RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780953|ref|YP_003065366.1| OmpA/MotB [Candidatus
Liberibacter asiaticus str. psy62]
         (190 letters)



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

 Score =  110 bits (275), Expect = 3e-25
 Identities = 51/157 (32%), Positives = 79/157 (50%), Gaps = 2/157 (1%)

Query: 30  LHKSNDTDIVNKRFGSSLDKAEDEFQMQLQDTGIVVSRIGDMITCYIPVHVSFVSEVF-L 88
           L  +    +     G  LD AE E + +    G    R    I   +P  V F  +   L
Sbjct: 35  LIGAGPGALGGAGAGVPLDVAEAELRAKEAGDGPAERRKARDIILNLPNDVLFDFDSSVL 94

Query: 89  EKKFLPMLQLIATILNKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGVSS 148
           + K    L  +A  L K P T I ++ HTDS G+ + N  +S+ RA+ +  YL+ +GV +
Sbjct: 95  KPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQALSERRAEAVADYLVSQGVVA 154

Query: 149 NRFISVRGFAYKYPIDTNDTKVGRQNNQRIEIQIFPR 185
           +R IS  G+  + PI +N T+ GR  N+R+EI+I P+
Sbjct: 155 DR-ISTVGYGEEKPIASNATEEGRAKNRRVEIKISPK 190


>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 =  106 bits (268), Expect = 3e-24
 Identities = 37/95 (38%), Positives = 57/95 (60%), Gaps = 1/95 (1%)

Query: 88  LEKKFLPMLQLIATILNKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGVS 147
           L  +  P+L  +A +L K P   I I+ HTDS G+   N  +S+ RA+ +  YL+ +GV 
Sbjct: 13  LTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKGVD 72

Query: 148 SNRFISVRGFAYKYPIDTNDTKVGRQNNQRIEIQI 182
           ++R I+  G+    PI +NDT+ GR  N+R+EI I
Sbjct: 73  ASR-ITAVGYGESRPIASNDTEEGRAKNRRVEIVI 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 = 71.3 bits (175), Expect = 2e-13
 Identities = 30/89 (33%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 88  LEKKFLPMLQLIATIL-NKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGV 146
           L  +    L  +A +L        I I+ HTDS G+ K N  +S  RA  + +YL+  G+
Sbjct: 9   LTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRGSAKYNWELSARRAQAVANYLVNHGI 68

Query: 147 SSNRFISVRGFAYKYPIDTNDTKVGRQNN 175
             +R ISV G+    P+ +ND+  GR  N
Sbjct: 69  PPSR-ISVEGYGESQPLASNDSDEGRAKN 96


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

 Score = 68.9 bits (168), Expect = 9e-13
 Identities = 39/151 (25%), Positives = 71/151 (47%), Gaps = 4/151 (2%)

Query: 40  NKRFGSSLDKAEDEFQMQLQDTGIVVSRIGDMITCYIPVHVSF-VSEVFLEKKFLPMLQL 98
           +++ G    + E + +    +  + V  + + +   I   + F      ++ +F  +L  
Sbjct: 94  SEKLGDLAKELESKPKDIELEHQLGVDDVEEGLVISISDSLMFASGSAVVQPEFRDLLLK 153

Query: 99  IATILNKFPSTVIAIQSHTDS---IGTLKNNLLISQERADVIKSYLIQRGVSSNRFISVR 155
           IA +L   P+  I I+ HTD+    G+  +N  +S  RA  +   LI  G+   + +SV 
Sbjct: 154 IAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAARAQSVVRVLINGGLVEAKRLSVV 213

Query: 156 GFAYKYPIDTNDTKVGRQNNQRIEIQIFPRG 186
           G+A   P+  NDT  GR  N+R+EI I  + 
Sbjct: 214 GYADTRPLADNDTAEGRAKNRRVEILILTKK 244


>gnl|CDD|145708 pfam02698, DUF218, DUF218 domain.  This large family of proteins
           contains several highly conserved charged amino acids,
           suggesting this may be an enzymatic domain (Bateman A
           pers. obs). The family includes SanA, which is involved
           in Vancomycin resistance. This protein may be involved
           in murein synthesis.
          Length = 148

 Score = 26.5 bits (59), Expect = 4.3
 Identities = 6/19 (31%), Positives = 13/19 (68%)

Query: 134 ADVIKSYLIQRGVSSNRFI 152
           A+V++ YL++ GV +   +
Sbjct: 49  AEVMRRYLVELGVPAEAIL 67


>gnl|CDD|145728 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase,
          carbamoyl-P binding domain. 
          Length = 140

 Score = 25.6 bits (57), Expect = 8.6
 Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 5/28 (17%)

Query: 45 SSLDKAEDEFQMQLQDTGIVVSRIGDMI 72
          SSL K E      L+DT  V+SR  D I
Sbjct: 74 SSLGKGES-----LKDTARVLSRYVDAI 96


>gnl|CDD|147081 pfam04739, AMPKBI, 5'-AMP-activated protein kinase beta subunit,
           interation domain.  This region is found in the beta
           subunit of the 5'-AMP-activated protein kinase complex,
           and its yeast homologues Sip1, Sip2 and Gal83, which are
           found in the SNF1 kinase complex. This region is
           sufficient for interaction of this subunit with the
           kinase complex, but is not solely responsible for the
           interaction, and the interaction partner is not known.
           The isoamylase N-terminal domain (pfam02922) is
           sometimes found in proteins belonging to this family.
          Length = 94

 Score = 25.7 bits (57), Expect = 9.0
 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)

Query: 76  IPVHVSFVSEVFLEKKFLPML--QLIATILNKFPST 109
           IP +   +      KK  P L   L+ TILNK  ++
Sbjct: 10  IPANFQDLLVAEEFKKEPPSLPPHLLKTILNKPTAS 45


  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
   0.322    0.137    0.380 

Gapped
Lambda     K      H
   0.267   0.0756    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,105,794
Number of extensions: 102847
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 216
Number of HSP's successfully gapped: 9
Length of query: 190
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,362,145
Effective search space: 444938790
Effective search space used: 444938790
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: 54 (24.5 bits)