RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780275|ref|YP_003064688.1| SsrA-binding protein [Candidatus Liberibacter asiaticus str. psy62] (159 letters) >1j1h_A Small protein B; SMPB, SSRA associated protein, OB fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Thermus thermophilus} SCOP: b.111.1.1 Length = 144 Score = 189 bits (481), Expect = 3e-49 Identities = 71/143 (49%), Positives = 96/143 (67%) Query: 12 KVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIP 71 V +NR+AR++Y I+ ++EAGI L GTEVKSLR KV+ + S+A FE+ E++L N YI Sbjct: 2 APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIA 61 Query: 72 EYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQ 131 Y + + N PRR RKLLL K E+ RL V + G+TLVP+KIYFN +G AK+ L LA+ Sbjct: 62 PYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLAR 121 Query: 132 GKKNYDKRETEKKRDWDRQKHRI 154 GKK Y+KR +KK R + Sbjct: 122 GKKAYEKRREDKKEAVRRALEEL 144 >1p6v_A SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA complex, RNA binding protein/RNA complex; 3.20A {Aquifex aeolicus} SCOP: b.111.1.1 PDB: 2ob7_B 1k8h_A 1zc8_K Length = 156 Score = 173 bits (439), Expect = 2e-44 Identities = 65/148 (43%), Positives = 91/148 (61%), Gaps = 2/148 (1%) Query: 11 KKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLR-VSKVNISDSYATFENDEIWLTNSY 69 +++N++A+ Y I+ ++EAGIVL G+EVKSLR V+ DS+ EN E WL N Y Sbjct: 6 IIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLY 65 Query: 70 IPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLAL 129 I Y A NH P R RKLLL KREI RLY V+ G T++P+K+Y+ K+ +AL Sbjct: 66 IAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWK-NNKVKVLIAL 124 Query: 130 AQGKKNYDKRETEKKRDWDRQKHRILRE 157 A+GKK YD+R K++ R+ R + Sbjct: 125 AKGKKLYDRRRELKEKAMKRELEREFKG 152 >1wjx_A Small protein B, SSRA-binding protein; RNA binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.70A {Thermus thermophilus} SCOP: b.111.1.1 PDB: 2czj_A* Length = 122 Score = 152 bits (386), Expect = 3e-38 Identities = 64/120 (53%), Positives = 86/120 (71%) Query: 14 VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEY 73 V +NR+AR++Y I+ ++EAGI L GTEVKSLR KV+ + S+A FE+ E++L N YI Y Sbjct: 3 VLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPY 62 Query: 74 LQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK 133 + + N PRR RKLLL K E+ RL V + G+TLVP+KIYFN +G AK+ L LA+GK Sbjct: 63 EKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 122 >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 = 32.2 bits (73), Expect = 0.056 Identities = 23/134 (17%), Positives = 41/134 (30%), Gaps = 49/134 (36%) Query: 3 LKSRGNPPKKVVSDNRK-------ARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSY 55 K P + +D+ ++ ++ E V +V L + Sbjct: 38 NKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQV--LNLC-------L 88 Query: 56 ATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVP--- 112 FEN YL+ N +IH L A + ++ T + Sbjct: 89 TEFENC-----------YLEGN-----------------DIHALAAKLLQENDTTLVKTK 120 Query: 113 --MKIYFNAKGLAK 124 +K Y A+ +AK Sbjct: 121 ELIKNYITARIMAK 134 Score = 31.5 bits (71), Expect = 0.087 Identities = 20/139 (14%), Positives = 43/139 (30%), Gaps = 47/139 (33%) Query: 26 IVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSY---------IPEYLQA 76 + FE L G ++ +L + +D T + + N + + Sbjct: 87 CLTEFENCY-LEGNDIHALAAKLLQEND--TTLVKTKELIKNYITARIMAKRPFDKKSNS 143 Query: 77 NRFNHYPRRNRKLL---------------LSKREIHRLYAAVRRD-----GMTLVPM--- 113 F N +L+ L R++++ Y + D TL + Sbjct: 144 ALFRAVGEGNAQLVAIFGGQGNTDDYFEEL--RDLYQTYHVLVGDLIKFSAETLSELIRT 201 Query: 114 -----KIYFNAKGLAKIDL 127 K++ +GL ++ Sbjct: 202 TLDAEKVF--TQGL---NI 215 Score = 29.1 bits (65), Expect = 0.45 Identities = 39/201 (19%), Positives = 54/201 (26%), Gaps = 100/201 (49%) Query: 9 PPKKVVSDNRKARYNYHIVRSFEAGIVLTGT-----EVKSLRVSKVNISDSYATFENDEI 63 PP ++ D S E G + +L +V Y + Sbjct: 320 PPS-ILED------------SLENN---EGVPSPMLSISNLTQEQV---QDY-------V 353 Query: 64 WLTNSYIPEYLQ-----AN---------------RFNHYPRRN---------------RK 88 TNS++P Q N N R+ RK Sbjct: 354 NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK 413 Query: 89 LLLSKR--EI------HRLYAA---VRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYD 137 L S R + H L A + +D LV + FNAK D+ + YD Sbjct: 414 LKFSNRFLPVASPFHSHLLVPASDLINKD---LVKNNVSFNAK-----DIQIPV----YD 461 Query: 138 KRETEKKRDWDRQKHRILREH 158 T D LR Sbjct: 462 ---TFDGSD--------LRVL 471 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 28.0 bits (61), Expect = 1.1 Identities = 22/88 (25%), Positives = 32/88 (36%), Gaps = 32/88 (36%) Query: 75 QANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKK 134 QA+R P RK RE R K L ++D A ++ Sbjct: 76 QADRLTQEPESIRKW----REEQR---------------------KRLQELDAASKVMEQ 110 Query: 135 NYDKRETEKK--RDWD-RQKHRILREHN 159 + RE KK +W+ RQ ++ E N Sbjct: 111 EW--REKAKKDLEEWNQRQSEQV--EKN 134 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 27.3 bits (59), Expect = 1.9 Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 12/33 (36%) Query: 93 KREIHRLYAAVRRDGMTLVPMKIYFN--AKGLA 123 K+ + +L A+ +K+Y + A LA Sbjct: 19 KQALKKLQAS----------LKLYADDSAPALA 41 >2ghj_A 50S ribosomal protein L20; folding intermediate, ribosomal protein extension, structural protein; 2.90A {Aquifex aeolicus} PDB: 1gyz_A Length = 118 Score = 26.2 bits (58), Expect = 3.9 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 7/49 (14%) Query: 84 RRNRKLLLSKREIHRLYAAVRRDGMT-------LVPMKIYFNAKGLAKI 125 R+ RK + I R+ AAVR G+ L I + K LA + Sbjct: 48 RKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADM 96 >2fzv_A Putative arsenical resistance protein; flavin binding protein, structural genomics, PSI, protein structure initiative; 1.70A {Shigella flexneri 2a str} SCOP: c.23.5.4 Length = 279 Score = 25.8 bits (56), Expect = 5.2 Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 3/59 (5%) Query: 9 PPKKV---VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIW 64 PP ++ R ++ V + G E + S + + D + ++ + Sbjct: 57 PPVRILLLYGSLRARSFSRLAVEEAARLLQFFGAETRIFDPSDLPLPDQVQSDDHPAVK 115 >1mve_A Truncated 1,3-1,4-beta-D-glucanase; circular-permutated jellyroll protein, hydrolase; 1.70A {Fibrobacter succinogenes} SCOP: b.29.1.2 PDB: 1zm1_A* 2r4a_A 3hr9_A 2r49_A Length = 243 Score = 25.5 bits (55), Expect = 6.1 Identities = 6/48 (12%), Positives = 14/48 (29%) Query: 40 EVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNR 87 + ++V K + W N + + + + NR Sbjct: 162 FINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGKGDWTFDGNR 209 >1vf1_A Glutathione S-transferase 3; detoxification; HET: GSH; 1.77A {Gallus gallus} PDB: 1vf2_A* 1vf3_A* 1vf4_A Length = 229 Score = 25.2 bits (54), Expect = 7.6 Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%) Query: 108 MTLVPMKIYFNAKGLA-KIDLALAQGKKNYDKRETEKKRDWDRQKH 152 M P+ YFN +G I LA +++ E + +++ Sbjct: 1 MAAKPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQ 46 >3i1n_Q 50S ribosomal protein L20; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_Q 3e1b_J 3e1d_J 1vs6_Q 3i1p_Q 3i1r_Q 3i1t_Q 3i20_Q 3i22_Q 2qam_Q* 1p85_O 1p86_O 2awb_Q 2aw4_Q 2i2v_Q 2j28_Q 2i2t_Q* 2qao_Q* 2qba_Q* 2qbc_Q* ... Length = 118 Score = 25.1 bits (55), Expect = 7.6 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 7/49 (14%) Query: 84 RRNRKLLLSKREIHRLYAAVRRDGMTLVPM-------KIYFNAKGLAKI 125 RR RK + I R+ AA R++G++ + + K LA I Sbjct: 50 RRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADI 98 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 0.319 0.134 0.387 Gapped Lambda K H 0.267 0.0737 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,367,728 Number of extensions: 59367 Number of successful extensions: 160 Number of sequences better than 10.0: 1 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 25 Length of query: 159 Length of database: 5,693,230 Length adjustment: 85 Effective length of query: 74 Effective length of database: 3,632,490 Effective search space: 268804260 Effective search space used: 268804260 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: 53 (24.2 bits)