RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780258|ref|YP_003064671.1| 50S ribosomal protein L2
[Candidatus Liberibacter asiaticus str. psy62]
         (278 letters)



>gnl|CDD|30439 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
           structure and biogenesis].
          Length = 275

 Score =  355 bits (912), Expect = 8e-99
 Identities = 158/276 (57%), Positives = 194/276 (70%), Gaps = 2/276 (0%)

Query: 1   MALKNFNPDTSGRRQLVMVDRNSLHSGKPIKSLTRGLCSKGGRNNTGRVTMRFRGGGHKN 60
           MA+K + P T GRR +V+VD   L  GKP KSL   L    GRNN GR+T+R RGGGHK 
Sbjct: 1   MAIKKYKPTTPGRRHMVVVDFAELTKGKPEKSLMGKLIKSQGRNNRGRITVRHRGGGHKR 60

Query: 61  RYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISSD 120
           RYRL+DFKR + G+ G V+ +EYDPNR+A IAL+ Y +G   YILAP+ L VGD + S  
Sbjct: 61  RYRLIDFKRNKDGIPGKVEDIEYDPNRSAPIALVVYEDGEKRYILAPEGLKVGDVIESGK 120

Query: 121 SAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSSG 180
            A D+KPGNA+PL  IP G+IVHNVE+KPG GGQ++RSAG+YA++V ++ +  ++RL SG
Sbjct: 121 DA-DIKPGNALPLGNIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGKEGNYVIVRLPSG 179

Query: 181 EMRFVHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMNPVDHPHGGGEGKT 240
           EMR V S C A+IG V+N  H      KAGRAR  G R  VRGVAMNPVDHPHGGGEG+ 
Sbjct: 180 EMRKVLSECRATIGVVANGGHILKPLGKAGRARHKGKRPTVRGVAMNPVDHPHGGGEGQH 239

Query: 241 SGGRNPCSPWGKLTKGKRTR-SNKSTDVFIARSRHK 275
            GG+ P  PWGK T GK+TR + K T  FI R R K
Sbjct: 240 PGGKPPTVPWGKPTPGKKTRIAAKRTGKFIVRRRKK 275


>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
          Length = 273

 Score =  316 bits (812), Expect = 5e-87
 Identities = 128/276 (46%), Positives = 174/276 (63%), Gaps = 7/276 (2%)

Query: 1   MALKNFNPDTSGRRQLVMVDRNSLHSGKPIKSLTRGLCSKG-GRNNTGRVTMRFRGGGHK 59
           MA++ +   T G R   +   +      P K+L  G    G GRNN G +T R RGGGHK
Sbjct: 1   MAIRLYKTYTPGTRNRSV---DEQVKSNPRKNLIYGQHRCGKGRNNRGIITARHRGGGHK 57

Query: 60  NRYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVISS 119
             YR +DF+R +  + G +  +EYDPNR A+I LI Y +G   YIL P+ L +GD ++S 
Sbjct: 58  RLYRKIDFRRNKKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILHPRGLKIGDTIVSG 117

Query: 120 DSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSS 179
             A  +K GNA+PL  IP+G+ +HN+E+ PGKGGQ++R+AG+ A+L+ ++   A L+L S
Sbjct: 118 TEA-PIKIGNALPLTNIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAKEGKSATLKLPS 176

Query: 180 GEMRFVHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMNPVDHPHGGGEGK 239
           GE+R +  +C A+IG V N D +N +  KAG  RWLG R  VRGV MNPVDHPHGGGEG+
Sbjct: 177 GEVRLISKNCSATIGQVGNVDVNNKSLGKAGSKRWLGKRPKVRGVVMNPVDHPHGGGEGR 236

Query: 240 TSGGRN-PCSPWGKLTKGKRTR-SNKSTDVFIARSR 273
              GR  P +PWGK   G++TR   K +D  I R R
Sbjct: 237 APIGRKKPVTPWGKPALGRKTRKRKKYSDNLILRRR 272


>gnl|CDD|146530 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
           domain. 
          Length = 130

 Score =  204 bits (521), Expect = 2e-53
 Identities = 80/130 (61%), Positives = 102/130 (78%), Gaps = 1/130 (0%)

Query: 125 VKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDRSRALLRLSSGEMRF 184
           +K GNA+PL+ IPVG+++HN+E+ PGKGGQ++RSAG+YA+++ ++     L+L SGE+R 
Sbjct: 1   IKIGNALPLKNIPVGTVIHNIELIPGKGGQLARSAGTYAQILAKEGKYVTLKLPSGEIRL 60

Query: 185 VHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMNPVDHPHGGGEGKTSGGR 244
           V S+C A+IG VSN DH+N    KAGR RWLG R  VRGVAMNPVDHPHGGGEG+TS GR
Sbjct: 61  VSSNCRATIGVVSNIDHNNKVLGKAGRNRWLGKRPTVRGVAMNPVDHPHGGGEGRTSIGR 120

Query: 245 N-PCSPWGKL 253
             P SPWGK 
Sbjct: 121 PPPVSPWGKP 130


>gnl|CDD|35659 KOG0438, KOG0438, KOG0438, Mitochondrial/chloroplast ribosomal
           protein L2 [Translation, ribosomal structure and
           biogenesis].
          Length = 312

 Score =  196 bits (500), Expect = 5e-51
 Identities = 112/268 (41%), Positives = 159/268 (59%), Gaps = 11/268 (4%)

Query: 1   MALKNFNPDTSGRRQLVMVDRNSLHSGKPIKSLTRGLCSKG-GRNNTGRVTMRFRGGGHK 59
             +    P T   R   ++ +  L    P + L   L   G GR+ TGR+ +R  GGGHK
Sbjct: 23  ARITVLKPGTPSLR-NGLLQQPDLKKSTPSRPLVESLKINGLGRDETGRIVVRHIGGGHK 81

Query: 60  NRYRLVDFKRGEYGLEGV-----VKRLEYDPNRTAFIALISYSNGSLAYILAPQRLSVGD 114
            RYR++DF R     +G      V  +EYDP R+A IAL++   G L YILA + L  GD
Sbjct: 82  QRYRMIDFARPRPIEQGTTTEERVIEIEYDPGRSAKIALVAGGTGELRYILATEGLKAGD 141

Query: 115 KVISSD----SAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQISRSAGSYARLVERDR 170
            ++SS      AV  K GNA+PL  +PVG+++HNVE+ PG+  Q +R+AG+ A ++ +  
Sbjct: 142 TILSSRKIPFMAVKGKEGNALPLGDLPVGTLIHNVEITPGRSAQFARAAGTSATILAKAG 201

Query: 171 SRALLRLSSGEMRFVHSSCMASIGAVSNQDHSNVNHAKAGRARWLGMRSHVRGVAMNPVD 230
             A+++L S   R V  +C+A++G VSN DH++    KAGR+RWLG R  VRGV M+ +D
Sbjct: 202 KFAIVQLPSKRERSVLRTCVATVGRVSNIDHNHRILGKAGRSRWLGKRPQVRGVLMSGLD 261

Query: 231 HPHGGGEGKTSGGRNPCSPWGKLTKGKR 258
           HP GGG+G+  G + P +PWGK  KG R
Sbjct: 262 HPKGGGKGRKIGRKKPVTPWGKPAKGLR 289


>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding domain.
           
          Length = 77

 Score =  119 bits (302), Expect = 6e-28
 Identities = 45/77 (58%), Positives = 57/77 (74%)

Query: 42  GRNNTGRVTMRFRGGGHKNRYRLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYSNGSL 101
           GRNN GR+T+R RGGGHK  YRL+DFKR +  ++G V  +EYDPNR+A IAL+ Y +G  
Sbjct: 1   GRNNPGRITVRHRGGGHKRLYRLIDFKRNKGNIKGKVIDIEYDPNRSAPIALVKYEDGEK 60

Query: 102 AYILAPQRLSVGDKVIS 118
            YILAP+ L VGD + S
Sbjct: 61  RYILAPEGLKVGDTIES 77


>gnl|CDD|37520 KOG2309, KOG2309, KOG2309, 60s ribosomal protein L2/L8
           [Translation, ribosomal structure and biogenesis].
          Length = 248

 Score = 96.6 bits (240), Expect = 8e-21
 Identities = 72/208 (34%), Positives = 107/208 (51%), Gaps = 19/208 (9%)

Query: 47  GRVTMRFRGGG-----HKNRY----RLVDFKRGEYGLEGVVKRLEYDPNRTAFIALISYS 97
           GRV    R  G     HK+R     R +D+      ++GVVK + +DP R A +A + + 
Sbjct: 2   GRVIRAQRKAGSIFKAHKHRKGAAKRTLDYAERHGYIKGVVKDIIHDPGRGAPLAKVVFR 61

Query: 98  NGSL--AYILAPQRLSVGDKVISSDSAVDVKPGNAMPLRFIPVGSIVHNVEMKPGKGGQI 155
           +        +A + +  G  V     A  +  GN +P+  +P G+IV NVE KPG  G +
Sbjct: 62  DYKKDKELFIAAEGMYTGQFVYCGKKA-QLNIGNVLPVGSMPEGTIVCNVEEKPGDRGAL 120

Query: 156 SRSAGSYARLV--ERDRSRALLRLSSGEMRFVHSSCMASIGAVSNQDHSNVNHAKAGRAR 213
           +R++G+YA ++    D  +  ++L SG  + V S+C A IG V+    ++    KAGRA 
Sbjct: 121 ARASGNYAIVIAHNPDTKKTRIKLPSGAKKVVQSACRAMIGVVAGGGRTDKPLLKAGRAY 180

Query: 214 WL-----GMRSHVRGVAMNPVDHPHGGG 236
                       VRGVAMNPV+HPHGGG
Sbjct: 181 HKYKAKRNCWPRVRGVAMNPVEHPHGGG 208


>gnl|CDD|114453 pfam05728, UPF0227, Uncharacterized protein family (UPF0227).
           Despite being classed as uncharacterized proteins, the
           members of this family are almost certainly enzymes that
           are distantly related to the pfam00561.
          Length = 187

 Score = 28.9 bits (65), Expect = 1.4
 Identities = 14/40 (35%), Positives = 16/40 (40%), Gaps = 2/40 (5%)

Query: 212 ARWLGMRSHVRGVAMNPVDHPHGGGEGKTSGGRNPCSPWG 251
           A WLG R  +R V  NP   P+    GK   G       G
Sbjct: 73  ATWLGFRCGLRQVLFNPAVRPYENLAGKL--GEQANPYTG 110


>gnl|CDD|145959 pfam03085, RAP-1, Rhoptry-associated protein 1 (RAP-1).  Members of
           this family are found in Babesia species. Though not in
           this Pfam family, rhoptry-associated proteins are also
           found in Plasmodium falciparum. Indeed, animal infection
           with Babesia may produce a pattern similar to human
           malaria. Rhoptry organelles form part of the apical
           complex in apicomplexan parasites. Rhoptry-associated
           proteins are antigenic, and generate partially
           protective immune responses in infected mammals. Thus
           RAPs are among the targeted vaccine antigens for
           babesial (and malarial) parasites. However, RAP-1
           proteins are encoded by by a multigene family; thus
           RAP-1 proteins are polymorphic, with B and T cell
           epitopes that are conserved among strains, but not
           across species. Antibodies to Babesia RAP-1 may also be
           helpful in the serological detection of Babesia
           infections.
          Length = 251

 Score = 27.7 bits (62), Expect = 3.8
 Identities = 15/54 (27%), Positives = 17/54 (31%), Gaps = 9/54 (16%)

Query: 39  SKGGRNNTGRVTMRFRGGGHKNRYRL---------VDFKRGEYGLEGVVKRLEY 83
           S   +N   R  MRFR GG    Y           V        LE  V +  Y
Sbjct: 102 SNPAKNRWKRFWMRFRKGGRYGAYHDFILNLLKKNVVLDADNTDLEAFVNKYLY 155


>gnl|CDD|133155 cd05488, Proteinase_A_fungi, Fungal Proteinase A , aspartic
           proteinase superfamily.  Fungal Proteinase A, a
           proteolytic enzyme distributed among a variety of
           organisms, is a member of the aspartic proteinase
           superfamily. In Saccharomyces cerevisiae, targeted to
           the vacuole as a zymogen, activation of proteinases A at
           acidic pH can occur by two different pathways: a
           one-step process to release mature proteinase A,
           involving the intervention of proteinase B, or a
           step-wise pathway via the auto-activation product known
           as pseudo-proteinase A. Once active, S. cerevisiae
           proteinase A is essential to the activities of other
           yeast vacuolar hydrolases, including proteinase B and
           carboxypeptidase Y. The mature enzyme is bilobal, with
           each lobe providing one of the two catalytically
           essential aspartic acid residues in the active site. The
           crystal structure of free proteinase A shows that flap
           loop is atypically pointing directly into the S(1)
           pocket of the enzyme.  Proteinase A preferentially
           hydrolyzes hydrophobic residues such as Phe, Leu or Glu
           at the P1 position and Phe, Ile, Leu or Ala at P1'.
           Moreover, the enzyme is inhibited by IA3, a natural and
           highly specific inhibitor produced by S. cerevisiae.
           This family of aspartate proteases is classified by
           MEROPS as the peptidase family A1 (pepsin A, clan AA).
          Length = 320

 Score = 26.6 bits (59), Expect = 8.2
 Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 83  YDPNRTAFIALISYSNGSLAYILAPQRLSVGDKVI 117
           Y  N T F   I Y +GSL   ++   LS+GD  I
Sbjct: 61  YKANGTEFK--IQYGSGSLEGFVSQDTLSIGDLTI 93


  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    0.134    0.396 

Gapped
Lambda     K      H
   0.267   0.0684    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,237,213
Number of extensions: 163955
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 11
Length of query: 278
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 185
Effective length of database: 4,254,100
Effective search space: 787008500
Effective search space used: 787008500
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: 57 (25.8 bits)