RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781146|ref|YP_003065559.1| hypothetical protein
CLIBASIA_05265 [Candidatus Liberibacter asiaticus str. psy62]
         (122 letters)



>gnl|CDD|58519 cd01842, SGNH_hydrolase_like_5, SGNH_hydrolase subfamily. SGNH
          hydrolases are a diverse family of lipases and
          esterases. The tertiary fold of the enzyme is
          substantially different from that of the alpha/beta
          hydrolase family and unique among all known hydrolases;
          its active site closely resembles the Ser-His-Asp(Glu)
          triad found in other serine hydrolases..
          Length = 183

 Score = 26.1 bits (57), Expect = 2.5
 Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 37 DFSKYGRKVIKNLREEKPEQYLRLISQILPRE 68
          D S+Y R  +K  RE     + +L   +LP E
Sbjct: 62 DLSRYQRNSMKTYRENLERLFSKL-DSVLPIE 92


>gnl|CDD|73272 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
           APPBP1. APPBP1 is part of the heterodimeric activating
           enzyme (E1), specific for the Rub family of
           ubiquitin-like proteins (Ubls). E1 enzymes are part of a
           conjugation cascade to attach Ub or Ubls, covalently to
           substrate proteins consisting of activating (E1),
           conjugating (E2), and/or ligating (E3) enzymes. E1
           activates ubiquitin(-like) by C-terminal adenylation,
           and subsequently forms a highly reactive thioester bond
           between its catalytic cysteine and Ubls C-terminus. E1
           also associates with E2 and promotes ubiquitin transfer
           to the E2's catalytic cysteine. Post-translational
           modification by Rub family of ubiquitin-like proteins
           (Ublps) activates SCF ubiquitin ligases and is involved
           in cell cycle control, signaling and embryogenesis.
           ABPP1 contains part of the adenylation domain..
          Length = 425

 Score = 26.0 bits (57), Expect = 3.0
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 6/63 (9%)

Query: 6   LLPIRKKYPCINRLSHKEISLQYLYQSVLTDD---FSKYGRKVIKNL---REEKPEQYLR 59
           LLP+    P +   + K I LQ +Y+     D     KY R+++K+L    +   ++ ++
Sbjct: 306 LLPLPGTLPDMTADTEKYIKLQNIYREKAEKDAAEVEKYVREILKSLGRSPDSISDKEIK 365

Query: 60  LIS 62
           L  
Sbjct: 366 LFC 368


>gnl|CDD|144174 pfam00481, PP2C, Protein phosphatase 2C.  Protein phosphatase 2C is
           a Mn++ or Mg++ dependent protein serine/threonine
           phosphatase.
          Length = 253

 Score = 25.4 bits (56), Expect = 4.0
 Identities = 8/20 (40%), Positives = 15/20 (75%), Gaps = 2/20 (10%)

Query: 73  DGITNGDQLTDEQLCEIIRS 92
           DG+   D L+D+++ +I+RS
Sbjct: 209 DGLW--DVLSDQEVVDIVRS 226


>gnl|CDD|143970 pfam00213, OSCP, ATP synthase delta (OSCP) subunit.  The ATP D
           subunit from E. coli is the same as the OSCP subunit
           which is this family. The ATP D subunit from metazoa are
           found in family pfam00401.
          Length = 171

 Score = 25.2 bits (56), Expect = 5.2
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 5/73 (6%)

Query: 31  QSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILPREKIKQDGITNGD-----QLTDEQ 85
           ++V     S+  +  +K L E      L  I++       +  GI          L++EQ
Sbjct: 58  KAVFGGKLSELTKNFLKLLAENGRLSLLPEIAEEFEELYNEHRGIVEATVTSAVPLSEEQ 117

Query: 86  LCEIIRSLEKELQ 98
           L  +  +LEK+  
Sbjct: 118 LKALKAALEKKTG 130


>gnl|CDD|147746 pfam05761, 5_nucleotid, 5' nucleotidase family.  This family of
           eukaryotic proteins includes 5' nucleotidase enzymes,
           such as purine 5'-nucleotidase EC:3.1.3.5.
          Length = 448

 Score = 24.9 bits (55), Expect = 5.3
 Identities = 4/26 (15%), Positives = 12/26 (46%)

Query: 87  CEIIRSLEKELQIFTDFKNKDAHSRE 112
             ++  LE+E++I    + +    + 
Sbjct: 320 ALVVPELEREIEILNTEQYRFEELQR 345


>gnl|CDD|176141 cd08450, PBP2_HcaR, The C-terminal substrate binding domain of
          LysR-type transcriptional regulator HcaR in involved in
          3-phenylpropionic acid catabolism, contains the type2
          periplasmic binding fold.  HcaR, a member of the LysR
          family of transcriptional regulators, controls the
          expression of the hcA1, A2, B, C, and D operon,
          encoding for the 3-phenylpropionate dioxygenase complex
          and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase,
          that oxidizes 3-phenylpropionate to
          3-(2,3-dihydroxyphenyl) propionate.  Dioxygenases play
          an important role in protecting the cell against the
          toxic effects of dioxygen. The expression of hcaR is
          negatively auto-regulated, as for other members of the
          LysR family, and is strongly repressed in the presence
          of glucose. This substrate-binding domain shows
          significant homology to the type 2 periplasmic binding
          proteins (PBP2), which are responsible for the uptake
          of a variety of substrates such as phosphate, sulfate,
          polysaccharides, lysine/arginine/ornithine, and
          histidine. The PBP2 bind their ligand in the cleft
          between these domains in a manner resembling a Venus
          flytrap. After binding their specific ligand with high
          affinity, they can interact with a cognate membrane
          transport complex comprised of two integral membrane
          domains and two cytoplasmically located ATPase domains.
          This interaction triggers the ligand translocation
          across the cytoplasmic membrane energized by ATP
          hydrolysis.
          Length = 196

 Score = 25.0 bits (55), Expect = 5.8
 Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 2/31 (6%)

Query: 44 KVIKNLREEKPEQYLRLISQILPR--EKIKQ 72
          +V+  LREE P+  + L S   P+  E + +
Sbjct: 17 EVLPILREEHPDLDVELSSLFSPQLAEALMR 47


>gnl|CDD|144807 pfam01346, FKBP_N, Domain amino terminal to FKBP-type
          peptidyl-prolyl isomerase.  This family is only found
          at the amino terminus of pfam00254. This domain is of
          unknown function.
          Length = 124

 Score = 24.8 bits (55), Expect = 5.8
 Identities = 9/28 (32%), Positives = 20/28 (71%), Gaps = 1/28 (3%)

Query: 72 QDGITNGD-QLTDEQLCEIIRSLEKELQ 98
          QD +   + +LTDE++ + +++ +K+LQ
Sbjct: 55 QDALAGKELKLTDEEIQKALQAFQKKLQ 82


>gnl|CDD|111230 pfam02316, Mu_DNA_bind, Mu DNA-binding domain.  This family
           consists of MuA-transposase and repressor protein CI.
           These proteins contain homologous DNA-binding domains at
           their N-termini which compete for the same DNA site
           within the Mu bacteriophage genome.
          Length = 136

 Score = 25.0 bits (54), Expect = 6.0
 Identities = 12/60 (20%), Positives = 27/60 (45%)

Query: 7   LPIRKKYPCINRLSHKEISLQYLYQSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILP 66
           LP+  +   + R    E       ++  T +   Y R++I +  +  P++  R + ++LP
Sbjct: 46  LPVETRAALLLRQGEIETGAGLFEKARPTLEAHTYDRELIWSKWDLAPDEQRRALEKLLP 105


>gnl|CDD|29049 cd00992, PDZ_signaling, PDZ domain found in a variety of
          Eumetazoan signaling molecules, often in tandem
          arrangements. May be responsible for specific
          protein-protein interactions, as most PDZ domains bind
          C-terminal polypeptides, and binding to internal
          (non-C-terminal) polypeptides and even to lipids has
          been demonstrated. In this subfamily of PDZ domains an
          N-terminal beta-strand forms the peptide-binding groove
          base, a circular permutation with respect to PDZ
          domains found in proteases..
          Length = 82

 Score = 24.4 bits (53), Expect = 7.3
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 11/63 (17%)

Query: 48 NLREEKPEQYLRLISQILPREKIKQDGITNGDQL-----------TDEQLCEIIRSLEKE 96
          +LR  K       +S++ P    ++ G+  GD++           T E+  E++++   E
Sbjct: 17 SLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDE 76

Query: 97 LQI 99
          + +
Sbjct: 77 VTL 79


>gnl|CDD|31056 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial
           oligomycin sensitivity protein) [Energy production and
           conversion].
          Length = 178

 Score = 24.0 bits (52), Expect = 9.5
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 19  LSHKEISLQY---LYQSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILPREKIKQDGI 75
           LS   +S +    L  S+         +  ++ L E K    L  I +   +   +  GI
Sbjct: 49  LSSPAVSAEDKKELLISIFKKIGDPLLQNFLRLLAENKRLNLLPEILEEFLKLAAESRGI 108

Query: 76  TNGD-----QLTDEQLCEIIRSLEKEL 97
              +     +L+DEQL ++   LEK+ 
Sbjct: 109 VEAEVTSAFELSDEQLTKLEAKLEKKF 135


>gnl|CDD|37920 KOG2709, KOG2709, KOG2709, Uncharacterized conserved protein
           [Function unknown].
          Length = 560

 Score = 23.9 bits (51), Expect = 9.8
 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 64  ILPREKIKQDGITNGDQLTDE-QLCEIIRSLEKELQIFTDFK 104
           + P    +  G+T G  L+ E Q   +I  LE  LQ FTDF 
Sbjct: 256 LFPDPTPQNPGMTVGILLSSEIQERRLIEELEIVLQEFTDFL 297


  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
   0.315    0.132    0.362 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,377,000
Number of extensions: 65568
Number of successful extensions: 180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 30
Length of query: 122
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,491,799
Effective search space: 179671960
Effective search space used: 179671960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.4 bits)