RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781078|ref|YP_003065491.1| hypothetical protein
CLIBASIA_04900 [Candidatus Liberibacter asiaticus str. psy62]
         (242 letters)



>gnl|CDD|110393 pfam01389, OmpA_membrane, OmpA-like transmembrane domain.  The
           structure of OmpA transmembrane domain shows that it
           consists of an eight stranded beta barrel. This family
           includes some other distantly related outer membrane
           proteins with low scores.
          Length = 175

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 17/110 (15%)

Query: 134 LKAGYSV-DSLLIYGMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYM 192
           LK  Y + D L +YG  G     ++ +     +     N K      G S +  +G++Y 
Sbjct: 81  LKLSYPLTDDLDVYGKVG---GALVRAD---YKFYEDANGKTGNHDTGVSPLFALGVEYA 134

Query: 193 VNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242
           V  ++++   Y+Y       +NN     D+ +  ++ +   ASLGI+  F
Sbjct: 135 VTPELAVRLEYQY-------LNNIG---DLHKQGKRPDNGSASLGISYRF 174


>gnl|CDD|33435 COG3637, COG3637, Opacity protein and related surface antigens
           [Cell envelope biogenesis, outer membrane].
          Length = 199

 Score = 34.2 bits (78), Expect = 0.030
 Identities = 24/156 (15%), Positives = 44/156 (28%), Gaps = 20/156 (12%)

Query: 93  LGHNIQLEDFVFGI---NCHTTAAKDDSTFYRL--KEKYFIYGDVVLKAGYSVDS-LLIY 146
            G+N++    V G+     +T  +   S        +    YG +     Y ++     Y
Sbjct: 58  AGYNLKYRYSVLGVEGSFTYTGQSGRYSGGSGKNQVDNKAWYGSLRAGPDYRINDRFSPY 117

Query: 147 GMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYMVNYDISLSASYRYI 206
           G  G     V        E   S +      G+      G G+ Y    ++++   Y Y 
Sbjct: 118 GGAGVAYGKV---KTSTDEVGGSADESKTKTGYA----YGAGVQYNPTDNVAIDLGYEYS 170

Query: 207 PHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242
                  +                 H   +G+   F
Sbjct: 171 -------DFGKKDGVDGGYSGDVKTHTVKVGVGYKF 199


>gnl|CDD|111657 pfam02784, Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase,
           pyridoxal binding domain.  These pyridoxal-dependent
           decarboxylases acting on ornithine, lysine, arginine and
           related substrates This domain has a TIM barrel fold.
          Length = 245

 Score = 32.2 bits (74), Expect = 0.12
 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 4/89 (4%)

Query: 98  QLEDFVFGINCHTTAAKDD-STFYRLKEKYFIYGDVVLKAGYSVDSLLIYGMGGFGGAYV 156
           +L   V G++ H  +   D   F +         D   + G+ +  L + G GGFG  Y 
Sbjct: 149 ELGLNVVGVHFHVGSGCTDAEAFVKAARDARNVFDQGAELGFELKILDL-G-GGFGVDYT 206

Query: 157 IDSSLEKVESDNSKNAKGRFDGHGSSVVL 185
                E+  ++    A      H     +
Sbjct: 207 GAEDFEEY-AEVINAALEEVFPHDPHPTI 234


>gnl|CDD|146513 pfam03922, OmpW, OmpW family.  This family includes outer membrane
           protein W (OmpW) proteins from a variety of bacterial
           species. This protein may form the receptor for S4
           colicins in E. coli.
          Length = 189

 Score = 27.8 bits (62), Expect = 2.5
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 184 VLGIGLDYMVNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242
               G+DYMVN D  ++    Y+   I +  +        +   K +  + S+G+   F
Sbjct: 133 AGQAGVDYMVNDDWLVNMDVWYM--FIDTTASYKLGGAKLKTKVKLDPWVFSIGLGYRF 189


>gnl|CDD|37417 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonuclease complex,
           subunit PM/SCL-100 (Rrp6) [Translation, ribosomal
           structure and biogenesis].
          Length = 687

 Score = 27.7 bits (61), Expect = 3.1
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 10/74 (13%)

Query: 31  PRKIDLFNEADNNVEYQDDEYGIWSGNYVGLHISRLYETHPLADTI--NRKTYNSLLPNG 88
           P  + +F+ AD ++        IW     G+++  L++T   +  +   R +   LL   
Sbjct: 264 PGIVKVFHGADTDI--------IWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLLECV 315

Query: 89  LGIELGHNIQLEDF 102
            G+      QL D+
Sbjct: 316 CGVLTNKKYQLADW 329


>gnl|CDD|34462 COG4853, COG4853, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 264

 Score = 26.8 bits (59), Expect = 5.6
 Identities = 11/56 (19%), Positives = 25/56 (44%)

Query: 1  MNFNGYGALFFVVFLSIVVPNHSLAVDLYLPRKIDLFNEADNNVEYQDDEYGIWSG 56
          M++    ++F VVFL + +   S+  +  + R      E++N    + D   + + 
Sbjct: 1  MDWKKTKSIFIVVFLLLNIFLVSIFFNKKVNRSHINLVESNNEENLKADNISVHAS 56


>gnl|CDD|32861 COG3047, OmpW, Outer membrane protein W [Cell envelope biogenesis,
           outer membrane].
          Length = 213

 Score = 26.8 bits (59), Expect = 6.1
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 177 DGHGSSVVLGIGLDYMVNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASL 236
           D  G       G+DYM+N D  L+   +Y+     +   +       +   K +  +  +
Sbjct: 150 DSWG--AAGQAGVDYMLNDDWLLNMDVKYMFIDTTAKYKAGLGGAKLKSKVKLDPWVFMI 207

Query: 237 GINMHF 242
           GI   F
Sbjct: 208 GIGYRF 213


>gnl|CDD|146437 pfam03797, Autotransporter, Autotransporter beta-domain.  Secretion
           of protein products occurs by a number of different
           pathways in bacteria. One of these pathways known as the
           type V pathway was first described for the IgA1
           protease. The protein component that mediates secretion
           through the outer membrane is contained within the
           secreted protein itself, hence the proteins secreted in
           this way are called autotransporters. This family
           corresponds to the presumed integral membrane
           beta-barrel domain that transports the protein. This
           domain is found at the C terminus of the proteins it
           occurs in. The N terminus contains the variable
           passenger domain that is translocated across the
           membrane. Once the passenger domain is exported it is
           cleaved auto-catalytically in some proteins, in others a
           different protease is used and in some cases no cleavage
           occurs.
          Length = 265

 Score = 26.3 bits (58), Expect = 7.9
 Identities = 26/117 (22%), Positives = 52/117 (44%), Gaps = 15/117 (12%)

Query: 90  GIELGHNIQL-EDFVFGIN-CHTTA-AKDDSTFYRLKEKYF---IYGDVVLKAGYSVDSL 143
           G +LG + +L  D + G+   ++ + +K D    + K   +   +Y       G  +D +
Sbjct: 33  GYQLGADARLGGDLILGLAFGYSFSKSKSDDGGGKGKSDSYGAGLYAQWNFDGGLYLDGV 92

Query: 144 LIYGMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYMVNYDISLS 200
           L YG          D+ + K    ++  AKG +D HG    L  G  + ++ +++L+
Sbjct: 93  LAYGR--------FDNDV-KRLGTSTGTAKGDYDSHGLGASLEAGYRFKLSGNLTLT 140


  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    0.140    0.414 

Gapped
Lambda     K      H
   0.267   0.0826    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,970,623
Number of extensions: 156104
Number of successful extensions: 331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 14
Length of query: 242
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,297,318
Effective search space: 648895018
Effective search space used: 648895018
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 (21.7 bits)
S2: 56 (25.2 bits)