RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P
[Candidatus Liberibacter asiaticus str. psy62]
         (126 letters)



>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
           protein L7/L12 refers to the large ribosomal subunit
           proteins L7 and L12, which are identical except that L7
           is acetylated at the N terminus. It is a component of
           the L7/L12 stalk, which is located at the surface of the
           ribosome. The stalk base consists of a portion of the
           23S rRNA and ribosomal proteins L11 and L10. An extended
           C-terminal helix of L10 provides the binding site for
           L7/L12. L7/L12 consists of two domains joined by a
           flexible hinge, with the helical N-terminal domain (NTD)
           forming pairs of homodimers that bind to the extended
           helix of L10. It is the only multimeric ribosomal
           component, with either four or six copies per ribosome
           that occur as two or three dimers bound to the L10
           helix. L7/L12 is the only ribosomal protein that does
           not interact directly with rRNA, but instead has
           indirect interactions through L10. The globular
           C-terminal domains of L7/L12 are highly mobile. They are
           exposed to the cytoplasm and contain binding sites for
           other molecules. Initiation factors, elongation factors,
           and release factors are known to interact with the
           L7/L12 stalk during their GTP-dependent cycles. The
           binding site for the factors EF-Tu and EF-G comprises
           L7/L12, L10, L11, the L11-binding region of 23S rRNA,
           and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
           has minimal effect on factor binding and it has been
           proposed that L7/L12 induces the catalytically active
           conformation of EF-Tu and EF-G, thereby stimulating the
           GTPase activity of both factors. In eukaryotes, the
           proteins that perform the equivalent function to L7/L12
           are called P1 and P2, which do not share sequence
           similarity with L7/L12. However, a bacterial L7/L12
           homolog is found in some eukaryotes, in mitochondria and
           chloroplasts. In archaea, the protein equivalent to
           L7/L12 is called aL12 or L12p, but it is closer in
           sequence to P1 and P2 than to L7/L12..
          Length = 127

 Score =  130 bits (330), Expect = 7e-32
 Identities = 81/127 (63%), Positives = 96/127 (75%), Gaps = 5/127 (3%)

Query: 3   NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAAS----EKTEF 58
            +E IVE L  LTL+EAAEL K LE+++GVSASA  +  A  A  A +AA+    EKTEF
Sbjct: 2   KVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAPAAAAAAAAEAEEKTEF 61

Query: 59  EVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLED 118
           +VVL+ F    KKIAVIKEVR IT LGLKEAK+LVESAPK LK G+SK+EA E+KKKLE+
Sbjct: 62  DVVLESFGA-AKKIAVIKEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEE 120

Query: 119 AGATVEL 125
           AGA VEL
Sbjct: 121 AGAKVEL 127


>gnl|CDD|177022 CHL00083, rpl12, ribosomal protein L12.
          Length = 131

 Score =  118 bits (298), Expect = 4e-28
 Identities = 71/131 (54%), Positives = 95/131 (72%), Gaps = 6/131 (4%)

Query: 1   MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPV-----SVVAPVAAEAGSAASEK 55
            + I  I+E+L SLTL+EAAEL K++E+ +GV ASAPV     S  A  AA+A     EK
Sbjct: 2   STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEK 61

Query: 56  TEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKK 115
           TEF+V+L+     K+ IAV+K VR++T LGLKEAKELVES PK++K G+SK+EA E KK+
Sbjct: 62  TEFDVILEEVPADKR-IAVLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQ 120

Query: 116 LEDAGATVELR 126
           LE+AGA V ++
Sbjct: 121 LEEAGAKVIIK 131


>gnl|CDD|30571 COG0222, RplL, Ribosomal protein L7/L12 [Translation, ribosomal
           structure and biogenesis].
          Length = 124

 Score =   99 bits (249), Expect = 1e-22
 Identities = 75/126 (59%), Positives = 93/126 (73%), Gaps = 3/126 (2%)

Query: 1   MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEV 60
               E I+E L  LT++E +EL K LE+++GV+A+APV+  A  AA A  AA EKTEF+V
Sbjct: 2   ALTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAGAA-AAEAAEEKTEFDV 60

Query: 61  VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAG 120
           VLK      KKIAVIK VR +T LGLKEAK+LVE APK LK G+SK+EA E+KKKLE+AG
Sbjct: 61  VLKSAGG--KKIAVIKVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAG 118

Query: 121 ATVELR 126
           A VEL+
Sbjct: 119 AKVELK 124


>gnl|CDD|36927 KOG1715, KOG1715, KOG1715, Mitochondrial/chloroplast ribosomal
           protein L12 [Translation, ribosomal structure and
           biogenesis].
          Length = 187

 Score = 91.2 bits (226), Expect = 7e-20
 Identities = 62/130 (47%), Positives = 82/130 (63%), Gaps = 7/130 (5%)

Query: 2   SNIESIVEKLSSLTLIEAAELSKRLEKEWGVS------ASAPVSVVAPVAAEAGSAASEK 55
             I  IV+++SSLTL+E ++L   L+K+  +       A+A  +           A  EK
Sbjct: 58  PKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDAGGAEEEAKKEK 117

Query: 56  TEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKK 115
           T F+V L+ FD    KI VIKEVRA+T LGLKEAK+LVE APK LK G++K+EA E+K+K
Sbjct: 118 TTFDVKLEKFD-ASSKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEK 176

Query: 116 LEDAGATVEL 125
           LE AGA V L
Sbjct: 177 LEAAGAKVVL 186


>gnl|CDD|144215 pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal
           domain. 
          Length = 68

 Score = 88.7 bits (221), Expect = 4e-19
 Identities = 48/69 (69%), Positives = 55/69 (79%), Gaps = 2/69 (2%)

Query: 57  EFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKL 116
           EF+VVL    D  KKIAVIK VR IT LGLKEAK+LVE APK +K G+SK+EA E+KKKL
Sbjct: 1   EFDVVLTSAGD--KKIAVIKVVREITGLGLKEAKDLVEGAPKVIKEGVSKEEAEEIKKKL 58

Query: 117 EDAGATVEL 125
           E+AGA VEL
Sbjct: 59  EEAGAKVEL 67


>gnl|CDD|34618 COG5013, NarG, Nitrate reductase alpha subunit [Energy production and
            conversion].
          Length = 1227

 Score = 25.7 bits (56), Expect = 4.1
 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 18   EAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDD-------PKK 70
            E  EL+K    + GV+   P    A  AAE   A S +T  +V +K +            
Sbjct: 919  EYDELAKLNGTKAGVAKGRPRIDTAIDAAEVILALSPETNGQVAVKAWAALEEITGRDHT 978

Query: 71   KIAVIKEVRAITDLGLKEAKELVESAP 97
             +A+ KE   I    ++     + S+P
Sbjct: 979  HLALNKEDEKIRFRDIQAQPRKIISSP 1005


>gnl|CDD|37077 KOG1866, KOG1866, KOG1866, Ubiquitin carboxyl-terminal hydrolase
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 944

 Score = 25.3 bits (55), Expect = 4.1
 Identities = 8/31 (25%), Positives = 15/31 (48%)

Query: 1  MSNIESIVEKLSSLTLIEAAELSKRLEKEWG 31
          + N++  V+ L +L  +  A  S +   EW 
Sbjct: 52 VYNLKRSVDCLMTLYYMFKATTSCQALYEWE 82


>gnl|CDD|37247 KOG2036, KOG2036, KOG2036, Predicted P-loop ATPase fused to an
           acetyltransferase [General function prediction only].
          Length = 1011

 Score = 24.9 bits (54), Expect = 6.7
 Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 13/70 (18%)

Query: 4   IESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAA-------EAGSAASEKT 56
            ++IVEK    T+   A   +      G SA+  +S+   VA         + S  + KT
Sbjct: 266 FDAIVEKTLRSTVSLTASRGR------GKSAALGLSIAGAVAFGYSNIYVTSPSPENLKT 319

Query: 57  EFEVVLKGFD 66
            FE V KGFD
Sbjct: 320 LFEFVFKGFD 329


>gnl|CDD|110511 pfam01514, YscJ_FliF, Secretory protein of YscJ/FliF family.  This
           family includes proteins that are related to the YscJ
           lipoprotein, and the amino terminus of FliF, the
           flageller M-ring protein. The members of the YscJ family
           are thought to be involved in secretion of several
           proteins. The FliF protein ring is thought to be part of
           the export apparatus for flageller proteins, based on
           the similarity to YscJ proteins.
          Length = 206

 Score = 24.6 bits (54), Expect = 8.1
 Identities = 11/21 (52%), Positives = 14/21 (66%)

Query: 100 LKTGLSKDEANEMKKKLEDAG 120
           L TGLS+ +ANE+   L  AG
Sbjct: 30  LYTGLSEKDANEVLAALLQAG 50


>gnl|CDD|176462 cd01357, Aspartase, Aspartase.  This subgroup contains Escherichia
           coli aspartase (L-aspartate ammonia-lyase), Bacillus
           aspartase and related proteins. It is a member of the
           Lyase class I family, which includes both aspartase
           (L-aspartate ammonia-lyase) and fumarase class II
           enzymes. Members of this family for the most part
           catalyze similar beta-elimination reactions in which a
           C-N or C-O bond is cleaved with the release of fumarate
           as one of the products. These proteins are active as
           tetramers. The four active sites of the homotetrameric
           enzyme are each formed by residues from three different
           subunits. Aspartase catalyzes the reversible deamination
           of aspartic acid.
          Length = 450

 Score = 24.4 bits (54), Expect = 9.5
 Identities = 8/21 (38%), Positives = 15/21 (71%)

Query: 74  VIKEVRAITDLGLKEAKELVE 94
           V++++  IT L LK A+ L++
Sbjct: 241 VVEKLSEITGLPLKRAENLID 261


>gnl|CDD|145572 pfam02503, PP_kinase, Polyphosphate kinase.  Polyphosphate kinase
           (Ppk) catalyses the formation of polyphosphate from ATP,
           with chain lengths of up to a thousand or more
           orthophosphate molecules.
          Length = 678

 Score = 24.3 bits (54), Expect = 9.8
 Identities = 8/19 (42%), Positives = 13/19 (68%), Gaps = 2/19 (10%)

Query: 107 DEANEMK--KKLEDAGATV 123
           DE N ++  ++LE+AG  V
Sbjct: 402 DEENNIRWARRLEEAGVHV 420


  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
   0.304    0.122    0.305 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,221,838
Number of extensions: 54474
Number of successful extensions: 186
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 48
Length of query: 126
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 43
Effective length of database: 4,470,190
Effective search space: 192218170
Effective search space used: 192218170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 51 (23.3 bits)