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)