RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780808|ref|YP_003065221.1| tRNA uridine
5-carboxymethylaminomethyl modification enzyme GidA [Candidatus
Liberibacter asiaticus str. psy62]
         (626 letters)



>gnl|CDD|179960 PRK05192, PRK05192, tRNA uridine 5-carboxymethylaminomethyl
           modification enzyme GidA; Validated.
          Length = 618

 Score = 1034 bits (2676), Expect = 0.0
 Identities = 330/619 (53%), Positives = 422/619 (68%), Gaps = 7/619 (1%)

Query: 3   NRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREI 62
              YDVIV+GGGHAGCEAA  AA++GA T L+TH   TIG MSCNPAIGG+ KGHLVREI
Sbjct: 2   PEEYDVIVVGGGHAGCEAALAAARMGAKTLLLTHNLDTIGQMSCNPAIGGIAKGHLVREI 61

Query: 63  DALDGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQREILSQENLDVIQG 122
           DAL G MG+  D  GIQFR+LN  KGPAVR  R QADR+LYR AM+  + +Q NLD+ QG
Sbjct: 62  DALGGEMGKAIDKTGIQFRMLNTSKGPAVRALRAQADRKLYRAAMREILENQPNLDLFQG 121

Query: 123 EVAGFNTEKNIISSIVMQDNSMIRCSTVVLTTGTFLRGVIHIGKLKIPAGRMGDSPSNSL 182
           EV     E   +  +V QD    R   VVLTTGTFLRG IHIG+     GR G+ PS  L
Sbjct: 122 EVEDLIVENGRVVGVVTQDGLEFRAKAVVLTTGTFLRGKIHIGEKNYSGGRAGEPPSIGL 181

Query: 183 FNSFMKFDFDTGRLKTGTPARLDGKTIIWDKTEKQFADERLIPFSFMTDKITNRQIECGI 242
             S  +  F+ GRLKTGTP R+DG++I + K E+Q  D+   PFSFMT+KI   Q+ C I
Sbjct: 182 SESLRELGFELGRLKTGTPPRIDGRSIDFSKLEEQPGDDPPPPFSFMTEKIHPPQVPCYI 241

Query: 243 TRTNLETHRIIMENIKHSAIYSGDIKSYGPRYCPSIEDKIVRFGERNGHQIFLEPEGLNT 302
           T TN ETH II EN+  S +YSG I+  GPRYCPSIEDKIVRF +++ HQIFLEPEGL+T
Sbjct: 242 TYTNEETHEIIRENLHRSPMYSGVIEGVGPRYCPSIEDKIVRFADKDRHQIFLEPEGLDT 301

Query: 303 DVVYPNGISTALPEEIQHQFIRTIPGLEKVNIIRPGYAIEYDYINPKELFPTLETKKISG 362
           + VYPNGIST+LPE++Q + +R+IPGLE   I+RPGYAIEYDY++P++L PTLETKKI G
Sbjct: 302 NEVYPNGISTSLPEDVQLEMLRSIPGLENAEILRPGYAIEYDYVDPRQLKPTLETKKIKG 361

Query: 363 LFLAGQINGTTGYEEAAAQGLVAGINSARKSNKLDCICFSRTDSYIGVMIDDLTSKGVLE 422
           LF AGQINGTTGYEEAAAQGL+AGIN+A K  + +     R+++YIGV+IDDL +KG  E
Sbjct: 362 LFFAGQINGTTGYEEAAAQGLIAGINAALKV-QGEPFILKRSEAYIGVLIDDLVTKGTKE 420

Query: 423 PYRMFTSRAEYRISLRPDNADNRLTPIGMKLGCIGERRQKRFAKYIQEYNFLRSLLKSLV 482
           PYRMFTSRAEYR+ LR DNAD RLT  G +LG + + R  RF +  +        LKS  
Sbjct: 421 PYRMFTSRAEYRLLLREDNADLRLTEKGYELGLVDDERWARFEEKKEAIEEEIERLKSTR 480

Query: 483 LTSKNLSSTSISFKQDGKTR--TAYEFLSYPDFSIQNLFSICPDARKFSSLVIERLQIES 540
           +T   L+        D   R  +  + L  P+ + ++L  + P+       V E+++IE 
Sbjct: 481 VTPDELN----ELGGDPLKREVSLLDLLRRPEITYEDLAKLDPELADLDPEVAEQVEIEI 536

Query: 541 SYAAYTGRQMIEAKEIKFEEKRLIPKDFDYSSLPALSNELKEKLSILKPFNLLQASKIEG 600
            Y  Y  RQ  E +++K  E + IP+D DY ++  LSNE +EKL+ ++P  + QAS+I G
Sbjct: 537 KYEGYIERQQEEIEKLKRLENKKIPEDIDYDAISGLSNEAREKLNKIRPETIGQASRISG 596

Query: 601 MTPAALNLLLIYIKKNTVK 619
           +TPA +++LL+Y+KK    
Sbjct: 597 VTPADISILLVYLKKRGRL 615


>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A.  GidA, the
           longer of two forms of GidA-related proteins, appears to
           be present in all complete eubacterial genomes so far,
           as well as Saccharomyces cerevisiae. A subset of these
           organisms have a closely related protein. GidA is absent
           in the Archaea. It appears to act with MnmE, in an
           alpha2/beta2 heterotetramer, in the
           5-carboxymethylaminomethyl modification of uridine 34 in
           certain tRNAs. The shorter, related protein, previously
           called gid or gidA(S), is now called TrmFO (see model
           TIGR00137).
          Length = 617

 Score =  781 bits (2019), Expect = 0.0
 Identities = 316/617 (51%), Positives = 405/617 (65%), Gaps = 9/617 (1%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREIDAL 65
           +DVIVIGGGHAGCEAA  AA++GA T L+T    TIG  SCNPAIGG  KG LV+EIDAL
Sbjct: 1   FDVIVIGGGHAGCEAALAAARMGAKTLLLTLNLDTIGKCSCNPAIGGPAKGILVKEIDAL 60

Query: 66  DGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQREILSQENLDVIQGEVA 125
            GLMG+ AD AG+QFRVLN  KGPAVR  R Q D+ LYR AM+  + +Q NL + QGEV 
Sbjct: 61  GGLMGKAADKAGLQFRVLNSSKGPAVRATRAQIDKVLYRKAMRNALENQPNLSLFQGEVE 120

Query: 126 GFNTEKN-IISSIVMQDNSMIRCSTVVLTTGTFLRGVIHIGKLKIPAGRMGDSPSNSLFN 184
               E N  I  +V QD    R   V++TTGTFLRG IHIG     AGR G+ PS  L  
Sbjct: 121 DLILEDNDEIKGVVTQDGLKFRAKAVIITTGTFLRGKIHIGDKSYSAGRAGEQPSIGLST 180

Query: 185 SFMKFDFDTGRLKTGTPARLDGKTIIWDKTEKQFADERLIPFSFMTDK-ITNRQIECGIT 243
           +  +  F  GRLKTGTP R+D ++I + K E Q  D     FSFM    +  +Q+ C +T
Sbjct: 181 TLRELGFKVGRLKTGTPPRIDKRSIDFSKLEVQHGDNPPPAFSFMNKNFLPLQQLPCYLT 240

Query: 244 RTNLETHRIIMENIKHSAIYSGDIKSYGPRYCPSIEDKIVRFGERNGHQIFLEPEGLNTD 303
            TN +TH +I  N+  S +YSG I+  GPRYCPSIEDK+VRF ++  HQIFLEPEGLN+D
Sbjct: 241 HTNPKTHDLIRSNLHRSPMYSGVIEGNGPRYCPSIEDKVVRFADKERHQIFLEPEGLNSD 300

Query: 304 VVYPNGISTALPEEIQHQFIRTIPGLEKVNIIRPGYAIEYDYINPKELFPTLETKKISGL 363
            +YPNG+ST+LPE++Q Q +R+IPGLE   I+RPGYAIEYD+ +P++L PTLETK I GL
Sbjct: 301 EIYPNGLSTSLPEDVQLQIVRSIPGLENAEILRPGYAIEYDFFDPRQLKPTLETKLIQGL 360

Query: 364 FLAGQINGTTGYEEAAAQGLVAGINSARKSNKLDCICFSRTDSYIGVMIDDLTSKGVLEP 423
           F AGQINGTTGYEEAAAQGL+AGIN+A K    +     R+++YIGV+IDDL +KG  EP
Sbjct: 361 FFAGQINGTTGYEEAAAQGLMAGINAALKLQNKEPFILKRSEAYIGVLIDDLVTKGTKEP 420

Query: 424 YRMFTSRAEYRISLRPDNADNRLTPIGMKLGCIGERRQKRFAKYIQEYNFLRSLLKSLVL 483
           YRMFTSRAEYR+ LR DNAD RLT IG +LG I + R  RF K  +        LKS  L
Sbjct: 421 YRMFTSRAEYRLLLREDNADFRLTEIGRELGLIDDERYARFLKKKENIEEEIQRLKSTWL 480

Query: 484 TS-----KNLSSTSISFKQDGKTRTAYEFLSYPDFSIQNLFSICPDARKFSSLVIERLQI 538
           T      + L +   S  +     +  + L  P+ +++ L  + P        V+E+++I
Sbjct: 481 TPSKEVKEELKNHLQSPLKRE--ASGEDLLRRPEMNLEKLTKLTPFLPALDEEVLEQVEI 538

Query: 539 ESSYAAYTGRQMIEAKEIKFEEKRLIPKDFDYSSLPALSNELKEKLSILKPFNLLQASKI 598
           +  Y  Y  +Q  E K++   E   IP  FDY  +P LS E +EKLS  +P ++ QAS+I
Sbjct: 539 QIKYEGYIKKQQDEIKKLDRLENVKIPATFDYRKVPGLSTEAREKLSKFRPLSIGQASRI 598

Query: 599 EGMTPAALNLLLIYIKK 615
            G+TPA +++LL+Y+KK
Sbjct: 599 SGITPADISILLVYLKK 615


>gnl|CDD|180023 PRK05335, PRK05335, tRNA (uracil-5-)-methyltransferase Gid;
           Reviewed.
          Length = 436

 Score = 83.7 bits (208), Expect = 1e-16
 Identities = 42/101 (41%), Positives = 58/101 (57%), Gaps = 2/101 (1%)

Query: 319 QHQFIRTIPGLEKVNIIRPGYAIEYDYIN-PKELFPTLETKKISGLFLAGQINGTTGYEE 377
           Q +  R IPGLE    +R G      +IN PK L PTL+ KK   LF AGQI G  GY E
Sbjct: 288 QKRVFRMIPGLENAEFVRYGVMHRNTFINSPKLLDPTLQLKKRPNLFFAGQITGVEGYVE 347

Query: 378 AAAQGLVAGINSARKSNKLDCICFSRTDSYIGVMIDDLTSK 418
           +AA GL+AGIN+AR +   + +    T + +G +++ +T  
Sbjct: 348 SAASGLLAGINAARLALGKEPVIPPPT-TALGALLNYITGA 387



 Score = 51.7 bits (125), Expect = 6e-07
 Identities = 39/147 (26%), Positives = 53/147 (36%), Gaps = 35/147 (23%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI---------THKTSTIGSMSCNPAIGGL----G 54
           V VIG G AG EAA   AK G    L           H T     + C+ +         
Sbjct: 5   VNVIGAGLAGSEAAWQLAKRGVPVELYEMRPVKKTPAHHTDGFAELVCSNSFRSDSLTNA 64

Query: 55  KGHLVREIDALDGLMGRVADAAGIQFRVLNVKKGPA-----VRGPRTQADRELYRLAMQR 109
            G L  E+  L  L+   ADA     RV      PA     V       DRE +   +  
Sbjct: 65  VGLLKEEMRRLGSLIMEAADAH----RV------PAGGALAV-------DREGFSEYVTE 107

Query: 110 EILSQENLDVIQGEVAGFNTEKNIISS 136
            + +   + VI+ EV     +  II++
Sbjct: 108 ALENHPLITVIREEVTEIPEDITIIAT 134


>gnl|CDD|129243 TIGR00137, gid_trmFO, tRNA:m(5)U-54 methyltransferase.  This model
           represents an orthologous set of proteins present in
           relatively few bacteria but very tightly conserved where
           it occurs. It is closely related to gidA
           (glucose-inhibited division protein A), which appears to
           be present in all complete eubacterial genomes so far
           and in Saccharomyces cerevisiae. It was designated gid
           but is now recognized as a tRNA:m(5)U-54
           methyltransferase and is now designated trmFO.
          Length = 433

 Score = 74.6 bits (183), Expect = 7e-14
 Identities = 35/111 (31%), Positives = 54/111 (48%), Gaps = 2/111 (1%)

Query: 309 GISTALPEEIQHQFIRTIPGLEKVNIIRPGYAIEYDYIN-PKELFPTLETKKISGLFLAG 367
           G  T L    Q +  R IPGLE    +R G      +IN P+ L  +L  K    LF AG
Sbjct: 277 GFQTNLRWGEQKRVFRLIPGLENAEFVRMGVMHRNTFINSPQLLTASLHFKDRQTLFFAG 336

Query: 368 QINGTTGYEEAAAQGLVAGINSARKSNKLDCICFSRTDSYIGVMIDDLTSK 418
           Q+ G  GY  + A G +AGIN+AR +     +     ++ +G + + +++ 
Sbjct: 337 QLTGVEGYVASTAGGWLAGINAARLALGEPLLTLP-AETMMGALFNYISTA 386



 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 35/130 (26%), Positives = 53/130 (40%), Gaps = 25/130 (19%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI---------THKTSTIGSMSCNPAIGGL----G 54
           V VIGGG AG EAA   A+ G    L           H T  +  + C+ ++G       
Sbjct: 3   VHVIGGGLAGSEAAWQLAQAGVPVILYEMRPEKLTPAHHTEDLAELVCSNSLGAKALDRA 62

Query: 55  KGHLVREIDALDGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQREILSQ 114
            G L  E+  L  L+   AD   +          PA  G     DR ++  ++  ++ S 
Sbjct: 63  AGLLKTEMRQLSSLIITAADRHAV----------PA--GGALAVDRGIFSRSLTEQVASH 110

Query: 115 ENLDVIQGEV 124
            N+ +I+ EV
Sbjct: 111 PNVTLIREEV 120


>gnl|CDD|180019 PRK05329, PRK05329, anaerobic glycerol-3-phosphate dehydrogenase
          subunit B; Validated.
          Length = 422

 Score = 49.9 bits (120), Expect = 2e-06
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTI----GSM 44
          +DV+VIGGG AG  AA  AA+ G   AL+      +    GS+
Sbjct: 3  FDVLVIGGGLAGLTAALAAAEAGKRVALVAKGQGALHFSSGSI 45


>gnl|CDD|180546 PRK06370, PRK06370, mercuric reductase; Validated.
          Length = 463

 Score = 45.2 bits (108), Expect = 6e-05
 Identities = 18/34 (52%), Positives = 19/34 (55%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
             + YD IVIG G AG   AA AA LG   ALI
Sbjct: 1  TPAQRYDAIVIGAGQAGPPLAARAAGLGMKVALI 34



 Score = 29.0 bits (66), Expect = 3.6
 Identities = 9/26 (34%), Positives = 16/26 (61%)

Query: 9   IVIGGGHAGCEAAAVAAKLGASTALI 34
           ++IGGG+ G E A +  + G+   +I
Sbjct: 175 VIIGGGYIGLEFAQMFRRFGSEVTVI 200


>gnl|CDD|149204 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
          oxidoreductase.  This family includes both class I and
          class II oxidoreductases and also NADH oxidases and
          peroxidases. This domain is actually a small NADH
          binding domain within a larger FAD binding domain.
          Length = 277

 Score = 45.0 bits (107), Expect = 6e-05
 Identities = 16/28 (57%), Positives = 19/28 (67%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALI 34
          DV++IGGG AG  AA   A+LG   ALI
Sbjct: 1  DVVIIGGGPAGLAAAIYLARLGLKVALI 28



 Score = 35.0 bits (81), Expect = 0.051
 Identities = 14/27 (51%), Positives = 19/27 (70%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI 34
           V+V+GGG+ G E AA  AKLGA   ++
Sbjct: 139 VVVVGGGYIGLELAAALAKLGAEVTVV 165


>gnl|CDD|162668 TIGR02032, GG-red-SF, geranylgeranyl reductase family.  This
          model represents a subfamily which includes
          geranylgeranyl reductases involved in chlorophyll and
          bacteriochlorophyll biosynthesis as well as other
          related enzymes which may also act on geranylgeranyl
          groups or related substrates.
          Length = 295

 Score = 44.6 bits (106), Expect = 8e-05
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGG 52
          YDV+V+G G AG  AA   A  G    L+  K S      C  A+  
Sbjct: 1  YDVVVVGAGPAGASAAYRLADKGLRVLLL-EKKSFPRYKPCGGALSP 46


>gnl|CDD|163151 TIGR03140, AhpF, alkyl hydroperoxide reductase, F subunit.  This
           enzyme is the partner of the peroxiredoxin (alkyl
           hydroperoxide reductase) AhpC which contains the
           peroxide-reactive cysteine. AhpF contains the reductant
           (NAD(P)H) binding domain (pfam00070) and presumably acts
           to resolve the disulfide which forms after oxidation of
           the active site cysteine in AphC. This proteins contains
           two paired conserved cysteine motifs, CxxCP and CxHCDGP.
          Length = 515

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 39/166 (23%), Positives = 68/166 (40%), Gaps = 50/166 (30%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREIDAL 65
           YDV+V+GGG AG  AA  AA+ G  TA++  +   IG                       
Sbjct: 213 YDVLVVGGGPAGAAAAIYAARKGLRTAMVAER---IG----------------------- 246

Query: 66  DGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQ-REILSQENLDVIQGEV 124
               G+V D  GI+    N+   P   G          +LA    E + Q  +D+++ + 
Sbjct: 247 ----GQVKDTVGIE----NLISVPYTTGS---------QLAANLEEHIKQYPIDLMENQR 289

Query: 125 AGFNTEKNIISSIVMQDNSMIRCSTVVLTTGTFLRGVIHIGKLKIP 170
           A     ++ +  + ++   +++  +V++ TG   R      KL +P
Sbjct: 290 AKKIETEDGLIVVTLESGEVLKAKSVIVATGARWR------KLGVP 329


>gnl|CDD|162675 TIGR02053, MerA, mercuric reductase.  This model represents the
           mercuric reductase found in the mer operon for the
           detoxification of mercury compounds. MerA is a
           FAD-containing flavoprotein which reduces Hg(II) to
           Hg(0) utilizing NADPH.
          Length = 463

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 9/118 (7%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREIDAL 65
           YD+++IG G A   AA  AA+LGAS A++      +G    N  +G +    L+R   A 
Sbjct: 1   YDLVIIGSGAAAFAAAIKAAELGASVAMVER--GPLGGTCVN--VGCVPSKMLLR---AA 53

Query: 66  DGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQREILSQENLDVIQGE 123
           +          G     + V  G  + G R   +    R     ++LS   +D ++G 
Sbjct: 54  EVAHYARKPPFGGLAATVAVDFGELLEGKREVVEEL--RHEKYEDVLSSYGVDYLRGR 109



 Score = 29.3 bits (66), Expect = 3.0
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI 34
           + VIGGG  G E A   A+LG+   ++
Sbjct: 169 LAVIGGGAIGVELAQAFARLGSEVTIL 195


>gnl|CDD|162312 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase.  The
          motif GGXCXXXGCXP near the N-terminus contains a
          redox-active disulfide.
          Length = 461

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 17/30 (56%), Positives = 21/30 (70%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          +YDV+VIGGG  G  AA  AA+LG   AL+
Sbjct: 1  AYDVVVIGGGPGGYVAAIRAAQLGLKVALV 30



 Score = 28.0 bits (63), Expect = 7.8
 Identities = 10/21 (47%), Positives = 15/21 (71%)

Query: 9   IVIGGGHAGCEAAAVAAKLGA 29
           ++IGGG  G E A++ A LG+
Sbjct: 174 VIIGGGVIGIEFASIFASLGS 194


>gnl|CDD|179973 PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase;
          Provisional.
          Length = 461

 Score = 42.8 bits (102), Expect = 3e-04
 Identities = 25/54 (46%), Positives = 29/54 (53%), Gaps = 13/54 (24%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAV-AAKLGASTALI----------THKTSTIGS 43
          M    YD++VIG G AG E AA+ AAKLG   A+I          TH T TI S
Sbjct: 1  MHMYDYDLVVIGSGPAG-EGAAMQAAKLGKRVAVIERYRNVGGGCTH-TGTIPS 52


>gnl|CDD|180579 PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed.
          Length = 471

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
             V+V+G G AG  AA  AA LG  T  +  + ST+G
Sbjct: 4  KTQVVVLGAGPAGYSAAFRAADLGLETVCV-ERYSTLG 40


>gnl|CDD|180516 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
          Length = 460

 Score = 42.1 bits (100), Expect = 4e-04
 Identities = 42/159 (26%), Positives = 62/159 (38%), Gaps = 26/159 (16%)

Query: 4   RSYDVIVIGGGHAGCEAAAVAAKLGASTALI---THKTS--TIGSMSCNPAIGGLGKGHL 58
             YDVIVIG G AG  AA  AAKLG   ALI       +   +G   C P+   +     
Sbjct: 2   EKYDVIVIGAGPAGYVAARRAAKLGKKVALIEKGPLGGTCLNVG---CIPSKALIAAAEA 58

Query: 59  VREIDALDGLMGRVADAAGIQFR-VLNVKKGPAVRGPRTQADRELYRLAMQREILSQENL 117
             E    +   G  AD   I F+ V+           R + +R+ +   +   +  +  +
Sbjct: 59  FHEAKHAEE-FGIHADGPKIDFKKVMA----------RVRRERDRFVGGVVEGLEKKPKI 107

Query: 118 DVIQGEVAGFNTEKNIISSIVMQDNSMIRCSTVVLTTGT 156
           D I+G  A F          V  +   I    +V+ TG+
Sbjct: 108 DKIKG-TARFVDPN-----TVEVNGERIEAKNIVIATGS 140


>gnl|CDD|162542 TIGR01812, sdhA_frdA_Gneg, succinate dehydrogenase or fumarate
          reductase, flavoprotein
          subunitGram-negative/mitochondrial subgroup.  This
          model represents the succinate dehydrogenase
          flavoprotein subunit as found in Gram-negative
          bacteria, mitochondria, and some Archaea. Mitochondrial
          forms interact with ubiquinone and are designated EC
          1.3.5.1, but can be degraded to 1.3.99.1. Some isozymes
          in E. coli and other species run primarily in the
          opposite direction and are designated fumarate
          reductase.
          Length = 566

 Score = 41.9 bits (99), Expect = 5e-04
 Identities = 20/46 (43%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGG 52
          DV+++G G AG  AA  AAK G +TA+I+ K     S +   A GG
Sbjct: 1  DVVIVGAGLAGLRAAVEAAKAGLNTAVIS-KVYPTRSHTV-AAQGG 44


>gnl|CDD|130488 TIGR01421, gluta_reduc_1, glutathione-disulfide reductase,
           animal/bacterial.  The tripeptide glutathione is an
           important reductant, e.g., for maintaining the cellular
           thiol/disulfide status and for protecting against
           reactive oxygen species such as hydrogen peroxide.
           Glutathione-disulfide reductase regenerates reduced
           glutathione from oxidized glutathione (glutathione
           disulfide) + NADPH. This model represents one of two
           closely related subfamilies of glutathione-disulfide
           reductase. Both are closely related to trypanothione
           reductase, and separate models are built so each of the
           three can describe proteins with conserved function.
           This model describes glutathione-disulfide reductases of
           animals, yeast, and a number of animal-resident
           bacteria.
          Length = 450

 Score = 41.7 bits (98), Expect = 6e-04
 Identities = 37/131 (28%), Positives = 59/131 (45%), Gaps = 11/131 (8%)

Query: 4   RSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREID 63
           + YD +VIGGG  G  +A  AA+ GA   L+  K   +G    N  +G + K  +    D
Sbjct: 1   KHYDYLVIGGGSGGIASARRAAEHGAKALLVEAK--KLGGTCVN--VGCVPKKVMWYASD 56

Query: 64  ALDGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRL-AMQREILSQENLDVIQG 122
               L  R+ DAA   F   N++        + + D  + RL  + ++ L +  +DVI G
Sbjct: 57  ----LAERMHDAADYGFYQ-NLENTFNWPELKEKRDAYVDRLNGIYQKNLEKNKVDVIFG 111

Query: 123 EVAGFNTEKNI 133
             A F  +  +
Sbjct: 112 H-ARFTKDGTV 121


>gnl|CDD|180529 PRK06327, PRK06327, dihydrolipoamide dehydrogenase; Validated.
          Length = 475

 Score = 41.4 bits (98), Expect = 7e-04
 Identities = 15/32 (46%), Positives = 20/32 (62%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          ++ +DV+VIG G  G  AA  AA+LG   A I
Sbjct: 2  SKQFDVVVIGAGPGGYVAAIRAAQLGLKVACI 33


>gnl|CDD|181001 PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase;
           Provisional.
          Length = 388

 Score = 41.0 bits (97), Expect = 8e-04
 Identities = 40/173 (23%), Positives = 68/173 (39%), Gaps = 37/173 (21%)

Query: 1   MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTS-----TIGSMSCNPAIGGLGK 55
           M     D+ VIGGG AG  AA   A+ GAS AL+  +       T   +   P+I     
Sbjct: 3   MEKEHTDIAVIGGGPAGLAAAIALARAGASVALVAPEPPYADLRTTALL--GPSI----- 55

Query: 56  GHLVREIDALDGLMGRVAD-AAGIQF-RVLNVKKGPAVRGPRTQ---------------A 98
               R ++ L GL  R+A  AA +Q  R+++   G  +R P  +                
Sbjct: 56  ----RFLERL-GLWARLAPHAAPLQSMRIVDA-TGRLIRAPEVRFRAAEIGEDAFGYNIP 109

Query: 99  DRELYRLAMQREILSQENLDVIQGEVAGFNTEKNIISSIVMQDNSMIRCSTVV 151
           +  L   A++  +    N+     E       ++ + ++ + D + +    VV
Sbjct: 110 NWLL-NRALEARVAELPNITRFGDEAESVRPREDEV-TVTLADGTTLSARLVV 160


>gnl|CDD|181141 PRK07845, PRK07845, flavoprotein disulfide reductase; Reviewed.
          Length = 466

 Score = 41.0 bits (97), Expect = 9e-04
 Identities = 15/27 (55%), Positives = 20/27 (74%)

Query: 8  VIVIGGGHAGCEAAAVAAKLGASTALI 34
          +++IGGG  G EAA VAA+LGA   +I
Sbjct: 4  IVIIGGGPGGYEAALVAAQLGADVTVI 30


>gnl|CDD|180558 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
          Length = 462

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
            YDVIVIG G  G  AA  AA+LG   A++
Sbjct: 3  FEYDVIVIGAGPGGYVAAIRAAQLGLKVAIV 33



 Score = 29.3 bits (67), Expect = 3.0
 Identities = 12/27 (44%), Positives = 18/27 (66%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI 34
           ++VIGGG+ G E A+  A LGA   ++
Sbjct: 175 LVVIGGGYIGVEFASAYASLGAEVTIV 201


>gnl|CDD|181124 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 626

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
           SYDV+VIG G AG  AA  A + G   A++ 
Sbjct: 7  HSYDVVVIGAGGAGLRAAIEARERGLRVAVVC 38


>gnl|CDD|183786 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
          Length = 578

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
          +  +DVIVIG G AG  AA  AA  G    L+  +T  +G
Sbjct: 14 DAEFDVIVIGAGAAGMSAALFAAIAGLKV-LLVERTEYVG 52


>gnl|CDD|180410 PRK06116, PRK06116, glutathione reductase; Validated.
          Length = 450

 Score = 38.6 bits (91), Expect = 0.006
 Identities = 17/29 (58%), Positives = 19/29 (65%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          YD+IVIGGG  G  +A  AA  GA  ALI
Sbjct: 5  YDLIVIGGGSGGIASANRAAMYGAKVALI 33


>gnl|CDD|181140 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase;
          Reviewed.
          Length = 557

 Score = 38.1 bits (89), Expect = 0.007
 Identities = 16/34 (47%), Positives = 21/34 (61%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          M  + YDV+V+G G AG  AA  AA  G ST ++
Sbjct: 3  MTVQEYDVVVVGSGAAGMVAALTAAHRGLSTVVV 36


>gnl|CDD|185217 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
           Provisional.
          Length = 517

 Score = 37.8 bits (89), Expect = 0.008
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHK 37
           YDV+V+GGG AG  AA  AA+ G  T ++  +
Sbjct: 212 YDVLVVGGGPAGAAAAIYAARKGIRTGIVAER 243



 Score = 28.6 bits (65), Expect = 4.4
 Identities = 10/15 (66%), Positives = 12/15 (80%)

Query: 7   DVIVIGGGHAGCEAA 21
            V VIGGG++G EAA
Sbjct: 353 RVAVIGGGNSGVEAA 367


>gnl|CDD|171762 PRK12839, PRK12839, hypothetical protein; Provisional.
          Length = 572

 Score = 37.5 bits (87), Expect = 0.009
 Identities = 19/38 (50%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
          +YDV+V+G G AG  +AAVAA  G +  L+  K ST G
Sbjct: 8  TYDVVVVGSG-AGGLSAAVAAAYGGAKVLVVEKASTCG 44


>gnl|CDD|162664 TIGR02023, BchP-ChlP, geranylgeranyl reductase.  This model
          represents a group of geranylgeranyl reductases
          specific for the biosyntheses of bacteriochlorophyll
          and chlorophyll. It is unclear whether the processes of
          isoprenoid ligation to the chlorin ring and reduction
          of the geranylgeranyl chain to a phytyl chain are
          necessarily ordered the same way in all species (see
          introduction to ).
          Length = 388

 Score = 37.5 bits (87), Expect = 0.010
 Identities = 24/66 (36%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVREIDAL 65
          YDV VIGGG +G  AA   A+ G  T L+    S     +  P  G +    L+ E D  
Sbjct: 1  YDVAVIGGGPSGATAAETLARAGIETILLERALS-----NIKPCGGAIPPC-LIEEFDIP 54

Query: 66 DGLMGR 71
          D L+ R
Sbjct: 55 DSLIDR 60


>gnl|CDD|180409 PRK06115, PRK06115, dihydrolipoamide dehydrogenase; Reviewed.
          Length = 466

 Score = 37.5 bits (87), Expect = 0.011
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCN 47
          SYDV++IGGG  G  AA  A +LG   A +  + ST+G    N
Sbjct: 3  SYDVVIIGGGPGGYNAAIRAGQLGLKVACVEGR-STLGGTCLN 44


>gnl|CDD|185416 PTZ00052, PTZ00052, thioredoxin reductase; Provisional.
          Length = 499

 Score = 37.5 bits (87), Expect = 0.011
 Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITH-KTSTIGS 43
          YD++VIGGG  G  AA  AA  G   AL  + K ST G+
Sbjct: 6  YDLVVIGGGSGGMAAAKEAAAHGKKVALFDYVKPSTQGT 44


>gnl|CDD|181345 PRK08274, PRK08274, tricarballylate dehydrogenase; Validated.
          Length = 466

 Score = 37.2 bits (87), Expect = 0.013
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
              DV+VIGGG+A   AA  A + GAS  L+
Sbjct: 2  ASMVDVLVIGGGNAALCAALAAREAGASVLLL 33


>gnl|CDD|162359 TIGR01438, TGR, thioredoxin and glutathione reductase
          selenoprotein.  This homodimeric, FAD-containing member
          of the pyridine nucleotide disulfide oxidoreductase
          family contains a C-terminal motif Cys-SeCys-Gly, where
          SeCys is selenocysteine encoded by TGA (in some
          sequence reports interpreted as a stop codon). In some
          members of this subfamily, Cys-SeCys-Gly is replaced by
          Cys-Cys-Gly. The reach of the selenium atom at the
          C-term arm of the protein is proposed to allow broad
          substrate specificity.
          Length = 484

 Score = 37.1 bits (86), Expect = 0.014
 Identities = 18/35 (51%), Positives = 20/35 (57%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTST 40
          YD+IVIGGG  G  AA  AA  GA   L+   T T
Sbjct: 3  YDLIVIGGGSGGLAAAKEAADYGAKVMLLDFVTPT 37


>gnl|CDD|181132 PRK07818, PRK07818, dihydrolipoamide dehydrogenase; Reviewed.
          Length = 466

 Score = 36.9 bits (86), Expect = 0.017
 Identities = 16/32 (50%), Positives = 21/32 (65%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHK 37
          YDV+V+G G  G  AA  AA+LG  TA++  K
Sbjct: 5  YDVVVLGAGPGGYVAAIRAAQLGLKTAVVEKK 36


>gnl|CDD|181289 PRK08205, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 583

 Score = 36.5 bits (85), Expect = 0.019
 Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          M    YDV+++G G AG  AA  A    A TA++T
Sbjct: 1  MQQHRYDVVIVGAGGAGMRAAIEAGP-RARTAVLT 34


>gnl|CDD|132421 TIGR03378, glycerol3P_GlpB, glycerol-3-phosphate dehydrogenase,
          anaerobic, B subunit.  Members of this protein family
          are the B subunit, product of the glpB gene, of a
          three-subunit, membrane-anchored, FAD-dependent
          anaerobic glycerol-3-phosphate dehydrogenase.
          Length = 419

 Score = 36.5 bits (85), Expect = 0.020
 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTI----GSM 44
          +DVI+IGGG AG   A   A+ G   A+I    S +    GS+
Sbjct: 1  FDVIIIGGGLAGLSCALRLAEAGKKCAIIAAGQSALHFSSGSL 43


>gnl|CDD|181564 PRK08849, PRK08849,
          2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
          hydroxylase; Provisional.
          Length = 384

 Score = 36.3 bits (84), Expect = 0.022
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHK 37
           YD+ V+GGG  G   A   AK G S A+I   
Sbjct: 3  KYDIAVVGGGMVGAATALGFAKQGRSVAVIEGG 35


>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 575

 Score = 36.2 bits (84), Expect = 0.023
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 4/50 (8%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGAST--ALITHKTSTIGSMSCNPAIGGL 53
          +DV+++GGG AGC AA    +L  S   A++  KT  I S S   A GG+
Sbjct: 4  HDVVIVGGGLAGCRAALEIKRLDPSLDVAVVA-KTHPIRSHSV-AAQGGI 51


>gnl|CDD|180333 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
          Length = 472

 Score = 36.0 bits (84), Expect = 0.028
 Identities = 43/169 (25%), Positives = 66/169 (39%), Gaps = 35/169 (20%)

Query: 3   NRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGG--LGKG---- 56
            + YD+++IGGG  G  AA  A +LG  TAL+               +GG  L KG    
Sbjct: 2   AKEYDLVIIGGGPGGYVAAIRAGQLGLKTALVEKG-----------KLGGTCLHKGCIPS 50

Query: 57  -HLVREIDALDGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQA--DRELYRLAMQRE-IL 112
             L+   +       + A   GI         GPA+   + Q   D  + RL      +L
Sbjct: 51  KALLHSAEVFQTA--KKASPFGISVS------GPALDFAKVQERKDGIVDRLTKGVAALL 102

Query: 113 SQENLDVIQGE--VAG---FNTEKNIIS-SIVMQDNSMIRCSTVVLTTG 155
            +  +DV  G   + G   F+     +S      +N MI    +++ TG
Sbjct: 103 KKGKIDVFHGIGRILGPSIFSPMPGTVSVETETGENEMIIPENLLIATG 151


>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed.
          Length = 581

 Score = 35.9 bits (83), Expect = 0.031
 Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 1/39 (2%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
             DV+VIG G AG  AA  AA  G    ++  K    G
Sbjct: 11 LECDVLVIGSGAAGLSAAVTAAWHGLKVIVV-EKDPVFG 48


>gnl|CDD|181594 PRK08958, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 588

 Score = 35.9 bits (83), Expect = 0.033
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          R +D +VIG G AG  AA   ++ G S AL++
Sbjct: 6  REFDAVVIGAGGAGMRAALQISQSGQSCALLS 37


>gnl|CDD|181641 PRK09078, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 598

 Score = 35.7 bits (83), Expect = 0.033
 Identities = 16/34 (47%), Positives = 20/34 (58%)

Query: 2  INRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          I+  YDV+V+G G AG  A    A+ G  TA IT
Sbjct: 9  IDHKYDVVVVGAGGAGLRATLGMAEAGLKTACIT 42


>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase;
          Reviewed.
          Length = 557

 Score = 35.5 bits (82), Expect = 0.040
 Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
           +YDV+V+G G  G  AA  AA  G    LI  K   +G
Sbjct: 5  ETYDVVVVGSGGGGMCAALAAADSGLEP-LIVEKQDKVG 42


>gnl|CDD|178083 PLN02464, PLN02464, glycerol-3-phosphate dehydrogenase.
          Length = 627

 Score = 35.5 bits (82), Expect = 0.041
 Identities = 12/32 (37%), Positives = 15/32 (46%)

Query: 3   NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
               DV+V+GGG  G   A  AA  G    L+
Sbjct: 69  AEPLDVLVVGGGATGAGVALDAATRGLRVGLV 100


>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
          Length = 1167

 Score = 35.5 bits (82), Expect = 0.043
 Identities = 19/38 (50%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMS 45
           VIV+GGG AGC AA  AA  GA   L+  K + +G  S
Sbjct: 412 VIVVGGGLAGCSAAIEAASCGAQVILL-EKEAKLGGNS 448


>gnl|CDD|161797 TIGR00275, TIGR00275, flavoprotein, HI0933 family.  The model
          when searched with a partial length search brings in
          proteins with a dinucleotide-binding motif (Rossman
          fold) over the initial 40 residues of the model,
          including oxidoreductases and dehydrogenases. Partially
          characterized members include an FAD-binding protein
          from Bacillus cereus and flavoprotein HI0933 from
          Haemophilus influenzae.
          Length = 400

 Score = 35.3 bits (82), Expect = 0.046
 Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 9  IVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGS 43
          I+IGGG AG  AA  AA+ G S  L+  K   IG 
Sbjct: 1  IIIGGGAAGLMAAITAAREGLSVLLL-EKNKKIGK 34



 Score = 34.9 bits (81), Expect = 0.065
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 10/47 (21%)

Query: 346 INPKELFPTLETKKISGLFLAGQ---INGTTG---YEEAAAQGLVAG 386
           INPK    T+E+K + GL+ AG+   ++G TG    + A + G +AG
Sbjct: 357 INPK----TMESKLVPGLYFAGEVLDVDGDTGGYNLQWAWSSGYLAG 399


>gnl|CDD|184334 PRK13800, PRK13800, putative oxidoreductase/HEAT
          repeat-containing protein; Provisional.
          Length = 897

 Score = 35.2 bits (81), Expect = 0.047
 Identities = 16/28 (57%), Positives = 20/28 (71%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALI 34
          DV+VIGGG AG  AA  AA+ GA+  L+
Sbjct: 15 DVLVIGGGTAGTMAALTAAEHGANVLLL 42


>gnl|CDD|183388 PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
          Length = 508

 Score = 35.1 bits (82), Expect = 0.058
 Identities = 14/28 (50%), Positives = 16/28 (57%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTAL 33
          YD++VIGGG  G   A  AA  G S  L
Sbjct: 7  YDLLVIGGGINGAGIARDAAGRGLSVLL 34


>gnl|CDD|185473 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone]
          flavoprotein subunit; Provisional.
          Length = 617

 Score = 34.3 bits (79), Expect = 0.094
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          +I+ +YD +V+G G AG  AA    +LG  TA I+
Sbjct: 25 VIDHTYDAVVVGAGGAGLRAALGLVELGYKTACIS 59


>gnl|CDD|162288 TIGR01292, TRX_reduct, thioredoxin-disulfide reductase.  This
          model describes thioredoxin-disulfide reductase, a
          member of the pyridine nucleotide-disulphide
          oxidoreductases (PFAM:PF00070).
          Length = 300

 Score = 34.1 bits (79), Expect = 0.098
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
          YDVI+IG G AG  AA  AA+    T +I    
Sbjct: 1  YDVIIIGAGPAGLTAAIYAARANLKTLIIEGME 33


>gnl|CDD|180382 PRK06069, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 577

 Score = 33.9 bits (78), Expect = 0.11
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLG---ASTALITHKTSTIGSMS 45
           YDV+++G G AG  AA  AA+      S A+++ KT  + S S
Sbjct: 5  KYDVVIVGSGLAGLRAAVAAAERSGGKLSVAVVS-KTQPMRSHS 47


>gnl|CDD|177739 PLN00128, PLN00128, Succinate dehydrogenase [ubiquinone]
          flavoprotein subunit.
          Length = 635

 Score = 33.7 bits (77), Expect = 0.14
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          +++ +YD +V+G G AG  AA   ++ G +TA IT
Sbjct: 46 IVDHTYDAVVVGAGGAGLRAAIGLSEHGFNTACIT 80


>gnl|CDD|130850 TIGR01790, carotene-cycl, lycopene cyclase family protein.  This
           family includes lycopene beta and epsilion cyclases
           (which form beta and delta carotene, respectively) from
           bacteria and plants as well as the plant
           capsanthin/capsorubin and neoxanthin cyclases which
           appear to have evolved from the plant lycopene cyclases.
           The plant lycopene epsilon cyclases also transform
           neurosporene to alpha zeacarotene.
          Length = 388

 Score = 33.6 bits (77), Expect = 0.15
 Identities = 26/153 (16%), Positives = 51/153 (33%), Gaps = 19/153 (12%)

Query: 7   DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGK-GHLVREIDAL 65
           D+ VIGGG AG   A   A+ G            +  +  +P I G    G    ++  L
Sbjct: 1   DLAVIGGGPAGLAIALELARPGLR----------VQLIEPHPPIPGNHTYGVWDDDLSDL 50

Query: 66  DGLMGRVADAAGIQFRVLNVKKGPAVRGPRTQADRELYRLAMQREILS---QENLDVIQG 122
                 +AD     +  +   + P        A   +    +  E+L    +  +  ++ 
Sbjct: 51  G-----LADCVEHVWPDVYEYRFPKQPRKLGTAYGSVDSTRLHEELLQKCPEGGVLWLER 105

Query: 123 EVAGFNTEKNIISSIVMQDNSMIRCSTVVLTTG 155
           +      +   +S++       I+   V+   G
Sbjct: 106 KAIHAEADGVALSTVYCAGGQRIQARLVIDARG 138


>gnl|CDD|178161 PLN02546, PLN02546, glutathione reductase.
          Length = 558

 Score = 33.7 bits (77), Expect = 0.16
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLG 54
           +D+  IG G  G  A+  A+  GAS A+     +TI S      +GG+G
Sbjct: 80  FDLFTIGAGSGGVRASRFASNFGASAAVCELPFATISS----DTLGGVG 124


>gnl|CDD|139246 PRK12814, PRK12814, putative NADPH-dependent glutamate synthase
           small subunit; Provisional.
          Length = 652

 Score = 33.2 bits (76), Expect = 0.19
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPA 49
           V+VIGGG+   +AA  A +LGA +  I ++  T   M  N A
Sbjct: 326 VVVIGGGNTAIDAARTALRLGAESVTILYR-RTREEMPANRA 366


>gnl|CDD|180907 PRK07251, PRK07251, pyridine nucleotide-disulfide oxidoreductase;
          Provisional.
          Length = 438

 Score = 33.2 bits (76), Expect = 0.20
 Identities = 15/29 (51%), Positives = 17/29 (58%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          YD+IVIG G AG   AA  A  G   AL+
Sbjct: 4  YDLIVIGFGKAGKTLAAKLASAGKKVALV 32


>gnl|CDD|183785 PRK12842, PRK12842, putative succinate dehydrogenase; Reviewed.
          Length = 574

 Score = 33.1 bits (76), Expect = 0.21
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLG 28
           + DV+VIG G  G  AA  A KLG
Sbjct: 8  LTCDVLVIGSGAGGLSAAITARKLG 32


>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
          hydroxylase; Reviewed.
          Length = 391

 Score = 33.0 bits (76), Expect = 0.21
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
          M N+  D+ ++GGG  G   A   A+ G S A++ H  
Sbjct: 1  MTNQPTDIAIVGGGMVGAALALGLAQHGFSVAVLEHAA 38


>gnl|CDD|183735 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
           subunit; Provisional.
          Length = 564

 Score = 33.3 bits (77), Expect = 0.22
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPA 49
           V+VIGGG+   +AA  A +LGA    I ++  T   M  +  
Sbjct: 270 VVVIGGGNTAMDAARTARRLGAEEVTIVYR-RTREDMPAHDE 310


>gnl|CDD|179368 PRK02106, PRK02106, choline dehydrogenase; Validated.
          Length = 560

 Score = 33.3 bits (77), Expect = 0.22
 Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 3/27 (11%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKL 27
          M    YD I+IG G AGC    +A +L
Sbjct: 1  MTTMEYDYIIIGAGSAGC---VLANRL 24


>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
          Length = 492

 Score = 32.9 bits (76), Expect = 0.24
 Identities = 13/31 (41%), Positives = 17/31 (54%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
             DV+V+G G AG  AA  AA  GA   ++
Sbjct: 19 DEADVVVVGFGAAGACAAIEAAAAGARVLVL 49


>gnl|CDD|178382 PLN02785, PLN02785, Protein HOTHEAD.
          Length = 587

 Score = 32.9 bits (75), Expect = 0.25
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 5  SYDVIVIGGGHAGCEAAA 22
          +YD IV+GGG AGC  AA
Sbjct: 55 AYDYIVVGGGTAGCPLAA 72


>gnl|CDD|181040 PRK07573, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 640

 Score = 32.9 bits (76), Expect = 0.25
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLG 28
          R +DVIV+G G AG  AAA   +LG
Sbjct: 34 RKFDVIVVGTGLAGASAAATLGELG 58


>gnl|CDD|162990 TIGR02733, desat_CrtD, C-3',4' desaturase CrtD.  Members of this
          family are slr1293, a carotenoid biosynthesis protein
          which was shown to be the C-3',4' desaturase (CrtD) of
          myxoxanthophyll biosynthesis in Synechocystis sp.
          strain PCC 6803, and close homologs (presumed to be
          functionally equivalent) from other cyanobacteria,
          where myxoxanthophyll biosynthesis is either known or
          expected. This enzyme can act on neurosporene and so
          presumably catalyzes the first step that is committed
          to myxoxanthophyll.
          Length = 492

 Score = 32.8 bits (75), Expect = 0.27
 Identities = 14/27 (51%), Positives = 17/27 (62%)

Query: 8  VIVIGGGHAGCEAAAVAAKLGASTALI 34
          V+VIG G AG  AAA+ AK G    L+
Sbjct: 4  VVVIGAGIAGLTAAALLAKRGYRVTLL 30


>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
          Length = 429

 Score = 32.6 bits (74), Expect = 0.28
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGS 43
          M +  +D IV+G G AG  AA V A+ G    L+  +  + G 
Sbjct: 1  MSDDKFDAIVVGAGVAGSVAALVMARAGLDV-LVIERGDSAGC 42


>gnl|CDD|162543 TIGR01813, flavo_cyto_c, flavocytochrome c.  This model describes
          a family of redox proteins related to the succinate
          dehydrogenases and fumarate reductases of E. coli,
          mitochondria, and other well-characterized systems. A
          member of this family from Shewanella frigidimarina
          NCIMB400 is characterized as a water-soluble
          periplasmic protein with four heme groups, a
          non-covalently bound FAD, and essentially
          unidirectional fumarate reductase activity. At least
          seven distinct members of this family are found in
          Shewanella oneidensis, a species able to use a wide
          variety of pathways for respiraton.
          Length = 439

 Score = 32.7 bits (75), Expect = 0.28
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLG 54
          DV+V+G G AG  AA  A K GA+  ++  K   IG    N AI   G
Sbjct: 1  DVVVVGSGFAGLSAALSAKKAGAANVVLLEKMPVIGG---NSAIAAGG 45


>gnl|CDD|178082 PLN02463, PLN02463, lycopene beta cyclase.
          Length = 447

 Score = 32.8 bits (75), Expect = 0.31
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          R  D++V+GGG AG   A   ++ G S   I
Sbjct: 27 RVVDLVVVGGGPAGLAVAQQVSEAGLSVCCI 57


>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase.  The family of known
           L-alanine dehydrogenases includes representatives from
           the Proteobacteria, Firmicutes, and Cyanobacteria, all
           with about 50 % identity or better. An outlier to this
           group in both sequence and gap pattern is the homolog
           from Helicobacter pylori, an epsilon division
           Proteobacteria, which must be considered a putative
           alanine dehydrogenase. Related proteins include
           saccharopine dehydrogenase and the N-terminal half of
           the NAD(P) transhydrogenase alpha subunit. All of these
           related proteins bind NAD and/or NADP.
          Length = 370

 Score = 32.2 bits (73), Expect = 0.38
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 7   DVIVIGGGHAGCEAAAVAAKLGASTALI 34
           DV +IGGG  G  AA +A  LGA+  ++
Sbjct: 169 DVTIIGGGVVGTNAAKMANGLGATVTIL 196


>gnl|CDD|180814 PRK07057, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 591

 Score = 32.1 bits (73), Expect = 0.39
 Identities = 11/33 (33%), Positives = 21/33 (63%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
           R +DV+++G G +G  A+   A+ G S A+++
Sbjct: 10 RRKFDVVIVGAGGSGMRASLQLARAGLSVAVLS 42


>gnl|CDD|180567 PRK06452, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 566

 Score = 32.2 bits (73), Expect = 0.39
 Identities = 15/35 (42%), Positives = 19/35 (54%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          M    YD +VIGGG AG  +A   A  G   A+I+
Sbjct: 1  MEKIEYDAVVIGGGLAGLMSAHEIASAGFKVAVIS 35


>gnl|CDD|130444 TIGR01377, soxA_mon, sarcosine oxidase, monomeric form.
          Sarcosine oxidase catalyzes the oxidative demethylation
          of sarcosine to glycine. The reaction converts
          tetrahydrofolate to 5,10-methylene-tetrahydrofolate.
          The enzyme is known in monomeric and heterotetrameric
          (alpha,beta,gamma,delta) forms.
          Length = 380

 Score = 32.1 bits (73), Expect = 0.39
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          +DVIV+G G  GC AA   AK G  T L+
Sbjct: 1  FDVIVVGAGIMGCFAAYHLAKHGKKTLLL 29


>gnl|CDD|178300 PLN02697, PLN02697, lycopene epsilon cyclase.
          Length = 529

 Score = 32.1 bits (73), Expect = 0.41
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 3   NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
           + + D++VIG G AG   AA +AKLG +  LI
Sbjct: 106 DGTLDLVVIGCGPAGLALAAESAKLGLNVGLI 137


>gnl|CDD|181346 PRK08275, PRK08275, putative oxidoreductase; Provisional.
          Length = 554

 Score = 31.9 bits (73), Expect = 0.46
 Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKL 27
            D++VIGGG AG   AA+ AK 
Sbjct: 9  ETDILVIGGGTAG-PMAAIKAKE 30


>gnl|CDD|183782 PRK12834, PRK12834, putative FAD-binding dehydrogenase; Reviewed.
          Length = 549

 Score = 32.2 bits (74), Expect = 0.46
 Identities = 14/29 (48%), Positives = 16/29 (55%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALI 34
           DVIV+G G AG  AAA  A  G    L+
Sbjct: 5  ADVIVVGAGLAGLVAAAELADAGKRVLLL 33


>gnl|CDD|162352 TIGR01424, gluta_reduc_2, glutathione-disulfide reductase, plant.
           The tripeptide glutathione is an important reductant,
          e.g., for maintaining the cellular thiol/disulfide
          status and for protecting against reactive oxygen
          species such as hydrogen peroxide.
          Glutathione-disulfide reductase regenerates reduced
          glutathione from oxidized glutathione (glutathione
          disulfide) + NADPH. This model represents one of two
          closely related subfamilies of glutathione-disulfide
          reductase. Both are closely related to trypanothione
          reductase, and separate models are built so each of the
          three can describe proteins with conserved function.
          This model describes glutathione-disulfide reductases
          of plants and some bacteria, including cyanobacteria.
          Length = 446

 Score = 32.1 bits (73), Expect = 0.47
 Identities = 14/28 (50%), Positives = 17/28 (60%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTAL 33
          YD+ VIG G  G  AA +AA  GA  A+
Sbjct: 3  YDLFVIGAGSGGVRAARLAANHGAKVAI 30



 Score = 30.2 bits (68), Expect = 1.7
 Identities = 9/30 (30%), Positives = 15/30 (50%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHK 37
           ++++GGG+   E A +   LG    LI   
Sbjct: 169 ILILGGGYIAVEFAGIWRGLGVQVTLIYRG 198


>gnl|CDD|179767 PRK04176, PRK04176, ribulose-1,5-biphosphate synthetase;
          Provisional.
          Length = 257

 Score = 32.1 bits (74), Expect = 0.50
 Identities = 15/38 (39%), Positives = 19/38 (50%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSM 44
          DV ++G G +G  AA   AK G   A+   K S  G M
Sbjct: 27 DVAIVGAGPSGLTAAYYLAKAGLKVAVFERKLSFGGGM 64


>gnl|CDD|180957 PRK07395, PRK07395, L-aspartate oxidase; Provisional.
          Length = 553

 Score = 31.9 bits (73), Expect = 0.53
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGAS--TALITHKTSTIGS 43
          ++   +DV+V+G G AG  A   A  L +     LIT  T    +
Sbjct: 5  ILPSQFDVLVVGSGAAGLYA---ALCLPSHLRVGLITKDTLKTSA 46


>gnl|CDD|162324 TIGR01372, soxA, sarcosine oxidase, alpha subunit family,
           heterotetrameric form.  This model describes the alpha
           subunit of a family of known and putative
           heterotetrameric sarcosine oxidases. Five operons of
           such oxidases are found in Mesorhizobium loti and three
           in Agrobacterium tumefaciens, a high enough copy number
           to suggest that not all members are share the same
           function. The model is designated as subfamily rather
           than equivalog for this reason.Sarcosine oxidase
           catalyzes the oxidative demethylation of sarcosine to
           glycine. The reaction converts tetrahydrofolate to
           5,10-methylene-tetrahydrofolate. The enzyme is known in
           monomeric and heterotetrameric (alpha,beta,gamma,delta)
           forms.
          Length = 985

 Score = 31.6 bits (72), Expect = 0.54
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 7   DVIVIGGGHAGCEAAAVAAKLGASTALI 34
           DV+V+G G AG  AA  AA+ GA   L+
Sbjct: 165 DVLVVGAGPAGLAAALAAARAGARVILV 192


>gnl|CDD|180733 PRK06854, PRK06854, adenylylsulfate reductase subunit alpha;
          Validated.
          Length = 608

 Score = 31.8 bits (73), Expect = 0.58
 Identities = 11/22 (50%), Positives = 15/22 (68%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLG 28
          D+++IGGG AGC AA  A +  
Sbjct: 13 DILIIGGGMAGCGAAFEAKEWA 34


>gnl|CDD|183783 PRK12835, PRK12835, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
          Length = 584

 Score = 31.3 bits (71), Expect = 0.71
 Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 27/105 (25%)

Query: 3   NRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLG-------- 54
           +R  DV+V+G G  G  AA  AA  G  T L+  K++  G  +   A+ G G        
Sbjct: 9   DREVDVLVVGSGGGGMTAALTAAARGLDT-LVVEKSAHFGGST---ALSGGGIWVPGAPA 64

Query: 55  ---KGH------LVREIDALDGLMGRVADAAGIQFRVLNVKKGPA 90
              +G+      + R +  + G  G V+ A    +    V   P 
Sbjct: 65  QRREGYVPDPEDVRRYLKQITG--GLVSAARLRAY----VDAAPQ 103


>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
          protein; Provisional.
          Length = 388

 Score = 31.5 bits (72), Expect = 0.74
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
           +DV+V+GGG  G   A   A+ G   AL+
Sbjct: 5  KFDVVVVGGGLVGASLALALAQSGLRVALL 34


>gnl|CDD|185420 PTZ00058, PTZ00058, glutathione reductase; Provisional.
          Length = 561

 Score = 31.1 bits (70), Expect = 0.78
 Identities = 16/32 (50%), Positives = 19/32 (59%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
             YD+IVIGGG  G  AA  AA+  A  AL+
Sbjct: 46 RMVYDLIVIGGGSGGMAAARRAARNKAKVALV 77


>gnl|CDD|185578 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
          Length = 567

 Score = 31.4 bits (71), Expect = 0.79
 Identities = 12/26 (46%), Positives = 15/26 (57%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLG 28
          N  YDVI++GG  AG   A   +K G
Sbjct: 31 NYDYDVIIVGGSIAGPVLAKALSKQG 56


>gnl|CDD|161807 TIGR00292, TIGR00292, thiazole biosynthesis enzyme.  This enzyme
          is involved in the biosynthesis of the thiamine
          precursor thiazole, and is repressed by thiamine.This
          family includes c-thi1, a Citrus gene induced during
          natural and ethylene induced fruit maturation and is
          highly homologous to plant and yeast thi genes involved
          in thiamine biosynthesis.
          Length = 254

 Score = 31.0 bits (70), Expect = 0.87
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSM 44
          DVI++G G +G  AA   AK G    ++    +  G  
Sbjct: 23 DVIIVGAGPSGLTAAYYLAKNGLKVCVLERSLAFGGGS 60


>gnl|CDD|114555 pfam05834, Lycopene_cycl, Lycopene cyclase protein.  This family
          consists of lycopene beta and epsilon cyclase proteins.
          Carotenoids with cyclic end groups are essential
          components of the photosynthetic membranes in all
          plants, algae, and cyanobacteria. These lipid-soluble
          compounds protect against photo-oxidation, harvest
          light for photosynthesis, and dissipate excess light
          energy absorbed by the antenna pigments. The
          cyclisation of lycopene (psi, psi-carotene) is a key
          branch point in the pathway of carotenoid biosynthesis.
          Two types of cyclic end groups are found in higher
          plant carotenoids: the beta and epsilon rings.
          Carotenoids with two beta rings are ubiquitous, and
          those with one beta and one epsilon ring are common;
          however, carotenoids with two epsilon rings are rare.
          Length = 374

 Score = 31.1 bits (71), Expect = 0.95
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 2/30 (6%)

Query: 7  DVIVIGGGHAGCEAAA--VAAKLGASTALI 34
          D++++G G AG   A     A+ G    LI
Sbjct: 1  DLVIVGAGLAGLLLALRLRQARPGLRVLLI 30


>gnl|CDD|161941 TIGR00585, mutl, DNA mismatch repair protein MutL.  All proteins in
           this family for which the functions are known are
           involved in the process of generalized mismatch repair.
           This family is based on the phylogenomic analysis of JA
           Eisen (1999, Ph.D. Thesis, Stanford University).
          Length = 312

 Score = 31.1 bits (71), Expect = 1.00
 Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 6/64 (9%)

Query: 459 RRQKRFAKYIQEYNFLRSLLKSLVLTSKNLSSTSISFKQDGKTRTAYEFLSYPDF---SI 515
            R+K      +E+  +  LL    L   ++   S S   DGK                 I
Sbjct: 156 VRRKFLKSPKKEFRKILDLLNRYALIHPDV---SFSLTHDGKKVLQLSTKPNQSLKERRI 212

Query: 516 QNLF 519
           +++F
Sbjct: 213 RSVF 216


>gnl|CDD|181125 PRK07804, PRK07804, L-aspartate oxidase; Provisional.
          Length = 541

 Score = 31.1 bits (71), Expect = 1.0
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          DV+V+G G AG  AA  A + G    ++T
Sbjct: 18 DVVVVGSGVAGLTAALAARRAGRRVLVVT 46


>gnl|CDD|179330 PRK01747, mnmC, bifunctional tRNA
           (mnm(5)s(2)U34)-methyltransferase/FAD-dependent
           cmnm(5)s(2)U34 oxidoreductase; Reviewed.
          Length = 662

 Score = 31.0 bits (71), Expect = 1.0
 Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 3/21 (14%)

Query: 7   DVIVIGGGHAGCEAAAVAAKL 27
           D  +IGGG AG    A+A  L
Sbjct: 262 DAAIIGGGIAGA---ALALAL 279


>gnl|CDD|180495 PRK06263, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 543

 Score = 30.7 bits (70), Expect = 1.1
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
          DV++IG G AG  AA  A +      +I  K 
Sbjct: 9  DVLIIGSGGAGARAAIEAERGK--NVVIVSKG 38


>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
          Length = 341

 Score = 30.6 bits (70), Expect = 1.4
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 7   DVIVIGGGHAGCEAAAVAAKLGASTALIT 35
           DV++ G G  G  AAAVA  +GA   +IT
Sbjct: 166 DVLITGAGPIGIMAAAVAKHVGARHVVIT 194


>gnl|CDD|184008 PRK13369, PRK13369, glycerol-3-phosphate dehydrogenase;
          Provisional.
          Length = 502

 Score = 30.3 bits (69), Expect = 1.4
 Identities = 13/33 (39%), Positives = 15/33 (45%)

Query: 1  MINRSYDVIVIGGGHAGCEAAAVAAKLGASTAL 33
              +YD+ VIGGG  G   A  AA  G    L
Sbjct: 2  AEPETYDLFVIGGGINGAGIARDAAGRGLKVLL 34


>gnl|CDD|178123 PLN02507, PLN02507, glutathione reductase.
          Length = 499

 Score = 30.2 bits (68), Expect = 1.6
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGGLGKGHLVR 60
          +D+ VIG G  G  AA  +A  GA   +       I S S    IGG+G   ++R
Sbjct: 26 FDLFVIGAGSGGVRAARFSANFGAKVGICELPFHPISSES----IGGVGGTCVIR 76


>gnl|CDD|171764 PRK12845, PRK12845, 3-ketosteroid-delta-1-dehydrogenase;
          Reviewed.
          Length = 564

 Score = 30.1 bits (68), Expect = 1.6
 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 13/81 (16%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGS----------MSCNPAIGGLGKG 56
          D++V+G G  G  AA  A +LG S  LI  K+S +G           +  +P +   G G
Sbjct: 18 DLLVVGSG-TGMAAALAAHELGLSV-LIVEKSSYVGGSTARSGGAFWLPASPVLDEAGAG 75

Query: 57 H-LVREIDALDGLMGRVADAA 76
            L R    LD ++G  A A 
Sbjct: 76 DTLERARTYLDSVVGGSAPAE 96


>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
           associated alcohol dehydrogenase.  This clade of
           zinc-binding alcohol dehydrogenases (members of
           pfam00107) are repeatedly associated with genes proposed
           to be involved with the catabolism of phosphonate
           compounds.
          Length = 280

 Score = 30.2 bits (68), Expect = 1.6
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTAL 33
           V+V+G G  G  AAA AA  GA+  +
Sbjct: 124 VLVVGAGMLGLTAAAAAAAAGAARVV 149


>gnl|CDD|132187 TIGR03143, AhpF_homolog, putative alkyl hydroperoxide reductase F
          subunit.  This family of thioredoxin reductase homologs
          is found adjacent to alkylhydroperoxide reductase C
          subunit predominantly in cases where there is only one
          C subunit in the genome and that genome is lacking the
          F subunit partner (also a thioredcxin reductase
          homolog) that is usually found (TIGR03140).
          Length = 555

 Score = 30.1 bits (68), Expect = 1.7
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
             YD+I+IGGG AG  A   A +    T +I
Sbjct: 2  EEIYDLIIIGGGPAGLSAGIYAGRAKLDTLII 33


>gnl|CDD|180743 PRK06912, acoL, dihydrolipoamide dehydrogenase; Validated.
          Length = 458

 Score = 30.1 bits (68), Expect = 1.8
 Identities = 14/27 (51%), Positives = 18/27 (66%)

Query: 8  VIVIGGGHAGCEAAAVAAKLGASTALI 34
          ++VIGGG AG  AA  AA+ G +  LI
Sbjct: 3  LVVIGGGPAGYVAAITAAQNGKNVTLI 29



 Score = 27.8 bits (62), Expect = 9.1
 Identities = 9/27 (33%), Positives = 19/27 (70%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALI 34
           ++++GGG  GCE A++ ++LG    ++
Sbjct: 173 LLIVGGGVIGCEFASIYSRLGTKVTIV 199


>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
           reductase subunit; Provisional.
          Length = 396

 Score = 29.9 bits (67), Expect = 1.9
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNP 48
           V+++G G  G E AA A +      +I    + +G     P
Sbjct: 147 VVIVGAGTIGLELAASATQRRCKVTVIELAATVMG--RNAP 185


>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
           subunit beta/2-polyprenylphenol hydroxylase;
           Provisional.
          Length = 944

 Score = 29.8 bits (67), Expect = 2.0
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 4   RSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
           +  +V VIGGG+   +AA  A +LG +  ++  +T
Sbjct: 446 KGKEVFVIGGGNTAMDAARTAKRLGGNVTIVYRRT 480


>gnl|CDD|181507 PRK08626, PRK08626, fumarate reductase flavoprotein subunit;
          Provisional.
          Length = 657

 Score = 29.9 bits (68), Expect = 2.1
 Identities = 12/25 (48%), Positives = 14/25 (56%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGAST 31
          D +VIG G AG   A  AA+ G  T
Sbjct: 7  DALVIGAGLAGLRVAIAAAQRGLDT 31


>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
          Validated.
          Length = 506

 Score = 29.8 bits (67), Expect = 2.2
 Identities = 10/30 (33%), Positives = 17/30 (56%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
           YD++++G G AG  AA  A   G +  ++
Sbjct: 61 KYDIVIVGAGGAGMSAAIEAKDAGMNPVIL 90


>gnl|CDD|173442 PTZ00153, PTZ00153, lipoamide dehydrogenase; Provisional.
          Length = 659

 Score = 29.9 bits (67), Expect = 2.2
 Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 6   YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG----SMSCNPAIGGLGKGHLVRE 61
           YDV +IG G  G  AA  A + G    + T    +IG    ++ C P+   L      RE
Sbjct: 117 YDVGIIGCGVGGHAAAINAMERGLKVIIFTGDDDSIGGTCVNVGCIPSKALLYATGKYRE 176

Query: 62  IDALDGL 68
           +  L  L
Sbjct: 177 LKNLAKL 183


>gnl|CDD|173619 PTZ00429, PTZ00429, beta-adaptin; Provisional.
          Length = 746

 Score = 29.5 bits (66), Expect = 2.5
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 556 IKFEEKRLIPKDFDYSSLPALSNELKEKLSILKPFNLLQ--------ASKIEGMTPAALN 607
           +K E+ RL+ K    S  P +  EL E  S +    +++        A K++ + P   N
Sbjct: 349 VKLEKLRLLLKLVTPSVAPEILKELAEYASGVDMVFVVEVVRAIASLAIKVDSVAPDCAN 408

Query: 608 LLLIYIKKNTVKLNEIV 624
           LLL  + +    L ++V
Sbjct: 409 LLLQIVDRRPELLPQVV 425


>gnl|CDD|162643 TIGR01989, COQ6, Ubiquinone biosynthesis mono0xygenase COQ6.
          This model represents the monooxygenase responsible for
          the 4-hydroxylateion of the phenol ring in the aerobic
          biosynthesis of ubiquinone.
          Length = 437

 Score = 29.7 bits (67), Expect = 2.6
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 4/44 (9%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPA 49
          +DV+++GGG  G    A+AA LG +          +     NP 
Sbjct: 1  FDVVIVGGGPVG---LALAAALGNNPLT-KDLKVLLLDAVDNPK 40


>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
          Length = 428

 Score = 29.5 bits (66), Expect = 2.7
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTS 39
          +D I++G G AG  AA V A+ GA   +I    S
Sbjct: 6  FDAIIVGAGLAGSVAALVLAREGAQVLVIERGNS 39


>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
          Length = 561

 Score = 29.3 bits (66), Expect = 2.7
 Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 1   MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCN 47
              R   V VIG G A   AA  A + GA   LI  +  TIG    N
Sbjct: 94  GNERPLHVAVIGSGGAAMAAALKAVEQGARVTLI--ERGTIGGTCVN 138


>gnl|CDD|183739 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol
           hydroxylase/glutamate synthase subunit beta;
           Provisional.
          Length = 752

 Score = 29.3 bits (66), Expect = 2.8
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKTS 39
           V V+GGG+   ++A  A +LGA    I ++ S
Sbjct: 573 VAVVGGGNTAMDSARTAKRLGAERVTIVYRRS 604


>gnl|CDD|181196 PRK08010, PRK08010, pyridine nucleotide-disulfide oxidoreductase;
          Provisional.
          Length = 441

 Score = 29.2 bits (65), Expect = 2.9
 Identities = 15/42 (35%), Positives = 18/42 (42%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCN 47
          Y  ++IG G AG   A   AK G   ALI    +  G    N
Sbjct: 4  YQAVIIGFGKAGKTLAVTLAKAGWRVALIEQSNAMYGGTCIN 45


>gnl|CDD|161923 TIGR00551, nadB, L-aspartate oxidase.  L-aspartate oxidase is the
          B protein, NadB, of the quinolinate synthetase complex.
          Quinolinate synthetase makes a precursor of the
          pyridine nucleotide portion of NAD. This model
          identifies proteins that cluster as L-aspartate oxidase
          (a flavoprotein difficult to separate from the set of
          closely related flavoprotein subunits of succinate
          dehydrogenase and fumarate reductase) by both UPGMA and
          neighbor-joining trees. The most distant protein
          accepted as an L-aspartate oxidase (NadB), that from
          Pyrococcus horikoshii, not only clusters with other
          NadB but is just one gene away from NadA.
          Length = 488

 Score = 29.4 bits (66), Expect = 3.0
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGS 43
          S DV+VIG G AG  AA   A  G    +++    T G+
Sbjct: 2  SCDVVVIGSGAAGLSAALALADQG-RVIVLSKAPVTEGN 39


>gnl|CDD|178472 PLN02884, PLN02884, 6-phosphofructokinase.
          Length = 411

 Score = 29.4 bits (66), Expect = 3.1
 Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 4/93 (4%)

Query: 248 ETHRIIMENIKHSAIYSGDIKSYGPRYCPSIEDKIVRFGERNGHQIFLEPEGLNTDVVYP 307
              R++++ IK+S+  S   +   P  C  +E  + R G R   +I+ EPE +   +V  
Sbjct: 5   NDDRVLLKVIKYSSPTSAGAECIDPD-CSWVEQWVHRAGPRK--KIYFEPEEVKAAIVTC 61

Query: 308 NGISTALPEEIQH-QFIRTIPGLEKVNIIRPGY 339
            G+   L + I+   F   I G++ +  I  GY
Sbjct: 62  GGLCPGLNDVIRQIVFTLEIYGVKNIVGIPFGY 94


>gnl|CDD|130383 TIGR01316, gltA, glutamate synthase (NADPH), homotetrameric.  This
           protein is homologous to the small subunit of NADPH and
           NADH forms of glutamate synthase as found in eukaryotes
           and some bacteria. This protein is found in numerous
           species having no homolog of the glutamate synthase
           large subunit. The prototype of the family, from
           Pyrococcus sp. KOD1, was shown to be active as a
           homotetramer and to require NADPH.
          Length = 449

 Score = 29.1 bits (65), Expect = 3.2
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 8   VIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
           V+VIGGG+   ++A  A +LGA    +  +T
Sbjct: 275 VVVIGGGNTAVDSARTALRLGAEVHCLYRRT 305


>gnl|CDD|130870 TIGR01811, sdhA_Bsu, succinate dehydrogenase or fumarate
          reductase, flavoprotein subunit, Bacillus subtilis
          subgroup.  This model represents the succinate
          dehydrogenase flavoprotein subunit as found in the
          low-GC Gram-positive bacteria and a few other lineages.
          This enzyme may act in a complete or partial TCA cycle,
          or act in the opposite direction as fumarate reductase.
          In some but not all species, succinate dehydrogenase
          and fumarate reductase may be encoded as separate
          isozymes.
          Length = 603

 Score = 29.0 bits (65), Expect = 3.2
 Identities = 14/28 (50%), Positives = 17/28 (60%)

Query: 8  VIVIGGGHAGCEAAAVAAKLGASTALIT 35
          VIV+G G AG  AAA  A+LG    L +
Sbjct: 1  VIVVGTGLAGGMAAAKLAELGYHVKLFS 28


>gnl|CDD|181663 PRK09126, PRK09126, hypothetical protein; Provisional.
          Length = 392

 Score = 29.1 bits (66), Expect = 3.2
 Identities = 11/31 (35%), Positives = 14/31 (45%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
             D++V+G G AG   A   A  G    LI
Sbjct: 2  MHSDIVVVGAGPAGLSFARSLAGSGLKVTLI 32


>gnl|CDD|163271 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
           Members of this family are the RepA (or ParA) protein
           involved in replicon partitioning. All known examples
           occur in bacterial species with two or more replicons,
           on a plasmid or the smaller chromosome. Note that an
           apparent exception may be seen as a pseudomolecule from
           assembly of an incompletely sequenced genome. Members of
           this family belong to a larger family that also includes
           the enzyme cobyrinic acid a,c-diamide synthase, but
           assignment of that name to members of this family would
           be in error.
          Length = 387

 Score = 29.2 bits (66), Expect = 3.3
 Identities = 13/22 (59%), Positives = 15/22 (68%)

Query: 473 FLRSLLKSLVLTSKNLSSTSIS 494
           FLRSL    VLT+  L ST+IS
Sbjct: 320 FLRSLFGDHVLTNPMLKSTAIS 341


>gnl|CDD|168991 PRK07524, PRK07524, hypothetical protein; Provisional.
          Length = 535

 Score = 29.2 bits (66), Expect = 3.7
 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)

Query: 8   VIVIGGG--HAGCEAAAVAAKLGASTALITH 36
           +I+ GGG   A     A+A +L A  AL  +
Sbjct: 205 LILAGGGALAAAAALRALAERLDAPVALTIN 235


>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase.  E. coli His-90
           modulates substrate specificity and is believed part of
           the active site.
          Length = 340

 Score = 29.1 bits (65), Expect = 3.8
 Identities = 11/32 (34%), Positives = 15/32 (46%)

Query: 7   DVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
            V+V G G  G  A AVA   GA   +++   
Sbjct: 164 SVLVTGAGPIGLMAIAVAKASGAYPVIVSDPN 195


>gnl|CDD|162827 TIGR02374, nitri_red_nirB, nitrite reductase [NAD(P)H], large
           subunit. 
          Length = 785

 Score = 29.0 bits (65), Expect = 3.9
 Identities = 15/36 (41%), Positives = 17/36 (47%)

Query: 1   MINRSYDVIVIGGGHAGCEAAAVAAKLGASTALITH 36
           M  R     VIGGG  G EAA     LG   ++I H
Sbjct: 136 MAQRFKKAAVIGGGLLGLEAAVGLQNLGMDVSVIHH 171


>gnl|CDD|162642 TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase,
          UbiH/UbiF/VisC/COQ6 family.  This model represents a
          family of FAD-dependent hydroxylases (monooxygenases)
          which are all believed to act in the aerobic ubiquinone
          biosynthesis pathway. A separate set of hydroxylases,
          as yet undiscovered, are believed to be active under
          anaerobic conditions. In E. coli three enzyme
          activities have been described, UbiB (which acts first
          at position 6, see TIGR01982), UbiH (which acts at
          position 4, ) and UbiF (which acts at position 5). UbiH
          and UbiF are similar to one another and form the basis
          of this subfamily. Interestingly, E. coli contains
          another hydroxylase gene, called visC, that is highly
          similar to UbiF, adjacent to UbiH and, when mutated,
          results in a phenotype similar to that of UbiH (which
          has also been named visB). Several other species appear
          to have three homologs in this family, although they
          assort themselves differently on phylogenetic trees
          (e.g. Xylella and Mesorhizobium) making it difficult to
          ascribe a specific activity to each one. Eukaryotes
          appear to have only a single homolog in this subfamily
          (COQ6) which complements UbiH, but also possess a
          non-orthologous gene, COQ7 which complements UbiF.
          Length = 385

 Score = 28.7 bits (65), Expect = 4.2
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHK 37
          D++++GGG  G   A   A+ G   ALI   
Sbjct: 1  DIVIVGGGMVGLALALALARSGLKIALIEAT 31


>gnl|CDD|180885 PRK07208, PRK07208, hypothetical protein; Provisional.
          Length = 479

 Score = 28.7 bits (65), Expect = 4.4
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 7  DVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGSMSCNPAIGG 52
           V++IG G AG  AA    K G    ++      +G +S      G
Sbjct: 6  SVVIIGAGPAGLTAAYELLKRGYPVTVL-EADPVVGGISRTVTYKG 50


>gnl|CDD|185592 PTZ00389, PTZ00389, 40S ribosomal protein S7; Provisional.
          Length = 184

 Score = 28.8 bits (65), Expect = 4.4
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 200 TPARLDGKT---IIWDKTEKQFADERLIPFSFMTDKITNRQIECGITRTN 246
           T  R+DG     +  D  +++  +E+L  FS +  K+T R +        
Sbjct: 135 TRVRVDGSKLLKVFLDPKDRKNVEEKLDAFSAVYKKLTGRDVVFEFPWDP 184


>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
          Length = 464

 Score = 28.4 bits (64), Expect = 5.0
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 2   INRSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKT 38
           I     V V+GGG+   +AA  A +LGA   ++  ++
Sbjct: 278 IKVGKKVAVVGGGNVAMDAARTALRLGAEVHIVYRRS 314


>gnl|CDD|183060 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
          Length = 376

 Score = 28.6 bits (65), Expect = 5.2
 Identities = 12/29 (41%), Positives = 14/29 (48%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          YDVIVIG G  G  A    A+ G     +
Sbjct: 4  YDVIVIGLGSMGSAAGYYLARRGLRVLGL 32


>gnl|CDD|162881 TIGR02485, CobZ_N-term, precorrin 3B synthase CobZ.  CobZ is
          essential for cobalamin biosynthesis (by knockout of
          the R. capsulatus gene ) and is complemented by the
          characterized precorrin 3B synthase CobG. The enzyme
          has been shown to contain flavin, heme and Fe-S cluster
          cofactors and is believed to require dioxygen as a
          substrate. This model identifies the N-terminal portion
          of the R. capsulatus gene which, in other species
          exists as a separate protein. The C-terminal portion is
          homologous to the 2-component signal transduction
          system protein CitB (TIGR02484).
          Length = 432

 Score = 28.3 bits (63), Expect = 5.8
 Identities = 14/25 (56%), Positives = 16/25 (64%)

Query: 10 VIGGGHAGCEAAAVAAKLGASTALI 34
          VIGGG AG  AA  A + GAS  L+
Sbjct: 1  VIGGGLAGLCAAIEARRAGASVLLL 25


>gnl|CDD|181247 PRK08137, PRK08137, amidase; Provisional.
          Length = 497

 Score = 28.2 bits (63), Expect = 5.9
 Identities = 31/90 (34%), Positives = 37/90 (41%), Gaps = 21/90 (23%)

Query: 20  AAAVAAKLGASTALITHKTSTIGSMSCNPAIGGL----------GKGHLVREIDALD--G 67
            AAVAA L    A +   T T GS++C  AI GL           +  +V    + D  G
Sbjct: 167 GAAVAAGL----AAVAIGTETDGSITCPAAINGLVGLKPTVGLVSRDGIVPISHSQDTAG 222

Query: 68  LMGR-VADAAGIQFRVLNVKKGPAVRGPRT 96
            M R VADAA     VL    G     P T
Sbjct: 223 PMTRTVADAA----AVLTAIAGGDPADPAT 248


>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB.  Members
           of this protein family are the bacterial ATP-dependent
           chaperone ClpB. This protein belongs to the AAA family,
           ATPases associated with various cellular activities
           (pfam00004). This molecular chaperone does not act as a
           protease, but rather serves to disaggregate misfolded
           and aggregated proteins.
          Length = 852

 Score = 28.4 bits (64), Expect = 6.1
 Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 7/48 (14%)

Query: 97  QADRELYRLAMQREIL-------SQENLDVIQGEVAGFNTEKNIISSI 137
           + DR + +L ++RE L       S+E L+ ++ E+A    E   +   
Sbjct: 409 ELDRRIIQLEIEREALKKEKDEASKERLEDLEKELAELEEEYADLEEQ 456


>gnl|CDD|130490 TIGR01423, trypano_reduc, trypanothione-disulfide reductase.
          Trypanothione, a glutathione-modified derivative of
          spermidine, is (in its reduced form) an important
          antioxidant found in trypanosomatids (Crithidia,
          Leishmania, Trypanosoma). This model describes
          trypanothione reductase, a possible antitrypanosomal
          drug target closely related to some forms of
          glutathione reductase.
          Length = 486

 Score = 28.4 bits (63), Expect = 6.3
 Identities = 11/25 (44%), Positives = 17/25 (68%)

Query: 3  NRSYDVIVIGGGHAGCEAAAVAAKL 27
          ++++D++VIG G  G EA   AA L
Sbjct: 1  SKAFDLVVIGAGSGGLEAGWNAATL 25


>gnl|CDD|181516 PRK08641, sdhA, succinate dehydrogenase flavoprotein subunit;
          Reviewed.
          Length = 589

 Score = 28.4 bits (64), Expect = 6.4
 Identities = 13/28 (46%), Positives = 16/28 (57%)

Query: 8  VIVIGGGHAGCEAAAVAAKLGASTALIT 35
          VIV+GGG AG  A   AA+ G    L +
Sbjct: 6  VIVVGGGLAGLMATIKAAEAGVHVDLFS 33


>gnl|CDD|178280 PLN02676, PLN02676, polyamine oxidase.
          Length = 487

 Score = 28.1 bits (63), Expect = 6.6
 Identities = 14/39 (35%), Positives = 19/39 (48%)

Query: 4  RSYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
           S  VI++G G +G  AA   ++ G    LI   T  IG
Sbjct: 25 PSPSVIIVGAGMSGISAAKTLSEAGIEDILILEATDRIG 63


>gnl|CDD|178411 PLN02815, PLN02815, L-aspartate oxidase.
          Length = 594

 Score = 28.1 bits (63), Expect = 6.8
 Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALIT 35
          +D +VIG G AG   A   A+ G + A+IT
Sbjct: 30 FDFLVIGSGIAGLRYALEVAEYG-TVAIIT 58


>gnl|CDD|184951 PRK14989, PRK14989, nitrite reductase subunit NirD; Provisional.
          Length = 847

 Score = 28.2 bits (63), Expect = 7.4
 Identities = 14/31 (45%), Positives = 16/31 (51%)

Query: 4   RSYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
           RS    V+GGG  G EAA     LG  T +I
Sbjct: 144 RSKRGAVVGGGLLGLEAAGALKNLGVETHVI 174


>gnl|CDD|148569 pfam07027, DUF1318, Protein of unknown function (DUF1318).  This
           family consists of several bacterial proteins of around
           100 residues in length and is often known as YdbL. The
           function of this family is unknown.
          Length = 95

 Score = 27.9 bits (63), Expect = 7.5
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)

Query: 353 PTLETKKISGLFLAG-QINGTTGY---EEAAAQGLVAGINSARK 392
             L+  K  GL   G Q++G  G        A+ LV  IN+ R+
Sbjct: 9   LDLDEAKAQGL--VGEQLDGYLGVVKGASPEARALVDDINNKRR 50


>gnl|CDD|165249 PHA02939, PHA02939, hypothetical protein; Provisional.
          Length = 144

 Score = 28.0 bits (62), Expect = 7.7
 Identities = 10/30 (33%), Positives = 23/30 (76%)

Query: 455 CIGERRQKRFAKYIQEYNFLRSLLKSLVLT 484
           CI E+R++++ K I+E+N ++ +++  VL+
Sbjct: 115 CIDEKRREKYLKLIEEFNKVKEMIEKTVLS 144


>gnl|CDD|151718 pfam11277, Med24_N, Mediator complex subunit 24 N-terminal.  This
           subunit of the Mediator complex appears to be conserved
           only from insects to humans. It is essential for correct
           retinal development in fish. Subunit composition of the
           mediator contributes to the control of differentiation
           in the vertebrate CNS as there are divergent functions
           of the mediator subunits Crsp34/Med27, Trap100/Med24,
           and Crsp150/Med14.
          Length = 991

 Score = 27.9 bits (62), Expect = 7.7
 Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 140 QDNSMIRCSTVV--LTTGTFLRGVIHIGKLKIPA 171
           Q+  + +C  V+  +   TFL  ++HIGKL+ P 
Sbjct: 151 QEEVLDQCLVVLERILQSTFLLALLHIGKLEEPE 184


>gnl|CDD|180946 PRK07364, PRK07364, 2-octaprenyl-6-methoxyphenyl hydroxylase;
          Validated.
          Length = 415

 Score = 28.1 bits (63), Expect = 7.8
 Identities = 13/30 (43%), Positives = 16/30 (53%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALI 34
          +YDV ++GGG  G   AA     G   ALI
Sbjct: 18 TYDVAIVGGGIVGLTLAAALKDSGLRIALI 47


>gnl|CDD|161671 TIGR00031, UDP-GALP_mutase, UDP-galactopyranose mutase.  The gene
          is known as glf, ceoA, and rfbD. It is known
          experimentally in E. coli, Mycobacterium tuberculosis,
          and Klebsiella pneumoniae.
          Length = 377

 Score = 27.8 bits (62), Expect = 8.0
 Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 5  SYDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIG 42
           +D I++G G +G   A + A+L     L+  K + IG
Sbjct: 1  MFDYIIVGAGLSGIVLANILAQLNKRV-LVVEKRNHIG 37


>gnl|CDD|132407 TIGR03364, HpnW_proposed, FAD dependent oxidoreductase TIGR03364.
           This clade of FAD dependent oxidoreductases (members
          of the pfam01266 family) is syntenically associated
          with a family of proposed phosphonatase-like enzymes
          (TIGR03351) and is also found (less frequently) in
          association with phosphonate transporter components. A
          likely role for this enzyme involves the oxidative
          deamination of an aminophosphonate differring slightly
          from 2-aminoethylphosphonate, possibly
          1-hydroxy-2-aminoethylphosphonate (see the comments for
          TIGR03351). Many members of the larger FAD dependent
          oxidoreductase family act as amino acid oxidative
          deaminases.
          Length = 365

 Score = 28.0 bits (63), Expect = 8.1
 Identities = 20/82 (24%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 6  YDVIVIGGGHAGCEAAAVAAKLGASTALITHKTSTIGS------MSCNPAIGGLGKGHLV 59
          YD+I++G G  G   A  AA+ G S  +I   +   G+              G   G   
Sbjct: 1  YDLIIVGAGILGLAHAYAAARRGLSVTVIERSSRAQGASVRNFGQVW---PTGQAPGPAW 57

Query: 60 REIDALDGLMGRVADAAGIQFR 81
                  +   +A  AGI  R
Sbjct: 58 DRARRSREIWLELAAKAGIWVR 79


>gnl|CDD|179352 PRK01911, ppnK, inorganic polyphosphate/ATP-NAD kinase;
           Provisional.
          Length = 292

 Score = 28.0 bits (63), Expect = 8.4
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 90  AVRGPRTQADRELYRLAMQREILSQENLDV-IQGEVAGFNTEKNIISSIV--MQDNSMIR 146
           A+ G   Q     Y   +  + L +   +V I+ +   F  +            DN  + 
Sbjct: 4   AIFGQTYQESASPYIQEL-FDELEERGAEVLIEEKFLDFLKQDLKFHPSYDTFSDNEELD 62

Query: 147 CSTVVLTT----GTFLRGVIHIGKLKIP-----AGRMG 175
            S  ++ +    GTFLR   ++G   IP      GR+G
Sbjct: 63  GSADMVISIGGDGTFLRTATYVGNSNIPILGINTGRLG 100


>gnl|CDD|152330 pfam11894, DUF3414, Protein of unknown function (DUF3414).  This
            family of proteins are functionally uncharacterized. This
            protein is found in eukaryotes. Proteins in this family
            are typically between 764 to 2011 amino acids in length.
            This protein has a conserved LLG sequence motif.
          Length = 1611

 Score = 27.7 bits (62), Expect = 8.6
 Identities = 12/54 (22%), Positives = 23/54 (42%)

Query: 453  LGCIGERRQKRFAKYIQEYNFLRSLLKSLVLTSKNLSSTSISFKQDGKTRTAYE 506
            L  +  R+     + + + N+L  L+ SL  T + L +      +     TA+E
Sbjct: 1412 LVHLDSRKDNFILESLSKSNYLSLLVDSLKATDEALQAALTPLPELLYELTAFE 1465


>gnl|CDD|162677 TIGR02061, aprA, adenosine phosphosulphate reductase, alpha
          subunit.  During dissimilatory sulfate reduction or
          sulfur oxidation, adenylylsulfate (APS) reductase
          catalyzes reversibly the two-electron reduction of APS
          to sulfite and AMP. Found in several bacterial lineages
          and in Archaeoglobales, APS reductase is a heterodimer
          composed of an alpha subunit containing a noncovalently
          bound FAD, and a beta subunit containing two [4Fe-4S]
          clusters. Described by this model is the alpha subunit
          of APS reductase, sharing common evolutionary origin
          with fumarate reductase/succinate dehydrogenase
          flavoproteins.
          Length = 614

 Score = 27.9 bits (62), Expect = 8.9
 Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 3/36 (8%)

Query: 7  DVIVIGGGHAGCEAAAVA---AKLGASTALITHKTS 39
          D++++GGG  GC AA  A           ++  K +
Sbjct: 1  DLLIVGGGMGGCGAAFEAVYWGDKKGLKIVLVEKAN 36


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.137    0.389 

Gapped
Lambda     K      H
   0.267   0.0741    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,185,828
Number of extensions: 680911
Number of successful extensions: 1543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1528
Number of HSP's successfully gapped: 163
Length of query: 626
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 527
Effective length of database: 3,855,281
Effective search space: 2031733087
Effective search space used: 2031733087
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: 60 (26.9 bits)