RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780935|ref|YP_003065348.1| rare lipoprotein A [Candidatus
Liberibacter asiaticus str. psy62]
         (276 letters)



>gnl|CDD|161866 TIGR00413, rlpA, rare lipoprotein A.  This is a family of
           prokaryotic proteins with unknown function. Lipoprotein
           annotation based on the presence of consensus
           lipoprotein signal sequence. Included in this family is
           the E. coli putative lipoprotein rlpA.
          Length = 208

 Score =  128 bits (322), Expect = 2e-30
 Identities = 53/94 (56%), Positives = 72/94 (76%)

Query: 90  GMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRGPY 149
           G+ASWYG  FHGR TANGEVY  + +TAAH TLP  +YV+VTN+ N  S++VR+NDRGP+
Sbjct: 1   GLASWYGPKFHGRKTANGEVYNMKALTAAHKTLPFNTYVKVTNLHNNRSVIVRINDRGPF 60

Query: 150 HSNRLIDLSNAAAKILRVEERGVSKVHVEYLGMA 183
             +R+IDLS+AAA+ + +  RGV +V +E L +A
Sbjct: 61  SDDRIIDLSHAAAREIGLISRGVGQVRIEVLHVA 94


>gnl|CDD|182636 PRK10672, PRK10672, rare lipoprotein A; Provisional.
          Length = 361

 Score =  119 bits (300), Expect = 8e-28
 Identities = 52/117 (44%), Positives = 70/117 (59%), Gaps = 9/117 (7%)

Query: 71  YQIMGRWYV----PRQYTAYAAVGMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLPS 126
           YQ  G+ Y     P  ++     G+A+ Y       LTA+GE +    +TAAHPTLP+PS
Sbjct: 61  YQRNGKSYKIVQDPSNFSQ---AGLAAIYDAEAGSNLTASGERFDPNALTAAHPTLPIPS 117

Query: 127 YVRVTNMENGISLVVRVNDRGPYHSNRLIDLSNAAAKILRVEERGVSKVHVEYLGMA 183
           YVRVTN+ NG  +VVR+NDRGPY   R+IDLS AAA  L       +KV ++ + +A
Sbjct: 118 YVRVTNLANGRMIVVRINDRGPYGPGRVIDLSRAAADRLNTSNN--TKVRIDPIIVA 172


>gnl|CDD|162614 TIGR01936, nqrA, NADH:ubiquinone oxidoreductase,
           Na(+)-translocating, A subunit.  This model represents
           the NqrA subunit of the six-protein, Na(+)-pumping
           NADH-quinone reductase of a number of marine and
           pathogenic Gram-negative bacteria. This oxidoreductase
           complex functions primarily as a sodium ion pump.
          Length = 447

 Score = 33.2 bits (76), Expect = 0.072
 Identities = 24/82 (29%), Positives = 29/82 (35%), Gaps = 10/82 (12%)

Query: 101 GRLTANGEVYGTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRGPYHSNRLIDLSNA 160
           G L   GE+     I  A P +  P YVR T   N   L     +      NRLI  S  
Sbjct: 247 GHLFLTGELLTERVIALAGPAVKKPRYVRTTKGANLSQLF--PGELTSEGENRLISGSVL 304

Query: 161 AAKILRVEERGVSKVHVEYLGM 182
             +  + EE         YLG 
Sbjct: 305 TGRKAKKEE--------AYLGR 318


>gnl|CDD|132116 TIGR03072, release_prfH, putative peptide chain release factor H.
           Members of this protein family are bacterial proteins
           homologous to peptide chain release factors 1 (RF-1,
           product of the prfA gene), and 2 (RF-2, product of the
           prfB gene). The member from Escherichia coli K-12,
           designated prfH, appears to be a pseudogene. This class
           I release factor is always found as the downstream gene
           of a two-gene operon.
          Length = 200

 Score = 29.7 bits (67), Expect = 0.82
 Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 12/55 (21%)

Query: 126 SYVRVTNMENGISLVVRVNDRGPYHSN----------RLIDLSNAAAKILRVEER 170
           S VR T++ +GIS  V+V      H+N          RL DL    A  LR E R
Sbjct: 128 SAVRATHLASGIS--VKVQSERSQHANKRLATLLLAVRLADLQQEQAAALRAERR 180


>gnl|CDD|148216 pfam06476, DUF1090, Protein of unknown function (DUF1090).  This
           family consists of several bacterial proteins of unknown
           function and is known as YqjC in E. coli.
          Length = 115

 Score = 28.0 bits (63), Expect = 3.0
 Identities = 5/21 (23%), Positives = 13/21 (61%)

Query: 231 NNCDDDSLQKQREISLRERKK 251
            +C D  L+ +R+  + E+++
Sbjct: 57  AHCTDAGLRAERQAKVEEKEQ 77


>gnl|CDD|177828 PLN02171, PLN02171, endoglucanase.
          Length = 629

 Score = 27.8 bits (62), Expect = 3.1
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 16/44 (36%)

Query: 89  VGMASW----YGKAFHGRLTANGEV--------YGTEYITAAHP 120
           V M SW    YGK    ++ A GE+        +GT+Y   AHP
Sbjct: 95  VTMMSWSIIEYGK----QMAAAGELGHAMDAVKWGTDYFIKAHP 134


>gnl|CDD|130079 TIGR01006, polys_exp_MPA1, polysaccharide export protein, MPA1
           family, Gram-positive type.  This family contains
           members from Low GC Gram-positive bacteria; they are
           proposed to have a function in the export of complex
           polysaccharides.
          Length = 226

 Score = 27.4 bits (61), Expect = 3.6
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 124 LPSYVRVTNMENGISLVVRVNDRGPYHSNRLID-----LSNAAAKILRVE 168
           L S V VTN  +   + + V D+ P  ++++ +      S    KI  V 
Sbjct: 106 LSSMVTVTNPTDTRLISISVKDKTPQDASKIANSLREVASKKIPKITNVS 155


>gnl|CDD|150741 pfam10101, DUF2339, Predicted membrane protein (DUF2339).  This
           domain, found in various hypothetical bacterial
           proteins, has no known function.
          Length = 738

 Score = 26.9 bits (60), Expect = 5.5
 Identities = 4/40 (10%), Positives = 10/40 (25%)

Query: 61  GGGRYFLGKPYQIMGRWYVPRQYTAYAAVGMASWYGKAFH 100
                +L    ++  R         +A   +A+       
Sbjct: 361 ALAAAWLLLAERLSRRRLRQGLAALFALAALAALALALTM 400


>gnl|CDD|148462 pfam06859, Bin3, Bicoid-interacting protein 3 (Bin3).  This family
           represents a conserved region of approximately 120
           residues within eukaryotic Bicoid-interacting protein 3
           (Bin3). Bin3, which shows similarity to a number of
           protein methyltransferases that modify RNA-binding
           proteins, interacts with Bicoid, which itself directs
           pattern formation in the early Drosophila embryo. The
           interaction might allow Bicoid to switch between its
           dual roles in transcription and translation. Note that
           family members contain a conserved HLN motif.
          Length = 110

 Score = 26.6 bits (59), Expect = 6.7
 Identities = 12/41 (29%), Positives = 18/41 (43%)

Query: 222 LTRSRTVHLNNCDDDSLQKQREISLRERKKSNLIPLPNGYS 262
           L+ ++ VHLN  D+   +  R I    R    LI  P  + 
Sbjct: 8   LSVTKWVHLNWGDEGLKRFFRRIYRLLRPGGILILEPQPWD 48


>gnl|CDD|162367 TIGR01450, recC, exodeoxyribonuclease V, gamma subunit.  This model
           describes the gamma subunit of exodeoxyribonuclease V.
           Species containing this protein should also have the
           alpha (TIGR01447) and beta (TIGR00609) subunits.
           Candidates from Borrelia and from the Chlamydias differ
           dramatically and score between trusted and noise
           cutoffs.
          Length = 1067

 Score = 26.6 bits (59), Expect = 8.0
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 149 YHSNRLIDLSNAAAKILRVE 168
           YHSNRL  L+   A +LR  
Sbjct: 4   YHSNRLDVLAALLAALLRDP 23


>gnl|CDD|132051 TIGR03006, pepcterm_polyde, polysaccharide deactylase family
           protein, PEP-CTERM locus subfamily.  Members of this
           protein family belong to the family of polysaccharide
           deacetylases (pfam01522). All are found in species that
           encode the PEP-CTERM/exosortase system predicted to act
           in protein sorting in a number of Gram-negative
           bacteria, and are found near the epsH homolog that is
           the putative exosortase gene. The highest scoring
           homologs below the trusted cutoff for this model are
           found in several species of Methanosarcina, an archaeal
           genus.
          Length = 265

 Score = 26.5 bits (59), Expect = 8.6
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)

Query: 53  VSGKRVPRGGGRYFLGKPYQIMGRWYVPR 81
           + G+ +P  GG YF   PY  + RW + R
Sbjct: 174 LGGRNLPAAGGGYFRLLPYA-LSRWALRR 201


>gnl|CDD|128886 smart00638, LPD_N, Lipoprotein N-terminal Domain. 
          Length = 574

 Score = 26.1 bits (58), Expect = 9.7
 Identities = 7/42 (16%), Positives = 15/42 (35%), Gaps = 6/42 (14%)

Query: 186 NGMDQEYLRSTVMVNSATVLPLGCQYREEIV------VIPYL 221
               Q YLR + ++   +++   C             ++ YL
Sbjct: 406 EVQKQPYLRESALLAYGSLVRRYCVNTPSCPDFVLEELLKYL 447


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.321    0.137    0.415 

Gapped
Lambda     K      H
   0.267   0.0655    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,600,032
Number of extensions: 291367
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 15
Length of query: 276
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 184
Effective length of database: 4,006,537
Effective search space: 737202808
Effective search space used: 737202808
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 (21.9 bits)
S2: 56 (25.5 bits)