RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780148|ref|YP_003064561.1| transcription antitermination
protein NusG [Candidatus Liberibacter asiaticus str. psy62]
         (177 letters)



>2jvv_A Transcription antitermination protein NUSG; transcription
           factor, transcription regulation, transcription
           termination; NMR {Escherichia coli} PDB: 2k06_A (A:)
          Length = 181

 Score =  149 bits (377), Expect = 2e-37
 Identities = 80/174 (45%), Positives = 118/174 (67%), Gaps = 1/174 (0%)

Query: 3   PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFP 62
            RWY+VQ +S  E +   S+   +    ++ L  E+ +P+E VV +R G++  SER+FFP
Sbjct: 7   KRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVVEIRGGQRRKSERKFFP 66

Query: 63  GYVLIKAVMTDKVYHTIKDTPKVIGFLG-TGENPSPVTDSEIEHIMNQVEAAVQRPVSSV 121
           GYVL++ VM D  +H ++  P+V+GF+G T + P+P++D E++ IMN+++    +P    
Sbjct: 67  GYVLVQMVMNDASWHLVRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKT 126

Query: 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
            FE GE V V+DGPFA FNG+V+ VD EKSR+ V V IFGR TPVEL ++QVEK
Sbjct: 127 LFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEK 180


>1nz8_A Transcription antitermination protein NUSG; transcription
           elongation, riken structural genomics/proteomics
           initiative, RSGI; NMR {Thermus thermophilus} (A:)
          Length = 119

 Score =  104 bits (261), Expect = 6e-24
 Identities = 34/114 (29%), Positives = 60/114 (52%), Gaps = 6/114 (5%)

Query: 4   RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRK-GRKVNSERRFFP 62
            WY V      E+KA  ++  R+   GL   + ++ IP+E VV +R+ G+K    ++ FP
Sbjct: 3   EWYAVHTLVGQEEKAKANLEKRIKAFGLQDKIFQVLIPTEEVVELREGGKKEVVRKKLFP 62

Query: 63  GYVLIKAVMTD-----KVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVE 111
           GY+ I+  + D     + +  ++ TP + GF+G G  P P++  E+ HI+    
Sbjct: 63  GYLFIQMDLGDEEEPNEAWEVVRGTPGITGFVGAGMRPVPLSPDEVRHILEVSG 116


>2oug_A Transcriptional activator RFAH; transcription factor,
           virulence, transcription pausing, transcription
           elongation; 2.10A {Escherichia coli} (A:1-98)
          Length = 98

 Score = 97.2 bits (242), Expect = 1e-21
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 9/104 (8%)

Query: 4   RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPG 63
            WY++       ++A E          L+        P   +  + +G++       FP 
Sbjct: 3   SWYLLYCKRGQLQRAQEH---------LERQAVNCLAPMITLEKIVRGKRTAVSEPLFPN 53

Query: 64  YVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIM 107
           Y+ ++         TI  T  V  F+  G +P+ V  + I  + 
Sbjct: 54  YLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLS 97


>1m1h_A Transcription antitermination protein NUSG; transcription
          termination, RNP motif, immunoglobulin fold, nucleic
          acid interaction; 1.95A {Aquifex aeolicus}
          (A:1-49,A:135-168)
          Length = 83

 Score = 80.4 bits (199), Expect = 1e-16
 Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 19/92 (20%)

Query: 1  MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRF 60
          +  +WY +QV    E +A E++   L   GL  LV E+ +P                   
Sbjct: 9  LEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVP------------------- 49

Query: 61 FPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTG 92
          FPGY+LIKA M DK+   I+ TP V   +  G
Sbjct: 50 FPGYILIKAHMNDKLLMAIEKTPHVFRPVMVG 81


>1nz9_A Transcription antitermination protein NUSG; transcription
           elongation, riken structural genomics/proteomics
           initiative, RSGI; NMR {Thermus thermophilus} (A:)
          Length = 58

 Score = 78.5 bits (194), Expect = 5e-16
 Identities = 28/57 (49%), Positives = 37/57 (64%)

Query: 119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK 175
           + V F  G++V V  GPFA F G V  ++ E+ +V V V IFGR TPVEL ++QV K
Sbjct: 1   AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVK 57


>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach
           chloroplast ribosome, ribonucleoprotein particle,
           macromolecular complex; 9.40A {Spinacea oleracea}
           (W:1-140)
          Length = 140

 Score = 29.5 bits (66), Expect = 0.28
 Identities = 8/42 (19%), Positives = 17/42 (40%)

Query: 117 PVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVV 158
            +     +VG+ V V  G      G +  + +  S V ++ +
Sbjct: 63  KLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDL 104


>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein
           complex, RNA-RNA complex, protein-RNA complex, peptidyl
           transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
           2.20A {Haloarcula marismortui} (T:20-120)
          Length = 101

 Score = 27.7 bits (62), Expect = 0.82
 Identities = 16/42 (38%), Positives = 22/42 (52%)

Query: 115 QRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
           +    +V    G+ V V  G FA   G V NVD +K+ +HVE
Sbjct: 16  EYGQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVE 57


>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal
           subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} (R:1-87)
          Length = 87

 Score = 26.6 bits (59), Expect = 2.1
 Identities = 10/40 (25%), Positives = 14/40 (35%)

Query: 117 PVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
               + F+ G+ V V  G      G V        +V VE
Sbjct: 10  HNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVE 49


>2gc4_D Cytochrome C-L; electron transfer, methylamine
          dehydrogenase, blue copper protein, oxidoreductase,
          electron transport; HET: TRQ HEM; 1.90A {Paracoccus
          denitrificans} (D:1-61,D:108-129)
          Length = 83

 Score = 26.4 bits (58), Expect = 2.2
 Identities = 9/15 (60%), Positives = 9/15 (60%)

Query: 81 DTPKVIGFLGTGENP 95
          DT  V  FL TGEN 
Sbjct: 24 DTEAVKHFLETGENV 38


>2d0w_A Cytochrome CL; electron transfer, electron transport; HET:
          HEM; 1.98A {Hyphomicrobium denitrificans}
          (A:1-63,A:110-130)
          Length = 84

 Score = 26.4 bits (58), Expect = 2.2
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 81 DTPKVIGFLGTGENP 95
          DTP V  F+ TG +P
Sbjct: 26 DTPAVKQFMQTGVDP 40


>1ycy_A Conserved hypothetical protein; structural genomics,
           southeast collaboratory for structural genomics, secsg,
           protein structure initiative; 2.80A {Pyrococcus
           furiosus} (A:)
          Length = 71

 Score = 25.6 bits (56), Expect = 3.9
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 126 GERVCVSDGPFASFNGIVKNVDEE 149
           G +V VS G   SF G +++ DEE
Sbjct: 16  GHKVAVSVGGDHSFTGTLEDFDEE 39


>2hlv_A Odorant-binding protein; domain swapping, transport protein;
           HET: LIK; 1.65A {Bos taurus} PDB: 1gt1_A* 1gt3_A*
           1gt4_A* 1gt5_A* 1hn2_A* 1obp_A 1g85_A 1pbo_A* (A:)
          Length = 160

 Score = 25.6 bits (55), Expect = 4.5
 Identities = 11/86 (12%), Positives = 20/86 (23%), Gaps = 10/86 (11%)

Query: 4   RWYIVQVYSNCEKKAVE--------SIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVN 55
            W  V + S   +K  E                 G       +    +      K  K +
Sbjct: 16  PWRTVYIGSTNPEKIQENGPFRTYFRELVFDDEKGTVDFYFSVKRDGKCKNVHVKATKQD 75

Query: 56  SERRF--FPGYVLIKAVMTDKVYHTI 79
                  + G  + K V   + +   
Sbjct: 76  DGTYVADYEGQNVFKIVSLSRTHLVA 101


>2q5w_E Molybdopterin-converting factor subunit 2; MOCO, MPT
           synthase, MOAD, MOAE, transferase, molybdenum cofactor
           biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_A*
           (E:)
          Length = 149

 Score = 24.8 bits (54), Expect = 6.1
 Identities = 7/46 (15%), Positives = 17/46 (36%), Gaps = 5/46 (10%)

Query: 132 SDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV 177
             G    F G V+   +     ++E   +     + +A  ++ +I 
Sbjct: 25  YQGAVVVFTGHVREWTKGVKTEYLEYEAY-----IPMAEKKLAQIG 65


>2do3_A Transcription elongation factor SPT5; KOW motif, structural
           genomics, NPPSFA, national project on protein structural
           and functional analyses; NMR {Homo sapiens} (A:)
          Length = 69

 Score = 25.0 bits (55), Expect = 6.4
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 6/47 (12%)

Query: 122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVEL 168
           +F++G+ V V  G F    G++  V+E        V++F  +T  EL
Sbjct: 17  YFKMGDHVKVIAGRFEGDTGLIVRVEEN------FVILFSDLTMHEL 57


>1bj7_A D 2; allergen, lipocalin; 1.80A {Bos taurus} (A:)
          Length = 156

 Score = 24.8 bits (53), Expect = 6.6
 Identities = 7/94 (7%), Positives = 23/94 (24%), Gaps = 10/94 (10%)

Query: 4   RWYIVQVYSNCEKKAVE--------SIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVN 55
            W I+   ++ + K VE             ++      +   +      ++     ++  
Sbjct: 15  EWRIIYAAADNKDKIVEGGPLRNYYRRIECINDCESLSITFYLKDQGTCLLLTEVAKRQE 74

Query: 56  SERRF--FPGYVLIKAVMTDKVYHTIKDTPKVIG 87
                  F G   ++ +   +             
Sbjct: 75  GYVYVLEFYGTNTLEVIHVSENMLVTYVENYDGE 108


>1e5p_A Aphrodisin; lipocalin, pheromone, hamster,; HET: MSE;
          1.63A {Mesocricetus auratus} (A:)
          Length = 151

 Score = 24.8 bits (53), Expect = 6.7
 Identities = 8/86 (9%), Positives = 19/86 (22%), Gaps = 10/86 (11%)

Query: 4  RWYIVQVYSNCEKKAVESIGGR------LSRSGLDHLVTEITIPSERVVSVRKGRKVNSE 57
          +WY + + ++  +K  E    R                    + +    S          
Sbjct: 9  KWYTIVIAADNLEKIEEGGPLRFYFRHIDCYKNCSEXEITFYVITNNQCSKTTVIGYLKG 68

Query: 58 ----RRFFPGYVLIKAVMTDKVYHTI 79
                 F G  + + +         
Sbjct: 69 NGTYETQFEGNNIFQPLYITSDKIFF 94


>2j01_Y 50S ribosomal protein L24; ribosome, tRNA, paromomycin,
           mRNA, translation; 2.8A {Thermus thermophilus} (Y:1-78)
          Length = 78

 Score = 24.6 bits (54), Expect = 8.3
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 126 GERVCVSDGPFASFNGIVKNVDEEKSRVHVE 156
           G+ V V+ G +    G VK V  +K  V VE
Sbjct: 10  GDTVLVASGKYKGRVGKVKEVLPKKYAVIVE 40


>2j16_A SDP-1, tyrosine-protein phosphatase YIL113W; hydrolase,
           hypothetical protein; 2.7A {Saccharomyces cerevisiae}
           PDB: 2j17_A* 2j16_B (A:)
          Length = 182

 Score = 24.4 bits (52), Expect = 8.5
 Identities = 6/91 (6%), Positives = 21/91 (23%), Gaps = 3/91 (3%)

Query: 47  SVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHI 106
                R  + E        +  + +  +  +       +   +     P+       + +
Sbjct: 10  LATDERSTDKESPNEDREFVPCSSLDVRRIYPKGPLLVLPEKIYLYSEPTVKELLPFDVV 69

Query: 107 MNQVEAAVQRPVSSVFFEVGERVCVSDGPFA 137
           +N    A +     +     E         +
Sbjct: 70  IN---VAEEANDLRMQVPAVEYHHYRWEHDS 97


>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding
           protein; 2.4A {Drosophila melanogaster} (B:1-79)
          Length = 79

 Score = 24.3 bits (53), Expect = 8.8
 Identities = 6/25 (24%), Positives = 9/25 (36%)

Query: 135 PFASFNGIVKNVDEEKSRVHVEVVI 159
           P A    ++K    E + V  E   
Sbjct: 11  PNAVIGRLIKEALPESASVSKEARA 35


  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
   0.318    0.136    0.389 

Gapped
Lambda     K      H
   0.267   0.0583    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,360,970
Number of extensions: 58995
Number of successful extensions: 216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 211
Number of HSP's successfully gapped: 31
Length of query: 177
Length of database: 4,956,049
Length adjustment: 83
Effective length of query: 94
Effective length of database: 2,150,234
Effective search space: 202121996
Effective search space used: 202121996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.1 bits)