RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780647|ref|YP_003065060.1| 50S ribosomal protein L27
[Candidatus Liberibacter asiaticus str. psy62]
         (90 letters)



>gnl|CDD|180080 PRK05435, rpmA, 50S ribosomal protein L27; Validated.
          Length = 82

 Score =  147 bits (374), Expect = 6e-37
 Identities = 55/83 (66%), Positives = 70/83 (84%), Gaps = 1/83 (1%)

Query: 1  MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIY 60
          MAHKK GGST+NGRDS  +RLG+K+ GGQ V AGNII+RQRGT++HPG+NVG GKDHT++
Sbjct: 1  MAHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLF 60

Query: 61 ALVDGHVRFFKKFSKGRAYVSVI 83
          ALVDG V+ F++  + R YVSV+
Sbjct: 61 ALVDGVVK-FERKGRNRKYVSVV 82


>gnl|CDD|161685 TIGR00062, L27, ribosomal protein L27.  Eubacterial, chloroplast,
          and mitochondrial. Mitochondrial members have an
          additional C-terminal domain.
          Length = 83

 Score =  115 bits (290), Expect = 2e-27
 Identities = 52/83 (62%), Positives = 68/83 (81%)

Query: 1  MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIY 60
          MA KK  GST+NGRDS  +RLG+K++GGQ V AG+II+RQRGT++HPG NVG+GKDHT++
Sbjct: 1  MATKKGVGSTKNGRDSEAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLF 60

Query: 61 ALVDGHVRFFKKFSKGRAYVSVI 83
          AL DG V+F KK  + R +VSV+
Sbjct: 61 ALSDGVVKFEKKGKRSRKFVSVV 83


>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
            beta/beta'; Provisional.
          Length = 2836

 Score = 27.7 bits (61), Expect = 0.67
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 12/69 (17%)

Query: 28   GQSVIAGNIIIRQ-RGTRYHPGLNVGLG-----------KDHTIYALVDGHVRFFKKFSK 75
            GQ V AG++I R  R +     +  GL            K+H I + +DG+V F +K  +
Sbjct: 2531 GQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRR 2590

Query: 76   GRAYVSVIP 84
            G+  + + P
Sbjct: 2591 GKRSILIKP 2599


>gnl|CDD|163268 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase. 
            Members of this protein family are
            L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
            product of the LYS2 gene. It is also called
            alpha-aminoadipate reductase. In fungi, lysine is
            synthesized via aminoadipate. Currently, all members of
            this family are fungal.
          Length = 1389

 Score = 27.3 bits (61), Expect = 0.86
 Identities = 24/81 (29%), Positives = 29/81 (35%), Gaps = 11/81 (13%)

Query: 15   DSAGQRLGLKKSGGQSVIAGNIIIRQ------RGTRYHPGLNVGLGKDHTIYALVDGHVR 68
            D  G   GL    GQS      IIR+      RG    PG   G  K        D    
Sbjct: 1138 DLMGSSKGLGTGYGQSKWVAEYIIREAGKRGLRGCIVRPGYVTGDSKTGATNT--DD--- 1192

Query: 69   FFKKFSKGRAYVSVIPKIEDT 89
            F  +  KG   + +IP I +T
Sbjct: 1193 FLLRMLKGCIQLGLIPNINNT 1213


>gnl|CDD|148939 pfam07596, SBP_bac_10, Protein of unknown function (DUF1559).  A
           large family of paralogous proteins apparently unique to
           planctomycetes.
          Length = 263

 Score = 24.7 bits (54), Expect = 5.8
 Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 11/67 (16%)

Query: 6   SGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTR-YHPGL-NVGLGKDHTIYALV 63
           SG S  +G ++     G   +       G+     RG    HPG  N  +          
Sbjct: 199 SGPSYGSGTNTTTPTNGSGPAPSGPGGGGDNGNANRGFGSAHPGGVNFLMA--------- 249

Query: 64  DGHVRFF 70
           DG VRF 
Sbjct: 250 DGSVRFI 256


>gnl|CDD|180950 PRK07373, PRK07373, DNA polymerase III subunit alpha; Reviewed.
          Length = 449

 Score = 24.6 bits (54), Expect = 6.2
 Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)

Query: 37 IIRQRGTRYHPGLNVGLGKDHTIYALVDGHVR---FFKKFSKGRAYVS 81
          II +R     P  ++G+ +DH  + L +G +    F K  S   AYV+
Sbjct: 4  IISRRSLGVQPVYDIGVAQDHN-FLLANGLIASNCFNKSHSTAYAYVT 50


>gnl|CDD|184527 PRK14131, PRK14131, N-acetylneuraminic acid mutarotase;
           Provisional.
          Length = 376

 Score = 24.2 bits (53), Expect = 6.9
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 46  HPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAY-VSV 82
           H GL      +  IYALV+G  +   +  +G AY VSV
Sbjct: 305 HEGLKKSWSDE--IYALVNGKWQKVGELPQGLAYGVSV 340


>gnl|CDD|182544 PRK10555, PRK10555, aminoglycoside/multidrug efflux system;
           Provisional.
          Length = 1037

 Score = 24.0 bits (52), Expect = 7.7
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 54  GKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKI 86
            K  T +A+++   + F K  + R   S  P I
Sbjct: 638 SKTGTSFAIIERATKAFNKIKEARVIASSPPAI 670


>gnl|CDD|183268 PRK11667, PRK11667, hypothetical protein; Provisional.
          Length = 163

 Score = 23.9 bits (52), Expect = 9.1
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 5  KSGGSTQNGRDSAGQRLGLKKSGGQSVIAGN 35
             GS+Q G  S     GL   GGQ++ AG+
Sbjct: 41 GQAGSSQQGGWSLSSLTGLLSGGGQALSAGS 71


>gnl|CDD|151457 pfam11010, DUF2848, Protein of unknown function (DUF2848).  This
          bacterial family of proteins has no known function.
          Length = 194

 Score = 23.7 bits (52), Expect = 9.5
 Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 5/22 (22%)

Query: 37 IIRQRGTRYHPGLNVGLGKDHT 58
          +IR  G        +G+G DHT
Sbjct: 61 LIRHEGRLL-----LGVGSDHT 77


>gnl|CDD|161766 TIGR00211, glyS, glycyl-tRNA synthetase, tetrameric type, beta
           subunit.  The glycyl-tRNA synthetases differ even among
           the eubacteria in oligomeric structure. In Escherichia
           coli and most others, it is a heterodimer of two alpha
           chains and two beta chains, encoded by tandem genes. The
           genes are similar, but fused, in Chlamydia trachomatis.
           By contrast, the glycyl-tRNA synthetases of Thermus
           thermophilus and of archaea and eukaryotes differ
           considerably; they are homodimeric, mutually similar,
           and not detected by this model.
          Length = 691

 Score = 24.0 bits (52), Expect = 9.7
 Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 3/39 (7%)

Query: 48  GLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKI 86
           G+NV   +D  I+    G   F +K  +G+    ++P +
Sbjct: 99  GINV---EDAEIFQTDKGEWLFVRKIHEGQPTKDLLPPL 134


>gnl|CDD|132166 TIGR03122, one_C_dehyd_C, formylmethanofuran dehydrogenase subunit
           C.  Members of this largely archaeal protein family are
           subunit C of the formylmethanofuran dehydrogenase.
           Nomenclature in some bacteria may reflect inclusion of
           the formyltransferase described by TIGR03119 as part of
           the complex, and therefore call this protein
           formyltransferase/hydrolase complex Fhc subunit C. Note
           that this model does not distinguish tungsten (FwdC)
           from molybdenum-containing (FmdC) forms of this enzyme.
          Length = 260

 Score = 23.8 bits (52), Expect = 9.8
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 16  SAGQRLGLKKSGGQSVIAGN 35
           +AG  LG +  GG+ +I GN
Sbjct: 152 NAGDYLGERMRGGEILIEGN 171


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.318    0.137    0.397 

Gapped
Lambda     K      H
   0.267   0.0722    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,463,075
Number of extensions: 80486
Number of successful extensions: 134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 133
Number of HSP's successfully gapped: 17
Length of query: 90
Length of database: 5,994,473
Length adjustment: 59
Effective length of query: 31
Effective length of database: 4,719,601
Effective search space: 146307631
Effective search space used: 146307631
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: 50 (23.1 bits)