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)