RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus
Liberibacter asiaticus str. psy62]
         (160 letters)



>gnl|CDD|32711 COG2885, OmpA, Outer membrane protein and related
           peptidoglycan-associated (lipo)proteins [Cell envelope
           biogenesis, outer membrane].
          Length = 190

 Score =  102 bits (256), Expect = 3e-23
 Identities = 38/110 (34%), Positives = 55/110 (50%), Gaps = 1/110 (0%)

Query: 41  QEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSI 99
                 ++ + V FD  S  ++P     L  L  +L+K+     L+EGH D  GS   + 
Sbjct: 74  ARDIILNLPNDVLFDFDSSVLKPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQ 133

Query: 100 ALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA 149
           AL  RRA AV +Y V++G+ A R+    YG+E P      E+  AKNRR 
Sbjct: 134 ALSERRAEAVADYLVSQGVVADRISTVGYGEEKPIASNATEEGRAKNRRV 183


>gnl|CDD|143586 cd07185, OmpA_C-like, Peptidoglycan binding domains similar to the
           C-terminal domain of outer-membrane protein OmpA.
           OmpA-like domains (named after the C-terminal domain of
           Escherichia coli OmpA protein) have been shown to
           non-covalently associate with peptidoglycan, a network
           of glycan chains composed of disaccharides, which are
           crosslinked via short peptide bridges. Well-studied
           members of this family include the Escherichia coli
           outer membrane protein OmpA, the Escherichia coli
           lipoprotein PAL, Neisseria meningitdis RmpM, which
           interact with the outer membrane, as well as the
           Escherichia coli motor protein MotB, and the Vibrio
           flagellar motor proteins PomB and MotY, which interact
           with the inner membrane.
          Length = 106

 Score =  101 bits (255), Expect = 7e-23
 Identities = 37/104 (35%), Positives = 54/104 (51%), Gaps = 1/104 (0%)

Query: 51  SVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAV 109
           +++FD  S  + P    +L  L   L+K+ D    IEGH D  GS   +  L  RRA AV
Sbjct: 3   TIYFDFGSAELTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDSRGSDAYNQELSERRAEAV 62

Query: 110 FNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
            +Y V++G+ ASR+    YG+  P      E+  AKNRR  + +
Sbjct: 63  ADYLVSKGVDASRITAVGYGESRPIASNDTEEGRAKNRRVEIVI 106


>gnl|CDD|144333 pfam00691, OmpA, OmpA family.  The Pfam entry also includes MotB
           and related proteins which are not included in the
           Prosite family.
          Length = 97

 Score = 76.3 bits (188), Expect = 3e-15
 Identities = 34/97 (35%), Positives = 43/97 (44%), Gaps = 2/97 (2%)

Query: 53  FFDTSSYSIRPADIQVLSNLGSWLE--KHDCDFLIEGHADELGSRNSSIALGLRRAYAVF 110
            FD  S  +     + L  L   L+  +      IEGH D  GS   +  L  RRA AV 
Sbjct: 1   LFDPGSAELTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRGSAKYNWELSARRAQAVA 60

Query: 111 NYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNR 147
           NY V  GI  SR+ V  YG+  P      ++  AKNR
Sbjct: 61  NYLVNHGIPPSRISVEGYGESQPLASNDSDEGRAKNR 97


>gnl|CDD|31551 COG1360, MotB, Flagellar motor protein [Cell motility and
           secretion].
          Length = 244

 Score = 51.9 bits (124), Expect = 8e-08
 Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 7/111 (6%)

Query: 50  DSVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADEL---GSRNSSIALGLRR 105
           DS+ F + S  ++P    +L  +   L      +  IEGH D +   GS  S+  L   R
Sbjct: 132 DSLMFASGSAVVQPEFRDLLLKIAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAAR 191

Query: 106 AYAVFNYFVARG-ISASRMKVTSYGKEMPSVYGHDEDAY-AKNRRAIVFLK 154
           A +V    +  G + A R+ V  Y    P +  +D     AKNRR  + + 
Sbjct: 192 AQSVVRVLINGGLVEAKRLSVVGYADTRP-LADNDTAEGRAKNRRVEILIL 241


>gnl|CDD|34136 COG4457, SrfB, Uncharacterized protein conserved in bacteria,
           putative virulence factor [Function unknown].
          Length = 1014

 Score = 28.8 bits (64), Expect = 0.68
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 52  VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFN 111
           V   + + ++    + ++ ++G+      C  LIE H DE    N +  L LR       
Sbjct: 238 VKTVSDTLNVPAVPVDLVLDVGN---SRTCGILIEDHPDENDGLNQTYELELRDLSK--P 292

Query: 112 YFVARGISASRMKVTS--YGKEMPSVYGHDEDAY 143
            +V      SR++     +GKE  SV     DA+
Sbjct: 293 EYVYNDPFESRVEFAQAEFGKEHFSVESGRPDAF 326


>gnl|CDD|35801 KOG0581, KOG0581, KOG0581, Mitogen-activated protein kinase
          kinase (MAP2K) [Signal transduction mechanisms].
          Length = 364

 Score = 26.8 bits (59), Expect = 2.9
 Identities = 14/58 (24%), Positives = 22/58 (37%)

Query: 17 SISGIDNLDTKISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGS 74
           +S  D L +   S +   N   L +   SS   +         I  +D++ L  LGS
Sbjct: 32 ILSARDTLPSTSESLELTDNSPPLSKISLSSSSANSELSEDDNGISLSDLERLGVLGS 89


>gnl|CDD|31696 COG1507, COG1507, Uncharacterized conserved protein [Function
           unknown].
          Length = 167

 Score = 26.5 bits (58), Expect = 3.1
 Identities = 15/31 (48%), Positives = 19/31 (61%)

Query: 119 SASRMKVTSYGKEMPSVYGHDEDAYAKNRRA 149
           +ASR++ T Y KEM    G DE+  A  RRA
Sbjct: 62  AASRLESTGYMKEMTERLGQDEELRAFYRRA 92


>gnl|CDD|30609 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
           metabolism].
          Length = 485

 Score = 26.0 bits (57), Expect = 4.4
 Identities = 8/18 (44%), Positives = 11/18 (61%)

Query: 48  VGDSVFFDTSSYSIRPAD 65
           VG  + FD+   SI+PA 
Sbjct: 251 VGKGITFDSGGISIKPAA 268


>gnl|CDD|163641 cd07398, MPP_YbbF-LpxH, Escherichia coli YbbF/LpxH and related
           proteins, metallophosphatase domain.  YbbF/LpxH is an
           Escherichia coli UDP-2,3-diacylglucosamine hydrolase
           thought to catalyze the fourth step of lipid A
           biosynthesis, in which a precursor
           UDP-2,3-diacylglucosamine is hydrolyzed to yield
           2,3-diacylglucosamine 1-phosphate and UMP.  YbbF belongs
           to the metallophosphatase (MPP) superfamily.  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 MPP superfamily 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).  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 = 217

 Score = 25.9 bits (57), Expect = 5.3
 Identities = 4/14 (28%), Positives = 6/14 (42%)

Query: 75  WLEKHDCDFLIEGH 88
              +   D +I GH
Sbjct: 184 LARRKGVDGVICGH 197


>gnl|CDD|144468 pfam00883, Peptidase_M17, Cytosol aminopeptidase family, catalytic
           domain.  The two associated zinc ions and the active
           site are entirely enclosed within the C-terminal
           catalytic domain in leucine aminopeptidase.
          Length = 312

 Score = 25.3 bits (56), Expect = 7.3
 Identities = 7/18 (38%), Positives = 10/18 (55%)

Query: 48  VGDSVFFDTSSYSIRPAD 65
           VG  + FD+   SI+P  
Sbjct: 84  VGKGITFDSGGISIKPGA 101


>gnl|CDD|146133 pfam03340, Pox_Rif, Poxvirus rifampicin resistance protein. 
          Length = 541

 Score = 25.4 bits (56), Expect = 8.4
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 28  ISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADI 66
           I S + ++ E+  +E F S   + +    S YSI   D 
Sbjct: 93  IESVNGIIWETGGEELFDSCRDNKIASKLSGYSIELNDF 131


  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
   0.318    0.132    0.372 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,800,125
Number of extensions: 84617
Number of successful extensions: 207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 16
Length of query: 160
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,405,363
Effective search space: 325996862
Effective search space used: 325996862
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: 41 (21.8 bits)
S2: 53 (24.2 bits)