RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780439|ref|YP_003064852.1| carbamoyl phosphate synthase
large subunit [Candidatus Liberibacter asiaticus str. psy62]
         (1162 letters)



>gnl|CDD|35591 KOG0370, KOG0370, KOG0370, Multifunctional pyrimidine synthesis
            protein CAD (includes carbamoyl-phophate synthetase,
            aspartate transcarbamylase, and glutamine
            amidotransferase) [General function prediction only].
          Length = 1435

 Score =  807 bits (2085), Expect = 0.0
 Identities = 429/1161 (36%), Positives = 639/1161 (55%), Gaps = 117/1161 (10%)

Query: 4    RQDLKTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADA 63
            R ++K +L++G+G + IGQA EFDYSG+QA KALKEE    IL+N N AT+ T   LAD 
Sbjct: 374  RVEVKKVLVLGSGGLSIGQAGEFDYSGSQAIKALKEENIFTILINPNIATVQTSKGLADK 433

Query: 64   TYTEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGVEMIGAKPETI 123
             Y  P+TPE V K+I+ ERPD IL T GGQTALN  + L + GV  +YGV+++G   +TI
Sbjct: 434  VYFLPVTPEYVTKVIKAERPDGILLTFGGQTALNCGVELDKAGVFAQYGVKVLGTPIQTI 493

Query: 124  DKAEDRSLFSKAMQNIPLATPKSILANATDIKEHDRKLHEEERENLKKTLSKEELDAALY 183
               EDR LF++A+  I                           E +  + +   ++ AL 
Sbjct: 494  ITTEDRDLFARALNEI--------------------------NEKIAPSEAVSTIEEALE 527

Query: 184  ALELKWNLEENDRKHRYICHAMAVAVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLE 243
            A E                            +G P+I+R ++ LGG G G A N  E  +
Sbjct: 528  AAE---------------------------RLGYPVIVRAAYALGGLGSGFANNEEELQD 560

Query: 244  IVENGLHASPTTEVLIEESVLGWKEYELEMMRDIKGNCIVVCSIENLDPMGVHTGDSITV 303
            +    L  + + ++L+E+S+ GWKE E E++RD   NCI VC++EN DP+G+HTGDSI V
Sbjct: 561  LAAQAL--ALSPQILVEKSLKGWKEVEYEVVRDAYDNCITVCNMENFDPLGIHTGDSIVV 618

Query: 304  APALTLTDKEYQLMRNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSAL 363
            AP+ TL+D+EYQ++R  AI V++ +GV  G  N+Q+A+NP + +  +IE+N R+SRSSAL
Sbjct: 619  APSQTLSDEEYQMLRTTAIKVIRHLGV-VGECNIQYALNPYSLEYRIIEVNARLSRSSAL 677

Query: 364  ASKATGFPIAKIAAKLAVGYTLDELGNDITGGKTPASFEPSIDYIVTKIPRFTFEKFPGS 423
            ASKATG+P+A  AAKLA+G  L EL N +T   T A FEPS+DY V KIPR+   KF   
Sbjct: 678  ASKATGYPLAYTAAKLALGIPLPELKNSVTK-TTTACFEPSLDYCVVKIPRWDLSKFQRV 736

Query: 424  DVTLTTSMKSVGEVMAIGRTFAESLQKALRGLETGLTGLDEIHIPSMESDNDPNALRSAI 483
               + +SMKSVGEVMAIGRTF E+ QKALR ++  L G               + L   +
Sbjct: 737  STEIGSSMKSVGEVMAIGRTFEEAFQKALRMVDPSLLGFMSTPFL--------DDLDEEL 788

Query: 484  SIPCPDRLRTVAQALRLGVSVEETHQSSNIDPWFIQQIKMIVDVEHRIREH---GLPKDF 540
            S P   R+  +A AL  G SV+  H+ + ID WF+ ++  IV++   +  H    LPK+ 
Sbjct: 789  STPTDRRVFAIAAALAKGYSVDRIHELTRIDKWFLYKLMNIVNIYKLLESHSLSSLPKEL 848

Query: 541  QNLQAIKAMGFSDARLSILSGIPCNEIRKIRHQMGLHPVFKCVDTCAGEFSSPTSYMYST 600
              L   K +GFSD +++   G     +R++R ++G+HP  K +DT A EF + T+Y+Y+T
Sbjct: 849  --LLRAKKLGFSDKQIAKFIGSTELAVRRLRKELGIHPFVKQIDTVAAEFPAQTNYLYTT 906

Query: 601  YETNFINKPVSEDKVSDRKKIVILGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINC 660
            Y           D   +   +++LG G  RIG  +EFD+C    + +L++ G +TIM+N 
Sbjct: 907  YNA------TEHDVDFNEHGVMVLGSGVYRIGSSVEFDWCAVGCARTLRKLGKKTIMVNY 960

Query: 661  NPETVSTDYDIADRLYFESLTEEDILEILRVEQQKGELVGIIVQFGGQTPLKLSKILEKN 720
            NPETVSTDYD  DRLYFE ++ E +++I  +E  +G    II+  GGQ P  ++  L +N
Sbjct: 961  NPETVSTDYDECDRLYFEEISYERVMDIYELENSEG----IIISVGGQLPNNIALKLHRN 1016

Query: 721  QIPILGTQPDSIDLAEDRDRFQKLLMELDLNQPRNGISHSVEHARLIACEIGFPLLIRPS 780
             + ILGT P+ ID AE+R +F ++L  + ++QP      S+E A+  A ++G+P+L+RPS
Sbjct: 1017 GVKILGTSPEMIDSAENRFKFSRMLDSIGVDQPAWKELTSLEEAKKFAEKVGYPVLVRPS 1076

Query: 781  YVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYL 840
            YVL G AM +VYSE+ L+ YL       VS +                   HP++   ++
Sbjct: 1077 YVLSGAAMNVVYSESDLKSYL--EQASAVSPD-------------------HPVVISKFI 1115

Query: 841  SDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQTKAL 900
              A EIDVDA+  + +V+V  I EH+E AG+HSGD+   LP + LS    + +      +
Sbjct: 1116 EGAKEIDVDAVASDGKVLVHAISEHVENAGVHSGDATLVLPPQDLSADTLERIKDIAAKV 1175

Query: 901  AGALNVIGLINVQYAIKDGKIYILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESLDA 960
            A AL + G  N+Q   KD ++ ++E N RASR+ PF++K +G     +A R I G  +  
Sbjct: 1176 AKALKITGPFNMQIIAKDNELKVIECNVRASRSFPFVSKTLGVDFIALATRAIMGVPV-- 1233

Query: 961  SIAAYGKRPDLSQIKHFAVKESVFPFNKFPGVDILLGPEMRSTGEVIGIDQDFPLAFAKS 1020
                      L    + AVK   F F++  G D +LG EM STGEV    +D   A+ K+
Sbjct: 1234 ------PPDLLLHPDYVAVKVPQFSFSRLAGADPVLGVEMASTGEVACFGEDRYEAYLKA 1287

Query: 1021 QLGIGVDLPHEGTVFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHG-LETQK 1079
             L  G  +P +  + +S+  + K  ++P  ++  KLG+K+ AT GTA F   +   E  +
Sbjct: 1288 MLSTGFKIPKKN-ILISI-GSYKPELLPSARDLAKLGYKLYATNGTADFYLENKYAEVSE 1345

Query: 1080 INKVLEGRPHIEDAISNRQVHLVINTTEGKKAIEDSKSLRRATLIRKIPYYTTIAGADAV 1139
                 + R  +     N  + LVIN       ++     RR  +   IP  T +  A   
Sbjct: 1346 EPTNDKLRELLA----NYNIDLVINLPRPSSFVDHGYKTRRLAVDFSIPLITDVKCAKLF 1401

Query: 1140 FQAIQALKAGNLEVHSLQSYR 1160
             +A++   + +++  +     
Sbjct: 1402 VEALKEKLS-HVDSMTSFRPV 1421



 Score =  146 bits (369), Expect = 4e-35
 Identities = 147/540 (27%), Positives = 234/540 (43%), Gaps = 70/540 (12%)

Query: 605  FINKPVSEDKVSDRKKIVILGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINCNPET 664
            FI +P       + KK+++LG G   IGQ  EFDY    A  +LKE    TI+IN N  T
Sbjct: 364  FITEPAKAAPRVEVKKVLVLGSGGLSIGQAGEFDYSGSQAIKALKEENIFTILINPNIAT 423

Query: 665  VSTDYDIADRLYFESLTEEDILEILRVEQQKGELVGIIVQFGGQT----PLKLSKI--LE 718
            V T   +AD++YF  +T E + ++++ E+      GI++ FGGQT     ++L K     
Sbjct: 424  VQTSKGLADKVYFLPVTPEYVTKVIKAERPD----GILLTFGGQTALNCGVELDKAGVFA 479

Query: 719  KNQIPILGTQPDSIDLAEDRDRFQKLLMELDLNQPRNGISHSVEHARLIACEIGFPLLIR 778
            +  + +LGT   +I   EDRD F + L E++     +    ++E A   A  +G+P+++R
Sbjct: 480  QYGVKVLGTPIQTIITTEDRDLFARALNEINEKIAPSEAVSTIEEALEAAERLGYPVIVR 539

Query: 779  PSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDS 838
             +Y LGG         N  ++ L D                  + QI         L + 
Sbjct: 540  AAYALGGLGSG---FAN-NEEELQDLA----------AQALALSPQI---------LVEK 576

Query: 839  YLSDAMEIDV----DALCQNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELI 894
             L    E++     DA    D  I V  +E+ +  GIH+GDS    PS++LS +    L 
Sbjct: 577  SLKGWKEVEYEVVRDAY---DNCITVCNMENFDPLGIHTGDSIVVAPSQTLSDEEYQMLR 633

Query: 895  SQTKALAGALNVIGLINVQYAIKDGKI--YILEVNPRASRTVPFIAKAIGFPVAKVAARI 952
            +    +   L V+G  N+QYA+    +   I+EVN R SR+    +KA G+P+A  AA++
Sbjct: 634  TTAIKVIRHLGVVGECNIQYALNPYSLEYRIIEVNARLSRSSALASKATGYPLAYTAAKL 693

Query: 953  IAGESLDAS--IAAYGKRPDLSQIKHFAVKESV-FPFNKFPGVDILLGPEMRSTGEVIGI 1009
              G  L                    + V +   +  +KF  V   +G  M+S GEV+ I
Sbjct: 694  ALGIPLPELKNSVTKTTTACFEPSLDYCVVKIPRWDLSKFQRVSTEIGSSMKSVGEVMAI 753

Query: 1010 DQDFPLAFAKSQLGIGVDL------------------PHEGTVFVSVRDADKKRIVPIIQ 1051
             + F  AF K+   +   L                  P +  VF       K   V  I 
Sbjct: 754  GRTFEEAFQKALRMVDPSLLGFMSTPFLDDLDEELSTPTDRRVFAIAAALAKGYSVDRIH 813

Query: 1052 NFKKLG----FKIMATEGTARFLESHGLETQKINKVLEGRPHIEDAISNRQVHLVINTTE 1107
               ++     +K+M      + LESH L +     +L  +   +   S++Q+   I +TE
Sbjct: 814  ELTRIDKWFLYKLMNIVNIYKLLESHSLSSLPKELLLRAK---KLGFSDKQIAKFIGSTE 870


>gnl|CDD|30806 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
           gene in MJ) [Amino acid transport and metabolism /
           Nucleotide transport and metabolism].
          Length = 400

 Score =  543 bits (1400), Expect = e-154
 Identities = 281/449 (62%), Positives = 331/449 (73%), Gaps = 56/449 (12%)

Query: 13  IGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADATYTEPITPE 72
           IG+GPIVIGQA EFDYSGTQACKALKEEGY ++LVNSNPATIMTDP+LAD  Y EPIT E
Sbjct: 1   IGSGPIVIGQAAEFDYSGTQACKALKEEGYGVVLVNSNPATIMTDPELADKVYIEPITKE 60

Query: 73  VVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGVEMIGAKPETIDKAEDRSLF 132
            V KIIEKERPDAILPT GGQTALN AL LK  GVL++YGVE++G+ PE I+ AED    
Sbjct: 61  PVEKIIEKERPDAILPTLGGQTALNAALELKEKGVLEKYGVEVVGSDPEAIEIAED---- 116

Query: 133 SKAMQNIPLATPKSILANATDIKEHDRKLHEEERENLKKTLSKEELDAALYALELKWNLE 192
                                            ++  K+ + +  +              
Sbjct: 117 ---------------------------------KKLFKEAMREIGIPVP----------- 132

Query: 193 ENDRKHRYICHAMAVAVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHAS 252
                   I H++  A +  DEIG P+I++PSF LGG+GGGIAYN  E  EI+E GL AS
Sbjct: 133 ------SRIAHSVEEADEIADEIGYPVIVKPSFGLGGSGGGIAYNEEELEEIIEEGLRAS 186

Query: 253 PTTEVLIEESVLGWKEYELEMMRDIKGNCIVVCSIENLDPMGVHTGDSITVAPALTLTDK 312
           P  EVLIEES++GWKE+E E++RD K NCIVVC++ENLDPMGVHTGDSITVAPA TLTDK
Sbjct: 187 PVEEVLIEESIIGWKEFEYEVVRDGKDNCIVVCNMENLDPMGVHTGDSITVAPAQTLTDK 246

Query: 313 EYQLMRNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPI 372
           EYQ++R+AAI V++EIG+E GG N+QFAV+P  G++ VIE+NPRVSRSSALASKATG+PI
Sbjct: 247 EYQMLRDAAIKVIREIGIE-GGCNIQFAVDPGGGELYVIEINPRVSRSSALASKATGYPI 305

Query: 373 AKIAAKLAVGYTLDELGNDITGGKTPASFEPSIDYIVTKIPRFTFEKFPGSDVTLTTSMK 432
           AK+AAKLAVGYTLDE+ NDIT G+TPASFEPS+DY+VTKIPRF FEKFPG+D  L T MK
Sbjct: 306 AKVAAKLAVGYTLDEIRNDIT-GRTPASFEPSLDYVVTKIPRFDFEKFPGADRRLGTQMK 364

Query: 433 SVGEVMAIGRTFAESLQKALRGLETGLTG 461
           SVGEVMAIGRTF E+LQKALR LE GL G
Sbjct: 365 SVGEVMAIGRTFEEALQKALRSLEIGLAG 393



 Score =  222 bits (567), Expect = 5e-58
 Identities = 133/424 (31%), Positives = 221/424 (52%), Gaps = 46/424 (10%)

Query: 624  LGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINCNPETVSTDYDIADRLYFESLTEE 683
            +G GP  IGQ  EFDY    A  +LKE G+  +++N NP T+ TD ++AD++Y E +T+E
Sbjct: 1    IGSGPIVIGQAAEFDYSGTQACKALKEEGYGVVLVNSNPATIMTDPELADKVYIEPITKE 60

Query: 684  DILEILRVEQQKGELVGIIVQFGGQTPL------KLSKILEKNQIPILGTQPDSIDLAED 737
             + +I+  E+       I+   GGQT L      K   +LEK  + ++G+ P++I++AED
Sbjct: 61   PVEKIIEKER----PDAILPTLGGQTALNAALELKEKGVLEKYGVEVVGSDPEAIEIAED 116

Query: 738  RDRFQKLLMELDLNQPRNGISHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSENML 797
            +  F++ + E+ +  P   I+HSVE A  IA EIG+P++++PS+ LGG    I Y+E   
Sbjct: 117  KKLFKEAMREIGIPVPS-RIAHSVEEADEIADEIGYPVIVKPSFGLGGSGGGIAYNE--- 172

Query: 798  QDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALC-QNDQ 856
                         EE++                   +L +  +    E + + +    D 
Sbjct: 173  -------------EELEEIIEEG-----LRASPVEEVLIEESIIGWKEFEYEVVRDGKDN 214

Query: 857  VIVVGIIEHIEEAGIHSGDSACSLPSRSLS----QQLKDELISQTKALAGALNVIGLINV 912
             IVV  +E+++  G+H+GDS    P+++L+    Q L+D  I   + +     + G  N+
Sbjct: 215  CIVVCNMENLDPMGVHTGDSITVAPAQTLTDKEYQMLRDAAIKVIREIG----IEGGCNI 270

Query: 913  QYAIKD--GKIYILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESLD---ASIAAYGK 967
            Q+A+    G++Y++E+NPR SR+    +KA G+P+AKVAA++  G +LD     I     
Sbjct: 271  QFAVDPGGGELYVIEINPRVSRSSALASKATGYPIAKVAAKLAVGYTLDEIRNDITGRTP 330

Query: 968  RPDLSQIKHFAVKESVFPFNKFPGVDILLGPEMRSTGEVIGIDQDFPLAFAKSQLGIGVD 1027
                  + +   K   F F KFPG D  LG +M+S GEV+ I + F  A  K+   + + 
Sbjct: 331  ASFEPSLDYVVTKIPRFDFEKFPGADRRLGTQMKSVGEVMAIGRTFEEALQKALRSLEIG 390

Query: 1028 LPHE 1031
            L  +
Sbjct: 391  LAGD 394


>gnl|CDD|145768 pfam02786, CPSase_L_D2, Carbamoyl-phosphate synthase L chain, ATP
           binding domain.  Carbamoyl-phosphate synthase catalyses
           the ATP-dependent synthesis of carbamyl-phosphate from
           glutamine or ammonia and bicarbonate. This important
           enzyme initiates both the urea cycle and the
           biosynthesis of arginine and/or pyrimidines. The
           carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes
           is a heterodimer of a small and large chain. The small
           chain promotes the hydrolysis of glutamine to ammonia,
           which is used by the large chain to synthesize carbamoyl
           phosphate. See pfam00988. The small chain has a GATase
           domain in the carboxyl terminus. See pfam00117. The ATP
           binding domain (this one) has an ATP-grasp fold.
          Length = 211

 Score =  241 bits (616), Expect = 1e-63
 Identities = 83/190 (43%), Positives = 115/190 (60%), Gaps = 7/190 (3%)

Query: 203 HAMAVAVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTT----EVL 258
                A+ A  EIG P+II+ +F  GG G GIA N  E  E+    L  +P      +VL
Sbjct: 25  ETEEEALAAAKEIGYPVIIKAAFGGGGLGMGIARNEEELAELFALALAEAPAAFGNPQVL 84

Query: 259 IEESVLGWKEYELEMMRDIKGNCIVVCSIENLDPMGVHTGDSITVAPALTLTDKEYQLMR 318
           +E+S+ G K  E +++RD  GNCI VC+ E  D     T  SI VAP+ TLTD+E Q++R
Sbjct: 85  VEKSLKGPKHIEYQVLRDAHGNCITVCNRECSDQR--RTQKSIEVAPSQTLTDEERQMLR 142

Query: 319 NAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAAK 378
            AA+ + + +G    G  V+FA++P +G+   IEMN R+  S ALA KATG+ +AK AAK
Sbjct: 143 EAAVKIARHLGYVGAG-TVEFALDPFSGEYYFIEMNTRLQVSHALAEKATGYDLAKEAAK 201

Query: 379 LAVGYTLDEL 388
           +A+GY L EL
Sbjct: 202 IALGYPLPEL 211



 Score =  112 bits (282), Expect = 6e-25
 Identities = 52/228 (22%), Positives = 90/228 (39%), Gaps = 24/228 (10%)

Query: 737 DRDRFQKLLMELDLNQPRN--GISHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSE 794
           D+  F+  + E  +       G   + E A   A EIG+P++I+ ++  GG  M I  +E
Sbjct: 1   DKVLFKAAMKEAGVPTVPGTAGPVETEEEALAAAKEIGYPVIIKAAFGGGGLGMGIARNE 60

Query: 795 NMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALC-Q 853
             L +     L                  +     G   +L +  L     I+   L   
Sbjct: 61  EELAELFALAL-----------------AEAPAAFGNPQVLVEKSLKGPKHIEYQVLRDA 103

Query: 854 NDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQTKALAGALNVIGLINVQ 913
           +   I V   E  ++    +  S    PS++L+ + +  L      +A  L  +G   V+
Sbjct: 104 HGNCITVCNRECSDQ--RRTQKSIEVAPSQTLTDEERQMLREAAVKIARHLGYVGAGTVE 161

Query: 914 YAI--KDGKIYILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESLD 959
           +A+    G+ Y +E+N R   +     KA G+ +AK AA+I  G  L 
Sbjct: 162 FALDPFSGEYYFIEMNTRLQVSHALAEKATGYDLAKEAAKIALGYPLP 209


>gnl|CDD|145769 pfam02787, CPSase_L_D3, Carbamoyl-phosphate synthetase large chain,
           oligomerisation domain.  Carbamoyl-phosphate synthase
           catalyses the ATP-dependent synthesis of
           carbamyl-phosphate from glutamine or ammonia and
           bicarbonate. The carbamoyl-phosphate synthase (CPS)
           enzyme in prokaryotes is a heterodimer of a small and
           large chain.
          Length = 122

 Score =  160 bits (407), Expect = 2e-39
 Identities = 55/123 (44%), Positives = 81/123 (65%), Gaps = 1/123 (0%)

Query: 479 LRSAISIPCPDRLRTVAQALRLGVSVEETHQSSNIDPWFIQQIKMIVDVEHRIREHGLPK 538
           L   +  P  +R+  +A+ALR G SVEE H+ + IDPWF+++IK IV++E  ++  G P 
Sbjct: 1   LLEKLRHPTDERIFAIAEALRRGYSVEEIHELTKIDPWFLEKIKEIVELEKELK-KGDPL 59

Query: 539 DFQNLQAIKAMGFSDARLSILSGIPCNEIRKIRHQMGLHPVFKCVDTCAGEFSSPTSYMY 598
               L   K +GFSDA+++ L G+   E+RK+R ++G+ PV+K VDTCA EF + T Y Y
Sbjct: 60  SDDLLLKAKKLGFSDAQIAKLLGVTEEEVRKLRKELGIRPVYKMVDTCAAEFEAKTPYYY 119

Query: 599 STY 601
           STY
Sbjct: 120 STY 122


>gnl|CDD|29636 cd01424, MGS_CPS_II, Methylglyoxal synthase-like domain from type II
            glutamine-dependent carbamoyl phosphate synthetase (CSP).
            CSP, a CarA and CarB heterodimer, catalyzes the
            production of carbamoyl phosphate which is subsequently
            employed in the metabolic pathways responsible for the
            synthesis of pyrimidine nucleotides or arginine. The
            MGS-like domain is the C-terminal domain of CarB and
            appears to play a regulatory role in CPS function by
            binding allosteric effector molecules, including UMP and
            ornithine..
          Length = 110

 Score =  158 bits (401), Expect = 9e-39
 Identities = 56/110 (50%), Positives = 76/110 (69%)

Query: 1032 GTVFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKVLEGRPHIE 1091
            GTVF+SV D DK   V I +   +LGFK++ATEGTA++L+  G+  + +NKV EGRP+I 
Sbjct: 1    GTVFISVADRDKPEAVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIV 60

Query: 1092 DAISNRQVHLVINTTEGKKAIEDSKSLRRATLIRKIPYYTTIAGADAVFQ 1141
            D I N ++ LVINT  GK+AI D  S+RRA L  K+PY+TT+  A A  +
Sbjct: 61   DLIKNGEIQLVINTPSGKRAIRDGFSIRRAALEYKVPYFTTLDTARAAVE 110


>gnl|CDD|145348 pfam02142, MGS, MGS-like domain.  This domain composes the whole
            protein of methylglyoxal synthetase and the domain is
            also found in Carbamoyl phosphate synthetase (CPS) where
            it forms a regulatory domain that binds to the allosteric
            effector ornithine. This family also includes inosicase.
            The known structures in this family show a common
            phosphate binding site.
          Length = 92

 Score =  103 bits (259), Expect = 4e-22
 Identities = 38/92 (41%), Positives = 53/92 (57%), Gaps = 5/92 (5%)

Query: 1045 RIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKVLEGRPH----IEDAISNRQVH 1100
             +V + +   +LGFK+ AT GTA+FL+  G+ T+ +NK  EGRP     I D I N ++ 
Sbjct: 1    GLVELAKALVELGFKLYATGGTAKFLKEAGIPTEVVNKTGEGRPGGRVQIGDLIKNGEID 60

Query: 1101 LVINTTEGKKA-IEDSKSLRRATLIRKIPYYT 1131
            LVINT    KA + D  ++RRA     IP  T
Sbjct: 61   LVINTLYPFKATVHDGYAIRRAAENIDIPLPT 92


>gnl|CDD|144029 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
           N-terminal domain.  Carbamoyl-phosphate synthase
           catalyses the ATP-dependent synthesis of
           carbamyl-phosphate from glutamine or ammonia and
           bicarbonate. This important enzyme initiates both the
           urea cycle and the biosynthesis of arginine and/or
           pyrimidines. The carbamoyl-phosphate synthase (CPS)
           enzyme in prokaryotes is a heterodimer of a small and
           large chain. The small chain promotes the hydrolysis of
           glutamine to ammonia, which is used by the large chain
           to synthesize carbamoyl phosphate. See pfam00988. The
           small chain has a GATase domain in the carboxyl
           terminus. See pfam00117.
          Length = 109

 Score = 92.5 bits (231), Expect = 5e-19
 Identities = 36/125 (28%), Positives = 49/125 (39%), Gaps = 24/125 (19%)

Query: 7   LKTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADATYT 66
           +K +L+   G I             +  +AL+E G   + VNSNP T+ T   LAD  Y 
Sbjct: 1   IKKVLVANRGEI-----------AVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYF 49

Query: 67  EP--------ITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGVEMIGA 118
                     +  E +  I EKE  DAI P   G   L+            + G+  IG 
Sbjct: 50  LGPGPASESYLNIERILDIAEKEGADAIHP---GYGFLSENAEFAEACE--KAGITFIGP 104

Query: 119 KPETI 123
            PE I
Sbjct: 105 SPEAI 109



 Score = 89.1 bits (222), Expect = 7e-18
 Identities = 34/126 (26%), Positives = 50/126 (39%), Gaps = 30/126 (23%)

Query: 619 KKIVILGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINCNPETVSTDYDIADRLYFE 678
           KK+++   G                   +L+E G ET+ +N NP+TVST   +AD  YF 
Sbjct: 2   KKVLVANRGEI-----------AVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYFL 50

Query: 679 S--------LTEEDILEILRVEQQKGELVGIIVQFGGQTPL----KLSKILEKNQIPILG 726
                    L  E IL+I   E       G      G   L    + ++  EK  I  +G
Sbjct: 51  GPGPASESYLNIERILDIAEKE-------GADAIHPGYGFLSENAEFAEACEKAGITFIG 103

Query: 727 TQPDSI 732
             P++I
Sbjct: 104 PSPEAI 109


>gnl|CDD|29632 cd00532, MGS-like, MGS-like domain. This domain composes the whole
            protein of methylglyoxal synthetase, which catalyzes the
            enolization of dihydroxyacetone phosphate (DHAP) to
            produce methylglyoxal. The family also includes the
            C-terminal domain in carbamoyl phosphate synthetase (CPS)
            where it catalyzes the last phosphorylation of a
            coaboxyphosphate intermediate to form the product
            carbamoyl phosphate and may also play a regulatory role.
            This family also includes inosine monophosphate
            cyclohydrolase. The known structures in this family show
            a common phosphate binding site..
          Length = 112

 Score = 77.7 bits (191), Expect = 2e-14
 Identities = 36/111 (32%), Positives = 55/111 (49%), Gaps = 5/111 (4%)

Query: 1034 VFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKVLE-GRPHIED 1092
            VF+SV D  K  +V +       GF + AT GT+R L   G+  + ++K  E G P ++ 
Sbjct: 2    VFLSVSDHVKAMLVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDA 61

Query: 1093 AISNR-QVHLVINTTEG---KKAIEDSKSLRRATLIRKIPYYTTIAGADAV 1139
            AI+ + +  +VIN  +    +   ED  +L R   + KIP  T  A A  V
Sbjct: 62   AIAEKGKFDVVINLRDPRRDRCTDEDGTALLRLARLYKIPVTTPNATAMFV 112


>gnl|CDD|30788 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
          Length = 449

 Score = 74.9 bits (184), Expect = 1e-13
 Identities = 66/295 (22%), Positives = 113/295 (38%), Gaps = 36/295 (12%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTT----EVLIEESV 263
           A+   +EIG P+I++ +   GG G  +  N  E     E     +        V +E+ +
Sbjct: 144 ALAIAEEIGYPVIVKAAAGGGGRGMRVVRNEEELEAAFEAARGEAEAAFGNPRVYLEKFI 203

Query: 264 LGWKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLMRN 319
            G +  E++++ D  GN I +    CSI+      +        AP+  LT++  + +  
Sbjct: 204 EGPRHIEVQVLGDGHGNVIHLGERDCSIQRRHQKVIEE------APSPLLTEELREKIGE 257

Query: 320 AAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAAKL 379
           AA+   K IG   G   V+F     NG+   IEMN R+     +    TG  + K   ++
Sbjct: 258 AAVRAAKLIG-YRGAGTVEFLY-DSNGEFYFIEMNTRLQVEHPVTEMVTGIDLVKEQIRI 315

Query: 380 AVGYTLDELGNDIT----------GGKTP-ASFEPS----IDYIVTKIPRFTFEKFPGSD 424
           A G  L     DI             + P  +F PS      Y     P    +      
Sbjct: 316 AAGEPLSLKQEDIKFRGHAIECRINAEDPLGNFLPSPGKITRYAPPGGPGVRVDSGVYDG 375

Query: 425 VTLTTSMKS-VGEVMAIGRTFAESLQKALRGLE----TGLTGLDEIHIPSMESDN 474
             +     S +G+V+  GRT  E++ +  R L+     G+     +    +   +
Sbjct: 376 YRVPPYYDSMIGKVIVHGRTRDEAIARMRRALDELVIDGIKTNIPLLQEILRDPD 430



 Score = 73.0 bits (179), Expect = 4e-13
 Identities = 56/300 (18%), Positives = 110/300 (36%), Gaps = 54/300 (18%)

Query: 712 KLSKILEKNQIPILGTQPDSIDLAEDRDRFQKLLMELDLNQP--RNGISHSVEHARLIAC 769
             ++   +  +  +G   ++I    D+   ++L+ +  +      +G     E A  IA 
Sbjct: 90  AFAEACAEAGLTFIGPSAEAIRRMGDKITARRLMAKAGVPVVPGSDGAVADNEEALAIAE 149

Query: 770 EIGFPLLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLL 829
           EIG+P++++ +   GGR M++V +E  L+                               
Sbjct: 150 EIGYPVIVKAAAGGGGRGMRVVRNEEELEA------------------------AFEAAR 185

Query: 830 GTHPLLFDSYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSACSL--------- 880
           G     F +       + ++   +  + I V ++       IH G+  CS+         
Sbjct: 186 GEAEAAFGNP-----RVYLEKFIEGPRHIEVQVLGDGHGNVIHLGERDCSIQRRHQKVIE 240

Query: 881 --PSRSLSQQLKDELISQTKALAGALNVIGLINVQYAI-KDGKIYILEVNPRASRTVPFI 937
             PS  L+++L++++       A  +   G   V++    +G+ Y +E+N R     P  
Sbjct: 241 EAPSPLLTEELREKIGEAAVRAAKLIGYRGAGTVEFLYDSNGEFYFIEMNTRLQVEHPVT 300

Query: 938 AKAIGFPVAKVAARIIAGESLDASIAAYGKRPDLSQIKH-----FAVKESVFPFNKFPGV 992
               G  + K   RI AGE L        K+ D+    H        ++ +  F   PG 
Sbjct: 301 EMVTGIDLVKEQIRIAAGEPLSL------KQEDIKFRGHAIECRINAEDPLGNFLPSPGK 354


>gnl|CDD|31240 COG1038, PycA, Pyruvate carboxylase [Energy production and
           conversion].
          Length = 1149

 Score = 66.1 bits (161), Expect = 5e-11
 Identities = 51/192 (26%), Positives = 91/192 (47%), Gaps = 18/192 (9%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTT----EVLIEESV 263
           A++  +E G P++I+ +   GG G  +  + ++  E  E     +       EV +E+ V
Sbjct: 150 ALEFAEEYGYPVMIKAAAGGGGRGMRVVRSEADLAEAFERAKSEAKAAFGNDEVYVEKLV 209

Query: 264 LGWKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLMRN 319
              K  E++++ D  GN + +    CS++            + VAPA  L+ +    + +
Sbjct: 210 ENPKHIEVQILGDTHGNVVHLFERDCSVQR------RHQKVVEVAPAPYLSPELRDEICD 263

Query: 320 AAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAAKL 379
            A+ + + IG  + G  V+F V+ ++GK   IE+NPR+     +  + TG  I K    +
Sbjct: 264 DAVKLARNIGYINAGT-VEFLVD-EDGKFYFIEVNPRIQVEHTITEEITGIDIVKAQIHI 321

Query: 380 AVGYTL--DELG 389
           A G TL   ELG
Sbjct: 322 AAGATLHTPELG 333



 Score = 57.2 bits (138), Expect = 3e-08
 Identities = 67/290 (23%), Positives = 122/290 (42%), Gaps = 45/290 (15%)

Query: 684 DILEILRVEQQKG-ELVGIIVQFGGQTPLKLSKILEKNQIPILGTQPDSIDLAEDRDRFQ 742
            I EI+R+ ++ G + +     F  + P + ++   +  I  +G +P+ +D+  D+ + +
Sbjct: 68  SIDEIIRIAKRSGADAIHPGYGFLSENP-EFARACAEAGITFIGPKPEVLDMLGDKVKAR 126

Query: 743 KLLMELDLN--QPRNGISHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSENMLQDY 800
              ++  +      +G   ++E A   A E G+P++I+ +   GGR M++V SE  L + 
Sbjct: 127 NAAIKAGVPVIPGTDGPIETIEEALEFAEEYGYPVMIKAAAGGGGRGMRVVRSEADLAEA 186

Query: 801 LLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALCQNDQVIVV 860
                      E K  + ND                        E+ V+ L +N + I V
Sbjct: 187 FERA-----KSEAKAAFGND------------------------EVYVEKLVENPKHIEV 217

Query: 861 GIIEHIEEAGIHSGDSACSL-----------PSRSLSQQLKDELISQTKALAGALNVIGL 909
            I+       +H  +  CS+           P+  LS +L+DE+      LA  +  I  
Sbjct: 218 QILGDTHGNVVHLFERDCSVQRRHQKVVEVAPAPYLSPELRDEICDDAVKLARNIGYINA 277

Query: 910 INVQYAI-KDGKIYILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESL 958
             V++ + +DGK Y +EVNPR         +  G  + K    I AG +L
Sbjct: 278 GTVEFLVDEDGKFYFIEVNPRIQVEHTITEEITGIDIVKAQIHIAAGATL 327


>gnl|CDD|35590 KOG0369, KOG0369, KOG0369, Pyruvate carboxylase [Energy production
           and conversion].
          Length = 1176

 Score = 59.2 bits (143), Expect = 7e-09
 Identities = 51/192 (26%), Positives = 91/192 (47%), Gaps = 20/192 (10%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRS------EFLEIVENGLHASPTTEVLIEE 261
           A++ + E GLP+II+ ++  GG G G+   RS       F       L A     + +E+
Sbjct: 176 ALEFVKEYGLPVIIKAAY--GGGGRGMRVVRSGEDVEEAFQRAYSEALAAFGNGTLFVEK 233

Query: 262 SVLGWKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLM 317
            +   +  E++++ D  GN + +    CS++      V       +APA TL  +    +
Sbjct: 234 FLEKPRHIEVQLLGDKHGNVVHLYERDCSVQRRHQKVVE------IAPAKTLPPEVRDAI 287

Query: 318 RNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAA 377
              A+ + K +G E+ G  V+F V+ K G+   IE+NPR+     +  + TG  + +   
Sbjct: 288 LTDAVKLAKHVGYENAGT-VEFLVDQK-GRHYFIEVNPRLQVEHTVTEEITGVDLVQAQI 345

Query: 378 KLAVGYTLDELG 389
            +A G +L +LG
Sbjct: 346 HVAEGASLPDLG 357



 Score = 41.5 bits (97), Expect = 0.001
 Identities = 66/295 (22%), Positives = 112/295 (37%), Gaps = 57/295 (19%)

Query: 760  SVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPN 819
            +VE A     E G P++I+ +Y  GGR M++V S         +     V E  +R Y  
Sbjct: 172  TVEEALEFVKEYGLPVIIKAAYGGGGRGMRVVRS--------GED----VEEAFQRAYSE 219

Query: 820  DKTGQINTLLGTHPLLFDSYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSACS 879
                      G   L  + +L     I+V  L      +V            H  +  CS
Sbjct: 220  ALAA-----FGNGTLFVEKFLEKPRHIEVQLLGDKHGNVV------------HLYERDCS 262

Query: 880  L-----------PSRSLSQQLKDELISQTKALAGALNVIGLINVQYAI-KDGKIYILEVN 927
            +           P+++L  +++D +++    LA  +       V++ + + G+ Y +EVN
Sbjct: 263  VQRRHQKVVEIAPAKTLPPEVRDAILTDAVKLAKHVGYENAGTVEFLVDQKGRHYFIEVN 322

Query: 928  PRASRTVPFIAKAIGFPVAKVAARIIAGESLDASIAAYGKRPDLSQIKHFAVKESVF--- 984
            PR         +  G  + +    +  G SL       G   D    + FA++  V    
Sbjct: 323  PRLQVEHTVTEEITGVDLVQAQIHVAEGASLP----DLGLTQDKITTRGFAIQCRVTTED 378

Query: 985  PFNKF-PGVDILLGPEMRSTGEVIGIDQDFPLAFAKSQLGIGVDLPHEGTVFVSV 1038
            P   F P    +   E+  +GE +GI  D   AFA + +      PH  ++ V V
Sbjct: 379  PAKGFQPDTGRI---EVFRSGEGMGIRLDGASAFAGAVIS-----PHYDSLLVKV 425


>gnl|CDD|35459 KOG0238, KOG0238, KOG0238, 3-Methylcrotonyl-CoA carboxylase,
           biotin-containing subunit/Propionyl-CoA carboxylase,
           alpha chain/Acetyl-CoA carboxylase, biotin carboxylase
           subunit [Lipid transport and metabolism, Amino acid
           transport and metabolism].
          Length = 670

 Score = 58.4 bits (141), Expect = 1e-08
 Identities = 47/194 (24%), Positives = 86/194 (44%), Gaps = 16/194 (8%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTT----EVLIEESV 263
           A +   EIG P++I+ +   GG G  IA++  EF E +E+    +  +     +L+E+ +
Sbjct: 140 AKKVAREIGYPVMIKATAGGGGKGMRIAWSEEEFEEGLESAKQEAAKSFGDDGMLLEKFI 199

Query: 264 LGWKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLMRN 319
              +  E+++  D  GN + +    CS++            I  APA  L ++  + +  
Sbjct: 200 DNPRHIEVQVFGDKHGNAVHLGERDCSVQR------RNQKIIEEAPAPNLPEETRRALGE 253

Query: 320 AAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAAKL 379
           AA+   K +G    G  V+F V+ K      +EMN R+     +    TG  + +   ++
Sbjct: 254 AAVRAAKAVGYVGAG-TVEFIVDSK-DNFYFMEMNTRLQVEHPVTEMITGTDLVEWQIRV 311

Query: 380 AVGYTLDELGNDIT 393
           A G  L     +I 
Sbjct: 312 AAGEPLPLKQEEIP 325



 Score = 58.4 bits (141), Expect = 1e-08
 Identities = 45/217 (20%), Positives = 87/217 (40%), Gaps = 41/217 (18%)

Query: 755 NGISHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIK 814
           +G   S E A+ +A EIG+P++I+ +   GG+ M+I +SE   ++ L         +E  
Sbjct: 131 HGEDQSDEEAKKVAREIGYPVMIKATAGGGGKGMRIAWSEEEFEEGLE-----SAKQEAA 185

Query: 815 RQYPNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSG 874
           + + +D             +L + ++ +   I+V               +    A +H G
Sbjct: 186 KSFGDDG------------MLLEKFIDNPRHIEVQVFG-----------DKHGNA-VHLG 221

Query: 875 DSACSL-----------PSRSLSQQLKDELISQTKALAGALNVIGLINVQYAI-KDGKIY 922
           +  CS+           P+ +L ++ +  L       A A+  +G   V++ +      Y
Sbjct: 222 ERDCSVQRRNQKIIEEAPAPNLPEETRRALGEAAVRAAKAVGYVGAGTVEFIVDSKDNFY 281

Query: 923 ILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESLD 959
            +E+N R     P      G  + +   R+ AGE L 
Sbjct: 282 FMEMNTRLQVEHPVTEMITGTDLVEWQIRVAAGEPLP 318


>gnl|CDD|34383 COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit
           [Lipid metabolism].
          Length = 645

 Score = 58.4 bits (141), Expect = 1e-08
 Identities = 52/196 (26%), Positives = 86/196 (43%), Gaps = 16/196 (8%)

Query: 206 AVAVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVEN----GLHASPTTEVLIEE 261
           A  V   +EIG P++I+ S   GG G  +     EF E +E+       +     V IE+
Sbjct: 142 AELVAIAEEIGYPVLIKASAGGGGKGMRVVETPEEFAEALESARREAKASFGDDRVFIEK 201

Query: 262 SVLGWKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLM 317
            +   +  E+++  D  GN + +    CS++            I  APA  LT++  + M
Sbjct: 202 YLDKPRHIEIQVFADQHGNVVHLGERDCSLQR------RHQKVIEEAPAPFLTEETREAM 255

Query: 318 RNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAA 377
             AA+A  K +G    G  V+F V+  +G    +EMN R+     +    TG  + +   
Sbjct: 256 GEAAVAAAKAVGYVGAG-TVEFIVDA-DGNFYFLEMNTRLQVEHPVTELITGIDLVEWQI 313

Query: 378 KLAVGYTLDELGNDIT 393
           ++A G  L    +DI 
Sbjct: 314 RVASGEKLPFTQDDIP 329



 Score = 49.9 bits (119), Expect = 4e-06
 Identities = 54/256 (21%), Positives = 95/256 (37%), Gaps = 43/256 (16%)

Query: 717 LEKNQIPILGTQPDSIDLAEDRDRFQKLLMELD--LNQPRNGISHSVEHARLIACEIGFP 774
           +E   +  +G    +I    D+   +KL  E         +G          IA EIG+P
Sbjct: 95  VEDAGLVFIGPSAGAIRAMGDKIAAKKLAAEAGVPTVPGYHGPIQDAAELVAIAEEIGYP 154

Query: 775 LLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPL 834
           +LI+ S   GG+ M++V +     + L          E K  + +D+            +
Sbjct: 155 VLIKASAGGGGKGMRVVETPEEFAEAL-----ESARREAKASFGDDR------------V 197

Query: 835 LFDSYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSACSL-----------PSR 883
             + YL     I++         +V            H G+  CSL           P+ 
Sbjct: 198 FIEKYLDKPRHIEIQVFADQHGNVV------------HLGERDCSLQRRHQKVIEEAPAP 245

Query: 884 SLSQQLKDELISQTKALAGALNVIGLINVQYAI-KDGKIYILEVNPRASRTVPFIAKAIG 942
            L+++ ++ +     A A A+  +G   V++ +  DG  Y LE+N R     P      G
Sbjct: 246 FLTEETREAMGEAAVAAAKAVGYVGAGTVEFIVDADGNFYFLEMNTRLQVEHPVTELITG 305

Query: 943 FPVAKVAARIIAGESL 958
             + +   R+ +GE L
Sbjct: 306 IDLVEWQIRVASGEKL 321


>gnl|CDD|29635 cd01423, MGS_CPS_I_III, Methylglyoxal synthase-like domain found in
            pyr1 and URA1-like carbamoyl phosphate synthetases (CPS),
            including ammonia-dependent CPS Type I, and
            glutamine-dependent CPS Type III. These are multidomain
            proteins, in which MGS is the C-terminal domain..
          Length = 116

 Score = 56.4 bits (136), Expect = 5e-08
 Identities = 27/104 (25%), Positives = 48/104 (46%), Gaps = 5/104 (4%)

Query: 1034 VFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKVLE----GRPH 1089
            + +S+    K  ++P  Q   KLG+K+ ATEGTA FL  +G+    +    E     +P 
Sbjct: 3    ILISIGSYSKPELLPTAQKLSKLGYKLYATEGTADFLLENGIPVTPVAWPSEEPQNDKPS 62

Query: 1090 IEDAISNRQVHLVIN-TTEGKKAIEDSKSLRRATLIRKIPYYTT 1132
            + + ++  ++ LVIN  +   K + D+  + R           T
Sbjct: 63   LRELLAEGKIDLVINLPSNRGKRVLDNDYVMRRAADDFAVPLIT 106


>gnl|CDD|35589 KOG0368, KOG0368, KOG0368, Acetyl-CoA carboxylase [Lipid transport
           and metabolism].
          Length = 2196

 Score = 52.7 bits (126), Expect = 7e-07
 Identities = 40/156 (25%), Positives = 77/156 (49%), Gaps = 15/156 (9%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGI--AYNRSEFLEIVENGLHASPTTEVLIEESVLG 265
            ++A ++IG P++I+ S   GG G GI    N  +F  + +   +  P + + + +    
Sbjct: 231 GLEAAEKIGFPVMIKASE--GGGGKGIRKVENEDDFKALFKQVQNEVPGSPIFLMKLADQ 288

Query: 266 WKEYELEMMRDIKGNCIVV----CSIENLDPMGVHTGDSITVAPALTLTDKEYQLMRNAA 321
            +  E++++ D  GN I +    CSI+      +      T+AP  T     ++ M  AA
Sbjct: 289 ARHLEVQLLADQYGNVISLFGRDCSIQRRHQKIIEEA-PATIAPPET-----FKKMEQAA 342

Query: 322 IAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRV 357
           + + K +G  S G  V++  +P +G+   +E+NPR+
Sbjct: 343 VRLAKLVGYVSAG-TVEYLYSPDDGEYYFLELNPRL 377


>gnl|CDD|32413 COG2232, COG2232, Predicted ATP-dependent carboligase related to
            biotin carboxylase [General function prediction only].
          Length = 389

 Score = 49.2 bits (117), Expect = 6e-06
 Identities = 77/386 (19%), Positives = 140/386 (36%), Gaps = 69/386 (17%)

Query: 647  SLKEAGFETIMI------NCNPETVSTDYDIADRLY--FESLTEEDILEILRVEQQKGEL 698
            S  + GFE   +      +   + +S   +    L   FE+L E+ ++E    E    ++
Sbjct: 27   SASKLGFEVYSVQYYDPADLPGDAISYLRERPGELLGRFENLDEQKLIEAA--EDLAEDV 84

Query: 699  VGIIVQFGGQTPLKLSKILEKNQIPILGTQPDS-IDLAEDRDRFQKLLMELDLNQPRNGI 757
               I+ F G   L+ S    +    + G +P+  +  A ++ +F + L  L + +P    
Sbjct: 85   DAPIIPFSGFEALRTSG---ELGCEVAGNEPEVKVVEASNKLKFYRKLEVLGMPEPSEKK 141

Query: 758  SHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQY 817
               +E       E    L+++P    GG    + + E        D  PG + +E     
Sbjct: 142  IEPLE-------EGEKTLILKPVSGAGGLVELVKFDEE-------DPPPGFIFQEFIEGR 187

Query: 818  PNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSA 877
            P   +             F S  SDA+ + V     NDQ+I    +       ++ G+  
Sbjct: 188  PVSVS-------------FISNGSDALTLAV-----NDQII--DGLRGEYSQFVYKGNLT 227

Query: 878  CSLPSRSLSQQLKDELISQTKALAGALNVIGLINVQYAIKDGKIYILEVNPRASRTVPFI 937
               P      +  + L  +   L   L ++G   V + + D   Y++EVNPR   T+  I
Sbjct: 228  ---PFPYEEVEEAERLAEE---LVEELGLVGSNGVDFVLNDKGPYVIEVNPRIQGTLECI 281

Query: 938  AKAIGFPVAKVAARIIAGESLDASIAAYGKRPDLSQIKHFAVKESVFPFNKFPGVDILLG 997
             ++ G  + ++  +   GE          +RP     + +A K  ++       V IL  
Sbjct: 282  ERSSGINLFRLHIQAFDGE--------LPERPK---PRGYACKRILYAPRTVR-VPILKL 329

Query: 998  PEMR---STGEVIGIDQDFPLAFAKS 1020
                     G VI   +      A S
Sbjct: 330  SWTHDIPRPGTVIEKGEPLCSVIASS 355


>gnl|CDD|31374 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
           enzymes [Cell envelope biogenesis, outer membrane].
          Length = 317

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 33/149 (22%), Positives = 61/149 (40%), Gaps = 13/149 (8%)

Query: 216 GLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTTEVLIEESVLGWKEYEL-EMM 274
           G PL ++P+      G        +    +E         +VL E+ + G +E E+  + 
Sbjct: 142 GFPLFVKPAREGSSVGRSPVNVEGDLQSALELAFKYD--RDVLREQGITG-REIEVGVLG 198

Query: 275 RDIKGNCIVVCSIENLDPM-------GVHTGDSITVAPALTLTDKEYQLMRNAAIAVLKE 327
            D +   + +  I              + TG +    PA  LTD+ ++ ++  A+   K 
Sbjct: 199 NDYEEQALPLGEIPPKGEEFYDYEAKYLSTGGAQYDIPA-GLTDEIHEEIKELALRAYKA 257

Query: 328 IGVESGGANVQFAVNPKNGKMVVIEMNPR 356
           +G   G A V F V+   G+ V++E+N  
Sbjct: 258 LGC-LGLARVDFFVDDDEGEFVLLEVNTN 285



 Score = 42.2 bits (99), Expect = 0.001
 Identities = 52/257 (20%), Positives = 90/257 (35%), Gaps = 44/257 (17%)

Query: 716 ILEKNQIPILGTQPDSIDLAEDRDRFQKLLMELDLNQPRNGISHSVEHARLIACEI---- 771
           +LE   IP +G    +   A D+   ++L     L           E++ +I  E+    
Sbjct: 82  LLELLGIPYVGKGVLASAGAMDKIVTKRLFKAEGLPVAPYVALTRDEYSSVIVEEVEEGL 141

Query: 772 GFPLLIRPSYVLGGRAMQIVYSENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGT 831
           GFPL ++P+          V  E  LQ  L         E   +    D+       +  
Sbjct: 142 GFPLFVKPAREGSSVGRSPVNVEGDLQSAL---------ELAFKY---DRDVLREQGI-- 187

Query: 832 HPLLFDSYLSDAMEIDVDALCQNDQVIVVGIIEHI---------EEAGIHSGDSACSLPS 882
                        EI+V  L  + +   + + E           E   + +G +   +P+
Sbjct: 188 ----------TGREIEVGVLGNDYEEQALPLGEIPPKGEEFYDYEAKYLSTGGAQYDIPA 237

Query: 883 RSLSQQLKDELISQTKALAGALNVIGLINVQYAIKD--GKIYILEVNPRASRT----VPF 936
             L+ ++ +E+         AL  +GL  V + + D  G+  +LEVN     T     P 
Sbjct: 238 G-LTDEIHEEIKELALRAYKALGCLGLARVDFFVDDDEGEFVLLEVNTNPGMTAMSLFPK 296

Query: 937 IAKAIGFPVAKVAARII 953
            A A G   A +  R +
Sbjct: 297 AAAAAGISFAILVLRFV 313


>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
           (MDR)/zinc-dependent alcohol dehydrogenase-like family. 
           The medium chain reductase/dehydrogenases
           (MDR)/zinc-dependent alcohol dehydrogenase-like family,
           which contains the zinc-dependent alcohol dehydrogenase
           (ADH-Zn) and related proteins, is a diverse group of
           proteins related to the first identified member, class I
           mammalian ADH.  MDRs display a broad range of activities
           and are distinguished from the smaller short chain
           dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P) binding-Rossmann fold domain of a
           beta-alpha form and an N-terminal catalytic domain with
           distant homology to GroES.  The MDR group contains a
           host of activities, including the founding alcohol
           dehydrogenase (ADH) , quinone reductase, sorbitol
           dehydrogenase, formaldehyde dehydrogenase, butanediol
           DH, ketose reductase, cinnamyl reductase, and numerous
           others. The zinc-dependent alcohol dehydrogenases (ADHs)
           catalyze the NAD(P)(H)-dependent interconversion of
           alcohols to aldehydes or ketones. ADH-like proteins
           typically form dimers (typically higher plants, mammals)
           or tetramers (yeast, bacteria), and generally 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. The active site zinc is
           coordinated by a histidine, two cysteines, and a water
           molecule. The second zinc seems to play a structural
           role, affects subunit interactions, and is typically
           coordinated by 4 cysteines. Other MDR members have only
           a catalytic zinc, and some contain no coordinated zinc.
          Length = 271

 Score = 43.1 bits (102), Expect = 5e-04
 Identities = 33/134 (24%), Positives = 49/134 (36%), Gaps = 27/134 (20%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLA-----D 62
            T+L++GAG +  G          Q  KA    G R+I+ + +   +    +LA     D
Sbjct: 136 DTVLVLGAGGV--GLLA------AQLAKAA---GARVIVTDRSDEKL----ELAKELGAD 180

Query: 63  AT--YTEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGVEMIGAKP 120
               Y E    E   ++      D ++   GG   L  AL L R G   R  V  +G   
Sbjct: 181 HVIDYKEE-DLEEELRLTGGGGADVVIDAVGGPETLAQALRLLRPGG--RIVV--VGGTS 235

Query: 121 ETIDKAEDRSLFSK 134
                 + R L  K
Sbjct: 236 GGPPLDDLRRLLFK 249


>gnl|CDD|29633 cd01421, IMPCH, Inosine monophosphate cyclohydrolase domain. This is
            the N-terminal domain in the purine biosynthesis pathway
            protein ATIC (purH). The bifunctional ATIC protein
            contains a C-terminal  ATIC formylase domain that
            formylates 5-aminoimidazole-4-carboxamide-ribonucleotide.
            The IMPCH domain then converts the
            formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to
            inosine monophosphate. This is the final step in de novo
            purine production..
          Length = 187

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 13/75 (17%)

Query: 1034 VFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKV------LEGR 1087
              +SV  +DK  +V   +   +LG +I++T GTA+FL+  G+    ++ +      L GR
Sbjct: 3    ALISV--SDKTGLVEFAKELVELGVEILSTGGTAKFLKEAGIPVTDVSDITGFPEILGGR 60

Query: 1088 -----PHIEDAISNR 1097
                 P I   I  R
Sbjct: 61   VKTLHPKIHGGILAR 75


>gnl|CDD|30487 COG0138, PurH, AICAR transformylase/IMP cyclohydrolase PurH (only IMP
            cyclohydrolase domain in Aful) [Nucleotide transport and
            metabolism].
          Length = 515

 Score = 39.4 bits (92), Expect = 0.005
 Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 8/61 (13%)

Query: 1033 TVFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKV------LEG 1086
               +SV  +DK  IV   +   +LG +I++T GTA+ L   G+   +++ +      L+G
Sbjct: 4    RALLSV--SDKTGIVEFAKALVELGVEILSTGGTAKLLAEAGIPVTEVSDITGFPEMLDG 61

Query: 1087 R 1087
            R
Sbjct: 62   R 62


>gnl|CDD|145680 pfam02655, ATP-grasp_3, ATP-grasp domain.  No functional
           information or experimental verification of function is
           known in this family. This family appears to be an
           ATP-grasp domain (Pers. obs. A Bateman).
          Length = 160

 Score = 38.1 bits (89), Expect = 0.013
 Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 14/93 (15%)

Query: 838 SYLSDAMEIDVDALCQNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQT 897
           S LSD        L  N Q     +I++     +++G      PSR+   +LK+EL    
Sbjct: 77  SLLSDG--EKALPLSVNRQ-----LIDNAGSGFVYAG---NLTPSRT---ELKEELEELA 123

Query: 898 KALAGAL-NVIGLINVQYAIKDGKIYILEVNPR 929
           + +  AL  + G + V   + D   Y++EVNPR
Sbjct: 124 EEVVEALPGLRGYVGVDLVLTDNGPYVIEVNPR 156



 Score = 33.1 bits (76), Expect = 0.42
 Identities = 35/172 (20%), Positives = 64/172 (37%), Gaps = 22/172 (12%)

Query: 188 KWNLEENDRKHRYICHAMAVAVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVEN 247
           K    +  +           A +  +E     I++P    GG G     N  E  E +EN
Sbjct: 4   KLKTYKALKNAGVPTPETLSAEEPTEE-EKKYIVKPRDGCGGEGVRFVENGREDEEFIEN 62

Query: 248 GLHASPTTEVLIEESVLGWKEYELEMMRDIKGNCIVVCS---IENLDPMGVHTGDSITVA 304
                    V+I+E + G +   + ++ D +    +  +   I+N     V+ G+     
Sbjct: 63  ---------VIIQEFIEG-EPLSVSLLSDGEKALPLSVNRQLIDNAGSGFVYAGNLT--- 109

Query: 305 PALTLTDKEYQLMRNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPR 356
           P+ T   +E   +   A  V++ +    G   V   +   +    VIE+NPR
Sbjct: 110 PSRTELKEE---LEELAEEVVEALPGLRGYVGVDLVLT--DNGPYVIEVNPR 156


>gnl|CDD|30949 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
           oxidoreductases [Energy production and conversion /
           General function prediction only].
          Length = 326

 Score = 36.9 bits (85), Expect = 0.032
 Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 13/108 (12%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDL-ADAT-- 64
           +T+L+ GA   V          G+ A +  K  G  ++ V S+   +    +L AD    
Sbjct: 144 ETVLVHGAAGGV----------GSAAIQLAKALGATVVAVVSSSEKLELLKELGADHVIN 193

Query: 65  YTEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYG 112
           Y E    E V ++   +  D +L T GG T   +  +L   G L   G
Sbjct: 194 YREEDFVEQVRELTGGKGVDVVLDTVGGDTFAASLAALAPGGRLVSIG 241


>gnl|CDD|30377 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
           formyltransferase (GAR transformylase) [Nucleotide
           transport and metabolism].
          Length = 394

 Score = 36.0 bits (83), Expect = 0.055
 Identities = 53/254 (20%), Positives = 99/254 (38%), Gaps = 44/254 (17%)

Query: 734 LAEDRDRFQKLLME-LDLNQPRNGISHSVEHARLIACEIGFPLLIRPSYVLGGRAMQIVY 792
           L  +R+  ++L  E L L   +   + S+E  R    +IGFP +++P     G+   +V 
Sbjct: 110 LTMNREGIRRLAAEELGLPTSKYRFADSLEELRAAVEKIGFPCVVKPVMSSSGKGQSVVR 169

Query: 793 SENMLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYLSDAMEIDVDALC 852
           S                 E++++ +   +  Q     G+  ++ + ++    EI +  + 
Sbjct: 170 SP----------------EDVEKAW---EYAQQGGRGGSGRVIVEEFVKFDFEITLLTVR 210

Query: 853 QNDQV-IVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQTKALAGALNVIGLIN 911
             D        I H +E     GD   S   + +S+   +E  S  K +  AL   GL  
Sbjct: 211 AVDGTGSFCAPIGHRQE----DGDYRESWQPQEMSEAALEEAQSIAKRVTDALGGRGLFG 266

Query: 912 VQYAIKDGKIYILEVNPRASRT--VPFI----------AKAI-GFPVAKV------AARI 952
           V+  +K  ++   EV+PR   T  V  I           +AI G P+ ++      A+ +
Sbjct: 267 VELFVKGDEVIFSEVSPRPHDTGMVTLISQDLSEFALHVRAILGLPIPEIRQISPAASAV 326

Query: 953 IAGESLDASIAAYG 966
           I  +    +    G
Sbjct: 327 ILAQETSQAPTFDG 340


>gnl|CDD|143431 cd07113, ALDH_PADH_NahF, Escherichia coli NAD+-dependent
           phenylacetaldehyde dehydrogenase PadA-like.
           NAD+-dependent, homodimeric, phenylacetaldehyde
           dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia
           coli involved in the catabolism of 2-phenylethylamine,
           and other related sequences, are present in this CD.
           Also included is the Pseudomonas fluorescens ST StyD
           PADH involved in styrene catabolism, the Sphingomonas
           sp. LB126 FldD protein involved in fluorene degradation,
           and the Novosphingobium aromaticivorans NahF
           salicylaldehyde dehydrogenase involved in the
           NAD+-dependent conversion of salicylaldehyde to
           salicylate.
          Length = 477

 Score = 34.7 bits (80), Expect = 0.15
 Identities = 42/125 (33%), Positives = 58/125 (46%), Gaps = 20/125 (16%)

Query: 297 TGDSITVAPALT--LTDKEYQLMRNAAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMN 354
           TG +I + P+    LT     L+R A +A  KE G+  G  NV   VN K      +  +
Sbjct: 169 TGCTIVIKPSEFTPLT-----LLRVAELA--KEAGIPDGVLNV---VNGKGAVGAQLISH 218

Query: 355 PRVSRSSALASKATGFPIAKIAAKLAVGYTLDELGNDITGGKTPASF--EPSIDYIVTKI 412
           P V++ S   S ATG  I + AA      TL EL     GGK  A+F  +  ID++V  +
Sbjct: 219 PDVAKVSFTGSVATGKKIGRQAASDLTRVTL-EL-----GGKNAAAFLKDADIDWVVEGL 272

Query: 413 PRFTF 417
               F
Sbjct: 273 LTAGF 277


>gnl|CDD|30500 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
           transport and metabolism].
          Length = 428

 Score = 34.8 bits (80), Expect = 0.15
 Identities = 61/300 (20%), Positives = 93/300 (31%), Gaps = 75/300 (25%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFL----EIVENGLHASPTTEVLIEESV 263
           A   +DE G P++++      G G  +A    E      E++E     S    V+IEE +
Sbjct: 130 AKAYIDEKGAPIVVKADGLAAGKGVIVAMTLEEAEAAVDEMLEGNAFGSAGARVVIEEFL 189

Query: 264 LGWKEYELEMMRDIKGNCIVVCSIENLDPM--------------GVHTGDSITVAPALTL 309
            G +E+ L                + + PM              G +TG     +PA  +
Sbjct: 190 DG-EEFSL----------QAFVDGKTVIPMPTAQDHKRAYDGDTGPNTGGMGAYSPAPFI 238

Query: 310 TDKEYQLMRNAAI-----AVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVS------ 358
           TD+  +      +      + KE     G       +     K  VIE N R        
Sbjct: 239 TDEVVERAVEEIVEPTVEGMAKEGYPFRGVLYAGLMLTADGPK--VIEFNARFGDPETQV 296

Query: 359 ---------------------RSSALASKATGFPIAKIAAKLAVGYTLD-ELGNDITGGK 396
                                    +     G  +  + A  A GY  D E G+ ITG +
Sbjct: 297 VLPLLESDLVELLLAAVDGKLDEVEILFWDKGAAVGVVLA--AEGYPGDPEKGDVITGDE 354

Query: 397 TPASFEPSIDYIVTKIPRFTFEKFPGSDVTLTTSMKSVGEVMAIGRTFAESLQKALRGLE 456
                   + +   K               L TS   V  V+  G T  E+ +KA   LE
Sbjct: 355 EAEEEGAKVFHAGVK---------LDDGGQLVTSGGRVLAVVGTGDTLEEAQEKAYEALE 405


>gnl|CDD|37766 KOG2555, KOG2555, KOG2555, AICAR transformylase/IMP
            cyclohydrolase/methylglyoxal synthase [Nucleotide
            transport and metabolism].
          Length = 588

 Score = 34.6 bits (79), Expect = 0.18
 Identities = 22/112 (19%), Positives = 44/112 (39%), Gaps = 18/112 (16%)

Query: 1042 DKKRIVPIIQNFKKLGFKIMATEGTARFLESHGLETQKINKV------LEGR-----PHI 1090
            DK  ++ + +   +LG  ++A+ GTA+ L   GL  + ++++      L GR     P +
Sbjct: 13   DKTGLLDLAKGLVELGVTLVASGGTAKMLRDAGLPVRDVSEITHFPEMLGGRVKTLHPAV 72

Query: 1091 EDAISNRQVHLVINTTEGKKAI-EDSKSLRRATLIRKIPYYTTIAGADAVFQ 1141
               I  R      +    +K + E         +    P+  T+A      +
Sbjct: 73   HGGILAR------DIESDEKDLKEQGIDKVDVVVCNLYPFKETVAKPGVTVE 118


>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase.  Sorbitol and aldose
           reductase are NAD(+) binding proteins of the polyol
           pathway, which interconverts glucose and fructose.
           Sorbitol dehydrogenase is tetrameric and has a single
           catalytic zinc per subunit. Aldose reductase catalyzes
           the NADP(H)-dependent conversion of glucose to sorbital,
           and SDH uses NAD(H) in the conversion of sorbitol to
           fructose.  NAD(P)(H)-dependent oxidoreductases are the
           major enzymes in the interconversion of alcohols and
           aldehydes, or ketones. The medium chain alcohol
           dehydrogenase family (MDR) have a NAD(P)(H)-binding
           domain in a Rossmann fold of a beta-alpha form. The
           N-terminal region typically has an all-beta catalytic
           domain. These proteins typically form dimers (typically
           higher plants, mammals) or tetramers (yeast, bacteria),
           and have 2 tightly bound zinc atoms per subunit.
          Length = 343

 Score = 34.4 bits (80), Expect = 0.18
 Identities = 24/112 (21%), Positives = 48/112 (42%), Gaps = 25/112 (22%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNP----------ATIMTD 57
            T+L+ GAGP  IG             KA      ++++ + +P          AT   +
Sbjct: 164 DTVLVFGAGP--IGLLT------AAVAKAFG--ATKVVVTDIDPSRLEFAKELGATHTVN 213

Query: 58  PDLADATYTEPITPEVVAKIIEKERPDAILPTTGGQTALNTAL-SLKRMGVL 108
               D     P + E +A+++  + PD ++  TG ++ + TA+ + +  G +
Sbjct: 214 VRTEDT----PESAEKIAELLGGKGPDVVIECTGAESCIQTAIYATRPGGTV 261


>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
           dehydrogenase related proteins, child 2.
           Glutathione-dependent formaldehyde dehydrogenases (FDHs)
           are members of the zinc-dependent/medium chain alcohol
           dehydrogenase family. Formaldehyde dehydrogenase (FDH)
           is a member of the zinc-dependent/medium chain alcohol
           dehydrogenase family.  FDH converts formaldehyde and NAD
           to formate and NADH. 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. 
           These tetrameric FDHs have a catalytic zinc that resides
           between the catalytic and NAD(H)binding domains and a
           structural zinc in a lobe of the catalytic domain. The
           medium chain alcohol dehydrogenase family (MDR) has a
           NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form. The N-terminal region typically has an
           all-beta catalytic domain. These proteins typically form
           dimers (typically higher plants, mammals) or tetramers
           (yeast, bacteria), and have 2 tightly bound zinc atoms
           per subunit.
          Length = 344

 Score = 34.2 bits (79), Expect = 0.24
 Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 23/113 (20%)

Query: 9   TLLIIGAGPIVIGQACEFDYSGTQACKALKEEGY-RIILVNSNPATIMTDPDLADATYTE 67
           T+ +IG GP+           G  A  + +  G  R+  V+  P  +    + A A   E
Sbjct: 170 TVAVIGCGPV-----------GLCAVLSAQVLGAARVFAVDPVPERL----ERAAALGAE 214

Query: 68  PITPE---VVAKIIEKER---PDAILPTTGGQTALNTALSL-KRMGVLDRYGV 113
           PI  E    V ++ E       D +L   GG  AL+ A  L +  GV+   GV
Sbjct: 215 PINFEDAEPVERVREATEGRGADVVLEAVGGAAALDLAFDLVRPGGVISSVGV 267


>gnl|CDD|30376 COG0026, PurK, Phosphoribosylaminoimidazole carboxylase (NCAIR
           synthetase) [Nucleotide transport and metabolism].
          Length = 375

 Score = 33.7 bits (77), Expect = 0.30
 Identities = 43/207 (20%), Positives = 82/207 (39%), Gaps = 37/207 (17%)

Query: 729 PDSIDLAEDRDRFQKLLMELDLNQPRNGISHSVEHARLIACEIGFPLLIRPSYVLG--GR 786
           PD++ +A+DR   ++ L +  L      +  S E     A ++GFP +++     G  G+
Sbjct: 91  PDALRIAQDRLVEKQFLDKAGLPVAPFQVVDSAEELDAAAADLGFPAVLKTRR-GGYDGK 149

Query: 787 AMQIVYSENMLQ--DYLLDTLPGLVSEEIKRQYPNDKTGQINTLLGTHPLLFDSYLSDAM 844
               + S+  L+     L      V EE                          ++    
Sbjct: 150 GQWRIRSDADLELRAAGLAEGGVPVLEE--------------------------FVPFER 183

Query: 845 EIDV-DALCQNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQTKALAGA 903
           EI V  A   + +V    + E++   GI     A   P+R +   L+ +     K +A  
Sbjct: 184 EISVIVARSNDGEVAFYPVAENVHRNGILRTSIA---PAR-IPDDLQAQAEEMAKKIAEE 239

Query: 904 LNVIGLINVQ-YAIKDGKIYILEVNPR 929
           L+ +G++ V+ +   DG++ + E+ PR
Sbjct: 240 LDYVGVLAVEFFVTPDGELLVNEIAPR 266


>gnl|CDD|173842 cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to
           fadE5.  Putative acyl-CoA dehydrogenase (ACAD).
           Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze
           the alpha,beta dehydrogenation of the corresponding
           trans-enoyl-CoA by FAD, which becomes reduced. The
           reduced form of ACAD is reoxidized in the oxidative
           half-reaction by electron-transferring flavoprotein
           (ETF), from which the electrons are transferred to the
           mitochondrial respiratory chain coupled with ATP
           synthesis. The ACD family includes the eukaryotic
           beta-oxidation, as well as amino acid catabolism
           enzymes. These enzymes share high sequence similarity,
           but differ in their substrate specificities. The
           mitochondrial ACD's are generally homotetramers and have
           an active site glutamate at a conserved position.
          Length = 407

 Score = 33.5 bits (77), Expect = 0.31
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 8/49 (16%)

Query: 216 GLPLIIRPSFTLGGTGGGIAYNRSEFLEIVEN--GLHASPTTEVLIEES 262
           GL L + P F   G   G+   R      +E   GLH SPT E++ + +
Sbjct: 184 GLSLFLVPKFLDDGERNGVTVAR------IEEKMGLHGSPTCELVFDNA 226


>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase.  L-threonine dehydrogenase
           (TDH) catalyzes the zinc-dependent formation of
           2-amino-3-ketobutyrate from L-threonine via NAD(H)-
           dependent oxidation.  THD is a member of the
           zinc-requiring, medium chain NAD(H)-dependent alcohol
           dehydrogenase family (MDR). MDRs  have a
           NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
           the major enzymes in the interconversion of alcohols and
           aldehydes, or ketones. The N-terminal region typically
           has an all-beta catalytic domain. These proteins
           typically form dimers (typically higher plants, mammals)
           or tetramers (yeast, bacteria) and have 2 tightly bound
           zinc atoms per subunit. Sorbitol and aldose reductase
           are NAD(+) binding proteins of the polyol pathway, which
           interconverts glucose and fructose.
          Length = 341

 Score = 33.0 bits (76), Expect = 0.45
 Identities = 24/102 (23%), Positives = 36/102 (35%), Gaps = 14/102 (13%)

Query: 8   KTLLIIGAGPI---VIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADAT 64
           K++LI G GPI    I  A     +G     A     YR+ L     A ++ +P   D  
Sbjct: 165 KSVLITGCGPIGLMAIAVA---KAAGASLVIASDPNPYRLELAKKMGADVVINPREED-- 219

Query: 65  YTEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMG 106
                    V  + +    D +L  +G   A+   L     G
Sbjct: 220 ------VVEVKSVTDGTGVDVVLEMSGNPKAIEQGLKALTPG 255


>gnl|CDD|33705 COG3919, COG3919, Predicted ATP-grasp enzyme [General function
            prediction only].
          Length = 415

 Score = 33.1 bits (75), Expect = 0.46
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 18/178 (10%)

Query: 892  ELISQTKALAGALNVIGLINV--QYAIKDGKIYILEVNPRASRTVPFIAKAIGFPVAKVA 949
            ++I   +    ++   GL+ V  +Y  +DG   +L+VNPR  R    +  A G+ + +  
Sbjct: 248  QVIQAARDFLESIEHTGLVEVEFKYDPRDGSYKLLDVNPRPWRWF-GLVTAAGYNLGRYL 306

Query: 950  ARIIAGESLDASIAAYGKRPDLSQIKHFAVKESVFPFNKFPGVDILLGPEMRSTGEVIGI 1009
                       +     K         + V++ V      P     +   + S     G 
Sbjct: 307  WADRINNE-TFTETIARKGTSWW----YLVRDKVAAKYLNPSGKEEIRRYINSFTGNRG- 360

Query: 1010 DQDFPLAFAKSQLGIGVDLPHEGTVFVSVRDADKKRIVPIIQNFKKLGFKIMATEGTA 1067
               + L ++       +D P       ++R     RI+   + +K  G K      TA
Sbjct: 361  ---WALFYSNDPSPGLIDKP-----LTAMRVL-FHRILGAFKTWKCYGHKRDGVSSTA 409


>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
           MDR/AHD-like proteins, including a protein annotated as
           a threonine dehydrogenase. L-threonine dehydrogenase
           (TDH) catalyzes the zinc-dependent formation of
           2-amino-3-ketobutyrate from L-threonine via
           NAD(H)-dependent oxidation. The zinc-dependent alcohol
           dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
           interconversion of alcohols to aldehydes or ketones.
           Zinc-dependent ADHs are medium chain
           dehydrogenase/reductase type proteins (MDRs) and have a
           NAD(P)(H)-binding domain in a Rossmann fold of an
           beta-alpha form. The N-terminal region typically has an
           all-beta catalytic domain. In addition to alcohol
           dehydrogenases, this group includes quinone reductase,
           sorbitol dehydrogenase, formaldehyde dehydrogenase,
           butanediol DH, ketose reductase, cinnamyl reductase, and
           numerous others.  These proteins typically form dimers
           (typically higher plants, mammals) or tetramers (yeast,
           bacteria), and generally have 2 tightly bound zinc atoms
           per subunit. The active site zinc is coordinated by a
           histidine, two cysteines, and a water molecule. The
           second zinc seems to play a structural role, affects
           subunit interactions, and is typically coordinated by 4
           cysteines.
          Length = 339

 Score = 32.7 bits (75), Expect = 0.65
 Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 15/104 (14%)

Query: 9   TLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYR-IILVNSNPATIMTDPDL-ADATYT 66
           T+L++GAGP+ +G             +AL   G   +I V+ +P  +     L AD    
Sbjct: 166 TVLVVGAGPVGLG--------ALMLARAL---GAEDVIGVDPSPERLELAKALGADFVIN 214

Query: 67  -EPITPEVVAKIIEKERPDAILPTTGGQTALNTAL-SLKRMGVL 108
                 + + ++      D  +  +G   A   AL +++  G L
Sbjct: 215 SGQDDVQEIRELTSGAGADVAIECSGNTAARRLALEAVRPWGRL 258


>gnl|CDD|32019 COG1834, COG1834, N-Dimethylarginine dimethylaminohydrolase [Amino
           acid transport and metabolism].
          Length = 267

 Score = 32.5 bits (74), Expect = 0.76
 Identities = 28/134 (20%), Positives = 46/134 (34%), Gaps = 17/134 (12%)

Query: 10  LLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLA-----DAT 64
           +L+ G   + IG +   +  G +  +A  EEGY + LV  +   +  D          A 
Sbjct: 123 VLMDGGDTVYIGYSFRTNLEGIEQLQAWLEEGYEVSLVRLDERYLHLDTVFNPLAEGLAL 182

Query: 65  YTEPITPEVVAKIIEKERPDAILPTTGGQTAL---------NTALSLKRMGV---LDRYG 112
              P   E    ++++   + I        AL         N  ++L R      L   G
Sbjct: 183 AYPPAFSEGANDVLKERGFELIEVPEEEAFALGCNVVSLGPNVVIALPRTPKAEQLAAAG 242

Query: 113 VEMIGAKPETIDKA 126
            E+I      I K 
Sbjct: 243 FEVIEVDLTEILKG 256


>gnl|CDD|176192 cd08230, glucose_DH, Glucose dehydrogenase.  Glucose dehydrogenase
           (GlcDH), a member of the medium chain
           dehydrogenase/zinc-dependent alcohol dehydrogenase-like
           family, catalyzes the NADP(+)-dependent oxidation of
           glucose to gluconate, the first step in the
           Entner-Doudoroff pathway, an alternative to or
           substitute for glycolysis or the pentose phosphate
           pathway. The medium chain dehydrogenases/reductase
           (MDR)/zinc-dependent alcohol dehydrogenase-like family,
           which contains the zinc-dependent alcohol dehydrogenase
           (ADH-Zn) and related proteins, is a diverse group of
           proteins related to the first identified member, class I
           mammalian ADH.  MDRs display a broad range of activities
           and are distinguished from the smaller short chain
           dehydrogenases  (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P) binding-Rossman fold domain of a
           beta-alpha form and an N-terminal catalytic domain with
           distant homology  to GroES.  The MDR group contains a
           host of activities, including the founding alcohol
           dehydrogenase (ADH), quinone reductase, sorbitol
           dehydrogenase, formaldehyde dehydrogenase, butanediol
           DH, ketose reductase, cinnamyl reductase, and numerous
           others. The zinc-dependent alcohol dehydrogenases (ADHs)
           catalyze the  NAD(P)(H)-dependent interconversion of
           alcohols to aldehydes or ketones. Active site zinc has a
           catalytic role, while structural zinc aids in stability.
          Length = 355

 Score = 32.2 bits (74), Expect = 0.83
 Identities = 26/110 (23%), Positives = 43/110 (39%), Gaps = 23/110 (20%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLAD---AT 64
           +  L++GAGPI           G  A   L+  G+ + ++N          D+ +   AT
Sbjct: 174 RRALVLGAGPI-----------GLLAALLLRLRGFEVYVLNRRDPPDPK-ADIVEELGAT 221

Query: 65  Y-TEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGV 113
           Y     TP    K++ +   D I+  TG        L+ + +  L   GV
Sbjct: 222 YVNSSKTPVAEVKLVGE--FDLIIEATG-----VPPLAFEALPALAPNGV 264


>gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the
           zinc-dependent alcohol dehydrogenases (ADH).  This group
           contains the hypothetical TM0436 alcohol dehydrogenase
           from Thermotoga maritima,  proteins annotated as
           5-exo-alcohol dehydrogenase, and other members of the
           medium chain dehydrogenases/reductase
           (MDR)/zinc-dependent alcohol dehydrogenase-like family. 
           MDR, which contains the zinc-dependent alcohol
           dehydrogenase (ADH-Zn) and related proteins, is a
           diverse group of proteins related to the first
           identified member, class I mammalian ADH.  MDRs display
           a broad range of activities and are distinguished from
           the smaller short chain dehydrogenases (~ 250 amino
           acids vs. the ~ 350 amino acids of the MDR).  The MDR
           proteins have 2 domains: a C-terminal NAD(P)
           binding-Rossmann fold domain of a beta-alpha form and an
           N-terminal catalytic domain with distant homology to
           GroES.  The MDR group contains a host of activities,
           including the founding alcohol dehydrogenase (ADH),
           quinone reductase, sorbitol dehydrogenase, formaldehyde
           dehydrogenase, butanediol DH, ketose reductase, cinnamyl
           reductase, and numerous others. The zinc-dependent
           alcohol dehydrogenases (ADHs) catalyze the
           NAD(P)(H)-dependent interconversion of alcohols to
           aldehydes or ketones. Active site zinc has a catalytic
           role, while structural zinc aids in stability.
          Length = 361

 Score = 32.2 bits (74), Expect = 0.95
 Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 18/106 (16%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGY-RIILVNSNPA------TIMTDPDL 60
            T+++ GAGP+           G  A  A K  G  R+I+++ +P           D  +
Sbjct: 179 DTVVVQGAGPL-----------GLYAVAAAKLAGARRVIVIDGSPERLELAREFGADATI 227

Query: 61  ADATYTEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMG 106
                 +P    +V  I      D ++  +G   A+   L L R G
Sbjct: 228 DIDELPDPQRRAIVRDITGGRGADVVIEASGHPAAVPEGLELLRRG 273


>gnl|CDD|32006 COG1821, COG1821, Predicted ATP-utilizing enzyme (ATP-grasp
           superfamily) [General function prediction only].
          Length = 307

 Score = 31.9 bits (72), Expect = 1.1
 Identities = 24/113 (21%), Positives = 44/113 (38%), Gaps = 11/113 (9%)

Query: 847 DVDALCQNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQTKALAGALNV 906
            V  L  N Q I+    E +   G    D         L ++  +E I   + + G   +
Sbjct: 184 KVLPLSVNRQFIIFAGSELVYNGGRTPIDH-------ELKREAFEEAIRAVECIPG---L 233

Query: 907 IGLINVQYAIKDGKIYILEVNPRASRTVPFIAKAIGFPVAKVAARIIAGESLD 959
            G + V   + D   Y++E+NPR +     +++     VA++      G+ L 
Sbjct: 234 NGYVGVDLVLSDE-PYVIEINPRPTTPTVGLSRVTPESVAELLLEGPTGKVLR 285


>gnl|CDD|31263 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
           dehydrogenases [Amino acid transport and metabolism /
           General function prediction only].
          Length = 350

 Score = 31.5 bits (71), Expect = 1.3
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 14/102 (13%)

Query: 9   TLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADATYT-- 66
           T++++GAGP  IG             K L      +I+V+ +P  +    +   A     
Sbjct: 171 TVVVVGAGP--IGLL------AIALAKLLGAS--VVIVVDRSPERLELAKEAGGADVVVN 220

Query: 67  --EPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMG 106
             E      + ++      D ++   G   AL+ AL   R G
Sbjct: 221 PSEDDAGAEILELTGGRGADVVIEAVGSPPALDQALEALRPG 262


>gnl|CDD|113104 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
          L-rhamnose is a saccharide required for the virulence
          of some bacteria. Its precursor, dTDP-L-rhamnose, is
          synthesized by four different enzymes the final one of
          which is RmlD. The RmlD substrate binding domain is
          responsible for binding a sugar nucleotide.
          Length = 284

 Score = 31.4 bits (72), Expect = 1.5
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 24/77 (31%)

Query: 10 LLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADATYTEPI 69
          +L+ GA     GQ       G +  + L E G  ++ ++          DL D       
Sbjct: 1  ILVTGAN----GQL------GRELTRLLAERGVEVVALDRPEL------DLTD------- 37

Query: 70 TPEVVAKIIEKERPDAI 86
           PE VA ++ + RPD +
Sbjct: 38 -PEAVAALVREARPDVV 53


>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD).  These
           alcohol dehydrogenases are related to the cinnamyl
           alcohol dehydrogenases (CAD), members of the medium
           chain dehydrogenase/reductase family.
           NAD(P)(H)-dependent oxidoreductases are the major
           enzymes in the interconversion of alcohols and
           aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
           (CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
           last step of monolignal metabolism in plant cells walls.
           CAD binds 2 zinc ions and is NADPH- dependent. CAD
           family members are also found in non-plant species, e.g.
           in yeast where they have an aldehyde reductase activity.
           The medium chain dehydrogenases/reductase
           (MDR)/zinc-dependent alcohol dehydrogenase-like family,
           which contains the zinc-dependent alcohol dehydrogenase
           (ADH-Zn) and related proteins, is a diverse group of
           proteins related to the first identified member, class I
           mammalian ADH.  MDRs display a broad range of activities
           and are distinguished from the smaller short chain
           dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P) binding-Rossmann fold domain of a
           beta-alpha form and an N-terminal catalytic domain with
           distant homology to GroES.  The MDR group contains a
           host of activities, including the founding alcohol
           dehydrogenase (ADH), quinone reductase, sorbitol
           dehydrogenase, formaldehyde dehydrogenase, butanediol
           DH, ketose reductase, cinnamyl reductase, and numerous
           others. The zinc-dependent alcohol dehydrogenases (ADHs)
           catalyze the NAD(P)(H)-dependent interconversion of
           alcohols to aldehydes or ketones.  Active site zinc has
           a catalytic role, while structural zinc aids in
           stability.  ADH-like proteins typically form dimers
           (typically higher plants, mammals) or tetramers (yeast,
           bacteria), and generally have 2 tightly bound zinc atoms
           per subunit. The active site zinc is coordinated by a
           histidine, two cysteines, and a water molecule. The
           second zinc seems to play a structural role, affects
           subunit interactions, and is typically coordinated by 4
           cysteines.
          Length = 341

 Score = 30.6 bits (70), Expect = 2.3
 Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 15/87 (17%)

Query: 30  GTQACKALKEEGYRIILVNSNPATIMTDPDL-----ADAT--YTEPITPEVVAKIIEKER 82
           G Q  KA+   G R+I ++     +    +L     ADA   + +    E V ++     
Sbjct: 182 GVQYAKAM---GLRVIAIDVGDEKL----ELAKELGADAFVDFKKSDDVEAVKELTGGGG 234

Query: 83  PDAILPTTGGQTALNTALS-LKRMGVL 108
             A++ T     A   AL  L+  G L
Sbjct: 235 AHAVVVTAVSAAAYEQALDYLRPGGTL 261


>gnl|CDD|37175 KOG1964, KOG1964, KOG1964, Nuclear pore complex, rNup107 component
           (sc Nup84) [Nuclear structure, Intracellular
           trafficking, secretion, and vesicular transport].
          Length = 800

 Score = 30.4 bits (68), Expect = 2.9
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 13/105 (12%)

Query: 796 MLQDYLLDTLPGLVSEEIKRQYPNDKTGQINTLL---GTHPLLFDSYLSDAMEIDVDALC 852
           +    +LD +  L+ E +      D+ GQ+   L    TH +LF   +S     +  +  
Sbjct: 391 LQNHLILDLIKELI-ESVVEWLEKDRNGQVPPHLLRIMTHLVLF-LRISGLEVNEDGS-- 446

Query: 853 QNDQVIVVGIIEHIEEAGIHSGDSACSLPSRSLSQQLKDELISQT 897
                I++  IE +  +G H    A    +R L + L+ E  S+ 
Sbjct: 447 ---AKIILTYIELLARSG-HKNLIA--FYTRFLPEDLQLEAYSRF 485


>gnl|CDD|143468 cd07150, ALDH_VaniDH_like, Pseudomonas putida vanillin
           dehydrogenase-like.  Vanillin dehydrogenase (Vdh,
           VaniDH) involved in the metabolism of ferulic acid and
           other related  sequences are included in this CD.  The
           E. coli vanillin dehydrogenase (LigV) preferred NAD+ to
           NADP+  and exhibited a broad substrate preference,
           including vanillin,  benzaldehyde, protocatechualdehyde,
           m-anisaldehyde, and p-hydroxybenzaldehyde.
          Length = 451

 Score = 30.4 bits (69), Expect = 3.2
 Identities = 25/77 (32%), Positives = 34/77 (44%), Gaps = 12/77 (15%)

Query: 324 VLKEIGVESGGANVQFAVNPKNGKMVVIEM--NPRVSRSSALASKATGFPIAKIAAKLAV 381
           +++E G+  G  NV        G  V  E+  +PRV   +   S A G  IA+ A +   
Sbjct: 168 IMEEAGLPKGVFNVV----TGGGAEVGDELVDDPRVRMVTFTGSTAVGREIAEKAGRHLK 223

Query: 382 GYTLDELGNDITGGKTP 398
             TL EL     GGK P
Sbjct: 224 KITL-EL-----GGKNP 234


>gnl|CDD|32398 COG2216, KdpB, High-affinity K+ transport system, ATPase chain B
           [Inorganic ion transport and metabolism].
          Length = 681

 Score = 30.2 bits (68), Expect = 3.5
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 4/57 (7%)

Query: 648 LKEAGFETIMINC-NPETVSTDYDIA--DRLYFESLTEEDILEILRVEQQKGELVGI 701
           L++ G +T+MI   NP T +     A  D    E+ T ED L ++R EQ +G LV +
Sbjct: 459 LRKMGIKTVMITGDNPLTAAAIAAEAGVDDFIAEA-TPEDKLALIRQEQAEGRLVAM 514


>gnl|CDD|31342 COG1148, HdrA, Heterodisulfide reductase, subunit A and related
           polyferredoxins [Energy production and conversion].
          Length = 622

 Score = 30.3 bits (68), Expect = 3.6
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 11/57 (19%)

Query: 607 NKPVSEDKVSDRKKIVILGGGPNRIGQGIEFDYCCCHASFSLKEAGFETIMINCNPE 663
            +P+ E KV   K ++++GGG      GI        A+  L + GF+  ++   P 
Sbjct: 113 LEPLEEIKVEVSKSVLVIGGGV----AGIT-------AALELADMGFKVYLVEKEPS 158


>gnl|CDD|31284 COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis,
          outer membrane].
          Length = 329

 Score = 30.1 bits (68), Expect = 4.1
 Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 18/70 (25%)

Query: 28 YSGTQACKALKEEGYRII----LVNSNPATIMTDP------DLADATYTEPITPEVVAKI 77
          Y G+   + L + G+ ++    L N +   ++         DL D          ++  +
Sbjct: 11 YIGSHTVRQLLKTGHEVVVLDNLSNGHKIALLKLQFKFYEGDLLDR--------ALLTAV 62

Query: 78 IEKERPDAIL 87
           E+ + DA++
Sbjct: 63 FEENKIDAVV 72


>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
           function prediction only].
          Length = 339

 Score = 29.8 bits (67), Expect = 5.0
 Identities = 25/113 (22%), Positives = 42/113 (37%), Gaps = 13/113 (11%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPDLADATYTE 67
           K + ++GAG +             Q  KA+   G  +I +  +   +     L       
Sbjct: 168 KWVAVVGAGGLGH--------MAVQYAKAM---GAEVIAITRSEEKLELAKKLGADHVIN 216

Query: 68  PITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDRYGVEMIGAKP 120
               + +  +  KE  DAI+ T G  T   +  +L+R G L   G+   G  P
Sbjct: 217 SSDSDALEAV--KEIADAIIDTVGPATLEPSLKALRRGGTLVLVGLPGGGPIP 267


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

 Score = 29.5 bits (66), Expect = 5.0
 Identities = 55/263 (20%), Positives = 97/263 (36%), Gaps = 55/263 (20%)

Query: 273 MMRDIKGNCIVVCSIENLDPMGVHTGDSIT----VAPALTLTDKEYQLMRNAAIAVLKEI 328
           M R +K    V      ++ + V  GD +     V PA  +++++ +      +      
Sbjct: 456 MNRHVKAGGKVEVDPVAIENLKVTRGDFLNALEDVKPAFGISEEDLERFVMNGMINWGPP 515

Query: 329 ---GVESGGANVQFAVNPKNGKMV-VIEMNPRVSRSSALASKA---TGFPIAKI-AAKLA 380
               ++ G   VQ   N +   +V V+   P  S  +ALA+K    + FP  KI + +  
Sbjct: 516 VTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDM 575

Query: 381 VGYTLDELGNDITGG-----KTPAS------FEPSIDYIVTKIPRFT----------FEK 419
           +G +       I        K+P S       E  +DY+    PRF+           +K
Sbjct: 576 IGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVPIG-PRFSNLVLQALLVLLKK 634

Query: 420 FPGSDVTL----TTSMKSVGEVMAIGRTFAESLQKALRGLETGLTGLDEIHIPSMESDND 475
            P     L    TTS + V + M I   F+                   IH+P++ +   
Sbjct: 635 QPPKGRKLLIFGTTSRREVLQEMGILDCFS-----------------STIHVPNLTTGEQ 677

Query: 476 PNALRSAISIPCPDRLRTVAQAL 498
              +   ++I   D +R +A+ L
Sbjct: 678 LLEVLEELNIFSDDEVRAIAEQL 700


>gnl|CDD|145188 pfam01887, SAM_adeno_trans, S-adenosyl-l-methionine hydroxide
           adenosyltransferase.  This is a family of proteins,
           previously known as DUF62, found in archaebacteria and
           bacteria. The structure of proteins in this family is
           similar to that of a bacterial fluorinating enzyme.
           S-adenosyl-l-methionine hydroxide adenosyltransferases
           utilizes a rigorously conserved amino acid side chain
           triad (Asp-Arg-His) which may have a role in activating
           water to hydroxide ion. This family used to be known as
           DUF62.
          Length = 258

 Score = 29.8 bits (68), Expect = 5.0
 Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 19/91 (20%)

Query: 373 AKIAAKLAVGYTLDELGNDITGG--KTPASFEPSID---------YI------VTKIPRF 415
           A  AA LA G  L+ELG +I           EPS++         YI      +T I R 
Sbjct: 131 APAAAHLARGGPLEELGPEIDPDSLVRLPLPEPSVEDDGIEGEVIYIDHFGNVITNITRE 190

Query: 416 TFEKFPGSDVTLTTSMKSVGEVMAIGRTFAE 446
            F    G  V +    +    ++   RT+ +
Sbjct: 191 LFGLGKGDRVEVRIRGEK--LILPFVRTYGD 219


>gnl|CDD|146510 pfam03915, AIP3, Actin interacting protein 3. 
          Length = 422

 Score = 29.6 bits (67), Expect = 5.1
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 2/93 (2%)

Query: 256 EVLIEESVLGWKEYELEMMRDIKGNCIVVCSIENLDPMGVHTGDSI-TVAPALTLTDKEY 314
           ++ I++ V G   YELE + DIK   ++V ++E LD +  H  DS+  ++  +    +  
Sbjct: 41  DIYIQDPVSG-VSYELEELSDIKDGSVLVLNVEELDEVKKHIDDSLGGLSEKIKSLKQAL 99

Query: 315 QLMRNAAIAVLKEIGVESGGANVQFAVNPKNGK 347
              +N  +  LKE+   +     + A  P    
Sbjct: 100 DDQQNTILQRLKELQQNAAKEVARPAAAPPPSS 132


>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family.  This
           group contains members identified as related to
           zinc-dependent alcohol dehydrogenase and other members
           of the MDR family. The medium chain
           dehydrogenases/reductase (MDR)/zinc-dependent alcohol
           dehydrogenase-like family, which contains the
           zinc-dependent alcohol dehydrogenase (ADH-Zn) and
           related proteins, is a diverse group of proteins related
           to the first identified member, class I mammalian ADH.
           MDRs display a broad range of activities and are
           distinguished from the smaller short chain
           dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
           acids of the MDR).  The MDR proteins have 2 domains: a
           C-terminal NAD(P)-binding Rossmann fold domain of a
           beta-alpha form and an N-terminal catalytic domain with
           distant homology to GroES.  The MDR group includes
           various activities, including the founding alcohol
           dehydrogenase (ADH), quinone reductase, sorbitol
           dehydrogenase, formaldehyde dehydrogenase, butanediol
           DH, ketose reductase, cinnamyl reductase, and numerous
           others. The zinc-dependent alcohol dehydrogenases (ADHs)
           catalyze the NAD(P)(H)-dependent interconversion of
           alcohols to aldehydes or ketones. Active site zinc has a
           catalytic role, while structural zinc aids in stability.
            ADH-like proteins typically form dimers (typically
           higher plants, mammals) or tetramers (yeast, bacteria),
           and generally have 2 tightly bound zinc atoms per
           subunit. The active site zinc is coordinated by a
           histidine, two cysteines, and a water molecule. The
           second zinc seems to play a structural role, affects
           subunit interactions, and is typically coordinated by 4
           cysteines.
          Length = 337

 Score = 29.5 bits (67), Expect = 5.3
 Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 28/104 (26%)

Query: 9   TLLIIGAGPIVIGQACEFDYSGTQACKALKEEGYRIILVNSNPATIMTDPD--------L 60
           T+L++GAGPI +G             +  K  G R+I+V+        D +         
Sbjct: 162 TVLVVGAGPIGLG-----------VIQVAKARGARVIVVD-------IDDERLEFARELG 203

Query: 61  ADATY--TEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSL 102
           AD T    +      + ++ + E  D ++  TG   ++  A+ L
Sbjct: 204 ADDTINVGDEDVAARLRELTDGEGADVVIDATGNPASMEEAVEL 247


>gnl|CDD|110097 pfam01071, GARS_A, Phosphoribosylglycinamide synthetase, ATP-grasp
           (A) domain.  Phosphoribosylglycinamide synthetase
           catalyses the second step in the de novo biosynthesis of
           purine. The reaction catalysed by
           Phosphoribosylglycinamide synthetase is the ATP-
           dependent addition of 5-phosphoribosylamine to glycine
           to form 5'phosphoribosylglycinamide. This domain is
           related to the ATP-grasp domain of biotin
           carboxylase/carbamoyl phosphate synthetase (see
           pfam02786).
          Length = 193

 Score = 29.5 bits (67), Expect = 6.1
 Identities = 34/172 (19%), Positives = 61/172 (35%), Gaps = 36/172 (20%)

Query: 208 AVQALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFLEIVENGLHASPTTE----VLIEESV 263
           A   + E G P +++      G G  +A +  E ++ V+  L      E    V+IEE +
Sbjct: 29  AKSYIREAGFPAVVKADGLAAGKGVIVAMDNEEAIKAVDEILEQKKFGEAGEPVVIEEFL 88

Query: 264 LGWKEYELEMMRDIKGNCIVVCSIENLDPM--------------GVHTGDSITVAPALTL 309
            G    E+ ++  + G  +         P+              G +TG     +PA  L
Sbjct: 89  EG---EEVSVLAFVDGKTVK--------PLPPAQDHKRLGEGDTGPNTGGMGAYSPAPVL 137

Query: 310 TDKEYQLMRNAAI-----AVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPR 356
           T +  + ++   +      + KE     G       +     K  V+E N R
Sbjct: 138 TPELLERIKETIVEPTVDGLRKEGIPYKGVLYAGLMLTKDGPK--VLEFNCR 187


>gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and
           fumarase class II enzymes.  This group contains
           aspartase (L-aspartate ammonia-lyase), fumarase class II
           enzymes, and related proteins. It is a member of the
           Lyase class I family. Members of this family for the
           most part catalyze similar beta-elimination reactions in
           which a C-N or C-O bond is cleaved with the release of
           fumarate as one of the products. These proteins are
           active as tetramers. The four active sites of the
           homotetrameric enzyme are each formed by residues from
           three different subunits. Aspartase catalyzes the
           reversible deamination of aspartic acid. Fumarase
           catalyzes the reversible hydration/dehydration of
           fumarate to L-malate during the Krebs cycle.
          Length = 450

 Score = 29.3 bits (67), Expect = 6.2
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 393 TGGKTPASFEPSIDYIVTKIPRFTFEKFPGSD--VTLTTSMKSVGEVMAIGRTFAESLQK 450
           TG   P  +    + +  ++   T   F  +      T +  ++ EV    +T A SL K
Sbjct: 229 TGLNAPPGY---AEKVAAELAELTGLPFVTAPNLFEATAAHDALVEVSGALKTLAVSLSK 285

Query: 451 A---LRGLETG-LTGLDEIHIPSME 471
               LR L +G   GL EI++P+ +
Sbjct: 286 IANDLRLLSSGPRAGLGEINLPANQ 310


>gnl|CDD|34435 COG4826, COG4826, Serine protease inhibitor [Posttranslational
           modification, protein turnover, chaperones].
          Length = 410

 Score = 29.2 bits (65), Expect = 6.4
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 4/41 (9%)

Query: 403 PSIDYIVTKIPRFTFEKFPGSDVTLTTSMKSVGEVMAIGRT 443
              D +  +IP+F FE    +   L  ++  +G V A   T
Sbjct: 292 EDQDEVEVEIPKFKFE----TKTELKDALIEMGVVDAFENT 328


>gnl|CDD|107353 cd06358, PBP1_NHase, Type I periplasmic-binding protein of the
           nitrile hydratase (NHase) system that selectively
           converts nitriles to corresponding amides.  This group
           includes the type I periplasmic-binding protein of the
           nitrile hydratase (NHase) system that selectively
           converts nitriles to corresponding amides, which are
           subsequently converted by amidases to yield free
           carboxylic acids and ammonia. NHases from bacteria and
           fungi have been purified and characterized. In
           Rhodococcus sp., the nitrile hydratase operon consists
           of six genes encoding NHase regulator 2, NHase regulator
           1, amidase, NHase alpha subunit, NHase beta subunit, and
           NHase activator. The operon produces a constitutive
           hydratase that has a broad substrate spectrum: aliphatic
           and aromatic nitriles, mononitriles and dinitriles,
           hydroxynitriles and amino-nitriles, and a constitutive
           amidase of equally low substrate specificity. NHases are
           metalloenzymes containing either cobalt or iron, and
           therefore can be classified into two subgroups: ferric
           NHases and cobalt NHases.
          Length = 333

 Score = 29.1 bits (66), Expect = 7.1
 Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 72  EVVAKIIEKERPDAILPTTGGQTALNTALSLKRMGVLDR 110
            V+ +I      DA+L T  GQ A+         G+ DR
Sbjct: 178 SVLERI-AASGADAVLSTLVGQDAVAFNRQFAAAGLRDR 215


>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases.  This
           group contains proteins identified as sorbitol
           dehydrogenases and other sugar dehydrogenases of the
           medium-chain dehydrogenase/reductase family (MDR), which
           includes zinc-dependent alcohol dehydrogenase and
           related proteins. Sorbitol and aldose reductase are
           NAD(+) binding proteins of the polyol pathway, which
           interconverts glucose and fructose. Sorbitol
           dehydrogenase is tetrameric and has a single catalytic
           zinc per subunit. NAD(P)(H)-dependent oxidoreductases
           are the major enzymes in the interconversion of alcohols
           and aldehydes, or ketones. Related proteins include
           threonine dehydrogenase, formaldehyde dehydrogenase, and
           butanediol dehydrogenase. The medium chain alcohol
           dehydrogenase family (MDR) has a NAD(P)(H)-binding
           domain in a Rossmann fold of a beta-alpha form. The
           N-terminal region typically has an all-beta catalytic
           domain. These proteins typically form dimers (typically
           higher plants, mammals) or tetramers (yeast, bacteria),
           and have 2 tightly bound zinc atoms per subunit. Horse
           liver alcohol dehydrogenase is a dimeric enzyme and each
           subunit has two domains. The NAD binding domain is in a
           Rossmann fold and the catalytic domain contains a zinc
           ion to which substrates bind. There is a cleft between
           the domains that closes upon formation of the ternary
           complex.
          Length = 343

 Score = 29.1 bits (66), Expect = 7.4
 Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 14/102 (13%)

Query: 8   KTLLIIGAGPIVIGQACEFDYSGTQACKALKEEGY-RIILVNSNPATIMTDPDL-ADATY 65
            T+++IGAG I           G  A + LK  G  R+I V+ +   +    +L AD T 
Sbjct: 161 DTVVVIGAGTI-----------GLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDTI 209

Query: 66  -TEPITPEVVAKIIEKERPDAILPTTGGQTALNTALSLKRMG 106
             +    E V ++ E    D ++   G    +  AL+L R G
Sbjct: 210 NPKEEDVEKVRELTEGRGADLVIEAAGSPATIEQALALARPG 251


>gnl|CDD|31945 COG1759, COG1759, ATP-utilizing enzymes of ATP-grasp superfamily
           (probably carboligases) [General function prediction
           only].
          Length = 361

 Score = 29.0 bits (65), Expect = 7.6
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 187 LKWNLEENDRKHRYICHAMAVAV----QALDEIGLPLIIRPSFTLGGTGGGIAYNRSEFL 242
           L+W  EE+ +    +     + +    ++ +EI  P+I++     GG G  IA +  EF 
Sbjct: 119 LRW--EEDRKLEYKLLEKAGLRIPKKYKSPEEIDRPVIVKLPGAKGGRGYFIASSPEEFY 176

Query: 243 EIVENGLHASPTTE-----VLIEESVLG 265
           E  E  L     TE       IEE V+G
Sbjct: 177 EKAERLLKRGVITEEDLKNARIEEYVVG 204


>gnl|CDD|30854 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
            dihydrolipoamide acyltransferase (E2) component, and
            related enzymes [Energy production and conversion].
          Length = 404

 Score = 28.8 bits (64), Expect = 8.1
 Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 1021 QLGIGVDLPHEGTVFVSVRDADKKRIVPIIQNFKKL 1056
             +GI VD P  G V   +RDADKK +  I +  K L
Sbjct: 268  NIGIAVDTPR-GLVVPVIRDADKKSLAEIAKEIKDL 302


>gnl|CDD|31216 COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy
           production and conversion].
          Length = 472

 Score = 28.8 bits (64), Expect = 9.9
 Identities = 28/87 (32%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 320 AAIAVLKEIGVESGGANVQFAVNPKNGKMVVIEMNPRVSRSSALASKATGFPIAKIAAKL 379
           A   +  E G+ +G  NV      + G  +V   +P V   S   S A G  IA  AA  
Sbjct: 178 ALAELAAEAGLPAGVLNVVTGGGAEVGDALVA--HPDVDAISFTGSTAVGRAIAAAAAAN 235

Query: 380 AVGYTLDELGNDITGGKTPASFEPSID 406
               TL EL     GGK+PA      D
Sbjct: 236 LKPVTL-EL-----GGKSPAIVLEDAD 256


  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
   0.318    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0772    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 13,770,662
Number of extensions: 761962
Number of successful extensions: 2297
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2235
Number of HSP's successfully gapped: 93
Length of query: 1162
Length of database: 6,263,737
Length adjustment: 104
Effective length of query: 1058
Effective length of database: 4,016,401
Effective search space: 4249352258
Effective search space used: 4249352258
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.0 bits)