RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780437|ref|YP_003064850.1| 30S ribosomal protein S21 [Candidatus Liberibacter asiaticus str. psy62] (95 letters) >3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus} Length = 190 Score = 66.9 bits (163), Expect = 1e-12 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%) Query: 20 VYVLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMR 78 V V+V DN E+ L ++++ GV++E K R +E R R EA +R+R+ Sbjct: 97 VQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRP 156 Query: 79 K 79 + Sbjct: 157 Q 157 >3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* 2qb9_U* ... Length = 71 Score = 49.7 bits (119), Expect = 1e-07 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 1/64 (1%) Query: 22 VLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKI 80 + VR+N + ALR K+ + GVL E++ R YEKP+ +R R K+ A++R K + + Sbjct: 4 IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARE 63 Query: 81 AQRE 84 R Sbjct: 64 NARR 67 >3ofo_U 30S ribosomal protein S21; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_U* 2wwl_U 3ofp_U Length = 51 Score = 44.7 bits (106), Expect = 5e-06 Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%) Query: 22 VLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIR 71 + VR+N + ALR K+ + GVL E++ R YEKP+ +R R K+ A++ Sbjct: 1 IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVK 51 >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 = 30.7 bits (69), Expect = 0.085 Identities = 21/106 (19%), Positives = 34/106 (32%), Gaps = 42/106 (39%) Query: 1 MLVFNAFRGI----FSEGREISAVY-VLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHY 55 + +F +G F E R++ Y VLV D L K E L EL Sbjct: 157 VAIFGG-QGNTDDYFEELRDLYQTYHVLVGD---------LIKFS-AE-TLSEL------ 198 Query: 56 EKPSQKRVRLKSEAIR-RSRKL--MRKIAQRE---------GAPVS 89 +R +A + ++ L + + P+S Sbjct: 199 -------IRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237 Score = 27.6 bits (61), Expect = 0.69 Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 20/84 (23%) Query: 2 LVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYE----- 56 L F + EG +I A L E ++K K +++ + Sbjct: 86 LCLTEFENCYLEGNDIHA---LAAKLLQENDTTLVKTK----ELIKN-----YITARIMA 133 Query: 57 -KPSQKRVR--LKSEAIRRSRKLM 77 +P K+ L + +L+ Sbjct: 134 KRPFDKKSNSALFRAVGEGNAQLV 157 Score = 25.7 bits (56), Expect = 2.8 Identities = 27/156 (17%), Positives = 44/156 (28%), Gaps = 79/156 (50%) Query: 7 FRGIF------SEGREISAVYVLVRD------NNVEQALRVL----------------KK 38 R S+G ++AV + D +V +A+ VL Sbjct: 263 LRSYLKGATGHSQGL-VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321 Query: 39 KM------QGEGV------LRELKMRGHYEK---------PSQKRVRLKSEAI-----RR 72 + EGV + L + + P+ K+V I + Sbjct: 322 SILEDSLENNEGVPSPMLSISNLT-QEQVQDYVNKTNSHLPAGKQV-----EISLVNGAK 375 Query: 73 S-------RKL------MRKIAQREGAPVSRLRQHR 95 + + L +RK AP S L Q R Sbjct: 376 NLVVSGPPQSLYGLNLTLRKA----KAP-SGLDQSR 406 >1zhv_A Hypothetical protein ATU0741; NESG, ATR8, structural genomics, PSI, protein structure initiative; 1.50A {Agrobacterium tumefaciens str} SCOP: d.58.18.8 d.58.18.8 Length = 134 Score = 26.0 bits (57), Expect = 2.4 Identities = 6/19 (31%), Positives = 12/19 (63%) Query: 21 YVLVRDNNVEQALRVLKKK 39 ++LVR N++E+ +L Sbjct: 103 HLLVRSNDLEKTADLLANA 121 >1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 104 Score = 25.6 bits (56), Expect = 2.8 Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 4/44 (9%) Query: 49 LKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLR 92 LK+ G Q +++ + KLM+ +R+G + ++R Sbjct: 27 LKVAGQDGSVVQFKIKRHTPL----SKLMKAYCERQGLSMRQIR 66 >3oet_A Erythronate-4-phosphate dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid; HET: NAD; 2.36A {Salmonella enterica subsp} Length = 381 Score = 25.7 bits (56), Expect = 2.9 Identities = 11/33 (33%), Positives = 16/33 (48%) Query: 4 FNAFRGIFSEGREISAVYVLVRDNNVEQALRVL 36 F+ R + E RE S++YV+ D L L Sbjct: 339 FDKLRKNYLERREWSSLYVMCDDETAAALLCKL 371 >3gke_A DDMC; rieske cluster, non-heme mononuclear iron, oxygenase, oxidoreductase; 1.75A {Stenotrophomonas maltophilia} PDB: 3gb4_A 3gl0_A* 3gl2_A* 3gob_A* 3gte_A 3gts_A* Length = 349 Score = 24.3 bits (51), Expect = 6.7 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%) Query: 50 KMRGHYEKPSQKRVRLKSEA-IRRSRKLMRKIAQREGA 86 + R + E + L + R + + K+ Q E A Sbjct: 303 RRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA 340 >1ujn_A Dehydroquinate synthase; riken structural genomics/proteomics initiative, RSGI, structural genomics, lyase; 1.80A {Thermus thermophilus HB8} SCOP: e.22.1.1 Length = 348 Score = 24.5 bits (52), Expect = 6.9 Identities = 6/34 (17%), Positives = 17/34 (50%), Gaps = 1/34 (2%) Query: 15 REISAVYVL-VRDNNVEQALRVLKKKMQGEGVLR 47 + V + + + +A +++++G G+LR Sbjct: 315 LAPGRLVVRPLPEGLLREAFAAWREELKGLGLLR 348 >1zvp_A Hypothetical protein VC0802; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Vibrio cholerae} SCOP: d.58.18.9 d.58.18.9 Length = 133 Score = 24.0 bits (52), Expect = 8.0 Identities = 5/18 (27%), Positives = 11/18 (61%) Query: 21 YVLVRDNNVEQALRVLKK 38 ++ V+ +QAL+ L + Sbjct: 112 HIFVQKEKAQQALQALGE 129 >1l2n_A Ubiquitin-like protein SMT3; structure, protein binding; NMR {Saccharomyces cerevisiae} SCOP: d.15.1.1 Length = 101 Score = 24.0 bits (52), Expect = 8.6 Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 6/39 (15%) Query: 57 KPSQKRVRLKSEAIRRS---RKLMRKIAQREGAPVSRLR 92 + K I+++ R+LM A+R+G + LR Sbjct: 29 SDGSSEIFFK---IKKTTPLRRLMEAFAKRQGKEMDSLR 64 >2z6v_A Putative uncharacterized protein; sulfotransferase, unknown function; HET: PLM; 2.60A {Mycobacterium avium} Length = 414 Score = 24.1 bits (51), Expect = 8.6 Identities = 6/51 (11%), Positives = 14/51 (27%) Query: 22 VLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRR 72 ++V + N ++ + L R Q + + R Sbjct: 57 LIVDEVNTSPVFTPFGRQRVLDDATNALGRRLQVHAYIQDHPEVLDAPVER 107 >2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1 Length = 94 Score = 23.7 bits (51), Expect = 9.4 Identities = 6/19 (31%), Positives = 12/19 (63%) Query: 74 RKLMRKIAQREGAPVSRLR 92 KLM+ +R+G + ++R Sbjct: 31 SKLMKAYCERQGLSMRQIR 49 >3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious disease, brucellosis, orchitis, epididymitis; 2.20A {Brucella melitensis} Length = 360 Score = 23.7 bits (51), Expect = 9.9 Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 3/26 (11%) Query: 70 IRRS---RKLMRKIAQREGAPVSRLR 92 I+++ R+LM A+R+G + LR Sbjct: 37 IKKTTPLRRLMEAFAKRQGKEMDSLR 62 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 0.323 0.136 0.367 Gapped Lambda K H 0.267 0.0706 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 780,553 Number of extensions: 33026 Number of successful extensions: 239 Number of sequences better than 10.0: 1 Number of HSP's gapped: 239 Number of HSP's successfully gapped: 45 Length of query: 95 Length of database: 5,693,230 Length adjustment: 61 Effective length of query: 34 Effective length of database: 4,214,346 Effective search space: 143287764 Effective search space used: 143287764 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 50 (23.1 bits)