RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764510|ref|YP_003065448.2| uroporphyrinogen-III synthase [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >gnl|CDD|31775 COG1587, HemD, Uroporphyrinogen-III synthase [Coenzyme metabolism]. Length = 248 Score = 83.2 bits (205), Expect = 5e-17 Identities = 50/242 (20%), Positives = 90/242 (37%), Gaps = 16/242 (6%) Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFIHDRE-SVFLAMQQSYGAIAITSSES 59 M +++TRP ++A ++K G P+ +PL + V L S + TS + Sbjct: 2 MRVLVTRPREQAEELAALLRKAGAEPLELPLIEIEPLPDLEVALEDLDSADWVVFTSPNA 61 Query: 60 LSTLPANF-------CRHTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKIIVEQKVL 112 + ++ I A+GE +A R+ G F +D ++ E L Sbjct: 62 VRFFFEALKEQGLDALKNKKIAAVGEKTAEALRKLGIKVDFIPEDGDS--EGLLEELPEL 119 Query: 113 FTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQNA--DAI 170 K ++ L G E+ L E +R ++ Y ++ E T+ LL+ DA+ Sbjct: 120 LKGGKRVLILRGNGGREVLEEKLEERGAEVREVEVYRTEPPPLDEATLIELLKLGEVDAV 179 Query: 171 LFYARSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVVTVACFPKETSLLK 226 +F + S+V +L + + A + V A P +L Sbjct: 180 VFTSSSAVRALLALAPESGIEFLERKRVASIGPRTAETLKELGITVDIAAEKPTLEALAD 239 Query: 227 LL 228 L Sbjct: 240 AL 241 >gnl|CDD|119440 cd06578, HemD, Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease. Length = 239 Score = 82.7 bits (205), Expect = 8e-17 Identities = 48/242 (19%), Positives = 88/242 (36%), Gaps = 19/242 (7%) Query: 3 IVITRPIKKALRTQEKIQKMGYIPVMMPLSYFIHDRESVFLAMQQ---SYGAIAITSSES 59 +++TRP +A ++ +G + +PL ++ A Y + TS + Sbjct: 1 VLVTRPRPQADELAALLEALGAEVLELPLIEIEPLDDAELDAALADLDEYDWLIFTSPNA 60 Query: 60 ----LSTLPANFCR---HTPIFAIGEASACLARQKGFTQIFHGKD-NSINLAKIIVEQKV 111 L R I A+G +A R+ G T F ++ +S L +++ Q Sbjct: 61 VEAFFEALEELGLRALAGLKIAAVGPKTAEALREAGLTADFVPEEGDSEGLLELLELQDG 120 Query: 112 LFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQNA-DAI 170 K ++ G + L E + ++ Y + ++ L + A DA+ Sbjct: 121 ---KGKRILRPRGGRAREDLAEALRERGAEVDEVEVYRTVPPDLDAELLELLEEGAIDAV 177 Query: 171 LFYARSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVVTVACFPKETSLLK 226 LF + S+V L + + A A+ VV VA P +LL+ Sbjct: 178 LFTSPSTVRNLLELLGKEGRALLKNVKIAAIGPRTAEALRELGLKVVIVAESPTLEALLE 237 Query: 227 LL 228 L Sbjct: 238 AL 239 >gnl|CDD|145641 pfam02602, HEM4, Uroporphyrinogen-III synthase HemD. This family consists of uroporphyrinogen-III synthase HemD EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea. This enzyme catalyses the reaction: Hydroxymethylbilane <=> uroporphyrinogen-III + H(2)O. Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, with pfam00590, however the aligned region corresponds with the uroporphyrinogen-III synthase EC:4.2.1.75 activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway. Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease. Length = 229 Score = 63.1 bits (154), Expect = 7e-11 Identities = 40/208 (19%), Positives = 70/208 (33%), Gaps = 25/208 (12%) Query: 14 RTQEKIQKMGYIPVMMPLSYFIHDRES---VFLAMQQSYGAIAITSSES----LSTLPAN 66 ++++G PV +PL + L Y + TS+ L Sbjct: 2 ELAALLEELGAEPVELPLIEIEPEDRDELDEALEDLGEYDWLIFTSANGVRAFFEALKEA 61 Query: 67 FC-----RHTPIFAIGEASACLARQKGFTQIFHGKD--NSINLAKIIVEQKVLFTPQKPL 119 + I A+G +A R+ G T F + LA+ + E K + Sbjct: 62 GADLRALANLKIAAVGPKTARALREAGLTPDFVPSAEGTAEGLAEELAELL----AGKRV 117 Query: 120 IYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQ--NADAILFYARSS 177 + L G + L E + + Y + A ++ LL+ DA++F + S+ Sbjct: 118 LLLRGNLGRDDLAEALREAGAKVDEVVVYRTVPPAELPEELRELLRAGEIDAVVFTSPST 177 Query: 178 VLYFFSLPLPAKISAAFLCLSNNIASAI 205 V F L + L +AI Sbjct: 178 VRSFLEL-----LPDEGELLKGVKVAAI 200 >gnl|CDD|144445 pfam00852, Glyco_transf_10, Glycosyltransferase family 10 (fucosyltransferase). This family of Fucosyltransferases are the enzymes transferring fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is know as glycosyltransferase family 10. Length = 353 Score = 31.9 bits (73), Expect = 0.14 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%) Query: 138 HKIPLRVIDCYYSQDIAYPE-TTMKNLLQNADAILFYARSSVLYFFSLPLPAK 189 L DC +I TT ++L ADA++F+ R +LP + Sbjct: 61 VPFDLN--DCPELFNIDGCFLTTNRSLYDEADAVVFHHRDISSDLSNLPKSPR 111 >gnl|CDD|107286 cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Length = 265 Score = 31.0 bits (71), Expect = 0.32 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 3/43 (6%) Query: 131 FEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQN---ADAI 170 F D L E+ + +R+I+ + D A + +K LL+ D I Sbjct: 135 FLDVLKENGLEVRIIEIQENFDDAEKKEEIKELLEEYPDIDGI 177 >gnl|CDD|132872 cd07186, CofD_like, LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. Length = 303 Score = 28.3 bits (64), Expect = 1.6 Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%) Query: 130 HFEDYLIEHKIPLRVIDCYYSQ-DIAYPETTMKNLLQNADAILF 172 HF++Y + + V D + + A P + +++AD ++ Sbjct: 146 HFQEYWVRRRGEPEVRDVRFVGAEEARPAPEVLEAIEDADLVII 189 >gnl|CDD|33438 COG3640, CooC, CO dehydrogenase maturation factor [Cell division and chromosome partitioning]. Length = 255 Score = 27.1 bits (60), Expect = 4.3 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 3 IVITRPIKKALRTQEKIQKMG 23 IV+ P K+LRT E+I+++ Sbjct: 160 IVVVDPSYKSLRTAERIKELA 180 >gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes. This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy. Length = 253 Score = 26.9 bits (60), Expect = 4.3 Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%) Query: 147 CYYSQDIAYPETTMKNLLQNADAILF 172 CY D+ +PE + L+ AD IL Sbjct: 143 CY---DLRFPELARELALKGADIILV 165 >gnl|CDD|31539 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]. Length = 278 Score = 27.1 bits (60), Expect = 4.6 Identities = 13/35 (37%), Positives = 18/35 (51%) Query: 198 SNNIASAIPASYKNVVTVACFPKETSLLKLLPLRR 232 S N+A+A+ K V+ V C PK S LL + Sbjct: 18 SQNLAAALAELGKKVLIVGCDPKADSTRLLLGGKA 52 >gnl|CDD|147686 pfam05664, DUF810, Protein of unknown function (DUF810). This family consists of several plant proteins of unknown function. Length = 674 Score = 26.6 bits (59), Expect = 5.3 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 8/55 (14%) Query: 181 FFSLPLPAKISAAFLCLSNNIASAIPAS---YKNVVTVACFPKETSLLKLLPLRR 232 FF LP+P + L + I A+ Y + V + KE + L PL R Sbjct: 569 FFGLPIPMHPT-----LLQALTEGIDAAFQKYTSKVKSSLGSKEDLVPPLPPLTR 618 >gnl|CDD|163613 cd00144, MPP_PPP_family, phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain. The PPP (phosphoprotein phosphatase) family is one of two known protein phosphatase families specific for serine and threonine. This family includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 225 Score = 26.6 bits (59), Expect = 6.1 Identities = 27/114 (23%), Positives = 40/114 (35%), Gaps = 23/114 (20%) Query: 94 HGKDNSINLAKIIVEQKVLFTPQKPLIYLG-----GKPRNFHFEDYLIEHKIP------L 142 HG +L +++ +K+ F P LI+LG G P + D L+ KI L Sbjct: 7 HG--CLDDLLRLL--EKIGFPPNDKLIFLGDYVDRG-PDSVEVIDLLLALKILPDNVILL 61 Query: 143 R------VIDCYYSQDIAYPETTMKNLLQNADAILFYARSSVLYFFSLPLPAKI 190 R +++ Y L + FF LPL A I Sbjct: 62 RGNHEDMLLNFLYGFYDEDEWIGGTLRLLKKLGEDLW-EEFNDVFFYLPLAALI 114 >gnl|CDD|176369 cd01774, Faf1_like2_UBX, Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Length = 85 Score = 26.0 bits (57), Expect = 7.9 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 13/74 (17%) Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHF------EDYLIEHKIPLRVIDCYYSQDIAYPETTM 160 VE++ LFT +I+ +F F E + I P RV+ C S+ P T + Sbjct: 17 VERRFLFTQSLRVIH------DFLFSLKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLL 70 Query: 161 KNLLQNADAILFYA 174 + L N++ +LF Sbjct: 71 EAGLSNSE-VLFVQ 83 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 0.325 0.138 0.405 Gapped Lambda K H 0.267 0.0662 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,758,193 Number of extensions: 140491 Number of successful extensions: 436 Number of sequences better than 10.0: 1 Number of HSP's gapped: 426 Number of HSP's successfully gapped: 14 Length of query: 232 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 141 Effective length of database: 4,297,318 Effective search space: 605921838 Effective search space used: 605921838 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.5 bits)