRPI 401
           VPGR E VG N  G  +  DYAH  ++LE  L+ ++ +  GR+I+VFG GGDRD     +
Sbjct: 1   VPGRLEVVGEN-NGVLVIDDYAHNPDALEAALQALKELFDGRLILVFGAGGDRDAEFHAL 59

Query: 402 MGKIALDLADIAIVTDDNPRSEDPEKIR 429
           +G +A  LAD+ I+T D PR+E+P    
Sbjct: 60  LGALAAALADVVILTGDYPRAEEPGAAI 87


>gnl|CDD|30633 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism].
          Length = 427

 Score = 88.4 bits (219), Expect = 4e-18
 Identities = 87/403 (21%), Positives = 149/403 (36%), Gaps = 67/403 (16%)

Query: 105 FASRLYGKHPE-NILAVTGTSGKSSVASFVQQICQRSG----------LSSF-------- 145
              RL        ++ V GT+GK S  +F++ I + +G          L SF        
Sbjct: 33  LLERLGNPQKSPPVIHVAGTNGKGSTCAFLESILREAGYKVGVYTSPHLLSFNERIRING 92

Query: 146 -QIGPTSTISSFAQ----DNRLTTPSPIYL----AKALSYLSSQGVTHVSVEASSHGLDQ 196
             I      ++F +       L   S  Y     A A  Y +   V    +E    G   
Sbjct: 93  EPISDEELAAAFERVEEAAGSLDLISLTYFEVLTAMAFLYFAEAKVDVAILEVGLGG--- 149

Query: 197 HRLDGIKLIAGS---FTNLGRDHIDY---HQTQQAYFNAKMRLFEELLPKESPAIIYA-- 248
            RLD   +I       T++G DH  +        A   A       ++    PA+I    
Sbjct: 150 -RLDATNVIEPDVSVITSIGLDHTAFLGDTLESIAREKAG------IIKAGKPAVIGEQQ 202

Query: 249 DDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPG 308
                  + +RA   G  +  +G   +         +      +    G   D   PL G
Sbjct: 203 PPEALNVIAERAEELGAPLFVLGPDFQ--------VLEEGNGFSFQGGGGLLDLPLPLLG 254

Query: 309 E-FQVYNALVAAGLCIAIG--IDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHT 365
              Q+ NA +A     A+G  I    + + L  +   PGR E +   S    I +D AH 
Sbjct: 255 GHHQIENAALAIAALEALGKEISEEAIRKGLANVD-WPGRLERL---SENPLILLDGAHN 310

Query: 366 SNSLEMILKNIRTI--TSGRIIVVFGCGGDRDQGKRPIMGKIALDLADIAIVTDDNPRSE 423
            ++   + + ++T+     R+ +VFG   D+D     ++  +   + +I       PR+ 
Sbjct: 311 PHAARALAETLKTLFNDRPRLTLVFGMLKDKDIA--GMLAALLPIVDEIYTTPLPWPRAL 368

Query: 424 DPEKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAG 466
           D E++ A    G  G +E  +  EA+  A+E  ++ D+++V G
Sbjct: 369 DAEELLA--FAGERGGVELDDVAEALELALEKADEDDLVLVTG 409


>gnl|CDD|144716 pfam01225, Mur_ligase, Mur ligase family, catalytic domain.  This
           family contains a number of related ligase enzymes which
           have EC numbers 6.3.2.*. This family includes: MurC,
           MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and
           MurF catalyse consecutive steps in the synthesis of
           peptidoglycan. Peptidoglycan consists of a sheet of two
           sugar derivatives, with one of these N-acetylmuramic
           acid attaching to a small pentapeptide. The pentapeptide
           is is made of L-alanine, D-glutamic acid,
           Meso-diaminopimelic acid and D-alanyl alanine. The
           peptide moiety is synthesized by successively adding
           these amino acids to UDP-N-acetylmuramic acid. MurC
           transfers the L-alanine, MurD transfers the D-glutamate,
           MurE transfers the diaminopimelic acid, and MurF
           transfers the D-alanyl alanine. This family also
           includes Folylpolyglutamate synthase that transfers
           glutamate to folylpolyglutamate.
          Length = 76

 Score = 67.2 bits (165), Expect = 9e-12
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 6/82 (7%)

Query: 29  KINEVSSDSRHIQAGWIFVAIVGNKEDGHLFIPQAIAQGAEAIVVSSAYSLQDFSATIRS 88
           +I+ +  DSR +  G +F+A+ G + DG  F   AIA GA A+V S+             
Sbjct: 1   EIHFIGIDSRGMSPGALFLALKGYRVDGSDFAESAIALGAVAVVSSA------IPRDPNP 54

Query: 89  NTPILVVDNTRKFLSLFASRLY 110
             P + V + R+ L+  A+R Y
Sbjct: 55  EVPGIPVIDRREALAELAARFY 76


>gnl|CDD|37736 KOG2525, KOG2525, KOG2525, Folylpolyglutamate synthase [Coenzyme
           transport and metabolism].
          Length = 496

 Score = 41.8 bits (98), Expect = 4e-04
 Identities = 81/369 (21%), Positives = 120/369 (32%), Gaps = 69/369 (18%)

Query: 78  SLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKH---PE-----NILAVTGTSGKSSV 129
           SLQ  +A I     +   D+  + L+L   R   +    PE     NI+ V GT GK S 
Sbjct: 30  SLQSNAALI---EKLRRQDDNPQGLTLPRMRKLLERLGNPEDQNSLNIIHVAGTKGKGST 86

Query: 130 ASFVQQICQRSGL------SSFQIGPTSTIS-----------------SFAQDNRLTT-- 164
            +F + I ++ GL      S   +     I                   + +        
Sbjct: 87  CAFTESILRQQGLRTGFYTSPHLLSVRERIRINGQPISEEKFTKYFWEVYERLKSTKLKE 146

Query: 165 -PSPIYL----AKALSYLSSQGVTHVSVEASSHGLDQHRLDGI----KLIAGSFTNLGRD 215
              P Y       A      + V    +E    G     LD      K +    T+LG D
Sbjct: 147 VSMPTYFEFLTLLAFHVFVKENVDVAVIEVGLGG----ELDATNVIEKPVVCGITSLGLD 202

Query: 216 HIDY-HQTQQAYFNAKMRLFEELLPKESPAIIYADDAYSKEVMK-RAHNAGCRVLSVGYQ 273
           H  +   T       K  +F+E      PA        +  V+K RA   G  +  V   
Sbjct: 203 HTSFLGNTLSEIAWEKAGIFKE----GVPAFTVPQPPEALNVLKERASELGVPLFVVPPL 258

Query: 274 GKFIHLKKVCAIHNKQQVTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVL 333
             +        +    Q + +           L  E+ + N  VA G+  A+     +  
Sbjct: 259 EAYELSGVNLGLIGTHQWSNAS------LAVQLASEWLIQNGRVAEGVLDALQTSGLIPP 312

Query: 334 EHLEKLHVV--PGRFEFVGTNSRGGRIYVDYAHTSNSLEMILKNIRTITSGR-----IIV 386
             L  L     PGR + +    RG    +D AHT  S E   K  R    G      +I+
Sbjct: 313 AFLSGLASTDWPGRLQILEYG-RGVTWLLDGAHTKESAEACAKWFRKAVRGLKKLTSLIL 371

Query: 387 VFGCGGDRD 395
           +F C  DRD
Sbjct: 372 LFNCTSDRD 380


>gnl|CDD|177020 CHL00081, chlI, Mg-protoporyphyrin IX chelatase.
          Length = 350

 Score = 31.5 bits (72), Expect = 0.49
 Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 6/66 (9%)

Query: 392 GDRDQGKRPIMGKIALDLADIAIVTDD--NPRSEDPEKIRAEIIHGIPGFIEKGNRIEAI 449
           GDR  GK   +  +   L +I +V DD  N    DPE +  E+       I+ G  IE  
Sbjct: 45  GDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDPELMSDEVREA----IQNGETIETE 100

Query: 450 RTAIEM 455
           +  I M
Sbjct: 101 KIKIPM 106


>gnl|CDD|31262 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
           [Energy production and conversion].
          Length = 366

 Score = 31.3 bits (71), Expect = 0.56
 Identities = 28/118 (23%), Positives = 39/118 (33%), Gaps = 21/118 (17%)

Query: 379 ITSGRIIVVFGCGGDRDQGKRPIMG-KIALDLADIAIVTDD---------------NPRS 422
           +  G  + VFG GG    G   I G K A     IA+  +                NP+ 
Sbjct: 183 VEPGDTVAVFGLGG---VGLAAIQGAKAAGAGRIIAVDINPEKLELAKKFGATHFVNPKE 239

Query: 423 EDP--EKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHIVTNG 478
            D   E I      G     E    +E +R A+E  ++    V+ G       I T  
Sbjct: 240 VDDVVEAIVELTDGGADYAFECVGNVEVMRQALEATHRGGTSVIIGVAGAGQEISTRP 297


>gnl|CDD|35667 KOG0446, KOG0446, KOG0446, Vacuolar sorting protein VPS1, dynamin,
           and related proteins [Intracellular trafficking,
           secretion, and vesicular transport, General function
           prediction only].
          Length = 657

 Score = 30.7 bits (69), Expect = 0.87
 Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 10/97 (10%)

Query: 390 CGGDRDQGKRPIMGKI-ALDLADIAIVTD----DNPRSEDPEKIRAEIIHGIPGFIEKGN 444
            G ++     PI  KI +  +A++ +V        P ++ P+ I  EI   I  +IEK N
Sbjct: 111 TGSNKGISPVPITLKIFSALVANLTLVDLPGLTKVPVADQPDDIEEEIKSMIEEYIEKPN 170

Query: 445 R-IEAIRTAIEMLNKQDVLVVAG----KGHETVHIVT 476
           R I A+  A   +     LVVA      G  T+ ++T
Sbjct: 171 RIILAVTPANSDIATSPALVVAREVDPGGSRTLEVIT 207


>gnl|CDD|32991 COG3178, COG3178, Predicted phosphotransferase related to Ser/Thr
           protein kinases [General function prediction only].
          Length = 351

 Score = 30.7 bits (69), Expect = 0.92
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 15/71 (21%)

Query: 113 HPENILAVTGTSGKSSVASFVQQICQRSGLSSFQ---IGPTS-TISSFAQDNRLTTPSPI 168
           H  N++     +G             R G+  FQ   IGP +  ++S  +D R+T     
Sbjct: 208 HSRNLMWTADRAGAD-----------RVGVLDFQDALIGPIAYDVASLLRDARVTWSPER 256

Query: 169 YLAKALSYLSS 179
            LA    Y ++
Sbjct: 257 ELALLDRYWAA 267


>gnl|CDD|33790 COG4031, COG4031, Predicted metal-binding protein [General function
           prediction only].
          Length = 227

 Score = 30.4 bits (68), Expect = 1.2
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 4/70 (5%)

Query: 331 LVLEHLEKLHVVPGRFEFVGTNSRGG-RIYVDYAHTSNSLEMILKNIRTITSGRIIVVFG 389
           LV +H     V+PG     G+   GG R+ V  A    +L ++L    ++   R++    
Sbjct: 148 LVAQHPYVKKVIPGVISAKGSAGGGGVRLKVTRADARGNLRLLLSEGSSVQEIRVVTT-- 205

Query: 390 CGGDRDQGKR 399
             G R++G+R
Sbjct: 206 -AGSREEGER 214


>gnl|CDD|133175 cd05043, PTK_Ryk, Pseudokinase domain of Ryk (Receptor related to
           tyrosine kinase).  Protein Tyrosine Kinase (PTK) family;
           Receptor related to tyrosine kinase (Ryk); pseudokinase
           domain. The PTKc (catalytic domain) family to which this
           subfamily belongs, is part of a larger superfamily that
           includes the catalytic domains of other kinases such as
           protein serine/threonine kinases, RIO kinases, and
           phosphoinositide 3-kinase (PI3K). PTKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           tyrosine (tyr) residues in protein substrates. Ryk is a
           receptor tyr kinase (RTK) containing an extracellular
           region with two leucine-rich motifs, a transmembrane
           segment, and an intracellular inactive pseudokinase
           domain. The extracellular region of Ryk shows homology
           to the N-terminal domain of Wnt inhibitory factor-1
           (WIF) and serves as the ligand (Wnt) binding domain of
           Ryk. Ryk is expressed in many different tissues both
           during development and in adults, suggesting a
           widespread function. It acts as a chemorepulsive axon
           guidance receptor of Wnt glycoproteins and is
           responsible for the establishment of axon tracts during
           the development of the central nervous system. In
           addition, studies in mice reveal that Ryk is essential
           in skeletal, craniofacial, and cardiac development.
           Thus, it appears Ryk is involved in signal transduction
           despite its lack of kinase activity. Ryk may function as
           an accessory protein that modulates the signals coming
           from catalytically active partner RTKs such as the Eph
           receptors.
          Length = 280

 Score = 29.7 bits (67), Expect = 2.0
 Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 25/93 (26%)

Query: 106 ASRLYGKHPENILAVTGTS--------------GKSSVASFVQQICQRSGLSSFQIGPTS 151
           +  LYG   +NIL +                     ++  F+QQ C+    ++ Q   T 
Sbjct: 59  SCLLYGLSHQNILPILHVCIEDGEPPFVLYPYMNWGNLKLFLQQ-CRLGEANNPQALSTQ 117

Query: 152 TISSFAQDNRLTTPSPIYLAKALSYLSSQGVTH 184
            +   A          I +A  +SYL  +GV H
Sbjct: 118 QLVHMA----------IQIACGMSYLHKRGVIH 140


>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
           Glutathione-dependent formaldehyde dehydrogenases (FDHs,
           Class III ADH) are members of the zinc-dependent/medium
           chain alcohol dehydrogenase family.  FDH converts
           formaldehyde and NAD(P) to formate and NAD(P)H. The
           initial step in this process the spontaneous formation
           of a S-(hydroxymethyl)glutathione adduct from
           formaldehyde and glutathione, followed by FDH-mediated
           oxidation (and detoxification) of the adduct to
           S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
           are the major enzymes in the interconversion of alcohols
           and aldehydes or ketones.  Alcohol dehydrogenase in the
           liver converts ethanol and NAD+ to acetaldehyde and
           NADH, while in yeast and some other microorganisms ADH
           catalyzes the conversion acetaldehyde to ethanol in
           alcoholic fermentation. Class III ADH are also known as
           glutathione-dependent formaldehyde dehydrogenase (FDH),
           which convert aldehydes to corresponding carboxylic acid
           and alcohol.  ADH is a member of the medium chain
           alcohol dehydrogenase family (MDR), which has a
           NAD(P)(H)-binding domain in a Rossmann fold of an
           beta-alpha form. The NAD(H)-binding region is comprised
           of 2 structurally similar halves, each of which contacts
           a mononucleotide.  A GxGxxG motif after the first
           mononucleotide contact half allows the close contact of
           the coenzyme with the ADH backbone.  The N-terminal
           catalytic domain has a distant homology to GroES.  These
           proteins typically form dimers (typically higher plants,
           mammals) or tetramers (yeast, bacteria), and have 2
           tightly bound zinc atoms per subunit, a catalytic zinc
           at the active site and a structural zinc in a lobe of
           the catalytic domain.  NAD(H) binding occurs in the
           cleft between the catalytic  and coenzyme-binding
           domains at the active site, and coenzyme binding induces
           a conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
          Length = 363

 Score = 29.0 bits (66), Expect = 2.7
 Identities = 31/113 (27%), Positives = 41/113 (36%), Gaps = 19/113 (16%)

Query: 379 ITSGRIIVVFGCGGDRD---QGKRPIMGK---IALDLAD----IAIV---TDD-NPRSED 424
           +  G  + V GCGG      QG R I G    IA+D       +A     T   N   +D
Sbjct: 180 VRPGDTVAVIGCGGVGLNAIQGAR-IAGASRIIAVDPVPEKLELARRFGATHTVNASEDD 238

Query: 425 PEKIRAEIIHGIPGF---IEKGNRIEAIRTAIEMLNKQDVLVVAGKGHETVHI 474
             +   ++  G  G     E   R   IR A+ M  K    VV G G     +
Sbjct: 239 AVEAVRDLTDGR-GADYAFEAVGRAATIRQALAMTRKGGTAVVVGMGPPGETV 290


>gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding
           domain of LysR-type transcriptional regulators, YofA and
           SoxR, contains the type 2 periplasmic binding fold.
           YofA is a LysR-like transcriptional regulator of cell
           growth in Bacillus subtillis. YofA controls cell
           viability and the formation of constrictions during cell
           division. YofaA positively regulates expression of the
           cell division gene ftsW, and thus is essential for cell
           viability during stationary-phase growth of Bacillus
           substilis. YofA shows significant homology to SoxR from
           Arthrobacter sp. TE1826. SoxR is a negative regulator
           for the sarcosine oxidase gene soxA. Sarcosine oxidase
           catalyzes the oxidative demethylation of sarcosine,
           which is involved in the metabolism of creatine and
           choline. The topology of this substrate-binding domain
           is most similar to that of the type 2 periplasmic
           binding proteins (PBP2), which are responsible for the
           uptake of a variety of substrates such as phosphate,
           sulfate, polysaccharides, lysine/arginine/ornithine, and
           histidine. The PBP2 bind their ligand in the cleft
           between these domains in a manner resembling a Venus
           flytrap. After binding their specific ligand with high
           affinity, they can interact with a cognate membrane
           transport complex comprised of two integral membrane
           domains and two cytoplasmically located ATPase domains.
           This interaction triggers the ligand translocation
           across the cytoplasmic membrane energized by ATP
           hydrolysis.
          Length = 193

 Score = 29.1 bits (66), Expect = 3.0
 Identities = 37/169 (21%), Positives = 61/169 (36%), Gaps = 52/169 (30%)

Query: 181 GVTHVSVEASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAKMRLFEE---- 236
           G T   ++     + + RLDG   +AG       +H    Q           +F+E    
Sbjct: 36  GTTGALIQ----AVLEGRLDGA-FVAGPV-----EHPRLEQEP---------VFQEELVL 76

Query: 237 LLPKESPAIIYADDAYSKEVMKRAHNAGCRVLSVGYQGKFIHLKKVCAIHNKQQVTISVE 296
           + PK  P +  A+D     ++  A  AGC      Y+ +         +   + +     
Sbjct: 77  VSPKGHPPVSRAEDLAGSTLL--AFRAGC-----SYRRRLEDWLAEEGVSPGKIM----- 124

Query: 297 GKDFDFLFPLPGEFQVYNAL---VAAGLCIAIGIDSALVLEHLEKLHVV 342
                       EF  Y+A+   VAAG+ IA+   S  VL+ L+    V
Sbjct: 125 ------------EFGSYHAILGCVAAGMGIALLPRS--VLDSLQGRGSV 159


>gnl|CDD|31522 COG1331, COG1331, Highly conserved protein containing a thioredoxin
           domain [Posttranslational modification, protein
           turnover, chaperones].
          Length = 667

 Score = 28.7 bits (64), Expect = 3.2
 Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 5/60 (8%)

Query: 314 NALVAAGLCIAIGIDSALVLEHLEKLHVVPGRFEFVGTNSRGGRIYVDYAHTSNSLEMIL 373
           N L+ A L  A       VL   E L       +F+  N    R+   Y     ++  +L
Sbjct: 413 NGLMIAALAEA-----GRVLGDPEYLEAAERAADFILDNLYVDRLLRRYRGGEAAVAGLL 467


>gnl|CDD|37624 KOG2413, KOG2413, KOG2413, Xaa-Pro aminopeptidase [Amino acid
           transport and metabolism].
          Length = 606

 Score = 28.3 bits (63), Expect = 4.8
 Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 127 SSVASFVQQICQRSGLSSFQIGPTSTI---SSFAQDNRLTTPSPIYLAKAL 174
             + S ++            I P +         +D+ +  PSPI  AKA+
Sbjct: 257 DQIWSDIKNWASAFADKKIWISPETNYGIGELIGEDHSMIDPSPISRAKAI 307


>gnl|CDD|33514 COG3719, Rna, Ribonuclease I [Translation, ribosomal structure and
           biogenesis].
          Length = 249

 Score = 28.4 bits (63), Expect = 4.9
 Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 222 TQQAYFNAKMRLFEELLPKESPAIIYADDAYS 253
           +Q+AYF    RLFEEL  K  P      D  +
Sbjct: 150 SQEAYFATTRRLFEEL--KLPPVRKLLADGKT 179


>gnl|CDD|39608 KOG4407, KOG4407, KOG4407, Predicted Rho GTPase-activating protein
           [General function prediction only].
          Length = 1973

 Score = 28.2 bits (62), Expect = 5.4
 Identities = 19/83 (22%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 62  QAIAQGAEAIVVSSAYSLQDFSATIRSNTPILVVDNTRKFLSLFASRLYGKHPENILAVT 121
           Q  ++   A    + + LQ F A   S+ P       +        R     P +  AV 
Sbjct: 758 QQTSRSLPAPHPPATHRLQRFIALFNSSKPSDGSGEHKPSRM---KRSRTSLPASRAAVP 814

Query: 122 GTSGKSSVASFVQQICQRSGLSS 144
           GT  +S V        Q   LS 
Sbjct: 815 GTILQSGVFRQTPVKHQEIALSK 837


>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
           binding fold superfamily.  Type 1 periplasmic binding
           fold superfamily. This model and hierarchy represent the
           ligand binding domains of the LacI family of
           transcriptional regulators, periplasmic binding proteins
           of the ABC-type transport systems, the family C
           G-protein couples receptors (GPCRs), membrane bound
           guanylyl cyclases including the family of natriuretic
           peptide receptors (NPRs), and the N-terminal
           leucine/isoleucine/valine- binding protein  (LIVBP)-like
           domains of the ionotropic glutamate receptors (iGluRs).
           In LacI-like transcriptional regulator and the bacterial
           periplasmic binding proteins the ligands are
           monosaccharides including lactose, ribose, fructose,
           xylose, arabinose, galactose/glucose, and other sugars,
           with a few exceptions.  Periplasmic sugar binding
           proteins are one of the components of ABC transporters
           and are involved in the active transport of
           water-soluble ligands. The LacI family of proteins
           consists of transcriptional regulators related to the
           lac repressor. In this case, the sugar binding domain
           binds a sugar which changes the DNA binding activity of
           the repressor domain. The periplasmic binding proteins
           are the primary receptors for chemotaxis and transport
           of many sugar based solutes. The core structures of
           periplasmic binding proteins are classified into two
           types, and they differ in number and order of beta
           strands: type 1 has  six beta strands, while type 2 has
           five beta strands per sub-domain. These two structural
           folds are thought to be distantly related via a common
           ancestor. Notably, while the N-terminal LIVBP-like
           domain of iGluRs belongs to the type 1
           periplasmic-binding fold protein superfamily, the
           glutamate-binding domain of the iGluR is structurally
           similar to the type 2 periplasmic-binding fold.
          Length = 269

 Score = 27.9 bits (62), Expect = 6.3
 Identities = 29/155 (18%), Positives = 51/155 (32%), Gaps = 11/155 (7%)

Query: 115 ENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTSTISSFAQDNRL--TTPSPIYLAK 172
           + +  + G    SS A  V ++   +G+    +   +T         +    P      +
Sbjct: 57  QGVDGIIGPPS-SSSALAVVELAAAAGIP--VVSLDATAPDLTGYPYVFRVGPDNEQAGE 113

Query: 173 AL-SYLSSQGVTHVSV-EASSHGLDQHRLDGIKLIAGSFTNLGRDHIDYHQTQQAYFNAK 230
           A   YL+ +G   V++         + RL+G K                    +  F A 
Sbjct: 114 AAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQA- 172

Query: 231 MRLFEELLPKESP-AIIYADDAYSKEVMKRAHNAG 264
             L + L     P AI   +D  +   +K A  AG
Sbjct: 173 --LLQLLKAAPKPDAIFACNDEMAAGALKAAREAG 205


>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase.  This group
           contains arabinose dehydrogenase (AraDH) and related
           alcohol dehydrogenases. AraDH is a member of the medium
           chain dehydrogenase/reductase family and catalyzes the
           NAD(P)-dependent oxidation of D-arabinose and other
           pentoses, the initial step in the metabolism of
           d-arabinose into 2-oxoglutarate. Like the alcohol
           dehydrogenases, AraDH binds a zinc in the catalytic
           cleft as well as a distal structural zinc. AraDH forms
           homotetramers as a dimer of dimers. AraDH replaces a
           conserved catalytic His with replace with Arg, compared
           to the canonical ADH site. NAD(P)(H)-dependent
           oxidoreductases are the major enzymes in the
           interconversion of alcohols and aldehydes, or ketones.
           Alcohol dehydrogenase in the liver converts ethanol and
           NAD+ to acetaldehyde and NADH, while in yeast and some
           other microorganisms ADH catalyzes the conversion
           acetaldehyde to ethanol in alcoholic fermentation.  ADH
           is a member of the medium chain alcohol dehydrogenase
           family (MDR), which has a NAD(P)(H)-binding domain in a
           Rossmann fold of a beta-alpha form. The NAD(H)-binding
           region is comprised of 2 structurally similar halves,
           each of which contacts a mononucleotide.  A GxGxxG motif
           after the first mononucleotide contact half allows the
           close contact of the coenzyme with the ADH backbone.
           The N-terminal catalytic domain has a distant homology
           to GroES.  These proteins typically form dimers
           (typically higher plants, mammals) or tetramers (yeast,
           bacteria), and have 2 tightly bound zinc atoms per
           subunit, a catalytic zinc at the active site and a
           structural zinc in a lobe of the catalytic domain.
           NAD(H) binding occurs in the cleft between the catalytic
           and coenzyme-binding domains at the active site, and
           coenzyme binding induces a conformational closing of
           this cleft. Coenzyme binding typically precedes and
           contributes to substrate binding. In human ADH
           catalysis, the zinc ion helps coordinate the alcohol,
           followed by deprotonation of a histidine, the ribose of
           NAD, a serine, then the alcohol, which allows the
           transfer of a hydride to NAD+, creating NADH and a
           zinc-bound aldehyde or ketone. In yeast and some
           bacteria, the active site zinc binds an aldehyde,
           polarizing it, and leading to the reverse reaction.
          Length = 340

 Score = 27.9 bits (63), Expect = 6.4
 Identities = 28/142 (19%), Positives = 44/142 (30%), Gaps = 47/142 (33%)

Query: 374 KNIRTITSGRIIVVFGCGG--------------------DRDQGKRPIMGKIALDL-ADI 412
           K +  +  G  +VV G GG                    DR +       K+A  L AD 
Sbjct: 160 KALPYLDPGSTVVVIGVGGLGHIAVQILRALTPATVIAVDRSEEAL----KLAERLGADH 215

Query: 413 AIVTDDNPRSEDPEKIRAEIIHGIPGFIEKGNRI--------EAIRTAIEMLNKQDVLVV 464
            +   D+   E    +R E+  G      +G           E +  A ++L K    V+
Sbjct: 216 VLNASDDVVEE----VR-ELTGG------RGADAVIDFVGSDETLALAAKLLAKGGRYVI 264

Query: 465 ---AGKGHETVHIVTNGEKKMS 483
               G G      +   E  + 
Sbjct: 265 VGYGGHGRLPTSDLVPTEISVI 286


>gnl|CDD|32226 COG2043, COG2043, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 237

 Score = 27.9 bits (62), Expect = 7.1
 Identities = 19/81 (23%), Positives = 25/81 (30%), Gaps = 14/81 (17%)

Query: 330 ALVLEHLEKLHVVPGRFEFVG------------TNSRGGRIYVDYAHTSNSLEMILKNIR 377
           ALV   LEK    P     +                 GGRI  D+A   +     +    
Sbjct: 123 ALVYAPLEKAEFEPDVVVIICKPAQAMRLIQAYLYFMGGRINGDFAGIQSLCADAV--AL 180

Query: 378 TITSGRIIVVFGCGGDRDQGK 398
              +G I +  GC G R    
Sbjct: 181 PYLTGEINITLGCSGSRKYAG 201


>gnl|CDD|29513 cd01192, INT_P22_C, P22-like integrases, site-specific
           recombinases, DNA breaking-rejoining enzymes, C-terminal
           catalytic domain. This CD includes various bacterial and
           phage integrases, including those similar to phage
           P22-like integrases, DLP12 and APSE-1..
          Length = 177

 Score = 27.6 bits (61), Expect = 7.6
 Identities = 11/46 (23%), Positives = 20/46 (43%)

Query: 102 LSLFASRLYGKHPENILAVTGTSGKSSVASFVQQICQRSGLSSFQI 147
           L +   +  G H   + A  G   +    +  +Q  QR+G+S F+ 
Sbjct: 77  LQVLKRQKAGAHKPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRW 122


>gnl|CDD|107389 cd06394, PBP1_iGluR_Kainate_KA1_2, N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the KA1 and KA2 subunits of Kainate receptor. 
           N-terminal leucine/isoleucine/valine-binding protein
           (LIVBP)-like domain of the KA1 and KA2 subunits of
           Kainate receptor. While this N-terminal domain belongs
           to the periplasmic-binding fold type I superfamily, the
           glutamate-binding domain of the iGluR is structurally
           homologous to the periplasmic-binding fold type II. The
           LIVBP-like domain of iGluRs is thought to play a role in
           the initial assembly of iGluR subunits, but it is not
           well understood how this domain is arranged and
           functions in intact iGluR. There are five types of
           kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
           which are structurally similar to AMPA and NMDA subunits
           of ionotropic glutamate receptors. KA1 and KA2 subunits
           can only form functional receptors with one of the
           GluR5-7 subunits. Moreover, GluR5-7 can also form
           functional homomeric receptor channels activated by
           kainate and glutamate when expressed in heterologous
           systems. Kainate receptors are involved in excitatory
           neurotransmission by activating postsynaptic receptors
           and in inhibitory neurotransmission by modulating
           release of the inhibitory neurotransmitter GABA through
           a presynaptic mechanism. Kainate receptors are closely
           related to AMPA receptors. In contrast of AMPA
           receptors, kainate receptors play only a minor role in
           signaling at synapses and their function is not well
           defined.
          Length = 333

 Score = 27.5 bits (61), Expect = 7.7
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 114 PENILAVTGTSGKSSVASFVQQICQRSGLSSFQIGPTST 152
           P+ +++V G S   + +S V  IC    +  F++GP  T
Sbjct: 63  PKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEET 101


>gnl|CDD|35838 KOG0618, KOG0618, KOG0618, Serine/threonine phosphatase 2C
           containing leucine-rich repeats, similar to SCN
           circadian oscillatory protein (SCOP) [Signal
           transduction mechanisms].
          Length = 1081

 Score = 27.7 bits (61), Expect = 7.7
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 128 SVASFVQQI-CQRSGLSSFQIGPTSTISSFAQDNRLTTPSPIYLAKALSYLS 178
           S  + ++ + C+R+ LS  +I   S  + +A  N LTT     +   L YL 
Sbjct: 196 SNLANLEVLHCERNQLSELEISGPSLTALYADHNPLTTLDVHPVPLNLQYLD 247


>gnl|CDD|145988 pfam03136, Pup_ligase, Pup-ligase protein.  Pupylation is a novel
           protein modification system found in some bacteria. This
           family of proteins are the enzyme that can conjugate
           proteins of the Pup family to lysine residues in target
           proteins marking them for degradation. The archetypal
           protein in this family is PafA (proteasome accessory
           factor) from Mycobacterium tuberculosis. It has been
           suggested that these proteins are related to
           gamma-glutamyl-cysteine synthetases.
          Length = 444

 Score = 27.6 bits (62), Expect = 8.3
 Identities = 7/10 (70%), Positives = 9/10 (90%)

Query: 355 GGRIYVDYAH 364
           G R+YVD+AH
Sbjct: 75  GARLYVDHAH 84


>gnl|CDD|38868 KOG3664, KOG3664, KOG3664, Predicted patched transmembrane receptor
           [Signal transduction mechanisms].
          Length = 999

 Score = 27.7 bits (61), Expect = 8.5
 Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 291 VTISVEGKDFDFLFPLPGEFQVYNALVAAGLCIAIGIDSALVL------EHLEKLHVVPG 344
           + +S+    F +   L  +F  Y  LVA  + I IG D   +        +L  LH    
Sbjct: 359 ICLSLGVALFFYAVVLGIDFFPYLNLVAVVVIIGIGADDVFLFLKIYERSNLRMLHTQSQ 418

Query: 345 RFEFVGTNSRG 355
              F    S  
Sbjct: 419 SASFFLELSDH 429


>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase.  Benzyl
           alcohol dehydrogenase is similar to liver alcohol
           dehydrogenase, but has some amino acid substitutions
           near  the active site, which may determine the enzyme's
           specificity of oxidizing aromatic substrates.  Also
           known as aryl-alcohol dehydrogenases, they catalyze the
           conversion of an aromatic alcohol + NAD+ to an aromatic
           aldehyde + NADH + H+.  NAD(P)(H)-dependent
           oxidoreductases are the major enzymes in the
           interconversion of alcohols and aldehydes, or ketones.
           Alcohol dehydrogenase in the liver converts ethanol and
           NAD+ to acetaldehyde and NADH, while in yeast and some
           other microorganisms ADH catalyzes the conversion
           acetaldehyde to ethanol in alcoholic fermentation.   ADH
           is a member of the medium chain alcohol dehydrogenase
           family (MDR), which has a NAD(P)(H)-binding domain in a
           Rossmann fold of a beta-alpha form.  The NAD(H)-binding
           region is comprised of 2 structurally similar halves,
           each of which contacts a mononucleotide.  A GxGxxG motif
           after the first mononucleotide contact half allows the
           close contact of the coenzyme with the ADH backbone.
           The N-terminal catalytic domain has a distant homology
           to GroES.  These proteins typically form dimers
           (typically higher plants, mammals) or tetramers (yeast,
           bacteria), and have 2 tightly bound zinc atoms per
           subunit, a catalytic zinc at the active site and a
           structural zinc in a lobe of the catalytic domain.
           NAD(H) binding occurs in the cleft between the catalytic
            and coenzyme-binding domains at the active site, and
           coenzyme binding induces a conformational closing of
           this cleft. Coenzyme binding typically precedes and
           contributes to substrate binding.  In human  ADH
           catalysis, the zinc ion helps coordinate the alcohol,
           followed by deprotonation of  a histidine, the ribose of
           NAD, a serine, then the alcohol, which allows the
           transfer of a hydride to NAD+, creating NADH and a
           zinc-bound aldehyde or ketone. In yeast and some
           bacteria, the active site zinc binds an aldehyde,
           polarizing it, and leading to the reverse reaction.
          Length = 365

 Score = 27.5 bits (62), Expect = 9.9
 Identities = 25/108 (23%), Positives = 36/108 (33%), Gaps = 28/108 (25%)

Query: 380 TSGRIIVVFGCGG--------DRDQGKRPIMGKIALDL------------ADIAIVTDDN 419
             G  I VFG G          +  G   I   IA+D+            A   I    N
Sbjct: 185 RPGSSIAVFGAGAVGLAAVMAAKIAGCTTI---IAVDIVDSRLELAKELGATHVI----N 237

Query: 420 PRSEDP-EKIRAEIIHGIPGFIEKGNRIEAIRTAIEMLNKQDVLVVAG 466
           P+ ED    IR     G+   ++       I  A++ L  +  L + G
Sbjct: 238 PKEEDLVAAIREITGGGVDYALDTTGVPAVIEQAVDALAPRGTLALVG 285


  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
   0.321    0.137    0.394 

Gapped
Lambda     K      H
   0.267   0.0739    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,870,572
Number of extensions: 315438
Number of successful extensions: 1057
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1037
Number of HSP's successfully gapped: 46
Length of query: 497
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 399
Effective length of database: 4,146,055
Effective search space: 1654275945
Effective search space used: 1654275945
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)