RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780172|ref|YP_003064585.1| general L-amino acid transport system permease protein [Candidatus Liberibacter asiaticus str. psy62] (386 letters) >3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1 Length = 217 Score = 61.3 bits (148), Expect = 3e-10 Identities = 42/210 (20%), Positives = 89/210 (42%), Gaps = 8/210 (3%) Query: 172 SLWGGLLVTLVISFFGIIISMPLGILLALGRNSNI---PVLRYACITFIELFRGVPLVTV 228 +W L +T V FFG +I +P+G+LL + R I L + +FR +P + + Sbjct: 12 GVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIIL 71 Query: 229 LFMASIMLPLFLPDTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGL 288 L + L A++ ++ A+ +IA ++ L I G EA+ ++G Sbjct: 72 LVWMIPFTRVI---VGTSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGA 128 Query: 289 SYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIINMFDLLGIVRVNFSESTWISS 348 + +Q +R +++P+ + ++ T I L S++ + L I + Sbjct: 129 TPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQIGYQYGYIGYNATV 188 Query: 349 VTPTTGLIFIGFVFWIFCFSISLYSVFIEK 378 + T L+ + + ++ F+ + + Sbjct: 189 M--NTVLVLLVILVYLIQFAGDRIVRAVTR 216 >3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: f.58.1.1 Length = 295 Score = 61.2 bits (148), Expect = 4e-10 Identities = 39/265 (14%), Positives = 90/265 (33%), Gaps = 21/265 (7%) Query: 113 MAQRWRPILVFLTGSILLTPMLIPSFPRKFLNSILLFGLFPIFSFFVLYGGLGLS----- 167 M + R F + + + +L+ + LF + + S Sbjct: 24 MKAKNRKTRKFEPLTFVFSFLLLV---------LFLFIFLTLSNMIFEQITEDFSGLVKA 74 Query: 168 IVETSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFR------ 221 S+ + ++L F ++++ LG + + I++ Sbjct: 75 AGNRSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFPGKRLVESIIDVPVVVPHTV 134 Query: 222 -GVPLVTVLFMASIMLPLFLPDTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQF 280 G+ L+TV ++ D L ++ + + Y+A R G +S+ Sbjct: 135 AGIALLTVFGSRGLIGEPLESYIQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLE 194 Query: 281 EAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIINMFDLLGIVRVNF 340 AA SLG + + +P + ++ G V T+ + + I+ + ++G + Sbjct: 195 NAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEFGAVVILAYYPMVGPTLIYD 254 Query: 341 SESTWISSVTPTTGLIFIGFVFWIF 365 ++ S + ++ I IF Sbjct: 255 RFISYGLSASRPIAVLLILVTLSIF 279 >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 = 48.8 bits (116), Expect = 2e-06 Identities = 56/306 (18%), Positives = 86/306 (28%), Gaps = 129/306 (42%) Query: 139 PRKFLNSILL-------FGLFPIFS--------F------FVLYGGLGLSIVETSLWGGL 177 K NS L L IF F + Y L +++ S Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFS--AET 194 Query: 178 LVTL------VISFFG----II-------------------ISMPL-GIL-LALGRNSNI 206 L L F I+ IS PL G++ LA Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA------- 247 Query: 207 PVLRYACIT----------FIELFRGVP-----LVTVLFMASIMLPLFLPDTWD-----V 246 Y +T +G LVT + +A D+W+ V Sbjct: 248 ---HY-VVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET-------DSWESFFVSV 296 Query: 247 DKLLRAL--LGV---SAFASAYIAEVLRGGLQ-SISKGQFEAANSLGLSYLQKMRLIIMP 300 K + L +GV A+ + + + L+ S+ E S LS + + Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSI---LEDSLENN--EGVPSPMLS----ISNLTQE 347 Query: 301 QVIKRVIPGIVNTFIGLFKDSSL-ISIINMFDLLGIVRVNF-----SES-----TWISSV 349 QV V N+ L + IS++N G N +S + Sbjct: 348 QVQDYV--NKTNSH--LPAGKQVEISLVN-----G--AKNLVVSGPPQSLYGLNLTLRKA 396 Query: 350 TPTTGL 355 +GL Sbjct: 397 KAPSGL 402 Score = 47.2 bits (112), Expect = 5e-06 Identities = 85/434 (19%), Positives = 128/434 (29%), Gaps = 195/434 (44%) Query: 2 IDSCKEFPYVRKRLLQP--SLPP----VYQRG--IIAWIHKNFFGTP-KDILLTALI--- 49 I E L V+ +G I+ W+ N TP KD LL+ I Sbjct: 188 IKFSAE-------TLSELIRTTLDAEKVFTQGLNILEWLE-NPSNTPDKDYLLSIPISCP 239 Query: 50 -ICLL-L--FSI--------PGIIHWVFLDAVWIGSNRTVCTTVSQGGI------QPDGW 91 I ++ L + + PG + +L T SQG + + D W Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELR-SYLKGA---------TGHSQGLVTAVAIAETDSW 289 Query: 92 ----NAACWA-----FIYDRYEQFIFGNYPMAQRWRPILVFLTGSILL----------TP 132 + A FI R + YP L SIL +P Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEA----YP--------NTSLPPSILEDSLENNEGVPSP 337 Query: 133 ML-IPSFPRKFL-------NSILLFGLFP----IF-SF------FVLYGGLGLSIVETSL 173 ML I + ++ + NS L P + S V+ G S+ Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHL-----PAGKQVEISLVNGAKNLVV-SGPPQSLY---- 387 Query: 174 WGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMAS 233 GL +TL P G+ S IP F E R + Sbjct: 388 --GLNLTLR------KAKAPSGL-----DQSRIP--------FSE--RKLKFSNR----- 419 Query: 234 IMLPLFLPDTWDVDKLLRALLGVSA-FASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQ 292 FLP V++ F S + A+ L L Sbjct: 420 -----FLP--------------VASPFHSHLL----------------VPASDLINKDLV 444 Query: 293 KMRLIIMPQVIKRVIPGIVNTFIGLFKD-----SSLI-SIINMFDLLGIVR--VNFSEST 344 K + + I+ IP + +TF G D S+ I++ I+R V + +T Sbjct: 445 KNNVSFNAKDIQ--IP-VYDTFDG--SDLRVLSGSISERIVDC-----IIRLPVKWETTT 494 Query: 345 WISSVTPTTGLI-F 357 T ++ F Sbjct: 495 ----QFKATHILDF 504 >2r6g_F Maltose transport system permease protein MALF; ABC transporter, catalytic intermediate, E. coli maltose transporter, MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP: e.70.1.1 f.58.1.1 PDB: 3fh6_F Length = 514 Score = 37.8 bits (87), Expect = 0.004 Identities = 27/173 (15%), Positives = 61/173 (35%), Gaps = 16/173 (9%) Query: 171 TSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLF 230 + T+V S + +++ +G++LA + + L VP + Sbjct: 275 KPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISIL 334 Query: 231 MASIMLPLFLPDTWDVDKLLRAL----------------LGVSAFASAYIAEVLRGGLQS 274 + + + + L + + + Y+ + G L++ Sbjct: 335 IFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKA 394 Query: 275 ISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISII 327 I +EA+ G Q I +P +IK + P ++ +F F + LI ++ Sbjct: 395 IPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLL 447 >1cii_A Colicin IA; bacteriocin, ION channel formation, transmembrane protein; 3.00A {Escherichia coli} SCOP: f.1.1.1 h.4.3.1 Length = 602 Score = 34.1 bits (77), Expect = 0.052 Identities = 10/29 (34%), Positives = 13/29 (44%) Query: 169 VETSLWGGLLVTLVISFFGIIISMPLGIL 197 ET + G LV F I+ LGI+ Sbjct: 549 TETIIAGNAATALVALVFSILTGSALGII 577 >3kvh_A Protein syndesmos; NUDT16-like, NUDT16L1, nudix, RNA regulation, RNA-binding, structural genomics consortium, SGC, RNA degradation; 1.70A {Homo sapiens} Length = 214 Score = 29.4 bits (66), Expect = 1.4 Identities = 9/24 (37%), Positives = 13/24 (54%) Query: 90 GWNAACWAFIYDRYEQFIFGNYPM 113 GW+ +C A +Y +FG PM Sbjct: 19 GWSHSCHAMLYAANPGQLFGRIPM 42 >1p1j_A Inositol-3-phosphate synthase; 1L-MYO-inositol 1-phosphate, NADH, isomerase, rossmann fold; HET: NAI; 1.70A {Saccharomyces cerevisiae} SCOP: c.2.1.3 d.81.1.3 PDB: 1jkf_A* 1la2_A* 1p1f_A 1jki_A* 1p1i_A* 1p1h_A* 1p1k_A* 1rm0_A* Length = 533 Score = 28.7 bits (64), Expect = 2.3 Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 7/42 (16%) Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135 D Y + I + S+L TP++I Sbjct: 411 SKVAMDEYYSELMLGGHNR-----ISIHNVCEDSLLATPLII 447 >1vko_A Inositol-3-phosphate synthase; CE21227, structural genomics, JCSG, protein structure initiative, PSI; HET: NAD; 2.30A {Caenorhabditis elegans} SCOP: c.2.1.3 d.81.1.3 Length = 537 Score = 28.3 bits (63), Expect = 2.9 Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 7/42 (16%) Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135 D Y IF +V T S+L +P++ Sbjct: 413 SKRAMDEYICSIFMGGKQT-----FVVHNTCEDSLLASPLIY 449 >2c1l_A Restriction endonuclease; BFII, domain fusion, hydrolase; HET: TAR TLA SRT MES; 1.9A {Bacillus firmus} Length = 358 Score = 27.6 bits (61), Expect = 4.5 Identities = 11/46 (23%), Positives = 20/46 (43%) Query: 338 VNFSESTWISSVTPTTGLIFIGFVFWIFCFSISLYSVFIEKTLHKG 383 + E+ W+S+ TP G +++ F + + Y F E G Sbjct: 20 IGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGG 65 >1u1i_A INO1, MIPS, MYO-inositol-1-phosphate synthase; NAD cofactor, metal IONS, isomerase; HET: NAD; 1.90A {Archaeoglobus fulgidus dsm 4304} SCOP: c.2.1.3 d.81.1.3 Length = 392 Score = 27.5 bits (61), Expect = 4.9 Identities = 5/42 (11%), Positives = 11/42 (26%), Gaps = 7/42 (16%) Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135 +D F M +I+ P+++ Sbjct: 305 NKTAFDFVHFKGFLGKLMK-----FYFIWDAIDAIVAAPLIL 341 >3bjx_A Halocarboxylic acid dehalogenase DEHI; plasmid, hydrolase; 2.30A {Pseudomonas putida} Length = 311 Score = 27.6 bits (61), Expect = 5.5 Identities = 7/24 (29%), Positives = 8/24 (33%) Query: 222 GVPLVTVLFMASIMLPLFLPDTWD 245 VP V P +LP W Sbjct: 46 RVPWVAFGCRVLATFPGYLPLAWR 69 >2ci1_A NG, NG-dimethylarginine dimethylaminohydrolase 1; NOS regulation, S-nitrosylation, zinc, MMA, ADMA, acetylation, metal-binding; HET: KOR CIT; 1.08A {Bos taurus} PDB: 2c6z_A* 2ci3_A 2ci4_A 2ci5_A* 2ci6_A 2ci7_A 2jaj_A* 2jai_A* Length = 275 Score = 27.4 bits (60), Expect = 5.9 Identities = 16/110 (14%), Positives = 35/110 (31%), Gaps = 7/110 (6%) Query: 192 MPLGILLALGRNSNIPVLRYACITFIEL-FRGVPLVTVLFMASIMLPLFLPDTWDVDKLL 250 + L + +N TF + VP+V L + S P+ + Sbjct: 127 TGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAG-PNLIAIGSSE 185 Query: 251 RALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMP 300 A + + ++ ++ AAN + L+ K +++ Sbjct: 186 SAQKAL-----KIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHR 230 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 0.331 0.147 0.466 Gapped Lambda K H 0.267 0.0568 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,435,076 Number of extensions: 160834 Number of successful extensions: 604 Number of sequences better than 10.0: 1 Number of HSP's gapped: 591 Number of HSP's successfully gapped: 39 Length of query: 386 Length of database: 5,693,230 Length adjustment: 94 Effective length of query: 292 Effective length of database: 3,414,294 Effective search space: 996973848 Effective search space used: 996973848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 58 (26.5 bits)