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)