RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780125|ref|YP_003064538.1| prophage antirepressor [Candidatus Liberibacter asiaticus str. psy62] (262 letters) >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 = 36.8 bits (85), Expect = 0.005 Identities = 51/376 (13%), Positives = 104/376 (27%), Gaps = 166/376 (44%) Query: 8 EFES-----NKIRTIV-----DKDQNIWFVAKDV------ATALGYENSNEA-----INA 46 EFE+ N I + + D + K++ A + ++ A Sbjct: 90 EFENCYLEGNDIHALAAKLLQENDTTL-VKTKELIKNYITARIMAKRPFDKKSNSALFRA 148 Query: 47 HCKGVAKRYPL-----KTEGGIQKVRIISEPDVYRLLVK-------------STLP-SAQ 87 +G A+ + T+ +++R + Y +LV A+ Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFEELRDLY--QTYHVLVGDLIKFSAETLSELIRTTLDAE 206 Query: 88 KF-------ERWVF-EEVLPTLRKTGSYSVEAP--------------------------K 113 K W+ P Y + P + Sbjct: 207 KVFTQGLNILEWLENPSNTPDK----DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE 262 Query: 114 LR-----------------ATSASTVLRVHKHLEELAKQA-------GLKDNQ------L 143 LR A + + + ++A G++ + L Sbjct: 263 LRSYLKGATGHSQGLVTAVAIAETDSW---ESFFVSVRKAITVLFFIGVRCYEAYPNTSL 319 Query: 144 ------------------LLKVNRGVTKITGVDQLEA-MDI--KHLPSSDNDEYLTITQI 182 +L + +T+ +Q++ ++ HLP+ + + I+ + Sbjct: 320 PPSILEDSLENNEGVPSPMLSI-SNLTQ----EQVQDYVNKTNSHLPA---GKQVEISLV 371 Query: 183 -GERLN-----PPQRARFLNKLLLK----RGLQVSKVSGGYRPTPKGEERGGKMCDVPM- 231 G + N PPQ LN L K GL S++ R K R +P+ Sbjct: 372 NGAK-NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK-LKFSNRF-----LPVA 424 Query: 232 -----QHVEGSTQQLK 242 + ++ + Sbjct: 425 SPFHSHLLVPASDLIN 440 >1y8a_A Hypothetical protein AF1437; structural genomics, protein structure initiative, PSI, midwest center for structural genomics, MCSG; 1.40A {Archaeoglobus fulgidus dsm 4304} SCOP: c.108.1.24 Length = 332 Score = 28.1 bits (62), Expect = 2.0 Identities = 8/105 (7%), Positives = 21/105 (20%), Gaps = 6/105 (5%) Query: 99 PTLRKTGSYSVEAPKLRATSASTVLRVHKHLEELAKQAGLKDNQLLLKVNRGVTKITGVD 158 Y K L AG+K+ + + + Sbjct: 50 RFFSNLSEYDDYLAYEVRREGYEAGYTLKLLTPFLAAAGVKNRDVERIAELSAKFVPDAE 109 Query: 159 Q----LEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLL 199 + L+ + S+ + + + + Sbjct: 110 KAMATLQERWTPVVISTSYTQ--YLRRTASMIGVRGELHGTEVDF 152 >2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus} Length = 244 Score = 27.0 bits (59), Expect = 4.2 Identities = 7/50 (14%), Positives = 14/50 (28%), Gaps = 2/50 (4%) Query: 174 DEYLTITQIGERLN-PPQRARFLNKLLLKRGL-QVSKVSGGYRPTPKGEE 221 + IT++ + L+ + L K G+ G Sbjct: 164 TKGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGKDRKVELNELGLN 213 >1lt8_A Betaine-homocysteine methyltransferase; homocysteine metabolism, homocysteinemia, zinc, thiol alkyl transfer; HET: CBH CIT; 2.05A {Homo sapiens} SCOP: c.1.26.1 PDB: 1lt7_A* 1umy_A Length = 406 Score = 27.1 bits (59), Expect = 4.6 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 3/76 (3%) Query: 128 HLEELAKQAGLKDNQLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLN 187 H+ +A++ + L + + +G+D ++ + E L I G N Sbjct: 306 HIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWENLRIA-SGRPYN 364 Query: 188 PPQRARFLNKLLLKRG 203 P + +G Sbjct: 365 PSMSKPD--GWGVTKG 378 >2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, RNA_POL_RPC34 domain, RNA polymerase III C39 subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85 Length = 81 Score = 26.3 bits (58), Expect = 6.3 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%) Query: 186 LNPPQRARFLNKLLLKRGLQVSKVSGG--YR 214 + QRA +N+LL L + + + G YR Sbjct: 42 IEAQQRAVAINRLLSMGQLDLLRSNTGLLYR 72 >1tnr_A Tumor necrosis factor beta; complex(lymphokine/receptor); 2.85A {Homo sapiens} SCOP: b.22.1.1 Length = 144 Score = 26.5 bits (58), Expect = 6.6 Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 3/28 (10%) Query: 230 PMQHVEG---STQQLKWNSNLLVSFLQN 254 P H+ G L W +N +FLQ+ Sbjct: 2 PAAHLIGDPSKQNSLLWRANTDRAFLQD 29 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} Length = 508 Score = 26.2 bits (57), Expect = 8.1 Identities = 30/139 (21%), Positives = 52/139 (37%), Gaps = 24/139 (17%) Query: 79 VKSTLPSAQKF----ERWVFEEVLPTLRKTGSYSVEAPKLRATSASTVLRVHKHLEELAK 134 V +++P Q R + +++ + + G Y T T + + + AK Sbjct: 183 VDASVPKPQAICLAPSRELARQIMDVVTEMGKY---------TEVKTAFGIKDSVPKGAK 233 Query: 135 QAGLKDNQLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARF 194 D Q+++ V + QL+A DIK + D L +G+ Q R Sbjct: 234 ----IDAQIVIGTPGTVMDLMKRRQLDARDIKVFVLDEADNMLDQQGLGD-----QSMRI 284 Query: 195 LNKLLLKRGLQVSKVSGGY 213 K LL R Q+ S + Sbjct: 285 --KHLLPRNTQIVLFSATF 301 >2tnf_A Protein (tumor necrosis factor alpha); lymphokine, cytokine, cytotoxin, transmembrane, glycoprotein, signal-anchor; 1.40A {Mus musculus} SCOP: b.22.1.1 PDB: 1a8m_A 1tnf_A 2tun_A 2az5_A* 4tsv_A 5tsw_A 2e7a_A 2zpx_A 2zjc_A Length = 156 Score = 26.1 bits (57), Expect = 8.5 Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%) Query: 228 DVPMQHVEG---STQQLKWNSNLLVSFLQN 254 D P+ HV +QL+W S + L N Sbjct: 10 DKPVAHVVANHQVEEQLEWLSQRANALLAN 39 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 0.315 0.132 0.378 Gapped Lambda K H 0.267 0.0521 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,136,459 Number of extensions: 94895 Number of successful extensions: 248 Number of sequences better than 10.0: 1 Number of HSP's gapped: 248 Number of HSP's successfully gapped: 10 Length of query: 262 Length of database: 5,693,230 Length adjustment: 91 Effective length of query: 171 Effective length of database: 3,487,026 Effective search space: 596281446 Effective search space used: 596281446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 56 (25.8 bits)