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)