Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431   3 FHEQKILPAVRQIKDLEKLLHSSYEYIVILDIHVGQLKSVISLAKQYCKKVFLHVDLIHGLQSDGHATEYLCQEFRPYGL 82
Cdd:COG1954    1 LAENPIIPAVRDLKDLEKALKSDVEVIFLLNGDIGNLKSIVKRLKQAGKKVFVHIDLIEGLSNDEYGIEYLKQEIKPDGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431  83 LSTKASVIMKAKQKGVVAIQRIFLIDSSAMEKSCNLLDKTKPDYIEVLPGAMTDIIAEVKERTGVPILAGGFIRTVEDVE 162
Cdd:COG1954   81 ISTKSNLIKAAKKEGLLTIQRLFLIDSSALETGIKLIEKSKPDAIEILPGIMPKVIKEIKKETGIPIIAGGLIRTKEDVE 160

                        170
                 ....*....|....*...
gi 446316431 163 RALNAGATAITTSKRELW 180
Cdd:COG1954  161 AALAAGAIAVSTSNKELW 178

Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431   3 FHEQKILPAVRQIKDLEKLLHSSYEYIVILDIHVGQLKSVISLAKQYCKKVFLHVDLIHGLQSDGHATEYLCQEFRPYGL 82
Cdd:COG1954    1 LAENPIIPAVRDLKDLEKALKSDVEVIFLLNGDIGNLKSIVKRLKQAGKKVFVHIDLIEGLSNDEYGIEYLKQEIKPDGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431  83 LSTKASVIMKAKQKGVVAIQRIFLIDSSAMEKSCNLLDKTKPDYIEVLPGAMTDIIAEVKERTGVPILAGGFIRTVEDVE 162
Cdd:COG1954   81 ISTKSNLIKAAKKEGLLTIQRLFLIDSSALETGIKLIEKSKPDAIEILPGIMPKVIKEIKKETGIPIIAGGLIRTKEDVE 160

                        170
                 ....*....|....*...
gi 446316431 163 RALNAGATAITTSKRELW 180
Cdd:COG1954  161 AALAAGAIAVSTSNKELW 178

HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446316431 135 TDIIAEVKERTGVPILAGGFIRTVEDVERALNAGATAI 172
Cdd:cd04732   62 LELIEEIVKAVGIPVQVGGGIRSLEDIERLLDLGVSRV 99

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446316431 135 TDIIAEVKERTGVPILAGGFIRTVEDVERALNAGAT 170
Cdd:PRK00748  63 LELIEAIVKAVDIPVQVGGGIRSLETVEALLDAGVS 98

Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431   3 FHEQKILPAVRQIKDLEKLLHSSYEYIVILDIHVGQLKSVISLAKQYCKKVFLHVDLIHGLQSDGHATEYLCQEFRPYGL 82
Cdd:COG1954    1 LAENPIIPAVRDLKDLEKALKSDVEVIFLLNGDIGNLKSIVKRLKQAGKKVFVHIDLIEGLSNDEYGIEYLKQEIKPDGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446316431  83 LSTKASVIMKAKQKGVVAIQRIFLIDSSAMEKSCNLLDKTKPDYIEVLPGAMTDIIAEVKERTGVPILAGGFIRTVEDVE 162
Cdd:COG1954   81 ISTKSNLIKAAKKEGLLTIQRLFLIDSSALETGIKLIEKSKPDAIEILPGIMPKVIKEIKKETGIPIIAGGLIRTKEDVE 160

                        170
                 ....*....|....*...
gi 446316431 163 RALNAGATAITTSKRELW 180
Cdd:COG1954  161 AALAAGAIAVSTSNKELW 178

Histidine biosynthesis protein; Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 446316431  132 GAMTDIIAEVKERTGVPILAGGFIRTVEDVERALNAGA 169
Cdd:pfam00977  59 PVNLDVVEEIAEEVFIPVQVGGGIRSLEDVERLLSAGA 96

HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446316431 135 TDIIAEVKERTGVPILAGGFIRTVEDVERALNAGATAI 172
Cdd:cd04732   62 LELIEEIVKAVGIPVQVGGGIRSLEDIERLLDLGVSRV 99

The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446316431 134 MTDIIAEVKERTGVPILAGGFIRTVEDVERALNAGA 169
Cdd:cd04731   59 MLDVVERVAEEVFIPLTVGGGIRSLEDARRLLRAGA 94

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446316431 135 TDIIAEVKERTGVPILAGGFIRTVEDVERALNAGAT 170
Cdd:PRK00748  63 LELIEAIVKAVDIPVQVGGGIRSLETVEALLDAGVS 98

Class I aldolases; Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446316431 131 PGAMTDIIAEVKERtgVPILAGGFIRTVEDVERALNAGATAITTS 175
Cdd:cd00945  159 VEDVKLMKEAVGGR--VGVKAAGGIKTLEDALAAIEAGADGIGTS 201

Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446316431 106 LIDSSAMEKSCNLLdktkPDYIEVLP--------GAMTDIIAEVKERTGVPILAGGFIRTVEDVERALNAGATAIT 173
Cdd:cd04723  145 FIGPEELLRRLAKW----PEELIVLDidrvgsgqGPDLELLERLAARADIPVIAAGGVRSVEDLELLKKLGASGAL 216

Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446316431 131 PGAMTDIIAEVKERTGVPILAGGFIRTVEDVERALNAG 168
Cdd:cd04734  270 PGPFLPLAARIKQAVDLPVFHAGRIRDPAEAEQALAAG 307

L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446316431 138 IAEVKERTGVPILAGGfIRTVEDVERALNAGATAITTS 175
Cdd:cd04737  213 IEFIAKISGLPVIVKG-IQSPEDADVAINAGADGIWVS 249

Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446316431 138 IAEVKERTGVPILAGGfIRTVEDVERALNAGATAI 172
Cdd:cd02809  164 LAWLRSQWKGPLILKG-ILTPEDALRAVDAGADGI 197

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 446316431 136 DIIAEVKERTGVPILAGGFIRTVEDVERALN 166
Cdd:cd02801  173 DYIAEIKEAVSIPVIANGDIFSLEDALRCLE 203