RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780520|ref|YP_003064933.1| flagellar basal body rod modification protein [Candidatus Liberibacter asiaticus str. psy62] (131 letters) >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 = 34.2 bits (77), Expect = 0.009 Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 17/46 (36%) Query: 16 KSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQME 61 K KK L Q A LKL + D + P A LA+ + ME Sbjct: 19 KQALKK-L-Q-ASLKL------YADDSAP-------A-LAIKATME 47 >2wyt_A Superoxide dismutase [CU-ZN]; oxidoreductase, disease mutation, amyotrophic lateral sclero antioxidant; HET: SO4; 1.00A {Homo sapiens} PDB: 2wyz_A* 1hl4_A 1spd_A 2c9v_A* 1hl5_A 1pu0_A 2c9u_A 2c9s_A* 2v0a_A* 3ecu_A 3kh3_A 3kh4_A 3gzp_A 2wko_A 3gzo_A 1uxl_A 3ecv_A 2yqx_A 2zky_A 1ozu_A ... Length = 153 Score = 27.5 bits (61), Expect = 0.84 Identities = 7/26 (26%), Positives = 11/26 (42%) Query: 92 NADGSISGVVNAIQVSSTGLTAITVD 117 DG + G++N Q S G + Sbjct: 9 KGDGPVQGIINFEQKESNGPVKVWGS 34 >3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, polymorphism, receptor, transcription, transcription regulation; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467 Score = 26.4 bits (57), Expect = 1.9 Identities = 9/66 (13%), Positives = 24/66 (36%), Gaps = 13/66 (19%) Query: 25 QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71 ++ L KH+ P +P + + + F ++ +++ L Sbjct: 398 REKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLM 457 Query: 72 ELLKSN 77 E+L++ Sbjct: 458 EMLEAP 463 >1xtm_B Hypothetical superoxide dismutase-like protein YOJM; SOD, Cu-Zn SOD, SOD-like, superoxide dismutase mutants, structural genomics; 1.60A {Bacillus subtilis} PDB: 1xtl_B 1s4i_B 1u3n_A Length = 175 Score = 25.7 bits (56), Expect = 3.4 Identities = 6/29 (20%), Positives = 11/29 (37%), Gaps = 1/29 (3%) Query: 89 NITNADGSISGVVNAIQVSSTGLTAITVD 117 + N +G G + + GL I + Sbjct: 25 QLVNREGKAVGFIEIKESDDEGLD-IHIS 52 >3l9y_A Cu-znsod1, superoxide dismutase [CU-ZN]; greek-KEY-barrel, antioxidant, copper, cytoplasm, metal- binding, oxidoreductase; 1.80A {Bombyx mori} PDB: 3l9e_A Length = 154 Score = 25.4 bits (55), Expect = 3.9 Identities = 5/23 (21%), Positives = 9/23 (39%) Query: 95 GSISGVVNAIQVSSTGLTAITVD 117 G +SG V Q ++ + Sbjct: 11 GDVSGTVFFDQQDEKSPVVVSGE 33 >3cc6_A Protein tyrosine kinase 2 beta; focal adhesion kinase, structural genomics, structural genomics consortium, SGC, alternative splicing; 1.60A {Homo sapiens} PDB: 3fzs_A* 3et7_A 3fzo_A* 3fzr_A* 3fzp_A* 3fzt_A* 3h3c_A* Length = 281 Score = 25.1 bits (54), Expect = 5.0 Identities = 12/38 (31%), Positives = 21/38 (55%) Query: 29 LKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQM 66 L L+T+ DP++ + +E V L+ QME+ + M Sbjct: 243 LYTLMTRCWDYDPSDRPRFTELVCSLSDVYQMEKDIAM 280 >1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A* Length = 237 Score = 25.0 bits (54), Expect = 6.0 Identities = 8/67 (11%), Positives = 22/67 (32%), Gaps = 13/67 (19%) Query: 25 QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71 + L I + + + Q+ + F ++ ++++ LQ Sbjct: 171 RSQVQVSLEDYINDRQYDSRGRFGEXXXXXPTLQSITWQMIEQIQFIKLFGMAKIDNLLQ 230 Query: 72 ELLKSNN 78 E+L + Sbjct: 231 EMLLGGS 237 >2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3e94_A* 1fby_A* 3fc6_A* 1rdt_A* 3fal_A* 1g5y_A* 1fm9_A* 1g1u_A 1fm6_A* 1k74_A* 2acl_A* 1xvp_A* ... Length = 240 Score = 24.7 bits (53), Expect = 7.8 Identities = 9/66 (13%), Positives = 24/66 (36%), Gaps = 13/66 (19%) Query: 25 QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71 ++ L KH+ P +P + + + F ++ +++ L Sbjct: 171 REKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLM 230 Query: 72 ELLKSN 77 E+L++ Sbjct: 231 EMLEAP 236 >1f1g_A Cuznsod, copper-zinc superoxide dismutase; nitric oxide, oxidoreductase; 1.35A {Saccharomyces cerevisiae} SCOP: b.1.8.1 PDB: 1f1a_A 1f18_A 1jcv_A 1b4l_A 1sdy_A 1yaz_A 1yso_A 2jcw_A 1f1d_A 1jk9_A 1b4t_A Length = 154 Score = 24.5 bits (53), Expect = 7.9 Identities = 8/26 (30%), Positives = 13/26 (50%) Query: 92 NADGSISGVVNAIQVSSTGLTAITVD 117 D +SGVV Q S + T ++ + Sbjct: 9 KGDAGVSGVVKFEQASESEPTTVSYE 34 >3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens} Length = 244 Score = 24.3 bits (52), Expect = 9.8 Identities = 10/67 (14%), Positives = 25/67 (37%), Gaps = 13/67 (19%) Query: 25 QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71 Q+ L ++ Q P +P + S V + F ++ + + ++ Sbjct: 168 QEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIR 227 Query: 72 ELLKSNN 78 ++L S + Sbjct: 228 DMLLSGS 234 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 0.307 0.121 0.306 Gapped Lambda K H 0.267 0.0561 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 855,570 Number of extensions: 30559 Number of successful extensions: 94 Number of sequences better than 10.0: 1 Number of HSP's gapped: 93 Number of HSP's successfully gapped: 25 Length of query: 131 Length of database: 5,693,230 Length adjustment: 82 Effective length of query: 49 Effective length of database: 3,705,222 Effective search space: 181555878 Effective search space used: 181555878 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 51 (23.8 bits)