RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase
subunit omega [Candidatus Liberibacter asiaticus str. psy62]
         (122 letters)



>3iyd_E DNA-directed RNA polymerase subunit omega; transcription,
          initiation, class I, activator, RNA polymerase,
          holoenzyme, sigma70, open complex, CAP, CRP,
          CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
          k-12} (E:)
          Length = 90

 Score = 93.6 bits (233), Expect = 9e-21
 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 4/81 (4%)

Query: 2  ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKP-TVDVGKDKNTVVALREIASGTLSP 60
          AR TV+D ++K+ NRF LVL+A+ R R +  G K   V    DK TV+ALREI  G ++ 
Sbjct: 1  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINN 60

Query: 61 DDLEEDFIHSLQKHVEIDEPD 81
            L+       Q+  E +  +
Sbjct: 61 QILDVR---ERQEQQEQEAAE 78


>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme,
          streptolydigin, antibiotic, transcription regulation;
          HET: STD; 2.40A {Thermus thermophilus} (E:1-77)
          Length = 77

 Score = 84.9 bits (210), Expect = 3e-18
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 15/77 (19%)

Query: 1  MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVG---------------KDKN 45
          MA   ++     VD+++ L ++ + R + L +       +                    
Sbjct: 1  MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNA 60

Query: 46 TVVALREIASGTLSPDD 62
             A++E+ +G L   +
Sbjct: 61 ETWAMKELLTGRLVFGE 77


>2dc0_A Probable amidase; structural genomics, NPPSFA, national
           project on protein structural and functional analyses;
           2.00A {Thermus thermophilus} (A:)
          Length = 434

 Score = 26.7 bits (57), Expect = 1.1
 Identities = 7/67 (10%), Positives = 21/67 (31%), Gaps = 1/67 (1%)

Query: 46  TVVALRE-IASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEALSFGQMSE 104
            ++  +  + +G  +P  L E+ +   +   + +      E +             +   
Sbjct: 2   DLLEAKRLLETGRTTPLALLEEALERAKAFQDRNALAYLDEEAARKEALALTEELRRGQV 61

Query: 105 GDLLEGI 111
              L G+
Sbjct: 62  RGPLHGL 68


>2gi3_A Glutamyl-tRNA(Gln) amidotransferase subunit A; TM1272,
          structural genomics, joint center for structural
          genomics, JCSG; HET: MSE MPD; 1.80A {Thermotoga
          maritima} (A:)
          Length = 476

 Score = 25.5 bits (54), Expect = 2.7
 Identities = 2/30 (6%), Positives = 12/30 (40%), Gaps = 1/30 (3%)

Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKH 74
            + + E +       + L +  + ++++ 
Sbjct: 8  RKLTIEECLKLSEEEREKLPQLSLETIKRL 37


>1o9p_A Malonamidase E2; malonate; 1.8A {Bradyrhizobium japonicum}
          (A:)
          Length = 414

 Score = 25.1 bits (53), Expect = 3.1
 Identities = 6/30 (20%), Positives = 14/30 (46%), Gaps = 1/30 (3%)

Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKH 74
          ++  L+  I +G LSP+        +++  
Sbjct: 3  SLADLQRRIETGELSPNAAIAQSHAAIEAR 32


>1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered
          double layers of alpha helices on TOP and bottom,
          hydrolase; HET: EPE; 1.40A {Stenotrophomonas
          maltophilia} (A:1-315,A:399-503)
          Length = 420

 Score = 24.0 bits (51), Expect = 6.4
 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 6/53 (11%)

Query: 46 TVVALRE-IASGTLSPDDLEEDFIHSLQKHVEIDEPDSPTENSDFSWHKPEAL 97
           V  L+  + +G L    L + ++    + +   +   P   +      P+AL
Sbjct: 12 DVADLQARMTAGELDSTTLTQAYL----QRIAALDRTGPRLRA-VIELNPDAL 59


>2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit,
          transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I
          2pmz_K 3hkz_K (K:27-95)
          Length = 69

 Score = 24.2 bits (53), Expect = 6.5
 Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 10/51 (19%)

Query: 26 RTRHLSQGAKPTVDVGKDKNT---VVALREIASGTLS-------PDDLEED 66
          R   L+ GA   +D+    +T    +A  E   G L        P+     
Sbjct: 13 RALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNGKIIL 63


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.313    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0619    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 924,403
Number of extensions: 37784
Number of successful extensions: 74
Number of sequences better than 10.0: 1
Number of HSP's gapped: 73
Number of HSP's successfully gapped: 9
Length of query: 122
Length of database: 4,956,049
Length adjustment: 73
Effective length of query: 49
Effective length of database: 2,488,284
Effective search space: 121925916
Effective search space used: 121925916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.3 bits)