RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781226|ref|YP_003065639.1| hypothetical protein
CLIBASIA_05665 [Candidatus Liberibacter asiaticus str. psy62]
         (129 letters)



>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
           (AHBA_syn). AHBA_syn family belongs to pyridoxal
           phosphate (PLP)-dependent aspartate aminotransferase
           superfamily (fold I). The members of this CD are
           involved in various biosynthetic pathways for secondary
           metabolites. Some well studied proteins in this CD are
           AHBA_synthase, protein product of pleiotropic regulatory
           gene degT,  Arnb aminotransferase and pilin
           glycosylation protein. The prototype of this family, the
           AHBA_synthase, is a dimeric PLP dependent enzyme.
           AHBA_syn is the terminal enzyme of
           3-amino-5-hydroxybenzoic acid (AHBA) formation which is
           involved in the biosynthesis of ansamycin antibiotics,
           including rifamycin B. Some members of this CD are
           involved in 4-amino-6-deoxy-monosaccharide D-perosamine
           synthesis. Perosamine is an important element in the
           glycosylation of several cell products, such as
           antibiotics and lipopolysaccharides of gram-positive and
           gram-negative bacteria. The pilin glycosylation protein
           encoded by gene pglA, is a galactosyltransferase
           involved in pilin glycosylation. Additionally, this CD
           consists of ArnB (PmrH) aminotransferase, a
           4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
           enzyme. This CD also consists of several predicted
           pyridoxal phosphate-dependent enzymes apparently
           involved in regulation of cell wall biogenesis. The
           catalytic lysine which is present in all characterized
           PLP dependent enzymes is replaced by histidine in some
           members of this CD..
          Length = 352

 Score = 29.8 bits (68), Expect = 0.23
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 23/70 (32%)

Query: 24  LKNRDKILERRRRRY------LKN---------KDKIRESYHQYYLKNKDKYREYKRRYY 68
           L+  D+I+ RRR         L +            ++ SYH Y ++   +  E      
Sbjct: 227 LEKLDEIIARRREIAERYKELLADLPGIRLPDVPPGVKHSYHLYVIRLDPEAGE------ 280

Query: 69  LKNRDKMREK 78
             +RD++ E 
Sbjct: 281 --SRDELIEA 288


>gnl|CDD|163652 cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related
           proteins, N-terminal metallophosphatase domain.  CD73 is
           a mammalian ecto-5'-nucleotidase expressed in
           endothelial cells and lymphocytes that catalyzes the
           conversion of 5'-AMP to adenosine in the final step of a
           pathway that generates adenosine from ATP.  This pathway
           also includes a CD39 nucleoside triphosphate
           dephosphorylase that mediates the dephosphorylation of
           ATP to ADP and then to 5'-AMP.  These enzymes all have
           an N-terminal metallophosphatase domain and a C-terminal
           5'nucleotidase domain.  The N-terminal
           metallophosphatase domain belongs to a large superfamily
           of distantly related metallophosphatases (MPPs) that
           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).  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 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 = 281

 Score = 27.5 bits (62), Expect = 1.00
 Identities = 9/21 (42%), Positives = 16/21 (76%)

Query: 105 EIEALEREIARLKAKPIEELI 125
           EIEA ++E  +LKA+ + ++I
Sbjct: 167 EIEAAQKEADKLKAQGVNKII 187


>gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A. 
          Length = 428

 Score = 27.5 bits (62), Expect = 1.00
 Identities = 25/108 (23%), Positives = 53/108 (49%), Gaps = 11/108 (10%)

Query: 21  RYYLKNRDKILERRRRRYLKNKDKIRESYH--QYYLKNKDKYREYKRRYYLKNRDKMREK 78
           + +L++R ++ +RR+   L+   K+ E  H  +  LK  +K         ++    + + 
Sbjct: 312 KEFLEHRLEVYKRRKEYLLE---KLEERLHILEGLLKALNKIDFVIEV--IRGSIDLNKA 366

Query: 79  ARQSYRKLYSKDS-WIAPEEPMG-MTKAEIEALEREIARLKAKPIEEL 124
            ++   +L    + ++  +  +  +TK EIE LE+EI  L+ + I EL
Sbjct: 367 KKELIEELSEIQADYLL-DMRLRRLTKEEIEKLEKEIEELEKE-IAEL 412


>gnl|CDD|30998 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA
           helicase) [Intracellular trafficking and secretion].
          Length = 822

 Score = 27.5 bits (61), Expect = 1.0
 Identities = 17/81 (20%), Positives = 27/81 (33%)

Query: 36  RRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAP 95
           R +L   D +RE  H      KD   EYKR  +    D + +      ++L+        
Sbjct: 727 REHLDAMDALREGIHLRGYAQKDPLIEYKREAFELFEDMLEDIKEDVVKRLFKVQVAEVE 786

Query: 96  EEPMGMTKAEIEALEREIARL 116
           EE   +   E    +      
Sbjct: 787 EEDRSLLAQEKALTQARALGK 807


>gnl|CDD|38228 KOG3018, KOG3018, KOG3018, Malonyl-CoA decarboxylase [Carbohydrate
           transport and metabolism].
          Length = 362

 Score = 26.2 bits (57), Expect = 2.9
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 44  KIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMGMTK 103
            +        L++  K  E +  + + NR+ +RE+    YR+        +P EP+    
Sbjct: 74  DLERGTWSSPLEDLQKLLEVEAVHPVVNREDVRERVGP-YRRCLGFSHPASPREPLVFIH 132

Query: 104 AEIEALEREIA 114
               AL   IA
Sbjct: 133 V---ALMETIA 140


>gnl|CDD|34782 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
           processing and modification].
          Length = 1175

 Score = 26.2 bits (57), Expect = 2.9
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 3/67 (4%)

Query: 33  RRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSW 92
           R RRR L N   I ES  +   ++    R   R+     R+  R+ +  S   + +  S 
Sbjct: 215 RLRRRMLMNPRAILESISR---ESAQLERNTARQQGEHARENGRDLSSDSNNNVINPVSD 271

Query: 93  IAPEEPM 99
             P   M
Sbjct: 272 NVPSRDM 278


>gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component
           [Carbohydrate transport and metabolism].
          Length = 500

 Score = 25.9 bits (57), Expect = 3.2
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 61  REYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMG-MTKAEIEALEREIAR 115
           RE  RR+ L +R  MR +AR+   +L      I P+  +G ++ A+ + +  EIAR
Sbjct: 108 REPTRRFGLIDRKAMRRRARELLARL---GLDIDPDTLVGDLSIAQRQMV--EIAR 158


>gnl|CDD|35636 KOG0415, KOG0415, KOG0415, Predicted peptidyl prolyl cis-trans
           isomerase [Posttranslational modification, protein
           turnover, chaperones].
          Length = 479

 Score = 26.1 bits (57), Expect = 3.2
 Identities = 13/78 (16%), Positives = 28/78 (35%)

Query: 7   TPEERMLCRREYKRRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRR 66
             ++R       +R           ER   R    ++  RE   +   + + +  E + R
Sbjct: 369 NSDDRERSESAQRRSPGEGRHQHSDERDDGRRQHRREDARELDRKSRFRKERESNEDEDR 428

Query: 67  YYLKNRDKMREKARQSYR 84
              + R++ R K+ +  R
Sbjct: 429 RSRRKRERTRNKSSRRER 446


>gnl|CDD|111439 pfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase.  This
           family includes N-methylhydaintoinase B which converts
           hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase
           EC:3.5.2.9 which catalyses the formation of L-glutamate
           from 5-oxo-L-proline. These enzymes are part of the
           oxoprolinase family and are related to pfam01968.
          Length = 527

 Score = 25.5 bits (56), Expect = 4.4
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 6/59 (10%)

Query: 69  LKNRDKMREKARQSYRKLYSKDSWIA--PEEPMGMTKAEIEALEREIARLKAKPIEELI 125
           L    +  E   +  R+L+ ++ + +  PE  +G  KA+I A ++ I R+  K I+E  
Sbjct: 152 LVKNGEFNE---ELIRQLFVRNPYPSRNPECNIGDLKAQIAANQKGIDRIG-KLIDEYG 206


>gnl|CDD|38823 KOG3617, KOG3617, KOG3617, WD40 and TPR repeat-containing protein
           [General function prediction only].
          Length = 1416

 Score = 25.4 bits (55), Expect = 4.5
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 20  RRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKA 79
            +Y  + RD+ L     +YL++  ++  +   +Y   KD +   + +      DK    A
Sbjct: 903 EQYVRRKRDESLYSWWGQYLESVGEMDAALS-FYSSAKDYFSMVRIKCIQGKTDKAARIA 961

Query: 80  RQS 82
            +S
Sbjct: 962 EES 964


>gnl|CDD|30540 COG0191, Fba, Fructose/tagatose bisphosphate aldolase [Carbohydrate
           transport and metabolism].
          Length = 286

 Score = 25.5 bits (56), Expect = 4.6
 Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 6/48 (12%)

Query: 43  DKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90
             +RE    Y  +N  +Y    R+Y     + M+E  ++  ++  S  
Sbjct: 243 AAVRE----YLAENPKEYDP--RKYLKPAIEAMKEVVKEKIKEFGSAG 284


>gnl|CDD|32946 COG3132, COG3132, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 215

 Score = 25.4 bits (55), Expect = 4.8
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 94  APEEPMGMTKAEIEALEREIARLKAK 119
           AP       +A +EALE+E+A L+A+
Sbjct: 182 APAAASSDLEARVEALEQEVAELRAR 207


>gnl|CDD|143419 cd07101, ALDH_SSADH2_GabD2, Mycobacterium tuberculosis
           succinate-semialdehyde dehydrogenase 2-like.
           Succinate-semialdehyde dehydrogenase 2 (SSADH2) and
           similar proteins are in this CD. SSADH1 (GabD1,
           EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
           of succinate semialdehyde to succinate.  SSADH activity
           in Mycobacterium tuberculosis is encoded by both gabD1
           (Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1
           was shown to be much higher than that of GabD2, and
           GabD2 (SSADH2) is likely to serve physiologically as a
           dehydrogenase for a different aldehyde(s).
          Length = 454

 Score = 25.0 bits (55), Expect = 5.7
 Identities = 8/17 (47%), Positives = 13/17 (76%)

Query: 21  RYYLKNRDKILERRRRR 37
           RYY +  +++L+ RRRR
Sbjct: 87  RYYARRAERLLKPRRRR 103


>gnl|CDD|35965 KOG0746, KOG0746, KOG0746, 60S ribosomal protein L3 and related
           proteins [Translation, ribosomal structure and
           biogenesis].
          Length = 384

 Score = 25.0 bits (54), Expect = 5.8
 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 62  EYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEE 97
           E KRR+Y KN  K ++KA   Y K +  +      E
Sbjct: 100 ECKRRFY-KNWHKSKKKAFTKYCKKWQDEDGKKQLE 134


>gnl|CDD|147119 pfam04802, SMK-1, Component of IIS longevity pathway SMK-1.  SMK-1
           is a component of the IIs longevity pathway which
           regulates aging in C.elegans. Specifically, SMK-1
           influences DAF-16-dependant regulation of the aging
           process by regulating the transcriptional specificity of
           DAF-16 activity. SMK-1 plays a role in longevity by
           modulating the transcriptional specificity of DAF-16.
          Length = 193

 Score = 24.8 bits (55), Expect = 6.4
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 4/41 (9%)

Query: 50  HQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90
           H+ +L    K++E      +KN  ++R+K  Q+YR  Y KD
Sbjct: 74  HRQFLTQNAKFKEVIP---IKN-PELRQKIHQTYRLQYLKD 110


>gnl|CDD|36758 KOG1545, KOG1545, KOG1545, Voltage-gated shaker-like K+ channel
           KCNA [Inorganic ion transport and metabolism].
          Length = 507

 Score = 24.5 bits (53), Expect = 7.9
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 8   PEERMLCRREYKRRYYL 24
           PEER L R E++R+ +L
Sbjct: 163 PEERPLPRNEFQRQVWL 179


>gnl|CDD|39002 KOG3798, KOG3798, KOG3798, Predicted Zn-dependent hydrolase
           (beta-lactamase superfamily) [General function
           prediction only].
          Length = 343

 Score = 24.6 bits (53), Expect = 9.0
 Identities = 8/23 (34%), Positives = 13/23 (56%)

Query: 51  QYYLKNKDKYREYKRRYYLKNRD 73
           +YYL+ +DK +E      LK+  
Sbjct: 307 EYYLEPRDKLKELMEAEGLKDTS 329


>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of  Nurr1, a
           member of  conserved family of nuclear receptors.  The
           ligand binding domain of nuclear receptor Nurr1: Nurr1
           belongs to the conserved family of nuclear receptors. It
           is a transcription factor that is expressed in the
           embryonic ventral midbrain and is critical for the
           development of dopamine (DA) neurons. Structural studies
           have shown that the ligand binding pocket of Nurr1 is
           filled by bulky hydrophobic residues, making it unable
           to bind to ligands. Therefore, it belongs to the class
           of orphan receptors. However, Nurr1 forms heterodimers
           with RXR and can promote signaling via its partner, RXR.
           Like other members of the nuclear receptor (NR)
           superfamily of ligand-activated transcription factors,
           Nurr1 has  a central well conserved DNA binding domain
           (DBD), a variable N-terminal domain, a flexible hinge
           and a C-terminal ligand binding domain (LBD).
          Length = 238

 Score = 24.6 bits (53), Expect = 9.2
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 8   PEERMLCRREYKRRYYLKNRD 28
           PE R LC +  +R +YLK  D
Sbjct: 200 PELRTLCTQGLQRIFYLKLED 220


>gnl|CDD|145880 pfam02956, TT_ORF1, TT viral orf 1.  TT virus (TTV), isolated
          initially from a Japanese patient with hepatitis of
          unknown aetiology, has since been found to infect both
          healthy and diseased individuals and numerous
          prevalence studies have raised questions about its role
          in unexplained hepatitis. ORF1 is a large 750 residue
          protein. The N-terminal half of this protein
          corresponds to the capsid protein.
          Length = 525

 Score = 24.5 bits (54), Expect = 9.3
 Identities = 9/24 (37%), Positives = 13/24 (54%)

Query: 15 RREYKRRYYLKNRDKILERRRRRY 38
           R  +RR  ++ R +   RRRRR 
Sbjct: 25 ARRRRRRRRVRRRRRGRRRRRRRR 48


>gnl|CDD|33234 COG3428, COG3428, Predicted membrane protein [Function unknown].
          Length = 494

 Score = 24.5 bits (53), Expect = 9.9
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 96  EEPMGMTKAEIEALEREIARLKAKPIEELIYKRG 129
           E   G  +AE E +EREIA   A  + E   K+ 
Sbjct: 117 ETAGGGGEAEAELVEREIAFELAALVREARVKKL 150


  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
   0.320    0.136    0.389 

Gapped
Lambda     K      H
   0.267   0.0615    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,749,306
Number of extensions: 94668
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 680
Number of HSP's successfully gapped: 163
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.1 bits)