RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3
[Candidatus Liberibacter asiaticus str. psy62]
         (221 letters)



>gnl|CDD|30436 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
           structure and biogenesis].
          Length = 218

 Score =  243 bits (621), Expect = 4e-65
 Identities = 111/214 (51%), Positives = 138/214 (64%), Gaps = 3/214 (1%)

Query: 2   RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNV 61
             G +  K+GMT V++  G  +PVTV+ +    VV  +T + +GY AVQVGAG+ K K V
Sbjct: 1   MLGFLGYKVGMTHVFDERGISVPVTVIEVPPNVVVQVKTYETDGYRAVQVGAGDRKAKRV 60

Query: 62  SKPMRGFFSSVNVSPKKKLFEFRVQKDD--DLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119
           +KP+ G F+   V PK+ L EFRV   D  +   VG   +   F  G+LVDVTG+T GKG
Sbjct: 61  NKPLVGHFAKAGVKPKRHLAEFRVGGGDVAEKFEVGQEITVDVFKEGELVDVTGVTKGKG 120

Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179
           F G MKR  F G  A+HG S+SHR  GS G RQ PGRVFK KKMAG MG  RVTV+NLEV
Sbjct: 121 FQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEV 180

Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213
           V VD +  LILVKG VPGAKK   ++VR + K+ 
Sbjct: 181 VKVDVENNLILVKGAVPGAKK-RLVVVRPAVKAK 213


>gnl|CDD|38351 KOG3141, KOG3141, KOG3141, Mitochondrial/chloroplast ribosomal
           protein L3 [Translation, ribosomal structure and
           biogenesis].
          Length = 310

 Score =  229 bits (584), Expect = 6e-61
 Identities = 101/215 (46%), Positives = 132/215 (61%), Gaps = 3/215 (1%)

Query: 2   RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRT-LDKNGYMAVQVGAGEAKVKN 60
           R GV+ARKLGM  +++ +G RIPVT+L +D+  V+ + T   K GY AVQVG G  K K 
Sbjct: 62  RVGVIARKLGMMPLWDKDGERIPVTILQVDDNHVIKYITPEAKGGYFAVQVGYGTVKPKK 121

Query: 61  VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
           ++K   G F S  V PK+ L EFRV  ++ LLP G+     +F  GQ VDVTG TIGKGF
Sbjct: 122 LTKAELGHFRSAGVPPKRHLREFRV-TEEALLPPGTPLFARHFKPGQYVDVTGKTIGKGF 180

Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
            G MKRH F G  A+HG S SHR  GS G    PGRV+  +KM G MG    T+K L+V 
Sbjct: 181 QGVMKRHGFKGGPASHGTSKSHRRPGSIGQGTTPGRVWPGRKMPGHMGNEWRTIKGLKVW 240

Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVN 215
            +D +  +I VKG VPG  K + + ++D+    V+
Sbjct: 241 KIDTELNVIWVKGSVPG-PKGNLVKIKDAILPTVD 274


>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated.
          Length = 207

 Score =  190 bits (484), Expect = 3e-49
 Identities = 88/201 (43%), Positives = 126/201 (62%), Gaps = 2/201 (0%)

Query: 1   MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60
           M  G++  K+GMT +++  G  IPVT+L +  C +   +TL  +GY A+Q+G  +   K 
Sbjct: 1   MSIGLLGTKIGMTQIFDETGNAIPVTILKVGPCVITQIKTLTTDGYNAIQIGYKQVSTKK 60

Query: 61  VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
           ++KP  G     NV P K L EFRV+  ++   VG   +   F+VGQLV+V+G +IGKGF
Sbjct: 61  LTKPQLGHLQKSNVPPLKYLKEFRVKSSEEF-EVGQPLTVDAFSVGQLVNVSGKSIGKGF 119

Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
           +G  KRHNF     THG S +HR+ GS G    PGRV+  KKMAGR+G  +VT+KNL+++
Sbjct: 120 AGLQKRHNFSRGPMTHG-SKNHRAPGSIGAGTTPGRVYPGKKMAGRLGNKKVTIKNLKIL 178

Query: 181 SVDDKRGLILVKGCVPGAKKN 201
            VD +  L+++KG VPG   N
Sbjct: 179 KVDSENNLLVLKGSVPGKPGN 199


>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3. 
          Length = 199

 Score =  175 bits (445), Expect = 9e-45
 Identities = 79/195 (40%), Positives = 105/195 (53%), Gaps = 5/195 (2%)

Query: 9   KLGMTCVY-NIEGRRIPVTVLHLDNCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPM 65
           K GMT ++   +G   PVTV+ +    VV  +T ++  +GY A+QVG    K   V K +
Sbjct: 1   KAGMTHIFTEKKGVLEPVTVIEVPPMVVVQVKTYEETNDGYKAIQVGLESIKKYRVVKRV 60

Query: 66  RGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMK 125
            G        PK  + EFRV   ++  P  ++     F  G+ VDVTG+T GKGF G MK
Sbjct: 61  LGHTQKRGTPPKAHVMEFRVNGGEEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVMK 120

Query: 126 RHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDK 185
           R  F  L   HG    HR  GS G    PGRVF   KMAG+MG +  T +NL++  +D +
Sbjct: 121 RWGFKRLPRKHGRGY-HRKPGSIG-AWHPGRVFPGVKMAGQMGNHHRTEQNLKIYRIDQE 178

Query: 186 RGLILVKGCVPGAKK 200
             L+LVKG VPG KK
Sbjct: 179 NNLLLVKGSVPGPKK 193


>gnl|CDD|40019 KOG4822, KOG4822, KOG4822, Predicted nuclear membrane protein
           involved in mRNA transport and sex determination via
           splicing modulation [RNA processing and modification,
           Signal transduction mechanisms].
          Length = 1906

 Score = 28.2 bits (62), Expect = 2.1
 Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 54  GEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTG 113
           GE+K K +  P    ++     P     E      + L+  GS  S S    G +V   G
Sbjct: 24  GESKFKRLCNPF--LYTPSAPYP----LEVEAVVTNHLVVRGSYRSLSLIVYGNIVKDLG 77

Query: 114 M 114
            
Sbjct: 78  Q 78


>gnl|CDD|110448 pfam01446, Rep_1, Replication protein.  Replication proteins (rep)
           are involved in plasmid replication. The Rep protein
           binds to the plasmid DNA and nicks it at the double
           strand origin (dso) of replication. The 3'-hydroxyl end
           created is extended by the host DNA replicase, and the
           5' end is displaced during synthesis. At the end of one
           replication round, Rep introduces a second single
           stranded break at the dso and ligates the ssDNA
           extremities generating one double-stranded plasmid and
           one circular ssDNA form. Complementary strand synthesis
           of the circular ssDNA is usually initiated at the
           single-stranded origin by the host RNA polymerase.
          Length = 232

 Score = 26.9 bits (60), Expect = 4.9
 Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 19/55 (34%)

Query: 57  KVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDD-------LLPVGSVFSPSYFT 104
           + K V K + G+  S  V+  K         D         LL V     PSYFT
Sbjct: 54  QYKKVKKNLLGYIRSTEVTVNK--------DDGSYHPHFHVLLMV----KPSYFT 96


>gnl|CDD|38005 KOG2794, KOG2794, KOG2794, Delta-aminolevulinic acid dehydratase
           [Coenzyme transport and metabolism].
          Length = 340

 Score = 26.1 bits (57), Expect = 9.2
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 65  MRGFFSSVNVSPKKKLFE-FRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFS 121
           +R +    N+SP   ++  F  + +DD  P+ S+       V +L +     + KG  
Sbjct: 27  LRAWQQETNISPANLIYPLFIHEGEDDFTPIDSMPGIYRLGVNRLKEELAPLVAKGLR 84


>gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA
           helicase [RNA processing and modification].
          Length = 1042

 Score = 25.8 bits (56), Expect = 9.2
 Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 1/41 (2%)

Query: 16  YNIEGRRIPVTVLHL-DNCQVVVHRTLDKNGYMAVQVGAGE 55
           + I GR  PV +++     +  V   + +   + +    G+
Sbjct: 525 FTIPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGD 565


  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
   0.321    0.137    0.405 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,581,360
Number of extensions: 129431
Number of successful extensions: 267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 256
Number of HSP's successfully gapped: 12
Length of query: 221
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,318,927
Effective search space: 565779437
Effective search space used: 565779437
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 (21.8 bits)
S2: 55 (25.0 bits)