RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780786|ref|YP_003065199.1| ribosome-binding factor A
[Candidatus Liberibacter asiaticus str. psy62]
         (128 letters)



>2e7g_A Putative ribosome-binding factor A; RBFA, structural
           genomics, NPPSFA, national project on protein structural
           and functional analyses; NMR {Homo sapiens} (A:)
          Length = 129

 Score = 95.6 bits (238), Expect = 2e-21
 Identities = 19/117 (16%), Positives = 40/117 (34%), Gaps = 3/117 (2%)

Query: 1   MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYI 60
             +   ++  R   +   +  AL  ++   E    L     + +S+V ++ D      Y 
Sbjct: 4   GSSGRKEDHARLRALNGLLYKALTDLLCTPEVSQELYDL-NVELSKVSLTPDFSACRAYW 62

Query: 61  S-LPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
                      + + L  +   +R  +      LR VP + F  D    +  +L+ L
Sbjct: 63  KTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQT-LRNVPPIVFVQDKGNAALAELDQL 118


>1pa4_A Probable ribosome-binding factor A; structural genomics,
           distant homology, BSGC structure funded by NIH, protein
           structure initiative, PSI; NMR {Mycoplasma pneumoniae}
           (A:)
          Length = 116

 Score = 84.0 bits (208), Expect = 6e-18
 Identities = 19/109 (17%), Positives = 44/109 (40%), Gaps = 4/109 (3%)

Query: 8   NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS 67
            S +  R+  ++   +    + +E  +  +      ++ V +S DL   TVY+       
Sbjct: 2   ASYKKERLENDIIRLINR-TVIHEIYNETVKT--GHVTHVKLSDDLLHVTVYLDCYNREQ 58

Query: 68  PDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
            DRV+ A N         +  +L  L    ++ F  D ++ +  ++ ++
Sbjct: 59  IDRVVGAFNQAKGVFSRVLAHNLY-LAKAVQIHFVKDKAIDNAMRIESI 106


>1jos_A RBFA, ribosome-binding factor A; RNA binding protein,
           structure 2 function project, S2F, structural genomics;
           1.70A {Haemophilus influenzae} (A:)
          Length = 128

 Score = 82.9 bits (205), Expect = 1e-17
 Identities = 33/114 (28%), Positives = 64/114 (56%), Gaps = 7/114 (6%)

Query: 6   PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD 65
            +  +R+ RV +E++  +   IL  E +D  I    +++S+V +S DL  A ++++   D
Sbjct: 2   AREFKRSDRVAQEIQKEIAV-ILQREVKDPRIGM--VTVSDVEVSSDLSYAKIFVTFLFD 58

Query: 66  ---VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
              ++ ++ +  L     +IR  +G+++R LR VPE+RF YD SL    +++ L
Sbjct: 59  HDEMAIEQGMKGLEKASPYIRSLLGKAMR-LRIVPEIRFIYDQSLVEGMRMSNL 111


>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH
           domain, structural genomics, NPPSFA; 1.84A {Thermus
           thermophilus HB8} (A:)
          Length = 95

 Score = 80.1 bits (198), Expect = 1e-16
 Identities = 18/101 (17%), Positives = 43/101 (42%), Gaps = 7/101 (6%)

Query: 9   SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP 68
           +     +  +++ AL   I     +D  +    +++  V +S D  V +VY+    +   
Sbjct: 2   AYGKAHLEAQLKRALAEEI--QALEDPRLFL--LTVEAVRLSKDGSVLSVYVEAFRE--E 55

Query: 69  DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQS 109
           +  + AL+   + +   + R +R +R +P L F    +  +
Sbjct: 56  EGALRALSRAERRLVAALARRVR-MRRLPRLEFLPWRASPA 95


  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
   0.325    0.138    0.406 

Gapped
Lambda     K      H
   0.267   0.0549    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 942,695
Number of extensions: 36528
Number of successful extensions: 149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 138
Number of HSP's successfully gapped: 6
Length of query: 128
Length of database: 4,956,049
Length adjustment: 76
Effective length of query: 52
Effective length of database: 2,386,869
Effective search space: 124117188
Effective search space used: 124117188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.4 bits)