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)