RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780930|ref|YP_003065343.1| nodulation protein (outer
membrane efflux protein) [Candidatus Liberibacter asiaticus str.
psy62]
         (452 letters)



>gnl|CDD|31727 COG1538, TolC, Outer membrane protein [Cell envelope biogenesis,
           outer membrane / Intracellular trafficking and
           secretion].
          Length = 457

 Score =  232 bits (593), Expect = 1e-61
 Identities = 126/454 (27%), Positives = 226/454 (49%), Gaps = 23/454 (5%)

Query: 14  LLAGCTVGPEYTKPHMPLLPTQFSIGNSKNLINIDTLKWWESFNDTSLNKLVKIALQQNL 73
           LLAGC + P Y  P    +P   +   +          WWE+FND  LN+LV +AL  N 
Sbjct: 3   LLAGCALLPPYLAP--AAVPAALAAAAAAAAAAAT---WWEAFNDAQLNQLVNLALAANP 57

Query: 74  TILQATERINAAKENILSVRADLFPSSYASISH-----------RFIPNLKTNSTGQLDS 122
            +  A   + AA+  +   RA L P   AS S+               +  +   G   +
Sbjct: 58  DLRVAAAEVEAARAQLRIARAALLPQLSASASYTRQTLAGGPLSSTGTDRNSYGYGLSLA 117

Query: 123 DWKIDLFGQRRH-IESSLANLDSAYAQVDIAKLNVISKLIPSYIDARHFKERISIAHQIL 181
            W +DLFG+ R  + ++ A   +A AQ++ A+L++ +++  +Y D    +E++++A + L
Sbjct: 118 SWLLDLFGRVRANVRAAEAAAKAARAQLEAARLSLAAEVATAYFDLLAAQEQLALAEETL 177

Query: 182 DLYKKNIELSHLKFTQGATSKLSLVKLEAEIKSIESDIPTLEKSFRMNVHNISTLLGYPA 241
              ++ +EL+  ++  G  ++L +++ EA++ S  + +   +       + ++ LLG   
Sbjct: 178 AAAEEQLELAEKRYDAGLATRLDVLQAEAQLASARAQLAAAQAQLAQARNALARLLGLEP 237

Query: 242 TEFLHYMQKQSNNFQPNLYIPINIGIPADLIRNRPDIRYQEKKLADSVAKIGIAKSDLYP 301
            E L           P L   +  G+P++ +  RPDI   E +LA + A IG A++   P
Sbjct: 238 GELL---DAPEPEALPALPPVLPDGLPSEALARRPDILAAEAQLAAANANIGAARAAFLP 294

Query: 302 SLSLNGSIALTH---DNSFPGYNTHWSFGPKLYLPIFDKGKIKSNIRRAESSAQEQYITW 358
           +LSL  S   +       F   +  WS GP L LPIFD G++++ +R+AE+        +
Sbjct: 295 TLSLTASYGRSSTNLSGLFGSSSRSWSVGPGLSLPIFDGGRLRARVRQAEAQYDAALAQY 354

Query: 359 QETVLNAIKEVENALTSINEDKKIVTKLQHAVELHKKSMSLSMINYRQGRYSLLDILDIE 418
           ++TVL A +EV +AL ++    + +  L+ AVE  ++++ L+   Y+ G  +LLD+LD +
Sbjct: 355 EQTVLTARQEVADALAALEAALEQLQALRQAVEAAQEALELARERYQAGVRTLLDVLDAQ 414

Query: 419 RATAKVEVDLSIAKRQLAKSYVDLYIAIGSGYNP 452
           R   +    L  A+     + V+LY A+G G++ 
Sbjct: 415 RTLLQARQALLQARYDYLVALVNLYKALGGGWDE 448


>gnl|CDD|145461 pfam02321, OEP, Outer membrane efflux protein.  The OEP family
           (Outer membrane efflux protein) form trimeric channels
           that allow export of a variety of substrates in Gram
           negative bacteria. Each member of this family is
           composed of two repeats. The trimeric channel is
           composed of a 12 stranded all beta sheet barrel that
           spans the outer membrane, and a long all helical barrel
           that spans the periplasm.
          Length = 186

 Score = 85.6 bits (212), Expect = 3e-17
 Identities = 47/178 (26%), Positives = 86/178 (48%), Gaps = 2/178 (1%)

Query: 272 IRNRPDIRYQEKKLADSVAKIGIAKSDLYPSLSLNGSIALTHDNSFPGYNTH--WSFGPK 329
           + N PD++  E ++  + A I +AKS+  P LSL+G      +NS  G +     S G  
Sbjct: 9   LENNPDLKAAEAEIEAARANIKLAKSEFLPDLSLSGGYGYNGNNSNGGGDDPRNGSVGLG 68

Query: 330 LYLPIFDKGKIKSNIRRAESSAQEQYITWQETVLNAIKEVENALTSINEDKKIVTKLQHA 389
           L  P+FD GK ++ ++ A++  +      ++       EV  A  ++   K+ +   + A
Sbjct: 69  LSQPLFDGGKRRARVKAAKAQLEAAEAQLEQARRQLRLEVAQAYLNLLAAKEQLELAKQA 128

Query: 390 VELHKKSMSLSMINYRQGRYSLLDILDIERATAKVEVDLSIAKRQLAKSYVDLYIAIG 447
           +EL ++++ L+   Y  G  SLLD+L  E    +  ++L  A+  L  +   L   +G
Sbjct: 129 LELAEEALELAEARYEAGLISLLDVLQAEVELLEARLELLEAEADLELARAQLEYLLG 186



 Score = 79.5 bits (196), Expect = 2e-15
 Identities = 41/186 (22%), Positives = 89/186 (47%), Gaps = 8/186 (4%)

Query: 61  LNKLVKIALQQNLTILQATERINAAKENILSVRADLFPSSYASISHRFIPNLKTNSTGQL 120
           L++L+ +AL+ N  +  A   I AA+ NI   +++  P    S  + +  N         
Sbjct: 1   LDELLALALENNPDLKAAEAEIEAARANIKLAKSEFLPDLSLSGGYGYNGNNSNGGGDDP 60

Query: 121 DS-------DWKIDLFGQRRH-IESSLANLDSAYAQVDIAKLNVISKLIPSYIDARHFKE 172
            +          +   G+RR  ++++ A L++A AQ++ A+  +  ++  +Y++    KE
Sbjct: 61  RNGSVGLGLSQPLFDGGKRRARVKAAKAQLEAAEAQLEQARRQLRLEVAQAYLNLLAAKE 120

Query: 173 RISIAHQILDLYKKNIELSHLKFTQGATSKLSLVKLEAEIKSIESDIPTLEKSFRMNVHN 232
           ++ +A Q L+L ++ +EL+  ++  G  S L +++ E E+     ++   E    +    
Sbjct: 121 QLELAKQALELAEEALELAEARYEAGLISLLDVLQAEVELLEARLELLEAEADLELARAQ 180

Query: 233 ISTLLG 238
           +  LLG
Sbjct: 181 LEYLLG 186


>gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease  HII.
           Ribonuclease (RNase) H is classified into two families,
           type I (prokaryotic RNase HI, eukaryotic RNase H1 and
           viral RNase H) and type II (prokaryotic RNase HII and
           HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
           RNase H endonucleolytically hydrolyzes an RNA strand
           when it is annealed to a complementary DNA strand in the
           presence of divalent cations, in DNA replication or
           repair. Some archaeal RNase HII show broad divalent
           cation specificity. It is proposed that three of the
           four acidic residues at the active site are involved in
           metal binding and the fourth one involved in the
           catalytic process in archaea. Most archaeal genomes
           contain multiple RNase H genes. Despite a lack of
           evidence for homology from sequence comparisons, type I
           and type II RNase H share a common fold and similar
           steric configurations of the four acidic active-site
           residues, suggesting identical or very similar catalytic
           mechanisms. It appears that type I and type II RNases H
           also have overlapping functions in cells, as
           over-expression of Escherichia coli RNase HII can
           complement an RNase HI deletion phenotype in E. coli.
          Length = 204

 Score = 28.3 bits (64), Expect = 4.9
 Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 6/29 (20%)

Query: 422 AKVEVDLSIAKRQLAKSYVDLYIAIGSGY 450
           AKVE D  I   +L + Y D     GSGY
Sbjct: 147 AKVERDREI--EELKEEYGD----FGSGY 169


>gnl|CDD|144459 pfam00873, ACR_tran, AcrB/AcrD/AcrF family.  Members of this family
           are integral membrane proteins. Some are involved in
           drug resistance. AcrB cooperates with a membrane fusion
           protein, AcrA, and an outer membrane channel TolC. The
           structure shows the AcrB forms a homotrimer.
          Length = 1021

 Score = 27.6 bits (62), Expect = 8.1
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 324 WSFGPKLYLPIFDKGKIKSNIRRAESSAQEQYITWQETVLNAIK---EVENALT 374
           +   PK +LP  D+G   ++ +    ++ +Q     + V   +K   EVE+   
Sbjct: 545 FVRIPKEFLPEEDEGVFVTSAQLPPGASLDQTQRVLKQVEKILKEKPEVESVFA 598


  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
   0.317    0.133    0.376 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,116,945
Number of extensions: 260270
Number of successful extensions: 644
Number of sequences better than 10.0: 1
Number of HSP's gapped: 639
Number of HSP's successfully gapped: 16
Length of query: 452
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 355
Effective length of database: 4,167,664
Effective search space: 1479520720
Effective search space used: 1479520720
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 (21.7 bits)
S2: 59 (26.4 bits)