RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

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



>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical
           bundle, structural genomics, PSI, protein structure
           initiative; 1.60A {Mycobacterium tuberculosis} SCOP:
           a.79.1.1
          Length = 156

 Score =  110 bits (275), Expect = 2e-25
 Identities = 39/143 (27%), Positives = 63/143 (44%), Gaps = 9/143 (6%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AV  L++ ++ G S  E++          + + D+          +   +  G
Sbjct: 10  RHQARKRAVALLFEAEVRGISAAEVVDTRAALA---EAKPDIAR-----LHPYTAAVARG 61

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V +   HID LI++     W+  RL  +  +ILR  V EL+    VP  V++ E V +A 
Sbjct: 62  VSEHAAHIDDLITAH-LRGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAK 120

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
           +    D P F+N VL +V     
Sbjct: 121 ELSTDDSPGFVNGVLGQVMLVTP 143


>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT
           site, phage lambda, lambdan antitermination; HET: NHE;
           1.30A {Escherichia coli K12} PDB: 3d3c_A 3imq_A 1ey1_A
          Length = 141

 Score =  100 bits (251), Expect = 1e-22
 Identities = 41/146 (28%), Positives = 68/146 (46%), Gaps = 14/146 (9%)

Query: 11  KLSHRRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFR 70
           + + RR  AR  AVQALY   +      ++  +     F A+ ++        VD+ +FR
Sbjct: 4   EPAARR-RARECAVQALYSWQLSQNDIADVEYQ-----FLAEQDVK------DVDVLYFR 51

Query: 71  VIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEY 130
            ++ GV     ++D L+   L        L  +  ++LR  + EL +   VP +V I+E 
Sbjct: 52  ELLAGVATNTAYLDGLMKPYL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEA 109

Query: 131 VCIAHDFFYGDEPKFINAVLDKVSRK 156
           + +A  F   D  KF+N VLDK +  
Sbjct: 110 IELAKSFGAEDSHKFVNGVLDKAAPV 135


>1q8c_A Hypothetical protein Mg027; structural genomics, NUSB, GI 3844637,
           BSGC structure funded by NIH, protein structure
           initiative, PSI; 2.00A {Mycoplasma genitalium} SCOP:
           a.79.1.2
          Length = 151

 Score = 94.7 bits (235), Expect = 1e-20
 Identities = 27/138 (19%), Positives = 59/138 (42%), Gaps = 7/138 (5%)

Query: 19  ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGV-- 76
            R+A V+ ++ +        E+I          DT+    + +  + ++ F   I     
Sbjct: 17  RRIAVVEFIFSLLFFLPKEAEVIQADFLEY---DTKERQLNEWQKLIVKAFSENIFSFQK 73

Query: 77  -MDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
            ++ +Q  + L       K S  ++D++  +++   + E    H+    ++ISE + I  
Sbjct: 74  KIEEQQLKNQLEIQTKYNKISGKKIDLLTTAVVLCALSEQK-AHNTDKPLLISEALLIMD 132

Query: 136 DFFYGDEPKFINAVLDKV 153
            +  G E K  +A+LDK+
Sbjct: 133 HYSQGAEKKQTHALLDKL 150


>2jr0_A Protein NUSB, N utilization substance protein B homolog;
           antiterminator, transcription; NMR {Aquifex aeolicus}
          Length = 148

 Score = 87.2 bits (215), Expect = 2e-18
 Identities = 32/144 (22%), Positives = 56/144 (38%), Gaps = 11/144 (7%)

Query: 15  RRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIH 74
            R  AR  A   LY+ D+ G +  E+  E    +   + +            E+ + ++ 
Sbjct: 3   YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKD----------AYEYAKKLVD 52

Query: 75  GVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIA 134
             +   + ID +I     + WS  RL  +  + LR GV ELI   S     +  + V + 
Sbjct: 53  TAVRHIEEIDSIIEKH-LKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLV 111

Query: 135 HDFFYGDEPKFINAVLDKVSRKEE 158
             +      KF+N VL  + +   
Sbjct: 112 KKYADEKAGKFVNGVLSAIYKAYI 135


>1tzv_A NUSB protein, N utilization substance protein B homolog;
           RNA-protein interaction, transcriptional
           antitermination, transcription regulation; 1.35A
           {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A
           1tzw_A 1tzx_A*
          Length = 142

 Score = 84.4 bits (208), Expect = 1e-17
 Identities = 43/141 (30%), Positives = 66/141 (46%), Gaps = 12/141 (8%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R   RLA  +AL+Q +       E I E        D   D          E  R  I G
Sbjct: 5   RRRMRLAVFKALFQHEFRRDEDLEQILE-----EILDETYD------KKAKEDARRYIRG 53

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           + +    ID LIS    EKWS +RL ++  ++LR    EL+    +P+EV I E + IA 
Sbjct: 54  IKENLSMIDDLISRY-LEKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAK 112

Query: 136 DFFYGDEPKFINAVLDKVSRK 156
            +   +  KF+N +LD+++++
Sbjct: 113 RYGTENSGKFVNGILDRIAKE 133


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 45.7 bits (108), Expect = 5e-06
 Identities = 35/172 (20%), Positives = 59/172 (34%), Gaps = 71/172 (41%)

Query: 13  SHRRGIARLAAV---QALYQIDIIGCSTT---EIISEYETYR--------FCADT--EL- 55
           +   G A+L A+   Q        G +     E+   Y+TY         F A+T  EL 
Sbjct: 148 AVGEGNAQLVAIFGGQ--------GNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELI 199

Query: 56  ----DVESVYLH-VDLE-WFRVIIHG---VMDRKQHIDLLIS---SC----LTEKWSFSR 99
               D E V+   +++  W    +       D+    D L+S   SC    + +   +  
Sbjct: 200 RTTLDAEKVFTQGLNILEW----LENPSNTPDK----DYLLSIPISCPLIGVIQLAHY-- 249

Query: 100 LDMILCSILRAGV--LELIEC------HS--VPVEVIISEYVCIAHDF--FY 139
             ++   +L  G    EL         HS  +   V I+E       +  F+
Sbjct: 250 --VVTAKLL--GFTPGELRSYLKGATGHSQGLVTAVAIAE----TDSWESFF 293


>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
           methyltransferase-fold, RNA-binding domain; 1.65A
           {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A
          Length = 429

 Score = 41.2 bits (95), Expect = 1e-04
 Identities = 25/138 (18%), Positives = 50/138 (36%), Gaps = 16/138 (11%)

Query: 19  ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMD 78
            R  A QA+ Q+   G S + I+   +        ++         D    + +  GV+ 
Sbjct: 7   LRSMAAQAVEQVVEQGQSLSNILPPLQ-------QKVS------DKDKALLQELCFGVLR 53

Query: 79  RKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFF 138
               +D LI+  +      +     +  ++  G+ +L+    +P    ++E V  A    
Sbjct: 54  TLSQLDWLINKLMARP--MTGKQRTVHYLIMVGLYQLLYTR-IPPHAALAETVEGAIAIK 110

Query: 139 YGDEPKFINAVLDKVSRK 156
                  IN VL +  R+
Sbjct: 111 RPQLKGLINGVLRQFQRQ 128


>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
          transcription factor, DNA-binding, DNA-directed RNA
          polymerase; 4.30A {Saccharomyces cerevisiae}
          Length = 197

 Score = 29.9 bits (67), Expect = 0.28
 Identities = 6/36 (16%), Positives = 11/36 (30%), Gaps = 1/36 (2%)

Query: 34 GCSTTEIISEYET-YRFCADTELDVESVYLHVDLEW 68
               +I+  +      CA   L +    +    EW
Sbjct: 28 KVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEW 63


>2z02_A Phosphoribosylaminoimidazole-succinocarboxamide synthase; 2-layer
           sandwich, ligase, purine biosynthesis, structural
           genomics; HET: ATP CIT; 2.03A {Methanocaldococcus
           jannaschii} PDB: 2yzl_A*
          Length = 242

 Score = 30.0 bits (67), Expect = 0.29
 Identities = 13/64 (20%), Positives = 24/64 (37%)

Query: 69  FRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIIS 128
                H V   K +++ LISS L E    + +       +    +   +   +P+EVI+ 
Sbjct: 41  GNGAKHDVKQGKGYLNALISSKLFEALEENGVKTHYIKYIEPRYMIAKKVEIIPIEVIVR 100

Query: 129 EYVC 132
               
Sbjct: 101 NIAA 104


>1f9y_A HPPK, protein (6-hydroxymethyl-7,8-dihydropterin
           pyrophosphokinase); pyrophosphoryl transfer, catalytic
           mechanism, folate, ternary complex; HET: APC HHR; 0.89A
           {Escherichia coli} SCOP: d.58.30.1 PDB: 1eq0_A 1dy3_A*
           1ex8_A* 1eqm_A* 1hka_A 1q0n_A* 1rao_A* 1rb0_A* 2f63_A
           2f65_A 3h4a_A* 3ip0_A* 1f9h_A* 1g4c_A 1kbr_A 1hq2_A*
           1im6_A 1tmm_A* 1tmj_A* 1rtz_A ...
          Length = 158

 Score = 26.9 bits (59), Expect = 2.5
 Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 2/43 (4%)

Query: 108 LRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVL 150
           + A +  L +     +  + S Y          D+P ++NA +
Sbjct: 18  VNAALKALGDIPESHILTVSSFYRTPPLGPQ--DQPDYLNAAV 58


>2wmf_A Fucolectin-related protein; hydrolase, glycoside hydrolase, blood
           group antigen, fucose utilization; 1.50A {Streptococcus
           pneumoniae} PDB: 2wmh_A* 2wmg_A*
          Length = 581

 Score = 26.8 bits (59), Expect = 2.7
 Identities = 5/42 (11%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 44  YETYRFCADTELDVESVYLHVDLEWFRVIIHG-VMDRKQHID 84
           +E   +   T       +    + +FR  I      +++ ++
Sbjct: 292 FECAAYTFMTNDVPTPAFTKGIIPFFRHAIQNPAPSKEEVVN 333


>1v8d_A Hypothetical protein (TT1679); X-RAY craytallography, structural
          genomics, riken structural genomics/proteomics
          initiative, RSGI; 2.16A {Thermus thermophilus} SCOP:
          c.140.1.1
          Length = 235

 Score = 25.5 bits (56), Expect = 6.5
 Identities = 5/15 (33%), Positives = 11/15 (73%)

Query: 29 QIDIIGCSTTEIISE 43
           + ++G ST+E++ E
Sbjct: 64 SLFVLGGSTSEVLGE 78


>3feh_A Centaurin-alpha-1; structural genomics consortium, GAP, GTPase
           activation, SGC, cytoplasm, metal-binding, nucleus,
           phosphoprotein, polymorphism; 1.90A {Homo sapiens} PDB:
           3fm8_C
          Length = 386

 Score = 25.2 bits (54), Expect = 7.0
 Identities = 7/34 (20%), Positives = 11/34 (32%), Gaps = 8/34 (23%)

Query: 39  EIISEYETYRFCADTELDVESVYLHVDLEWFRVI 72
            I++    + F  +TE D          EW    
Sbjct: 342 TIVTPDRKFLFACETESDQR--------EWVAAF 367


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.325    0.139    0.416 

Gapped
Lambda     K      H
   0.267   0.0544    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,493,352
Number of extensions: 65108
Number of successful extensions: 172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 15
Length of query: 170
Length of database: 5,693,230
Length adjustment: 86
Effective length of query: 84
Effective length of database: 3,608,246
Effective search space: 303092664
Effective search space used: 303092664
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: 53 (24.6 bits)