RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780923|ref|YP_003065336.1| hypothetical protein
CLIBASIA_04110 [Candidatus Liberibacter asiaticus str. psy62]
         (365 letters)



>gnl|CDD|33549 COG3754, RgpF, Lipopolysaccharide biosynthesis protein [Cell
           envelope biogenesis, outer membrane].
          Length = 595

 Score =  136 bits (345), Expect = 7e-33
 Identities = 71/226 (31%), Positives = 101/226 (44%), Gaps = 8/226 (3%)

Query: 115 KAKIAIVVHLYYIDLWIEIANLLSNLSISFDLHVTLVT-ESASIKSEILKIFPA-ARIHI 172
             KIA+ +H+YY DL  E   L  N    +DL +T  T +  +     L   P  A + +
Sbjct: 292 IQKIAVHLHVYYTDLLDEFLALAENTPFPYDLILTTDTPDKVAEIQRALARKPKNAFVRV 351

Query: 173 MENHGRDVLPFLILLETEQLSNYDYVCKIHGKKSKRKGYSWWEGDLWRRWLFYDLLGAPG 232
           +EN GRD+ P L LL   +   YD VC++H KKS +    +W G+LWR     +LL + G
Sbjct: 352 VENRGRDIGPLLHLLRDLKGDRYDLVCRLHTKKSGQ--ADFWAGELWRHHTIDNLLASRG 409

Query: 233 VVFKIIRTFDTHRDIGMIGSRAYRYPNKYCDYTCSLGKNREMICTLAGRMGI--TFQDQK 290
            V   +  F  +  +G      +R    Y     +  +NR  +  L   MG+        
Sbjct: 410 YVTNALEIFADNPSVGADIPPFFRLN--YPTEGIAWFENRAAVADLLRLMGMNVKTDRNT 467

Query: 291 LDFFAGTMFWVRTEALDPIKNLRLSRYFEPKVHKALDGEIEHAVER 336
                GTMFW R  AL P+  L L     P      DG + HA+ER
Sbjct: 468 FVAAYGTMFWFRPRALRPLFELELGWNDFPAEPLPQDGHLAHAIER 513


>gnl|CDD|113802 pfam05045, RgpF, Rhamnan synthesis protein F.  This family consists
           of a group of proteins which are related to the
           Streptococcus rhamnose-glucose polysaccharide assembly
           protein (RgpF). Rhamnan backbones are found in several O
           polysaccharides of phytopathogenic bacteria and are
           regarded as pathogenic factors.
          Length = 498

 Score =  117 bits (294), Expect = 6e-27
 Identities = 74/230 (32%), Positives = 112/230 (48%), Gaps = 18/230 (7%)

Query: 117 KIAIVVHLYYIDLWIEIANLLSNLSISFDLHVTLVTE--SASIKSEILKIFPA--ARIHI 172
           KIA+  H+YY+D+  EI     N+  S+DL +T  T+   A I+  + K   A  A + +
Sbjct: 266 KIAVHAHVYYVDMLDEILTAFKNIPFSYDLIITTDTDDKKAEIEEILAKRKGAKNAIVRV 325

Query: 173 MENHGRDVLPFLILLETEQLSN-YDYVCKIHGKKSKRKGYSWWEGDLWRRWLFYDLLGAP 231
           ++N GRD+ P LI L+ E + + YD VC+ H KKS +    +W G+ ++  L  +LL   
Sbjct: 326 VQNRGRDMSPLLISLKDELVDDRYDLVCRFHTKKSPQA--DFWAGESFKEELIDNLLKPR 383

Query: 232 GVVFKIIRTFDTHRDIGMIGSRA--YRYPNKYCDYTCSLGKNREMICTLAGRMGITFQDQ 289
           G    I+  F+ +  IG++       RYP        +  +N   +  LA RMGI  +  
Sbjct: 384 GYADNILAMFEQNPSIGLVIPDIVHIRYPT----IGNAWNENAPEMNKLARRMGIKKKFD 439

Query: 290 KLDFFA--GTMFWVRTEALDPIKNLRLS-RYFEPKVHKALDGEIEHAVER 336
                A  GTMFW R EAL  +  L      F  +     D  + HA+ER
Sbjct: 440 DNTPVASYGTMFWFRPEALKKLFELEWKWEDFPNEPLP--DNSLLHAIER 487


>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
           a cobalt transport family found in bacteria, archaea,
           and eukaryota.  The transition metal cobalt is an
           essential component of many enzymes and must be
           transported into cells in appropriate amounts when
           needed.  This ABC transport system of the CbiMNQO family
           is involved in cobalt transport in association with the
           cobalamin (vitamin B12) biosynthetic pathways.  Most of
           cobalt (Cbi) transport systems possess a separate CbiN
           component, the cobalt-binding periplasmic protein, and
           they are encoded by the conserved gene cluster cbiMNQO. 
           Both the CbiM and CbiQ proteins are integral cytoplasmic
           membrane proteins, and the CbiO protein has the linker
           peptide and the Walker A and B motifs commonly found in
           the ATPase components of the ABC-type transport
           systems..
          Length = 211

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 6/67 (8%)

Query: 278 LAGRMGITFQDQKLDFFAGTMFWVRTEALDPIKNLRLSRY-FEPKVHKALD--GEIEHAV 334
           L  ++G+ FQ+    FF  T   V  E    ++NL L     E +V +AL+  G      
Sbjct: 73  LRRKVGLVFQNPDDQFFGPT---VEEEVAFGLENLGLPEEEIEERVEEALELVGLEGLRD 129

Query: 335 ERCFSLS 341
              F+LS
Sbjct: 130 RSPFTLS 136


  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
   0.327    0.141    0.458 

Gapped
Lambda     K      H
   0.267   0.0658    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,806,313
Number of extensions: 265173
Number of successful extensions: 694
Number of sequences better than 10.0: 1
Number of HSP's gapped: 687
Number of HSP's successfully gapped: 11
Length of query: 365
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 270
Effective length of database: 4,210,882
Effective search space: 1136938140
Effective search space used: 1136938140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.3 bits)