RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780546|ref|YP_003064959.1| hypothetical protein
CLIBASIA_02165 [Candidatus Liberibacter asiaticus str. psy62]
         (423 letters)



>gnl|CDD|30179 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
           PP-loop faimly implicated in cell cycle control [Cell
           division and chromosome partitioning]. This is a
           subfamily of Adenine nucleotide alpha hydrolases
           superfamily.Adeninosine nucleotide alpha hydrolases
           superfamily  includes N type ATP PPases and ATP
           sulphurylases. It forms a apha/beta/apha fold which
           binds to Adenosine group.  This domain has  a strongly
           conserved motif SGGXD at the N terminus..
          Length = 185

 Score =  175 bits (446), Expect = 1e-44
 Identities = 76/189 (40%), Positives = 104/189 (55%), Gaps = 7/189 (3%)

Query: 21  HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRL 80
            ILVAVSGG DSM LL  L  +   +    ++  A+ VDH LR  + +E  +V+D+C++L
Sbjct: 1   KILVAVSGGPDSMALLHLLSEL---KPRLGLRLVAVHVDHGLRPESDEEAAFVADLCAKL 57

Query: 81  RIAHSV-VSWKNSKPQTGLMAAAREARYALISEHAKTINATLIMTAHTFDDQLETVYMRS 139
            I   + V     KP   L AAAREARY   +E AK   A +++TAH  DDQ ETV MR 
Sbjct: 58  GIPLYILVVALAPKPGGNLEAAAREARYDFFAEIAKEHGADVLLTAHHADDQAETVLMRL 117

Query: 140 QRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCRREDIRSFLLQRNISWCEDPSNTDDRF 199
            R       GL+GM   I +     + RP L   R +I ++L +  + W EDPSN D R+
Sbjct: 118 LR--GSGLRGLAGMPARIPFG-GGRLIRPLLGITRAEIEAYLRENGLPWWEDPSNEDPRY 174

Query: 200 ERVRVRRFV 208
            R R+R  +
Sbjct: 175 TRNRIRHEL 183


>gnl|CDD|144677 pfam01171, ATP_bind_3, PP-loop family.  This family of proteins
           belongs to the PP-loop superfamily.
          Length = 182

 Score =  167 bits (424), Expect = 7e-42
 Identities = 72/187 (38%), Positives = 94/187 (50%), Gaps = 7/187 (3%)

Query: 21  HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRL 80
            ILVAVSGG DSM LL  L  +   +    I  +A  VDH LRE +  E ++V ++C +L
Sbjct: 1   KILVAVSGGPDSMALLYLLKKL---KPKFGIDLTAAHVDHGLREESDREAQFVKELCRQL 57

Query: 81  RIAHSVVSWK-NSKPQTGLMAAAREARYALISEHAKTINATLIMTAHTFDDQLETVYMRS 139
            I   V+      K    L  AAREARY    E AK   A +++TAH  DDQ ET  MR 
Sbjct: 58  NIPLEVLRVDVAKKSGLNLEEAAREARYDFFEEIAKKNGAEVLLTAHHADDQAETFLMRL 117

Query: 140 QRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCRREDIRSFLLQRNISWCEDPSNTDDRF 199
            R       GL+G+           I RP L+  + +I  +L +  I W ED SN D R+
Sbjct: 118 LRG--SGLAGLAGIAPVRPLA-GGRIVRPLLKVTKSEIEEYLKEHGIPWVEDESNADLRY 174

Query: 200 ERVRVRR 206
            R R+R 
Sbjct: 175 TRNRIRH 181


>gnl|CDD|30386 COG0037, MesJ, Predicted ATPase of the PP-loop superfamily
           implicated in cell cycle control [Cell division and
           chromosome partitioning].
          Length = 298

 Score =  144 bits (363), Expect = 5e-35
 Identities = 66/219 (30%), Positives = 95/219 (43%), Gaps = 14/219 (6%)

Query: 1   MFLSPIES--VRFFVRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISV 58
                +E    R      +    ILVAVSGG DS+ LL  L          +I+  A+ V
Sbjct: 1   CLREKLERKVKRAIREFNLIEYKILVAVSGGKDSLALLHLLK-----ELGRRIEVEAVHV 55

Query: 59  DHCLRETAKDEVRYVSDVCSRLRIAHSVVSW-----KNSKPQTGLMAAAREARYALISEH 113
           DH LR  +  E   V  +C +L I   V        + +     + AA R  R  L+ + 
Sbjct: 56  DHGLRGYSDQEAELVEKLCEKLGIPLIVERVTDDLGRETLDGKSICAACRRLRRGLLYKI 115

Query: 114 AKTINATLIMTAHTFDDQLETVYMRSQRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCR 173
           AK + A  I T H  DDQ ET  M   R       GL GM     ++  L I RP L  R
Sbjct: 116 AKELGADKIATGHHLDDQAETFLMNLLRG--SGLRGLRGMPPKRPFEGGLLIIRPLLYVR 173

Query: 174 REDIRSFLLQRNISWCEDPSNTDDRFERVRVRRFVRDID 212
            ++I  +  ++ + + ED SN D R+ R R+R  +  ++
Sbjct: 174 EKEIELYAKEKGLPYIEDESNYDLRYTRNRIREELLPLE 212


>gnl|CDD|30180 cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine
           nucleotide alpha hydrolases superfamily.Adeninosine
           nucleotide alpha hydrolases superfamily  includes N type
           ATP PPases and ATP sulphurylases. It forms a
           apha/beta/apha fold which  binds to Adenosine group.
           This subfamily   of proteins is predicted to  bind ATP.
           This domainhas  a strongly conserved motif SGGKD at the
           N terminus..
          Length = 185

 Score = 75.3 bits (185), Expect = 3e-14
 Identities = 42/174 (24%), Positives = 69/174 (39%), Gaps = 12/174 (6%)

Query: 22  ILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRLR 81
           ILVA+SGG DS+ LL  L   L  R     +  A++VD  +     + +  V  +   L 
Sbjct: 2   ILVALSGGKDSLVLLHVLKK-LQRRYPYGFELEALTVDEGIPGYRDESLEVVERLAEELG 60

Query: 82  IAHSVVSWKNSKPQTGLMAAARE---------ARYALISEHAKTINATLIMTAHTFDDQL 132
           I   +VS+K        +               R  L+++ AK + A  + T H  DD+ 
Sbjct: 61  IELEIVSFKEEYTDDIEVKKRGGKSPCSLCGVLRRGLLNKIAKELGADKLATGHNLDDEA 120

Query: 133 ETVYMRSQRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCRREDIRSFLLQRNI 186
           ET+ M   R    + M    +      D  +   RP +  R ++I  +     +
Sbjct: 121 ETLLMNLLRGGILRLMRPGPILYLDEGD--VTRIRPLVYVREKEIVLYAELNGL 172


>gnl|CDD|31794 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
           [General function prediction only].
          Length = 269

 Score = 34.5 bits (79), Expect = 0.058
 Identities = 52/310 (16%), Positives = 102/310 (32%), Gaps = 58/310 (18%)

Query: 1   MFLSPIESVRFFVRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDH 60
           M LS +E ++  ++       ++VA SGG DS  L       L D          ++V  
Sbjct: 2   MLLSKLERLKKAIKEK---KKVVVAFSGGVDSSLLAKLAKEALGDN--------VVAVTV 50

Query: 61  CLRETAKDEVRYVSDVCSRLRIAHSVVSWKNSKPQTGLMAAAR-----EARYALISEHAK 115
                 + E+    ++   + I H  +      P+       R      A Y+ + E A+
Sbjct: 51  DSPYIPRREIEEAKNIAKEIGIRHEFIKMNRMDPEFKENPENRCYLCKRAVYSTLVEEAE 110

Query: 116 TINATLIMTAHTFDDQLETVYMRSQRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCR-- 173
                ++       D      +   R       GL       L +L +    P       
Sbjct: 111 KRGYDVVADGTNASD------LFDYRP------GLR-----ALKELGIR--SPLAEFGIT 151

Query: 174 REDIRSFLLQRNISWCEDPSNT--DDRF---ERVRVRRFVRDIDLHALYLKMKKFQDLRV 228
           +++IR       +   + PS      R    E + V    + ++    +L+    + +RV
Sbjct: 152 KKEIREIAKSLGLPTWDKPSMACLASRIPYGEEITVEDLKK-VEEAEEFLRELGVRQIRV 210

Query: 229 K--VNNAVAMLIPKYLTVHMRSIIAISQDILNIDSTLLFYLLRVSAAICGGQISLPGYRS 286
           +   N AV  + P+     +  +  I   +  +         +V+       + L GYRS
Sbjct: 211 RSEDNLAVIEVGPEEPEKLLNEVEEIDDKLKKVGF------RKVT-------LDLEGYRS 257

Query: 287 MERVMLFLKS 296
            +      ++
Sbjct: 258 GKLNKTIKEA 267


>gnl|CDD|30865 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
          transport and metabolism].
          Length = 315

 Score = 32.4 bits (74), Expect = 0.22
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 7/60 (11%)

Query: 13 VRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDH-CLRETAKDEVR 71
          +R  V    +++A+SGG DS    +  H  + D+       + + VDH  LR+   ++V 
Sbjct: 15 IREQVGDGKVILALSGGVDSSVAAVLAHRAIGDQ------LTCVFVDHGLLRKGEAEQVV 68


>gnl|CDD|30185 cd01998, tRNA_Me_trans, tRNA methyl transferase. This family
          represents
          tRNA(5-methylaminomethyl-2-thiouridine)-
          methyltransferase which is involved in the biosynthesis
          of the modified nucleoside
          5-methylaminomethyl-2-thiouridine present in the wobble
          position of some tRNAs. This family of enzyme only
          presents in bacteria and eukaryote. The  archaeal
          counterpart of this enzyme performs same function, but
          is completely unrelated in sequence..
          Length = 349

 Score = 31.7 bits (72), Expect = 0.38
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 21 HILVAVSGGSDS---MGLLIAL-HSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDV 76
           ++VA+SGG DS     LL    + V+    F K          C    ++++++    V
Sbjct: 1  KVVVAMSGGVDSSVAAALLKEQGYEVIG--VFMKNWDEDDGKGGC---CSEEDLKDARRV 55

Query: 77 CSRLRIAHSVVSWKN 91
            +L I H VV+++ 
Sbjct: 56 ADQLGIPHYVVNFEK 70


>gnl|CDD|30177 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
          nucleotide alpha hydrolases superfamily. Adenine
          nucleotide alpha hydrolases superfamily  includes N
          type ATP PPases and ATP sulphurylases. It forms a
          apha/beta/apha fold which  binds to Adenosine group.
          This subfamily   of proteins probably binds ATP. This
          domain is about 200 amino acids long with a strongly
          conserved motif SGGKD at the N terminus..
          Length = 202

 Score = 31.7 bits (72), Expect = 0.39
 Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 8/67 (11%)

Query: 22 ILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRLR 81
          + VA SGG DS  LL A    L DR        A++    L    + E+     +   + 
Sbjct: 1  VAVAFSGGVDSTLLLKAAVDALGDRVL------AVTATSPL--FPRRELEEAKRLAKEIG 52

Query: 82 IAHSVVS 88
          I H V+ 
Sbjct: 53 IRHEVIE 59


>gnl|CDD|30184 cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase.
          It contains two subdomains; the ATP pyrophosphatase
          domain which closes to the N-termial and the
          dimerization domain at C-terminal end. The ATP-PPase is
          a twisted, five-stranded parallel beta-sheet sandwiched
          between helical layers. It has a signature
          nucleotide-binding motif, or P-loop, at the end of the
          first-beta strand.The dimerization domain formed by the
          C-terminal 115 amino acid for prokaryotic proteins. It
          is adjacent to teh ATP-binding site of the ATP-PPase
          subdomain. The largest difference between the primary
          sequence of prokaryotic and eukaryotic GMP synthetase
          map to the dimerization domain.Eukaryotic GMP
          synthetase has several large insertions relative to
          prokaryotes..
          Length = 295

 Score = 30.9 bits (70), Expect = 0.62
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 8/60 (13%)

Query: 21 HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYVSDVCSRL 80
           +++A+SGG DS    + LH  + DR       + + VD+ L    K+E   V ++ S+L
Sbjct: 1  KVILALSGGVDSTVAAVLLHKAIGDR------LTCVFVDNGLLR--KNEAERVEELFSKL 52


>gnl|CDD|35262 KOG0039, KOG0039, KOG0039, Ferric reductase, NADH/NADPH oxidase and
           related proteins [Inorganic ion transport and
           metabolism, Secondary metabolites biosynthesis,
           transport and catabolism].
          Length = 646

 Score = 30.7 bits (69), Expect = 0.75
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 17/136 (12%)

Query: 251 AISQDILNIDSTLLFYLLRVSAAICGGQISLPGYRSMERVMLFLKSGKRGCVS--IGRVV 308
           A SQD+   +  +L         + GG    P    ++ ++  +  G+    +      +
Sbjct: 458 APSQDVFKYEVLVL---------VGGGIGVTPFASILKDLLNKISLGRTKAPTSDYSDSL 508

Query: 309 IDRRANFLWITRAVRNLPTLILYPEETTVWDGRYQFQNLSDSLIQIGPQSYRKADVPSGI 368
             ++  F W+TR  R+         E   +D      +    L      SY + D  S +
Sbjct: 509 KLKKVYFYWVTREQRSFEWFKGLLTEVEEYD-----SSGVIELHNYVTSSYEEGDARSAL 563

Query: 369 PPIIAQRALSSMPSKE 384
             ++ Q+ L +    +
Sbjct: 564 IQMV-QKLLHAKNGVD 578


>gnl|CDD|48196 cd03321, mandelate_racemase, Mandelate racemase (MR) catalyzes the
           Mg2+-dependent 1,1-proton transfer reaction that
           interconverts the enantiomers of mandelic acid. MR is
           the first enzyme in the bacterial pathway that converts
           mandelic acid to benzoic acid and allows this pathway to
           utilize either enantiomer of mandelate. MR belongs to
           the enolase superfamily of enzymes, characterized by the
           presence of an enolate anion intermediate which is
           generated by abstraction of the alpha-proton of the
           carboxylate substrate by an active site residue and is
           stabilized by coordination to the essential Mg2+ ion..
          Length = 355

 Score = 29.6 bits (66), Expect = 1.6
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 13/83 (15%)

Query: 127 TFDDQLETVYMRSQRDYAEKGMGLSGMCDTILYDLNLWISRPFLRCRREDIRSFLLQRNI 186
           T D+ L  V  RS R     G+GL  M D   Y+ +L +     R +  D      Q  +
Sbjct: 168 TADEDLAVV--RSIRQAVGDGVGL--MVD---YNQSLTVPEAIERGQALD------QEGL 214

Query: 187 SWCEDPSNTDDRFERVRVRRFVR 209
           +W E+P+   D     R+   +R
Sbjct: 215 TWIEEPTLQHDYEGHARIASALR 237


>gnl|CDD|146126 pfam03331, LpxC, UDP-3-O-acyl N-acetylglycosamine deacetylase.  The
           enzymes in this family catalyse the second step in the
           biosynthetic pathway for lipid A.
          Length = 276

 Score = 29.2 bits (66), Expect = 2.2
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 122 IMTAHTFDDQLETVYMRSQRDYAEKGMGLSGMCD-TILYDLNLWISRPFLRCRREDIRSF 180
           I  A TF    E  Y+RS      KG+   G  +  I++D +  ++ P LR   E +R  
Sbjct: 183 IAPARTFGFMREIEYLRS------KGLIKGGSLENAIVFDDDKVLNPPGLRFEDEPVRHK 236

Query: 181 LL 182
           +L
Sbjct: 237 IL 238


>gnl|CDD|30830 COG0482, TrmU, Predicted
          tRNA(5-methylaminomethyl-2-thiouridylate)
          methyltransferase, contains the PP-loop ATPase domain
          [Translation, ribosomal structure and biogenesis].
          Length = 356

 Score = 28.7 bits (64), Expect = 3.4
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 22/80 (27%)

Query: 22 ILVAVSGGSDS---MGLL-------IALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVR 71
          +LV +SGG DS     LL       I L     D   G                +++++R
Sbjct: 6  VLVGMSGGVDSSVAAYLLKEQGYEVIGLFMKNWDEDGGG------------GCCSEEDLR 53

Query: 72 YVSDVCSRLRIAHSVVSWKN 91
              V  +L I   VV ++ 
Sbjct: 54 DAERVADQLGIPLYVVDFEK 73


>gnl|CDD|38051 KOG2840, KOG2840, KOG2840, Uncharacterized conserved protein with
           similarity to predicted ATPase of the PP-loop
           superfamily [General function prediction only].
          Length = 347

 Score = 28.0 bits (62), Expect = 4.7
 Identities = 28/147 (19%), Positives = 52/147 (35%), Gaps = 15/147 (10%)

Query: 14  RSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRETAKDEVRYV 73
           +       + +  SGG DS  +L  +   L++R    ++   +S+D  +R    D +  V
Sbjct: 46  KLFARGERVAIGASGGKDST-VLAYVLDALNERHDYGLRLFLLSIDEGIRGYRDDSLEAV 104

Query: 74  SDVCSRLRIAHSVVSWK--------NSKPQTGLMAAAREA------RYALISEHAKTINA 119
                +  +   +VS+K        +                    R   +   A  + A
Sbjct: 105 KRNGVQYGLPLCIVSYKDLYGEWTMDEIVSEIGQEIRNNCTFCGVFRRQALDRGADVLGA 164

Query: 120 TLIMTAHTFDDQLETVYMRSQRDYAEK 146
             ++T H  DD  ETV M   R  + +
Sbjct: 165 AELVTGHNADDWAETVLMNLLRGDSAR 191


>gnl|CDD|144363 pfam00733, Asn_synthase, Asparagine synthase.  This family is
           always found associated with pfam00310. Members of this
           family catalyse the conversion of aspartate to
           asparagine.
          Length = 195

 Score = 28.0 bits (63), Expect = 5.1
 Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 15/105 (14%)

Query: 6   IESVRFFVRSLVYPAHILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVDHCLRET 65
            ++V+   R L     + V +SGG DS   LIA  ++ + +S   +K    SV      +
Sbjct: 7   RDAVK---RRLRADVPVGVLLSGGLDSS--LIA--ALAARQSSPPLK--TFSVG--FEGS 55

Query: 66  AKDEVRYVSDVCSRLRIAHSVVSWKNSKPQTGLMAAAREARYALI 110
             DE  Y   V   L   H  +       +  L+ A  E  Y L 
Sbjct: 56  DYDEAPYAELVADHLGTDHHEI---IVTEEE-LLDALPEVIYHLE 96


>gnl|CDD|30168 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
          phosphosulphate (PAPS) reductase enzymes or PAPS
          sulphotransferase. PAPS reductase is part of the
          adenine nucleotide alpha hydrolases superfamily also
          including N type ATP PPases and ATP sulphurylases. A
          highly modified version of the P loop, the fingerprint
          peptide of mononucleotide-binding proteins, is present
          in the active site of the protein, which appears to be
          a positively charged cleft containing a number of
          conserved arginine and lysine residues. Although PAPS
          reductase has no ATPase activity, it shows a striking
          similarity to the structure of the ATP pyrophosphatase
          (ATP PPase) domain of GMP synthetase, indicating that
          both enzyme families have evolved from a common
          ancestral nucleotide-binding fold.   The enzyme uses
          thioredoxin as an electron donor for the reduction of
          PAPS to phospho-adenosine-phosphate (PAP) . It is also
          found in NodP nodulation protein P from Rhizobium
          meliloti which has ATP sulphurylase activity (sulphate
          adenylate transferase) ..
          Length = 173

 Score = 27.7 bits (61), Expect = 6.3
 Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 10/74 (13%)

Query: 21 HILVAVSGGSDSMGLLIALHSVLSDRSFGKIKFSAISVD--HCLRETAKDEVRYVSDVCS 78
          +++V+ SGG DS  LL      L            I +D  +   ET      +V  V  
Sbjct: 1  NVVVSFSGGKDSTVLLHLALKAL----PELKPVPVIFLDTGYEFPET----YEFVDRVAE 52

Query: 79 RLRIAHSVVSWKNS 92
          R  +   VV   +S
Sbjct: 53 RYGLPLVVVRPPDS 66


  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
   0.326    0.139    0.415 

Gapped
Lambda     K      H
   0.267   0.0726    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,192,152
Number of extensions: 278054
Number of successful extensions: 745
Number of sequences better than 10.0: 1
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 17
Length of query: 423
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 327
Effective length of database: 4,189,273
Effective search space: 1369892271
Effective search space used: 1369892271
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: 59 (26.5 bits)