RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780297|ref|YP_003064710.1| peptide deformylase
[Candidatus Liberibacter asiaticus str. psy62]
         (170 letters)



>gnl|CDD|144794 pfam01327, Pep_deformylase, Polypeptide deformylase. 
          Length = 155

 Score =  205 bits (525), Expect = 4e-54
 Identities = 78/154 (50%), Positives = 108/154 (70%), Gaps = 1/154 (0%)

Query: 4   KPLVIFPDPILRRVSRPIEKINSD-IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVID 62
            P+V +PDP+LR+ ++P+E+ + + +  LID+MLE MY+ +G+GLAA QIGV  R+ VID
Sbjct: 2   LPIVTYPDPVLRQKAKPVEEFDDEELKELIDDMLETMYAANGVGLAAPQIGVSKRIFVID 61

Query: 63  LQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQ 122
           + D      P+V INP+II+ S++    +EGCLS+P  R +V+R   ITVRY D N    
Sbjct: 62  VGDEDGEPEPLVLINPEIISASEETVEGEEGCLSVPGLRGEVERPKRITVRYQDLNGNEH 121

Query: 123 IIYADGLLATCLQHELDHLNGILFIDHLSRLKRD 156
            + ADG LA  LQHE+DHL+GILFID LS+LKR 
Sbjct: 122 ELEADGFLARVLQHEIDHLDGILFIDRLSKLKRL 155


>gnl|CDD|30591 COG0242, Def, N-formylmethionyl-tRNA deformylase [Translation,
           ribosomal structure and biogenesis].
          Length = 168

 Score =  203 bits (519), Expect = 1e-53
 Identities = 83/167 (49%), Positives = 123/167 (73%), Gaps = 1/167 (0%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
           M  + +V +PDP LR+V++P+E+++ ++  LID+MLE MY+ +G+GLAA QIG+  R+ V
Sbjct: 1   MAIREIVKYPDPRLRQVAKPVEEVDDELRQLIDDMLETMYAAEGVGLAAPQIGISKRIFV 60

Query: 61  IDLQDHAHRK-NPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNA 119
           ID+++    K  P+V INP+II+ S++    +EGCLS+P  R +V+R   ITV+Y+D N 
Sbjct: 61  IDVEEDGRPKEPPLVLINPEIISKSEETLTGEEGCLSVPGVRGEVERPERITVKYLDRNG 120

Query: 120 QHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLV 166
           + Q + A+GLLA C+QHE+DHLNG+LFID LS LKRD + KK+ KL 
Sbjct: 121 KPQELEAEGLLARCIQHEIDHLNGVLFIDRLSPLKRDRLKKKLKKLK 167


>gnl|CDD|29602 cd00487, Pep_deformylase, Polypeptide or peptide deformylase; a
           family of metalloenzymes that catalyzes the removal of
           the N-terminal formyl group in a growing polypeptide
           chain following translation initiation during protein
           synthesis in prokaryotes. These enzymes utilize Fe(II)
           as the catalytic metal ion, which can be replaced with a
           nickel or cobalt ion with no loss of activity. There are
           two types of peptide deformylases, types I and II, which
           differ in structure only in the outer surface of the
           domain. Because these enzymes are essential only in
           prokaryotes (although eukaryotic gene sequences have
           been found), they are a target for a new class of
           antibacterial agents..
          Length = 141

 Score =  179 bits (457), Expect = 2e-46
 Identities = 68/141 (48%), Positives = 101/141 (71%)

Query: 6   LVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQD 65
           +V +PDP+LR+ ++P+E+ + ++  LID+M E MY+  G+GLAA QIGV  R+ VID+ D
Sbjct: 1   IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPD 60

Query: 66  HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIY 125
             +++ P+V INP+II  S +    +EGCLS+P YR +V+R   +TVRY+D +     + 
Sbjct: 61  EENKEPPLVLINPEIIESSGETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELE 120

Query: 126 ADGLLATCLQHELDHLNGILF 146
           A+G LA C+QHE+DHLNGILF
Sbjct: 121 AEGFLARCIQHEIDHLNGILF 141


>gnl|CDD|38347 KOG3137, KOG3137, KOG3137, Peptide deformylase [Translation,
           ribosomal structure and biogenesis].
          Length = 267

 Score =  119 bits (299), Expect = 4e-28
 Identities = 54/162 (33%), Positives = 88/162 (54%), Gaps = 17/162 (10%)

Query: 6   LVIFPDPILRRVSRPIEKI---NSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVID 62
           +V + DP+LR  ++ +++    + ++ NL+D M +VM  TDG+GL+A Q+GV  +L+V++
Sbjct: 81  IVEYGDPVLRAKAKRVDRAQIGDENLQNLVDAMFDVMRKTDGVGLSAPQVGVPVQLMVLE 140

Query: 63  LQDHAHRKNP--------------MVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSA 108
                 R+ P              +V +NPK+  +SD    + EGCLS+P + A+V R  
Sbjct: 141 PAGALCRECPEPGRAERQMEPFKLIVLVNPKLKKYSDKLVPFDEGCLSVPGFYAEVVRPQ 200

Query: 109 FITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHL 150
            + +   D   +   I A G  A   QHE DHL G+LF D +
Sbjct: 201 SVKIDGRDITGERFSISASGWPARIFQHEYDHLEGVLFFDKM 242


>gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR).  QOR catalyzes the
           conversion of a quinone + NAD(P)H to a hydroquinone +
           NAD(P)+. Quinones are cyclic diones derived from
           aromatic compounds. Membrane bound QOR acts in the
           respiratory chains of bacteria and mitochondria, while
           soluble QOR acts to protect from toxic quinones (e.g.
           DT-diaphorase) or as a soluble eye-lens protein in some
           vertebrates (e.g. zeta-crystalin). QOR reduces quinones
           through a semi-quinone intermediate via a
           NAD(P)H-dependent single electron transfer. QOR is a
           member of the medium chain dehydrogenase/reductase
           family, but lacks the zinc-binding sites of the
           prototypical alcohol dehydrogenases of this group.
           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 = 323

 Score = 28.6 bits (65), Expect = 0.98
 Identities = 9/18 (50%), Positives = 11/18 (61%)

Query: 44  GIGLAAVQIGVLYRLVVI 61
           G+GLAAVQ+       VI
Sbjct: 151 GVGLAAVQLAKALGARVI 168


>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
           NAD(P)(H)-dependent oxidoreductases are the major
           enzymes in the interconversion of alcohols and
           aldehydes, or ketones. This group has the characteristic
           catalytic and structural zinc sites of the
           zinc-dependent alcohol dehydrogenases.  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 = 345

 Score = 28.0 bits (63), Expect = 1.5
 Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)

Query: 44  GIGLAAVQIGVLY--RLVVIDLQDHA 67
           G+GL+AV I      R++ +D+ D  
Sbjct: 176 GVGLSAVMIASALGARVIAVDIDDDK 201


>gnl|CDD|29356 cd01172, RfaE_like, RfaE encodes a bifunctional ADP-heptose
           synthase involved in the biosynthesis of the
           lipopolysaccharide (LPS) core precursor
           ADP-L-glycero-D-manno-heptose. LPS plays an important
           role in maintaining the structural integrity of the
           bacterial outer membrane of gram-negative bacteria. RfaE
           consists of two domains, a sugar kinase domain,
           represented here, and a domain belonging to the
           cytidylyltransferase superfamily..
          Length = 304

 Score = 26.3 bits (58), Expect = 4.9
 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 31  LIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVY 90
           LI+ + E +   D + L+    GVL   V+  L   A      V ++PK      D+S Y
Sbjct: 124 LIERIAERLPEADVVILSDYGKGVLTPRVIEALIAAARELGIPVLVDPK----GRDYSKY 179

Query: 91  QEGCLSIPDYR 101
           +   L  P+ +
Sbjct: 180 RGATLLTPNEK 190


>gnl|CDD|48606 cd03057, GST_N_Beta, GST_N family, Class Beta subfamily; GSTs are
          cytosolic dimeric proteins involved in cellular
          detoxification by catalyzing the conjugation of
          glutathione (GSH) with a wide range of endogenous and
          xenobiotic alkylating agents, including carcinogens,
          therapeutic drugs, environmental toxins and products of
          oxidative stress. The GST fold contains an N-terminal
          TRX-fold domain and a C-terminal alpha helical domain,
          with an active site located in a cleft between the two
          domains. Unlike mammalian GSTs which detoxify a broad
          range of compounds, the bacterial class Beta GSTs
          exhibit limited GSH conjugating activity with a narrow
          range of substrates. In addition to GSH conjugation,
          they also bind antibiotics and reduce the antimicrobial
          activity of beta-lactam drugs. The structure of the
          Proteus mirabilis enzyme reveals that the cysteine in
          the active site forms a covalent bond with GSH..
          Length = 77

 Score = 26.3 bits (58), Expect = 5.0
 Identities = 9/28 (32%), Positives = 16/28 (57%)

Query: 52 IGVLYRLVVIDLQDHAHRKNPMVFINPK 79
          +G+ + LV +DL+    +    + INPK
Sbjct: 21 LGLPFELVRVDLRTKTQKGADYLAINPK 48


>gnl|CDD|48602 cd03053, GST_N_Phi, GST_N family, Class Phi subfamily; composed
          of plant-specific class Phi GSTs and related fungal and
          bacterial proteins. GSTs are cytosolic dimeric proteins
          involved in cellular detoxification by catalyzing the
          conjugation of glutathione (GSH) with a wide range of
          endogenous and xenobiotic alkylating agents, including
          carcinogens, therapeutic drugs, environmental toxins
          and products of oxidative stress. The GST fold contains
          an N-terminal TRX-fold domain and a C-terminal alpha
          helical domain, with an active site located in a cleft
          between the two domains. The class Phi GST subfamily
          has experience extensive gene duplication. The
          Arabidopsis and Oryza genomes contain 13 and 16 Phi
          GSTs, respectively. They are primarily responsible for
          herbicide detoxification together with class Tau GSTs,
          showing class specificity in substrate preference. Phi
          enzymes are highly reactive toward chloroacetanilide
          and thiocarbamate herbicides. Some Phi GSTs have other
          functions including transport of flavonoid pigments to
          the vacuole, shoot regeneration and GSH peroxidase
          activity..
          Length = 76

 Score = 25.9 bits (57), Expect = 5.7
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 47 LAAVQIGVLYRLVVIDLQDHAHRKNPMVFINP--KIITFSD-DFSVYQ 91
          L   + GV Y LV +DL    H+    +  NP  +I    D D  +++
Sbjct: 18 LCLEEKGVDYELVPVDLTKGEHKSPEHLARNPFGQIPALEDGDLKLFE 65


>gnl|CDD|146776 pfam04315, DUF462, Protein of unknown function, DUF462.  This
           family consists of bacterial proteins of uncharacterized
           function.
          Length = 165

 Score = 25.2 bits (56), Expect = 10.0
 Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%)

Query: 121 HQIIYADGLLATCLQHELDH 140
           H+II+A G  A+ L HE+ H
Sbjct: 33  HRIIFAHGFFASAL-HEIAH 51


  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
   0.327    0.143    0.418 

Gapped
Lambda     K      H
   0.267   0.0705    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,118,491
Number of extensions: 108950
Number of successful extensions: 306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 16
Length of query: 170
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,383,754
Effective search space: 363851582
Effective search space used: 363851582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.6 bits)