RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780549|ref|YP_003064962.1| signal peptide protein [Candidatus Liberibacter asiaticus str. psy62] (271 letters) >1lr0_A TOLA protein; domain-swapping, TONB, protein transport; 1.91A {Pseudomonas aeruginosa} SCOP: d.212.1.1 Length = 129 Score = 50.0 bits (119), Expect = 6e-07 Identities = 15/102 (14%), Positives = 33/102 (32%), Gaps = 12/102 (11%) Query: 175 SQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRM 234 + ++ N V W P + + V++ ++ G + G + Sbjct: 27 TGSLDDLIVNLVSQQWRRPPSARN--GMSVEVLIEMLPDGTITNASVSRSSG-----DKP 79 Query: 235 LRENARKAVIKSQAF----RLSPSTY-KSWRNITLFFVPSKM 271 +A AV +L +T+ +R + F P + Sbjct: 80 FDSSAVAAVRNVGRIPEMQQLPRATFDSLYRQRRIIFKPEDL 121 >1tol_A G3P - TOLA, protein (fusion protein consisting of minor coat protein, glycine rich linker, TOLA,...; bacteriophage M13, phage infection; 1.85A {Enterobacteria phage M13} SCOP: b.37.1.1 d.212.1.1 PDB: 1s62_A Length = 222 Score = 49.9 bits (119), Expect = 6e-07 Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 13/92 (14%) Query: 180 AIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENA 239 +++ + + + S + + +L G + +++ GG + + A Sbjct: 134 GQIKSAIESKFYDASSYAG---KTCTLRIKLAPDGML---LDIKPEGGDPALCQ-----A 182 Query: 240 RKAVIKSQAFRLSPS--TYKSWRNITLFFVPS 269 A K PS Y+ ++N L F P+ Sbjct: 183 ALAAAKLAKIPKPPSQAVYEVFKNAPLDFKPA 214 >3hj3_A Chain A, crystal structure of DHFR; TS, enzyme, crossover, non-active site, oxidoreductase; HET: UMP CB3 MTX NDP; 2.70A {Cryptosporidium hominis} PDB: 1qzf_A* 1sej_A* 3dl5_A* 3dl6_A* 2oip_A* Length = 521 Score = 35.3 bits (81), Expect = 0.016 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A V + I W+I D K F K+ Sbjct: 12 ASVLSSGIGINGQLPWSISEDLKFFSKI 39 >3irm_A Bifunctional dihydrofolate reductase-thymidylate; DHFR-TS antifolate complex, methyltransfe multifunctional enzyme, NADP; HET: 1CY; 2.10A {Trypanosoma cruzi} PDB: 3inv_A* 3irn_A* 3iro_A* 2h2q_A* 3cl9_A* 3clb_A* 3hbb_A* 3kjs_A* Length = 521 Score = 35.0 bits (80), Expect = 0.021 Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A+ + I + WN+P D K F+ L Sbjct: 28 AVDEHGGIGDGRSIPWNVPEDMKFFRDL 55 >2h2q_A Bifunctional dihydrofolate reductase-thymidylate synthase; bifunctional enzyme in complex with NADP and DUMP, oxidoreductase, transferase; HET: NAP DU; 2.40A {Trypanosoma cruzi} PDB: 3cl9_A* 3clb_A* 3hbb_A* Length = 521 Score = 34.6 bits (79), Expect = 0.027 Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 7/52 (13%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVG 226 A+ I + WN+P D K F+ V + K N V+G Sbjct: 28 AVDERGGIGDGRSIPWNVPEDMKFFR--DVTTKLRGKNVKPSPAKRNAVVMG 77 >3cse_A Dihydrofolate reductase; protein-ligand complex, oxidoreductase; HET: NAP N22; 1.60A {Candida glabrata} PDB: 3eej_A* 3eek_A* 3eel_A* 3eem_A* Length = 227 Score = 33.2 bits (75), Expect = 0.059 Identities = 7/45 (15%), Positives = 18/45 (40%), Gaps = 5/45 (11%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKLRVKMHFQLNQKGFVLGK 219 A++ I W + + K F+++ + Q ++G+ Sbjct: 12 ALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGR 56 >3ix9_A Dihydrofolate reductase; central beta sheet surrounded by 4 alpha helices, oxidoreductase; HET: NDP MTX; 1.95A {Streptococcus pneumoniae} Length = 190 Score = 33.4 bits (76), Expect = 0.061 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 13/50 (26%) Query: 161 LLSKVEKSSRKRIPSQDAIAIV---RNRVIAN-----WNIPSDFKRFKKL 202 L+ + K+I +AI VI W +P++ + FK+ Sbjct: 13 LVPRGSHGMTKKI-----VAIWAQDEEGVIGKDNRLPWYLPAELQHFKET 57 >3jwk_A Dihydrofolate reductase; oxidoreductase; HET: NAP 5WB; 2.08A {Bacillus anthracis} PDB: 3jw5_A* 3jwf_A* 3jwc_A* 3jvx_A* 3jwm_A* 3jw3_A* 3e0b_A* 3dat_A* 2qk8_A* 3fl8_A* 3fl9_A* 2kgk_A* Length = 168 Score = 33.3 bits (76), Expect = 0.063 Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A+ NRVI W +PS+ + KK Sbjct: 14 AMDENRVIGKDNNLPWRLPSELQYVKKT 41 >3dl5_A Dihydrofolate reductase, DHFR; enzyme active site mutant, enzyme-ligand complex, , oxidoreductase; HET: UMP CB3 DHF NDP; 2.74A {Cryptosporidium hominis} PDB: 3dl6_A* 1qzf_A* 1sej_A* 2oip_A* Length = 521 Score = 33.0 bits (75), Expect = 0.064 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A V + I W+I D K F K+ Sbjct: 12 ASVLSSGIGINGQLPWSISEDLKFFSKI 39 >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 = 33.0 bits (75), Expect = 0.083 Identities = 61/382 (15%), Positives = 99/382 (25%), Gaps = 180/382 (47%) Query: 18 LLLLYFNFNVQLLVPISRREMLSVDNIYNEDYHSSKYKKIEEPVVQFKG----SSQENLV 73 L L + + LLVP + + + E ++ + EP F ++ LV Sbjct: 9 LTLSHGSLEHVLLVPTA---SFFIASQLQEQFNKI----LPEPTEGFAADDEPTTPAELV 61 Query: 74 RDF------SVQENG----------------DRFSDQTKTHA------TENETK------ 99 F V+ + + + + HA EN+T Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKE 121 Query: 100 ------------RSSSSKGEQALKESALLRMPVSPYDKQKISKATNKEQDL------QGI 141 + K SAL R L QG Sbjct: 122 LIKNYITARIMAKRPFDKKSN----SALFR------------AVGEGNAQLVAIFGGQGN 165 Query: 142 S---FAEKKSI-DTVVVRPDKKELLSKV---------EKSSRKRIPSQ--DAIAIVRNRV 186 + F E + + T +L+ +++ +Q + Sbjct: 166 TDDYFEELRDLYQTY--HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLN--------- 214 Query: 187 IANW-----NIPS-DFKRFKKL---RVKM---------HFQLNQKGFVLGKINVDVVGGT 228 I W N P D+ L + H+ V K ++G T Sbjct: 215 ILEWLENPSNTPDKDY-----LLSIPISCPLIGVIQLAHYV------VTAK----LLGFT 259 Query: 229 --ELVRRMLR-------------------------ENARKAV-----I--KSQ-AF---R 250 EL R L+ + RKA+ I + A+ Sbjct: 260 PGEL-RSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTS 318 Query: 251 LSPSTYK-SWRNITLFFVPSKM 271 L PS + S N VPS M Sbjct: 319 LPPSILEDSLENN--EGVPSPM 338 >3dfr_A Dihydrofolate reductase; oxido-reductase; HET: NDP MTX; 1.70A {Lactobacillus casei} SCOP: c.71.1.1 PDB: 1ao8_A* 1bzf_A* 1dis_A* 1diu_A* 1lud_A* 2hm9_A* 2hqp_A* Length = 162 Score = 32.8 bits (74), Expect = 0.088 Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A RN +I W++P D F+ Sbjct: 6 AQNRNGLIGKDGHLPWHLPDDLHYFRAQ 33 >2w3w_A Dihydrofolate reductase; nonclassical antifolates, one-carbon metabolism, lipophilic antifolates, NADP, oxidoreductase; HET: VG9 NDP; 1.60A {Mycobacterium avium} PDB: 2w3v_A* Length = 167 Score = 32.4 bits (73), Expect = 0.12 Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A + VI W++P D RFK++ Sbjct: 11 AQSTSGVIGRGGDIPWSVPEDLTRFKEV 38 >1aoe_A DHFR, dihydrofolate reductase; oxidoreductase, antifungal target; HET: NDP GW3; 1.60A {Candida albicans} SCOP: c.71.1.1 PDB: 1ai9_A* 1ia1_A* 1ia2_A* 1ia3_A* 1ia4_A* 1m78_A* 1m79_A* 1m7a_A* Length = 192 Score = 31.8 bits (71), Expect = 0.18 Identities = 6/47 (12%), Positives = 16/47 (34%), Gaps = 5/47 (10%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKLRVKMHFQLNQKGFVLGKIN 221 A+ I W + + + FK + + + ++G+ Sbjct: 12 ALKPALGIGYKGKMPWRLRKEIRYFKDVTTRTTKPNTRNAVIMGRKT 58 >3e0b_A Dihydrofolate reductase; oxidoreductase; HET: NAP N22; 2.25A {Bacillus anthracis} PDB: 3dat_A* 2qk8_A* 3fl8_A* 3fl9_A* 2kgk_A* Length = 166 Score = 31.9 bits (72), Expect = 0.18 Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A+ NRVI W +PS+ + KK Sbjct: 12 AMDENRVIGKDNNLPWRLPSELQYVKKT 39 >2fzi_A Dihydrofolate reductase; trimethoprim derivatives, ring stacking interactions, oxidoreductase; HET: NAP DH3; 1.60A {Pneumocystis carinii} SCOP: c.71.1.1 PDB: 1daj_A* 1cd2_A* 1e26_A* 1klk_A* 1ly3_A* 1ly4_A* 1s3y_A* 2cd2_A* 2fzh_A* 1dyr_A* 3cd2_A* 4cd2_A* 1vj3_A* Length = 206 Score = 31.0 bits (69), Expect = 0.28 Identities = 5/29 (17%), Positives = 12/29 (41%), Gaps = 5/29 (17%) Query: 179 IAIVRNRVIAN-----WNIPSDFKRFKKL 202 +A+ + I W + + FK++ Sbjct: 11 VALTTSYGIGRSNSLPWKLKKEISYFKRV 39 >1df7_A DHFR, dihydrofolate reductase; structure-based inhibitor design, folateanalogs, rossmann fold, nicotinamide adenine dinucleotide; HET: NDP MTX; 1.70A {Mycobacterium tuberculosis} SCOP: c.71.1.1 PDB: 1dg5_A* 1dg7_A* 1dg8_A* 2cig_A* Length = 159 Score = 30.4 bits (68), Expect = 0.40 Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 5/27 (18%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKK 201 A + VI W +P D F++ Sbjct: 7 AQATSGVIGRGGDIPWRLPEDQAHFRE 33 >1zdr_A Dihydrofolate reductase; DHFR, NADP, oxidoreductase; 2.00A {Geobacillus stearothermophilus} Length = 164 Score = 30.5 bits (68), Expect = 0.40 Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 5/27 (18%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKK 201 A+ NRVI W++P+D FK+ Sbjct: 7 AMDENRVIGKDNRLPWHLPADLAYFKR 33 >3ia4_A Dihydrofolate reductase; NADPH, methotrexate, oxidoreductase; HET: NDP MTX; 1.70A {Moritella profunda} PDB: 3ia5_A Length = 162 Score = 30.3 bits (68), Expect = 0.43 Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 5/27 (18%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKK 201 A+ NRVI W++P++ + FK+ Sbjct: 8 ALANNRVIGLDNKMPWHLPAELQLFKR 34 >1cz3_A Dihydrofolate reductase; dimer, hyperthermophIle, oxidoreductase; 2.10A {Thermotoga maritima} SCOP: c.71.1.1 PDB: 1d1g_A* Length = 168 Score = 30.6 bits (68), Expect = 0.45 Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 4/33 (12%) Query: 179 IAIVRNRVIAN----WNIPSDFKRFKKLRVKMH 207 +A+ + IA+ W+ D K F+K+ ++ Sbjct: 7 LAMDVSGKIASSVESWSSFEDRKNFRKITTEIG 39 >3nrr_A Dihydrofolate reductase-thymidylate synthase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, niaid, DHFR; HET: NAP D16 UMP; 1.80A {Babesia bovis} PDB: 3kjr_A* 3i3r_A* 3k2h_A* Length = 515 Score = 30.3 bits (68), Expect = 0.45 Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 6/29 (20%) Query: 180 AIVRNRVIAN-----W-NIPSDFKRFKKL 202 A+ N+VI + W +I DF+ + Sbjct: 20 AVALNKVIGHKNQIPWPHITHDFRFLRNG 48 >2w9h_A DHFR, dihydrofolate reductase; NADP, trimethoprim, oxidoreductase, one-carbon metabolism; HET: TOP; 1.48A {Staphylococcus aureus} PDB: 2w9g_A* 3fyw_X* 3fyv_X* 3fy8_X* 3fy9_X* 3fq0_A* 3f0b_X* 3fqc_A* 3fqz_A* 3f0u_X* 3fqf_A* 3fqo_A* 3fqv_A* 2w9s_A* 2w9t_A Length = 159 Score = 30.0 bits (67), Expect = 0.52 Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 5/27 (18%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKK 201 A RVI W++P+D K KK Sbjct: 8 AHDLQRVIGFENQLPWHLPNDLKHVKK 34 >3kjr_A Dihydrofolate reductase/thymidylate synthase; microfluidics, slipchip,structural genomics, PSI-2, protein structure initiative; HET: NAP NHE; 1.95A {Babesia bovis T2BO} PDB: 3i3r_A* 3k2h_A* Length = 511 Score = 30.0 bits (67), Expect = 0.53 Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 8/54 (14%) Query: 179 IAIVRNRVIAN-----W-NIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVG 226 +A+ N+VI + W +I DF+ + + NV + G Sbjct: 15 VAVALNKVIGHKNQIPWPHITHDFRFLR--NGTTYIPPEVLSKNPDIQNVVIFG 66 >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 = 30.0 bits (66), Expect = 0.54 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 11/32 (34%) Query: 107 EQALKE-SALLRMPVSPY-DKQ----KISKAT 132 +QALK+ A L++ Y D I KAT Sbjct: 19 KQALKKLQASLKL----YADDSAPALAI-KAT 45 Score = 28.4 bits (62), Expect = 1.7 Identities = 8/27 (29%), Positives = 16/27 (59%), Gaps = 5/27 (18%) Query: 158 KKELLSKVEKSSRKRIPSQD---AIAI 181 +K+ L K++ S ++ + D A+AI Sbjct: 18 EKQALKKLQAS--LKLYADDSAPALAI 42 >3dau_A Dihydrofolate reductase; oxidoreductase, pseudo-rossmann fold, adenine nucleotide binding domain, antibiotic resistance; HET: MTX NAP; 1.50A {Escherichia coli K12} PDB: 1ddr_A* 1dds_A* 1ra9_A* 1dre_A* 1drh_A* 1dyi_A* 1dyh_A* 1jol_A* 1jom_A* 1ra1_A* 1dyj_A* 1ra3_A* 1ra8_A* 1ra2_A* 1rb2_A* 1rb3_A* 1rc4_A* 1rd7_A* 1re7_A* 1rf7_A* ... Length = 159 Score = 29.3 bits (65), Expect = 0.95 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 5/28 (17%) Query: 180 AIVRNRVIAN-----WNIPSDFKRFKKL 202 A+ +RVI WN+P+D FK+ Sbjct: 7 ALAVDRVIGMENAMPWNLPADLAWFKRN 34 >3jsu_A Dihydrofolate reductase-thymidylate synthase; rossmann fold, oxidoreductase, transferase; HET: KA5 NDP UMP; 2.70A {Plasmodium falciparum} Length = 608 Score = 27.7 bits (61), Expect = 2.5 Identities = 7/56 (12%), Positives = 18/56 (32%), Gaps = 1/56 (1%) Query: 190 WN-IPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVI 244 W I D K F+ + ++ +K ++ + + + V+ Sbjct: 48 WKCISLDMKYFRAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVV 103 >1kmv_A DHFR, dihydrofolate reductase; oxidoreductase, antiparasitic drugs, lipophilic antifolates; HET: LII NDP; 1.05A {Homo sapiens} SCOP: c.71.1.1 PDB: 1dhf_A* 1hfr_A* 1drf_A* 1kms_A* 1ohj_A* 1ohk_A* 1pd8_A* 1pd9_A* 1pdb_A 1s3u_A* 1s3v_A* 1s3w_A* 1u72_A* 1yho_A* 2c2s_A* 2c2t_A* 2dhf_A* 3ghw_A* 3fs6_A* 1mvs_A* ... Length = 186 Score = 27.4 bits (60), Expect = 3.9 Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 6/46 (13%) Query: 180 AIVRNRVIAN-----W-NIPSDFKRFKKLRVKMHFQLNQKGFVLGK 219 A+ +N I W + ++F+ F+++ + Q ++GK Sbjct: 9 AVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGK 54 >2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Length = 229 Score = 26.4 bits (57), Expect = 6.6 Identities = 9/60 (15%), Positives = 21/60 (35%), Gaps = 6/60 (10%) Query: 152 VVVRPDKKELLSKVEKSSRKRIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLN 211 V PD + ++ + + ++ +R W K + V + F++N Sbjct: 170 FDVTPDGRVDNVQILSAKPANMFEREVKNAMR-----RWR-YEPGKPGSGIVVNILFKIN 223 >1vdr_A DHFR, dihydrofolate reductase; oxidoreductase, halophilic enzyme; 2.55A {Haloferax volcanii} SCOP: c.71.1.1 PDB: 2ith_A 2jyb_A Length = 162 Score = 25.9 bits (56), Expect = 10.0 Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 6/28 (21%) Query: 180 AIVRNRVIAN------WNIPSDFKRFKK 201 A+ NRVI +IP+D K+++ Sbjct: 8 ALAENRVIGRDGELPWPSIPADKKQYRS 35 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 0.317 0.131 0.359 Gapped Lambda K H 0.267 0.0571 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,158,960 Number of extensions: 95709 Number of successful extensions: 253 Number of sequences better than 10.0: 1 Number of HSP's gapped: 252 Number of HSP's successfully gapped: 37 Length of query: 271 Length of database: 5,693,230 Length adjustment: 91 Effective length of query: 180 Effective length of database: 3,487,026 Effective search space: 627664680 Effective search space used: 627664680 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 (21.7 bits) S2: 56 (25.7 bits)