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)