RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780345|ref|YP_003064758.1| transcription antitermination
protein NusB [Candidatus Liberibacter asiaticus str. psy62]
         (170 letters)



>gnl|CDD|31124 COG0781, NusB, Transcription termination factor [Transcription].
          Length = 151

 Score =  118 bits (297), Expect = 8e-28
 Identities = 54/146 (36%), Positives = 82/146 (56%), Gaps = 6/146 (4%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AVQALYQ ++ G  + E I E          E +++      D E+FR ++ G
Sbjct: 10  RRQARELAVQALYQWELSGSVSAEDILED---IEEEFVENELD--IELADSEYFRSLVKG 64

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V++ ++ +D LIS  L  KWS  RLD++  +ILR  + EL+    VP +V+I+E + +A 
Sbjct: 65  VLENQEELDELISPHLK-KWSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIELAK 123

Query: 136 DFFYGDEPKFINAVLDKVSRKEEIKR 161
            F   D  KF+N VLDK+++K   K 
Sbjct: 124 KFSGEDSHKFVNGVLDKIAKKLRPKE 149


>gnl|CDD|144570 pfam01029, NusB, NusB family.  The NusB protein is involved in the
           regulation of rRNA biosynthesis by transcriptional
           antitermination.
          Length = 126

 Score =  100 bits (251), Expect = 2e-22
 Identities = 41/138 (29%), Positives = 65/138 (47%), Gaps = 13/138 (9%)

Query: 18  IARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVM 77
            AR  A+QALY ++  G S  E++ +              E+     D  +   +++GV+
Sbjct: 2   NARELALQALYAVEERGASLNELLDKLL------------EADLDERDRAFATELVYGVL 49

Query: 78  DRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDF 137
              + +D LI+  L E W   RLD +  +ILR    EL+    +P  V I+E V +A  F
Sbjct: 50  RNLEELDALIAK-LLENWPLERLDPVDRAILRLAAYELLYLDDIPPHVAINEAVELAKKF 108

Query: 138 FYGDEPKFINAVLDKVSR 155
                  F+N VL K++R
Sbjct: 109 GGEKSAGFVNGVLRKIAR 126


>gnl|CDD|29565 cd00619, Terminator_NusB, Transcription termination factor NusB (N
           protein-Utilization Substance B). NusB plays a key role
           in the regulation of ribosomal RNA biosynthesis in
           eubacteria by modulating the efficiency of
           transcriptional antitermination. NusB along with other
           Nus factors (NusA, NusE/S10 and NusG) forms the core
           complex with the boxA element of the nut site of the
           rRNA operons. These interactions help RNA polymerase to
           counteract polarity during transcription of rRNA operons
           and allow stable antitermination. The transcription
           antitermination system can be appropriated by some
           bacteriophages such as lambda, which use the system to
           switch between the lysogenic and lytic modes of phage
           propagation..
          Length = 130

 Score = 90.7 bits (225), Expect = 2e-19
 Identities = 43/141 (30%), Positives = 64/141 (45%), Gaps = 12/141 (8%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AVQALY  ++            E      +             L +   ++ G
Sbjct: 1   RRRARELAVQALYAWEL------APEILAEVVSL-LELLQYKSKK----VLPFALKLVRG 49

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V++  + ID LI   L   WS  RL ++  +ILR  V EL+    VP  V+I+E + +A 
Sbjct: 50  VLENIEEIDELIEKHL-RNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAK 108

Query: 136 DFFYGDEPKFINAVLDKVSRK 156
            F   D  KF+N VLDK+++ 
Sbjct: 109 RFGGDDSHKFVNGVLDKIAKD 129


>gnl|CDD|29564 cd00447, NusB_Sun, RNA binding domain of NusB (N
           protein-Utilization Substance B) and Sun (also known as
           RrmB or Fmu) proteins. This family includes two
           orthologous groups exemplified by the transcription
           termination factor NusB and the N-terminal domain of the
           rRNA-specific 5-methylcytidine transferase
           (m5C-methyltransferase) Sun. The NusB protein plays a
           key role in the regulation of ribosomal RNA biosynthesis
           in eubacteria by modulating the efficiency of
           transcriptional antitermination. NusB along with other
           Nus factors (NusA, NusE/S10 and NusG) forms the core
           complex with the boxA element of the nut site of the
           rRNA operons. These interactions help RNA polymerase to
           counteract polarity during transcription of rRNA operons
           and allow stable antitermination. The transcription
           antitermination system can be appropriated by some
           bacteriophages such as lambda, which use the system to
           switch between the lysogenic and lytic modes of phage
           propagation. The m5C-methyltransferase Sun shares the
           N-terminal non-catalytic RNA-binding domain with NusB..
          Length = 129

 Score = 77.7 bits (191), Expect = 2e-15
 Identities = 44/141 (31%), Positives = 70/141 (49%), Gaps = 15/141 (10%)

Query: 19  ARLAAVQALYQIDI-IGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVM 77
           AR  A QALYQ++I  G S   ++S  E            +      D  +   +++GV+
Sbjct: 2   AREIAFQALYQVEIRNGISLEAVLSALE------------KLQLAKKDRPFALELVYGVL 49

Query: 78  DRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIEC-HSVPVEVIISEYVCIAHD 136
                +D +IS  L +KW   RLD +  +ILR  + EL +  + VP  V I+E V +A  
Sbjct: 50  RNLPELDDIISPLL-KKWLLDRLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKR 108

Query: 137 FFYGDEPKFINAVLDKVSRKE 157
           F   D  KF+N VL +++++ 
Sbjct: 109 FGDDDSAKFVNGVLRRIAKES 129


>gnl|CDD|29566 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
           the methyltransferase Sun. The rRNA-specific
           5-methylcytidine transferase Sun, also known as RrmB or
           Fmu shares the RNA-binding non-catalytic domain with the
           transcription termination factor NusB. The precise
           biological role of this domain in Sun is unknown,
           although it is likely to be involved in
           sequence-specific RNA binding. The C-terminal
           methyltransferase domain of Sun has been shown to
           catalyze formation of m5C at position 967 of 16S rRNA in
           Escherichia coli..
          Length = 126

 Score = 42.9 bits (101), Expect = 4e-05
 Identities = 29/139 (20%), Positives = 52/139 (37%), Gaps = 15/139 (10%)

Query: 19  ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMD 78
           AR  A + L  +   G S   ++S  +            +      D      +++G + 
Sbjct: 3   ARSTAAEVLRDVLQRGASLNAVLSALQ------------KKDKSDRDRGLATELVYGTLR 50

Query: 79  RKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFF 138
               +D +I+  L  K      D  + ++LR G+ +L     VP    + E V IA    
Sbjct: 51  WLALLDWIINPLL--KKPDVGKDPDVRNLLRLGLYQL-LYLDVPPHAAVDETVEIAKIRK 107

Query: 139 YGDEPKFINAVLDKVSRKE 157
                  +NAVL +  R++
Sbjct: 108 DLGRAGLVNAVLRRFERED 126


  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
   0.325    0.139    0.416 

Gapped
Lambda     K      H
   0.267   0.0776    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,069,965
Number of extensions: 105287
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 8
Length of query: 170
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,383,754
Effective search space: 363851582
Effective search space used: 363851582
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: 54 (24.5 bits)