RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781101|ref|YP_003065514.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Candidatus Liberibacter asiaticus str. psy62] (472 letters) >gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]. Length = 451 Score = 376 bits (968), Expect = e-105 Identities = 175/464 (37%), Positives = 244/464 (52%), Gaps = 14/464 (3%) Query: 4 LWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQK 63 L T +L + G +G P +G+SIDSR + P + F A+KG +DGHDFI A+ Sbjct: 2 LLTLDELADILGGALVGADPVVV-SGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAA 60 Query: 64 GAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTK 123 GA V+V ++ ++ + V V D L AL KLA A R + A +IAITGS GKTTTK Sbjct: 61 GAAAVLVARPVLPP--AIPLVVLLVLDTLEALGKLAKAYRQKFNAKVIAITGSNGKTTTK 118 Query: 124 EMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVR 183 EML LS+ K +A G++NN IG+PLTL R+P D ++ + E+GM+H GEI L+ + R Sbjct: 119 EMLAAILSTKGKVHATPGNFNNEIGLPLTLLRLPADTEYAVLEMGMNHPGEIAELSEIAR 178 Query: 184 PHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALG 243 P IAVIT I AHL F E IA AKAEI GL G LN D+ + AK +G Sbjct: 179 PDIAVITNIGEAHLEGFGSREGIAEAKAEILAGLRPEGIAILNADNPLLKNWAAK---IG 235 Query: 244 IKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIV 303 + SFG + DF+ E S + ++G E G H N L + Sbjct: 236 NAKVLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALA 295 Query: 304 SILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQI 363 L D++ L P +GR + L TLID+SYNANP SM+AA+ +L+ + Sbjct: 296 LELGLDLEEIAAGLKELKPVKGRLEVI---LLANGKTLIDDSYNANPDSMRAALDLLAAL 352 Query: 364 SPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIH 423 + IAVLGDM E+GE S+ H ++ E I V+L G A+ +AL Sbjct: 353 PG---RKGIAVLGDMLELGEESEELHEEVGEYAVEAGIDLVFLVGELSKAIAEALGN--K 407 Query: 424 VHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEE 467 Y + L +++ L GDVV+VK S ++++ LL + Sbjct: 408 GIYFADKEELITSLKALLRKGDVVLVKGSRGMKLEKVVDALLGK 451 >gnl|CDD|31112 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]. Length = 475 Score = 112 bits (282), Expect = 2e-25 Identities = 93/370 (25%), Positives = 138/370 (37%), Gaps = 33/370 (8%) Query: 27 VNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVF 86 G+++DSR + + F A G DGHDFI A+ GA VVV D+ + +PV Sbjct: 10 PTGLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDIKLAEA--GVPVI 67 Query: 87 GVDDVLGAL--NKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIG--- 141 V G L LA K +I +TG+ GKTTT +L L + K A IG Sbjct: 68 VVTGTNGKLTTLALAFYGLPSGKLKVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGTEG 127 Query: 142 -SYNNHIGVP-----------LTLARMPVD--VDFGIFELGMSHLGEIRFLTHLVRPHIA 187 + I P L R +D + + E SH G ++ V + Sbjct: 128 DELSPGILEPTGLTTPEALDLQNLLRDLLDRGAEIAVME-VSSH-GLVQGRVEGVTFDVG 185 Query: 188 VITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTI 247 V T ++ HL +E +AKA +FE L +G +N DD K + Sbjct: 186 VFTNLSRDHLDYHGTMEYYGAAKAVLFESLPHSGEAVINPDDGHGLDYKERLKNALGD-Y 244 Query: 248 YSFGKSKNADFQLRKWKQCSEQSWM-EVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSIL 306 ++G + + S + G E G N L + L Sbjct: 245 ITYGCDFKRPDLDYRGIEESSSGSDFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALAL 304 Query: 307 TADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPH 366 D++ + L P GR + G ++D Y NP ++ A+ + H Sbjct: 305 GVDLEDILAGLETLKPVPGRMELVNIG---GKLVIVD--YAHNPDGLEKALRAV---RLH 356 Query: 367 GEGRRIAVLG 376 GR I V G Sbjct: 357 AAGRLIVVFG 366 >gnl|CDD|31116 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]. Length = 459 Score = 109 bits (274), Expect = 2e-24 Identities = 93/426 (21%), Positives = 161/426 (37%), Gaps = 56/426 (13%) Query: 45 AIKGPHYDGHDFILHAVQKGAGLVVVNTDM------VASIGSLSIPVFGVDDVLGALNKL 98 A+ + GHD A +VVV+ + + + IPV ++L L Sbjct: 50 ALGIEIFIGHD---AENILDADVVVVSNAIKEDNPEIVAALERGIPVISRAEMLAEL--- 103 Query: 99 AVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKK--TYACIGSYNNHIGVPLTLARM 156 +R + T IA+ G+ GKTTT ML L + T+ IG + G T AR+ Sbjct: 104 -----MRFR-TSIAVAGTHGKTTTTSMLAWVLEAAGLDPTFL-IGGILKNFG---TNARL 153 Query: 157 PVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEG 216 D+ + E S H P +A++T I HL + +E I A Sbjct: 154 G-SGDYFVAEADESD----SSFLHY-NPRVAIVTNIEFDHLDYYGDLEAIKQAFHHFVRN 207 Query: 217 LEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQL 276 + G + DD L+ + ++G AD++ +Q + +V Sbjct: 208 VPFYGRAVVCGDD---PNLRELLSRGCWSPVVTYGFDDEADWRAENIRQDGSGTTFDVLF 264 Query: 277 QGKSMEVVHHGI-GYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALN 335 +G+ + V + G H N L + + L D + +AL+ F +G +R+ Sbjct: 265 RGEELGEVKLPLPGRHNVLNALAAIAVARELGIDPEAIAEALASF---QGVKRRFELKGE 321 Query: 336 QGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGD------MCEMGELSQSF- 388 T+ID+ Y +P +KA ++ Q P G R +AV + + +++ Sbjct: 322 VNGVTVIDD-YAHHPTEIKATLAAARQKVPGG-KRIVAVFQPHRYSRTRDLLDDFAKALS 379 Query: 389 HIDLAEVLSLY-----NISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVD 443 D +L +Y I L + + + HV + D L + Sbjct: 380 DADEVILLDVYAAGEEPIEGDV----SSEDLAEKIRQPGHVDVPDLDD-LVELLAKVAQP 434 Query: 444 GDVVVV 449 GDV++ Sbjct: 435 GDVILF 440 >gnl|CDD|31114 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]. Length = 448 Score = 96.9 bits (241), Expect = 1e-20 Identities = 89/357 (24%), Positives = 134/357 (37%), Gaps = 38/357 (10%) Query: 101 AARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVP-LTLARMPVD 159 RL +A I+AITG+ GKTTT ++ L + G+ IG P L L Sbjct: 103 FYRLSGEAPIVAITGTNGKTTTTSLIAHLLKAAGLDALLGGN----IGTPALELLEQAEP 158 Query: 160 VDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEK 219 D + EL L T +RP IAVI I+ HL +E A+AK I EG + Sbjct: 159 ADVYVLELSSFQL----ETTSSLRPEIAVILNISEDHLDRHGSMENYAAAKLRILEG--Q 212 Query: 220 TGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGK 279 T +N DD LK + + F + E L Sbjct: 213 TEVAVINADD---AYLKTLADEATKARVIWFSFGEPLADGDY-IYDGKLVFKGEKLLPAD 268 Query: 280 SMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFF 339 +++ G H +N L L + L + ++ALS F R + F Sbjct: 269 ELKLP----GAHNLENALAALALARALGVPPEAILEALSSFTGLPHRLEFVGEKDGVLF- 323 Query: 340 TLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLY 399 I++S N + AA+S +G I + G + + S LAE+L+ Sbjct: 324 --INDSKATNVDATLAALSGF-------DGPVILIAGGDDKGADFS-----PLAEILAKV 369 Query: 400 NISHVWLSGFHVLALKDAL-PRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSC 455 I + L G + AL + ET++ + GDVV++ S +C Sbjct: 370 -IKKLVLIGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQPGDVVLL--SPAC 423 >gnl|CDD|144716 pfam01225, Mur_ligase, Mur ligase family, catalytic domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. Length = 76 Score = 58.3 bits (142), Expect = 4e-09 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 2/73 (2%) Query: 27 VNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVF 86 ++ I IDSR ++P F A+KG DG DF A+ GA VV + + + +P Sbjct: 2 IHFIGIDSRGMSPGALFLALKGYRVDGSDFAESAIALGAVAVVSSA--IPRDPNPEVPGI 59 Query: 87 GVDDVLGALNKLA 99 V D AL +LA Sbjct: 60 PVIDRREALAELA 72 >gnl|CDD|145824 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. Length = 87 Score = 47.3 bits (113), Expect = 1e-05 Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 8/71 (11%) Query: 334 LNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLA 393 N G + D Y NP +++AA+ L ++ +GR I V G G+ FH L Sbjct: 10 ENNGVLVIDD--YAHNPDALEAALQALKEL---FDGRLILVFGA---GGDRDAEFHALLG 61 Query: 394 EVLSLYNISHV 404 + + + Sbjct: 62 ALAAALADVVI 72 >gnl|CDD|30633 COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism]. Length = 427 Score = 40.3 bits (94), Expect = 0.001 Identities = 49/226 (21%), Positives = 90/226 (39%), Gaps = 32/226 (14%) Query: 158 VDVDFGIFELGMSHLGEIRF-LTHLVRPHIAVITTIAPAHLSNFSG--IEEIASAKAEIF 214 VD I E+G+ R T+++ P ++VIT+I H + F G +E IA KA I Sbjct: 136 AKVDVAILEVGLG----GRLDATNVIEPDVSVITSIGLDH-TAFLGDTLESIAREKAGII 190 Query: 215 EGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEV 274 + + ++ ++ ++ LG DFQ+ + Sbjct: 191 KAGKPAVIGEQQPPEA-LNVIAERAEELGAPLFVL-----GPDFQVLEEGN-----GFSF 239 Query: 275 QLQGKSMEVVHHGIGYHM-AQNMLMTLGIVSILTADV--DTAIKAL-SVFHPKEGRGKRY 330 Q G +++ +G H +N + + + L ++ + K L +V P GR +R Sbjct: 240 QGGGGLLDLPLPLLGGHHQIENAALAIAALEALGKEISEEAIRKGLANVDWP--GRLER- 296 Query: 331 RCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLG 376 L++ L+D ++ NP + +A L + R V G Sbjct: 297 ---LSENPLILLDGAH--NPHAARALAETLKTLFND-RPRLTLVFG 336 >gnl|CDD|145608 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation. Length = 205 Score = 30.9 bits (71), Expect = 0.76 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 6/39 (15%) Query: 339 FTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGD 377 F ++DE+ N P MK L++I G ++ V GD Sbjct: 122 FIILDEAQNTTPEQMK---MFLTRI---GFNSKMVVTGD 154 >gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl alcohol dehydrogenase is similar to liver alcohol dehydrogenase, but has some amino acid substitutions near the active site, which may determine the enzyme's specificity of oxidizing aromatic substrates. Also known as aryl-alcohol dehydrogenases, they catalyze the conversion of an aromatic alcohol + NAD+ to an aromatic aldehyde + NADH + H+. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 365 Score = 30.2 bits (69), Expect = 1.5 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 8/54 (14%) Query: 61 VQKGAGLVVVNTDMVASIGSLSIPVFGVDDV-LGALNKLAVAARLRSKATIIAI 113 +Q GAG V+N + GS SI VFG V L A+ +AA++ TIIA+ Sbjct: 171 IQTGAG-AVLNV-LKPRPGS-SIAVFGAGAVGLAAV----MAAKIAGCTTIIAV 217 >gnl|CDD|37195 KOG1984, KOG1984, KOG1984, Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]. Length = 1007 Score = 29.6 bits (66), Expect = 2.2 Identities = 27/139 (19%), Positives = 48/139 (34%), Gaps = 43/139 (30%) Query: 338 FFTLIDESYNANPASMKAAI-----SVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDL 392 F +ID SYNA A SVL + R+ + + Sbjct: 420 FVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGI---------------VTF 464 Query: 393 AEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSS 452 + + +N+S +L + D +D +F+ +DG + V + Sbjct: 465 DKTVHFFNLSSNLAQP-QMLIVSD-------------VDDVFV----PFLDG--LFVNPN 504 Query: 453 NSCGFYRLINLLLEEFPAI 471 S ++I LLL+ P + Sbjct: 505 ES---RKVIELLLDSIPTM 520 >gnl|CDD|145357 pfam02153, PDH, Prephenate dehydrogenase. Members of this family are prephenate dehydrogenases EC:1.3.1.12 involved in tyrosine biosynthesis. Length = 258 Score = 28.9 bits (65), Expect = 3.3 Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 13/72 (18%) Query: 178 LTHLVRPHIAVITTIAPAHL---SNFSGIEEIASAKAEIFEG-------LEKTGTIFLNY 227 + ++ P H + SG +A+A +FE EKT T L Sbjct: 85 IVKDAEQLLSDGVGFIPGHPMAGTEKSGP---DAARANLFENAPVILTPTEKTDTEALAL 141 Query: 228 DDSFFELLKAKS 239 E + AK Sbjct: 142 VRELLEGIGAKV 153 >gnl|CDD|147730 pfam05735, TSP_C, Thrombospondin C-terminal region. This region is found at the C-terminus of thrombospondin and related proteins. Length = 201 Score = 28.5 bits (64), Expect = 4.2 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 17/63 (26%) Query: 214 FEGLEKTGTIFLN--YDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSW 271 FEG++ GT F+N DD + +G + FG N+ F + WK+ +EQ++ Sbjct: 32 FEGVDFEGTFFINTTTDDDY----------VG----FVFGYQSNSKFYVVMWKK-AEQTY 76 Query: 272 MEV 274 + Sbjct: 77 WQA 79 >gnl|CDD|73403 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.. Length = 294 Score = 28.3 bits (63), Expect = 4.7 Identities = 13/42 (30%), Positives = 21/42 (50%) Query: 76 ASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSV 117 SI SL +P G+D L + ++ +K I++TGS Sbjct: 61 GSINSLGLPNLGLDYYLEYIRTISDGLPGSAKPFFISVTGSA 102 >gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201 Score = 27.9 bits (63), Expect = 6.6 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 10/59 (16%) Query: 165 FELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTI 223 F + MS +GE+ FL L +A + +AP + IE + E+ E LE +G I Sbjct: 2 FRIAMSDIGEMYFLPRL----LAALREVAP-GVR----IETVRLPVDELEEALE-SGEI 50 >gnl|CDD|100086 cd03084, phosphohexomutase, The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.. Length = 355 Score = 27.7 bits (62), Expect = 8.1 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 7/57 (12%) Query: 276 LQGKSMEVVH---HGIGYHMAQNMLMTLGI-VSILTADVDTAIKALSVFHPKEGRGK 328 L K +VV +G+G +A +L LG V L + D +P G Sbjct: 108 LSNKKFKVVVDSVNGVGGPIAPQLLEKLGAEVIPLNCEPD---GNFGNINPDPGSET 161 >gnl|CDD|30198 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.. Length = 220 Score = 27.5 bits (61), Expect = 9.1 Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 2/24 (8%) Query: 110 IIAITGSV--GKTTTKEMLTIALS 131 II I GSV GK+TT +L LS Sbjct: 1 IIGIAGSVAVGKSTTARVLQALLS 24 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.322 0.137 0.401 Gapped Lambda K H 0.267 0.0680 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,636,328 Number of extensions: 303538 Number of successful extensions: 757 Number of sequences better than 10.0: 1 Number of HSP's gapped: 740 Number of HSP's successfully gapped: 26 Length of query: 472 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 375 Effective length of database: 4,167,664 Effective search space: 1562874000 Effective search space used: 1562874000 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 (21.9 bits) S2: 59 (26.6 bits)