RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 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}
           (A:)
          Length = 156

 Score =  108 bits (272), Expect = 4e-25
 Identities = 39/143 (27%), Positives = 60/143 (41%), Gaps = 9/143 (6%)

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

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

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


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

 Score =  106 bits (266), Expect = 1e-24
 Identities = 33/143 (23%), Positives = 57/143 (39%), Gaps = 11/143 (7%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  A   LY+ D+ G +  E+  E    +   + +            E+ + ++  
Sbjct: 4   RKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKD----------AYEYAKKLVDT 53

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
            +   + ID +I   L + WS  RL  +  + LR GV ELI   S     +  + V +  
Sbjct: 54  AVRHIEEIDSIIEKHL-KGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVK 112

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
            +      KF+N VL  + +   
Sbjct: 113 KYADEKAGKFVNGVLSAIYKAYI 135


>1tzv_A NUSB protein, N utilization substance protein B homolog;
           RNA-protein interaction, transcriptional
           antitermination, transcription regulation; 1.35A
           {Thermotoga maritima} (A:)
          Length = 142

 Score =  106 bits (266), Expect = 2e-24
 Identities = 44/143 (30%), Positives = 67/143 (46%), Gaps = 12/143 (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  L EKWS +RL ++  ++LR    EL+    +P+EV I E + IA 
Sbjct: 54  IKENLSMIDDLISRYL-EKWSLNRLSVVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAK 112

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
            +   +  KF+N +LD+++++  
Sbjct: 113 RYGTENSGKFVNGILDRIAKEHA 135


>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 (A:)
          Length = 141

 Score =  103 bits (259), Expect = 1e-23
 Identities = 40/143 (27%), Positives = 65/143 (45%), Gaps = 13/143 (9%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           R  AR  AVQALY   +      ++  +     F A+ ++        VD+ +FR ++ G
Sbjct: 8   RRRARECAVQALYSWQLSQNDIADVEYQ-----FLAEQDVK------DVDVLYFRELLAG 56

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V     ++D L+   L        L  +  ++LR  + EL +   VP +V I+E + +A 
Sbjct: 57  VATNTAYLDGLMKPYL--SRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAK 114

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
            F   D  KF+N VLDK +    
Sbjct: 115 SFGAEDSHKFVNGVLDKAAPVIR 137


>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet,
           methyltransferase-fold, RNA-binding domain; 1.65A
           {Escherichia coli} (A:1-142)
          Length = 142

 Score = 92.6 bits (230), Expect = 3e-20
 Identities = 26/143 (18%), Positives = 52/143 (36%), Gaps = 16/143 (11%)

Query: 16  RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHG 75
           +   R  A QA+ Q+   G S + I+   +        ++  +      D    + +  G
Sbjct: 4   QRNLRSMAAQAVEQVVEQGQSLSNILPPLQQ-------KVSDK------DKALLQELCFG 50

Query: 76  VMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAH 135
           V+     +D LI+         +     +  ++  G+ +L     +P    ++E V  A 
Sbjct: 51  VLRTLSQLDWLINKL--MARPMTGKQRTVHYLIMVGLYQL-LYTRIPPHAALAETVEGAI 107

Query: 136 DFFYGDEPKFINAVLDKVSRKEE 158
                     IN VL +  R++E
Sbjct: 108 AIKRPQLKGLINGVLRQFQRQQE 130


>1f86_A Transthyretin Thr119Met variant; protein stability, X-RAY
           amyloidogenesis, transport protein; HET: T44; 1.10A
           {Homo sapiens} (A:)
          Length = 115

 Score = 27.8 bits (62), Expect = 0.75
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 13/58 (22%)

Query: 46  TYRFCADT-----ELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS 98
            Y+   DT      L +   + H +        +    R+  I  L+S      +S+S
Sbjct: 59  IYKVEIDTKSYWKALGISPFHEHAE---VVFTANDSGPRRYTIAALLSP-----YSYS 108


>2hdv_A SH2-B PH domain containing signaling mediator 1 gamma
           isoform; adapter protein, signaling protein; 2.00A {Mus
           musculus} PDB: 2hdx_A* 1rpy_A 1rqq_C* (A:)
          Length = 111

 Score = 28.1 bits (62), Expect = 0.76
 Identities = 13/83 (15%), Positives = 22/83 (26%), Gaps = 10/83 (12%)

Query: 63  HVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVP 122
                WF    HG++ R +   L++         F    ++  S  R G   L       
Sbjct: 6   LSGYPWF----HGMLSRLKAAQLVLEGGTGSHGVF----LVRQSETRRGECVLTFNFQGK 57

Query: 123 VEVIISEYVCIAHDFFYGDEPKF 145
            + +       A          F
Sbjct: 58  AKHLRLSL--NAAGQCRVQHLHF 78


>2gr8_A Adhesin; trimeric autotransporter, adhesion, protein
          secretion, microbial pathogenesis, membrane protein;
          2.00A {Haemophilus influenzae} (A:)
          Length = 99

 Score = 27.4 bits (61), Expect = 1.1
 Identities = 8/35 (22%), Positives = 10/35 (28%), Gaps = 4/35 (11%)

Query: 3  IQDNKKDLKLSHRRGIARLAAVQALYQIDIIGCST 37
          +    K        G A   A   L Q  + G S 
Sbjct: 18 VPRGSKRA----DAGTASALAASQLPQATMPGKSM 48


>1l6j_A Matrix metalloproteinase-9; twisted beta sheet flanked by
          helices, hydrolase; 2.50A {Homo sapiens} (A:201-256)
          Length = 56

 Score = 26.2 bits (58), Expect = 2.3
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 35 CSTTEIISEYETYRFCADTE 54
          CSTT      + + FC    
Sbjct: 37 CSTTANYDTDDRFGFCPSER 56


>3cym_A Uncharacterized protein BAD_0989; structural genomics,
           unknown function, ribonuclease D, exonuclease; 2.10A
           {Bifidobacterium adolescentis ATCC15703} (A:338-440)
          Length = 103

 Score = 25.9 bits (57), Expect = 3.2
 Identities = 7/21 (33%), Positives = 12/21 (57%)

Query: 108 LRAGVLELIECHSVPVEVIIS 128
           +R  V ++ E    PVE++I 
Sbjct: 32  VRKAVSQIAEDTRTPVEIVIK 52


>1ck7_A Protein (gelatinase A); hydrolase (metalloprotease),
          FULL-length, metalloproteinase; 2.80A {Homo sapiens}
          (A:256-313)
          Length = 58

 Score = 25.5 bits (56), Expect = 3.9
 Identities = 8/24 (33%), Positives = 11/24 (45%)

Query: 35 CSTTEIISEYETYRFCADTELDVE 58
          C TTE     + Y FC +T +   
Sbjct: 33 CGTTEDYDRDKKYGFCPETAMSTV 56


>1n8i_A Probable malate synthase G; glyoxylate pathway, acetyl
           coenzyme A, isocitrate lyase, persistence, GLCB,
           structural genomics, PSI; 2.10A {Mycobacterium
           tuberculosis} (A:1-579)
          Length = 579

 Score = 25.3 bits (55), Expect = 4.6
 Identities = 8/31 (25%), Positives = 15/31 (48%)

Query: 62  LHVDLEWFRVIIHGVMDRKQHIDLLISSCLT 92
           LH+++        G  DR    D+++ S +T
Sbjct: 237 LHIEILIDPESQVGTTDRAGVKDVILESAIT 267


>1v8d_A Hypothetical protein (TT1679); X-RAY craytallography,
          structural genomics, riken structural
          genomics/proteomics initiative, RSGI; 2.16A {Thermus
          thermophilus} (A:1-213)
          Length = 213

 Score = 25.1 bits (55), Expect = 5.4
 Identities = 5/15 (33%), Positives = 11/15 (73%)

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


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
           translation termination, ATP-binding, cytoplasm,
           hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
           (A:1-326)
          Length = 326

 Score = 25.1 bits (54), Expect = 6.0
 Identities = 12/154 (7%), Positives = 36/154 (23%), Gaps = 31/154 (20%)

Query: 31  DIIGCSTT----------EIISEYETYRF------CADTELDVESVYLHV-DLEWFRVII 73
           ++IG S +           ++S  +           A +      +   V ++  +  + 
Sbjct: 160 NMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAICLAPSRELARQIMDVVTEMGKYTEVK 219

Query: 74  HGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCI 133
                +                +   +  ++        L+  +     V V+      +
Sbjct: 220 TAFGIKDSVPKGAKIDAQIVIGTPGTVMDLMKR----RQLDARDIK---VFVLDEADNML 272

Query: 134 AHDFFYGDEPKFINAVLDKVSRKEEIKRSGCVSA 167
                          +   + R     +    SA
Sbjct: 273 DQQGLGDQ----SMRIKHLLPRN---TQIVLFSA 299


>1j7m_A Matrix metalloproteinase 2; beta sheet, alpha helix,
          hydrolase; NMR {Homo sapiens} (A:)
          Length = 72

 Score = 24.8 bits (54), Expect = 6.0
 Identities = 6/21 (28%), Positives = 9/21 (42%)

Query: 35 CSTTEIISEYETYRFCADTEL 55
          C+TT    +   + FC D   
Sbjct: 49 CATTANYDDDRKWGFCPDQGW 69


>1ck7_A Protein (gelatinase A); hydrolase (metalloprotease),
          FULL-length, metalloproteinase; 2.80A {Homo sapiens}
          (A:194-255)
          Length = 62

 Score = 24.7 bits (54), Expect = 6.5
 Identities = 8/21 (38%), Positives = 9/21 (42%)

Query: 35 CSTTEIISEYETYRFCADTEL 55
          CSTT    +   Y FC    L
Sbjct: 37 CSTTYNFEKDGKYGFCPHEAL 57


>1v5u_A SBF1, SET binding factor 1; MTMR5, the pleckstrin homology
           domain, structural genomics, riken structural
           genomics/proteomics initiative, RSGI; NMR {Mus musculus}
           (A:)
          Length = 117

 Score = 24.4 bits (52), Expect = 9.2
 Identities = 6/34 (17%), Positives = 11/34 (32%), Gaps = 8/34 (23%)

Query: 39  EIISEYETYRFCADTELDVESVYLHVDLEWFRVI 72
           ++ +    Y FCA      +        +W   I
Sbjct: 81  DVKTTRRVYNFCAQDVPSAQ--------QWVDRI 106


>2fl7_A Regulatory protein SIR3; ORC, silencing, chromatin,
           transcription; 1.85A {Saccharomyces cerevisiae} PDB:
           2fvu_A (A:56-232)
          Length = 177

 Score = 24.5 bits (53), Expect = 9.4
 Identities = 5/33 (15%), Positives = 11/33 (33%)

Query: 128 SEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIK 160
           +  V + H+         +   +    R  E+K
Sbjct: 13  TYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELK 45


  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    0.139    0.416 

Gapped
Lambda     K      H
   0.267   0.0499    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,315,157
Number of extensions: 56660
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 35
Length of query: 170
Length of database: 4,956,049
Length adjustment: 82
Effective length of query: 88
Effective length of database: 2,184,039
Effective search space: 192195432
Effective search space used: 192195432
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: 51 (24.0 bits)