RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780570|ref|YP_003064983.1| phosphoribosylglycinamide formyltransferase [Candidatus Liberibacter asiaticus str. psy62] (205 letters) >gnl|CDD|30647 COG0299, PurN, Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]. Length = 200 Score = 247 bits (633), Expect = 1e-66 Identities = 90/188 (47%), Positives = 124/188 (65%) Query: 4 KNIVIFISGEGTNMLSLIQATKKNDYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIPYKD 63 K I + SG G+N+ ++I A K AEIV V SD ++A L +A K +PT + K+ Sbjct: 1 KKIAVLASGNGSNLQAIIDAIKGGKLDAEIVAVISDKADAYALERAAKAGIPTVVLDRKE 60 Query: 64 YISRREHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLHT 123 + SR ++A++ L PDL+ LAGYMR+L +F+ ++ +ILNIHPSLLP FPGLH Sbjct: 61 FPSREAFDRALVEALDEYGPDLVVLAGYMRILGPEFLSRFEGRILNIHPSLLPAFPGLHA 120 Query: 124 HRRVLQSGIKITGCTVHMVTANMDEGPIIAQAAVPVSSQDTESSLSQKVLSAEHLLYPLA 183 H + L++G+K++GCTVH VT +D GPIIAQAAVPV DT +L +VL EH LYPLA Sbjct: 121 HEQALEAGVKVSGCTVHFVTEGVDTGPIIAQAAVPVLPGDTAETLEARVLEQEHRLYPLA 180 Query: 184 LKYTILGK 191 +K G+ Sbjct: 181 VKLLAEGR 188 >gnl|CDD|144222 pfam00551, Formyl_trans_N, Formyl transferase. This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function. Length = 181 Score = 193 bits (493), Expect = 2e-50 Identities = 74/181 (40%), Positives = 109/181 (60%) Query: 4 KNIVIFISGEGTNMLSLIQATKKNDYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIPYKD 63 I + ISG G+N+ +L+ A +K + EIV V ++ A GL +A + +P +K+ Sbjct: 1 MKIAVLISGTGSNLQALLDALRKGGHEVEIVAVVTNKDKAAGLERAEQAGIPVEVFEHKN 60 Query: 64 YISRREHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLHT 123 + R + + + L+++ PDLI LAGYMR+L +F++++ KILNIHPSLLP F G Sbjct: 61 FTPRSQFDSELADSLAALAPDLIVLAGYMRILPPEFLQAFPGKILNIHPSLLPRFRGAAP 120 Query: 124 HRRVLQSGIKITGCTVHMVTANMDEGPIIAQAAVPVSSQDTESSLSQKVLSAEHLLYPLA 183 +R L++G K TG TVH V +D GPI+AQ AVP+ DT +L +V EH P A Sbjct: 121 IQRALEAGDKETGVTVHQVDEELDTGPILAQKAVPILPDDTSETLYNRVAELEHKALPEA 180 Query: 184 L 184 L Sbjct: 181 L 181 >gnl|CDD|38286 KOG3076, KOG3076, KOG3076, 5'-phosphoribosylglycinamide formyltransferase [Carbohydrate transport and metabolism]. Length = 206 Score = 188 bits (479), Expect = 9e-49 Identities = 80/185 (43%), Positives = 116/185 (62%), Gaps = 2/185 (1%) Query: 3 RKNIVIFISGEGTNMLSLIQATKKN--DYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIP 60 R + + ISG G+N+ +LI AT+ A++V V S+ GL +A +PT IP Sbjct: 6 RARVAVLISGTGSNLQALIDATRDGSLGPNADVVLVISNKKGVYGLERAADAGIPTLVIP 65 Query: 61 YKDYISRREHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPG 120 +K + SR +++ + L + DL+CLAGYMR+LS +F+ +I+NIHP+LLP F G Sbjct: 66 HKRFASREKYDNELAEVLLELGTDLVCLAGYMRILSGEFLSQLPKRIINIHPALLPAFKG 125 Query: 121 LHTHRRVLQSGIKITGCTVHMVTANMDEGPIIAQAAVPVSSQDTESSLSQKVLSAEHLLY 180 LH ++ L++G+K++GCTVH V +D GPIIAQ AVPV DT SL Q+V AEH + Sbjct: 126 LHAIKQALEAGVKLSGCTVHFVIEEVDTGPIIAQMAVPVIPGDTLESLEQRVHDAEHKAF 185 Query: 181 PLALK 185 A+K Sbjct: 186 VEAIK 190 >gnl|CDD|31131 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]. Length = 287 Score = 139 bits (352), Expect = 5e-34 Identities = 66/186 (35%), Positives = 99/186 (53%), Gaps = 3/186 (1%) Query: 3 RKNIVIFISGEGTNMLSLIQATKKNDYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIPYK 62 RK I I +S E + L+ + + PAEIV V S++ + + LV + +P IP Sbjct: 90 RKRIAILVSKEDHCLGDLLYRWRIGELPAEIVAVISNHDDLRPLV--ERFDIPFHHIP-V 146 Query: 63 DYISRREHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLH 122 ++ E E +L L DL+ LA YM++LS DFVE + KI+NIH S LP F G + Sbjct: 147 TKENKAEAEARLLELLEEYGADLVVLARYMQILSPDFVERFPGKIINIHHSFLPAFIGAN 206 Query: 123 THRRVLQSGIKITGCTVHMVTANMDEGPIIAQAAVPVSSQDTESSLSQKVLSAEHLLYPL 182 + + + G+K+ G T H VTA++DEGPII Q + V + L + E L+ Sbjct: 207 PYHQAYERGVKLIGATAHYVTADLDEGPIIEQDVIRVDHAYSVEDLVRAGRDVEKLVLAR 266 Query: 183 ALKYTI 188 A+K + Sbjct: 267 AVKAHL 272 >gnl|CDD|30572 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]. Length = 307 Score = 80.6 bits (199), Expect = 3e-16 Identities = 50/184 (27%), Positives = 83/184 (45%), Gaps = 20/184 (10%) Query: 7 VIFISGEGTNMLSLIQATKKNDYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIPYKDYIS 66 ++F GT ++ + EIV V + G R +K+ P P K Sbjct: 4 IVFF---GTPEFAVPSLEALIEAGHEIVAVVTQPDKPAG----RGKKL--TPSPVKRLAL 54 Query: 67 RRE---------HEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPL 117 ++ L +L+++ PDLI + Y ++L ++ ++ +N+HPSLLP Sbjct: 55 ELGIPVFQPEKLNDPEFLEELAALDPDLIVVVAYGQILPKEILDLPPYGCINLHPSLLPR 114 Query: 118 FPGLHTHRRVLQSGIKITGCTVHMVTANMDEGPIIAQAAVPVSSQDTESSLSQKV--LSA 175 + G + + +G TG T+ + +D G I+AQ VP+ DT SL K+ L A Sbjct: 115 YRGAAPIQWAILNGDTETGVTIMQMDEGLDAGDILAQREVPIEPDDTAGSLHDKLAELGA 174 Query: 176 EHLL 179 E LL Sbjct: 175 ELLL 178 >gnl|CDD|38292 KOG3082, KOG3082, KOG3082, Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]. Length = 338 Score = 60.8 bits (147), Expect = 2e-10 Identities = 34/112 (30%), Positives = 52/112 (46%), Gaps = 7/112 (6%) Query: 78 LSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLHTHRRVLQSGIKITGC 137 L L A + RLL + +N+HPSLLP + G +R L +G +TG Sbjct: 77 LMRPDDQLAITASFGRLLPFKLLNQLPYGGINVHPSLLPKYRGAAPVQRALLNGDTLTGV 136 Query: 138 TVH-MVTANMDEGPIIAQAAVPV----SSQDTESSLSQKVLSAEHLLYPLAL 184 T+ + D+GPI+AQ + V ++ + +SLS L A L+ L Sbjct: 137 TIQTIDPKRFDKGPILAQEYLAVNPKETAPELTASLSS--LGANLLIRSLYN 186 >gnl|CDD|37663 KOG2452, KOG2452, KOG2452, Formyltetrahydrofolate dehydrogenase [Nucleotide transport and metabolism]. Length = 881 Score = 46.2 bits (109), Expect = 6e-06 Identities = 37/158 (23%), Positives = 70/158 (44%), Gaps = 12/158 (7%) Query: 32 EIVGVFS---DNSNAQGL-VKARKEKVPTFPIPYKDYISRREHEKAILMQLSSIQPDLIC 87 E+VGVF+ + A L ++A K+ VP F Y + ++ + ++ + ++ +L Sbjct: 25 EVVGVFTVPDKDGKADPLGLEAEKDGVPVFK--YSRWRAKAQALPDVVAKYQALGAELNV 82 Query: 88 LAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLHTHRRVLQSGIKITGCTVHMVTANMD 147 L + + + + + ++ + HPSLLP G L G K G ++ +D Sbjct: 83 LPFCSQFIPMEIISAPRHGSIIYHPSLLPRHRGASAINWTLIHGDKKGGFSIFWADDGLD 142 Query: 148 EGPIIAQAAVPVSSQDTESSLSQKVLSAEHLLYPLALK 185 G ++ Q V DT S+L + L+P +K Sbjct: 143 TGDLLLQKECEVLPDDTVSTLYNR------FLFPEGIK 174 >gnl|CDD|39014 KOG3810, KOG3810, KOG3810, Micronutrient transporters (folate transporter family) [Coenzyme transport and metabolism]. Length = 433 Score = 28.8 bits (64), Expect = 1.2 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 2/53 (3%) Query: 58 PIPYKDYISRREHEKAI--LMQLSSIQPDLICLAGYMRLLSRDFVESYKNKIL 108 + Y R E + ++ L +++ + L G LL RD E Y N L Sbjct: 184 RVKRSLYFHRLEDKISVGDLEEMNPQASYMSYLRGAFVLLWRDLQECYSNPRL 236 >gnl|CDD|163650 cd07407, MPP_YHR202W_N, Saccharomyces cerevisiae YHR202W and related proteins, N-terminal metallophosphatase domain. YHR202W is an uncharacterized Saccharomyces cerevisiae UshA-like protein with two domains, an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 282 Score = 28.4 bits (64), Expect = 1.4 Identities = 13/50 (26%), Positives = 22/50 (44%) Query: 77 QLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPLFPGLHTHRR 126 +++ DLI + G+M + + + I I P F G H+H R Sbjct: 182 AINNEDVDLILVLGHMPVRDDAEFKVLHDAIRKIFPDTPIQFLGGHSHVR 231 >gnl|CDD|36486 KOG1272, KOG1272, KOG1272, WD40-repeat-containing subunit of the 18S rRNA processing complex [RNA processing and modification]. Length = 545 Score = 26.8 bits (59), Expect = 4.8 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 6/71 (8%) Query: 60 PYKDYISRREHEKAILMQLSSIQPDLICL----AGYMRLLSRDFVESYKNKILNIHPSLL 115 P++ R+E E L L I P+LI L G + S + + ++ P Sbjct: 422 PFETRKQRQEKEVRSL--LEKIPPELISLDPRVIGIVDEPSLEEKKDEIERLFEEKPPEA 479 Query: 116 PLFPGLHTHRR 126 P T R Sbjct: 480 GALPRHKTKGR 490 >gnl|CDD|31075 COG0731, COG0731, Fe-S oxidoreductases [Energy production and conversion]. Length = 296 Score = 26.4 bits (58), Expect = 5.1 Identities = 11/41 (26%), Positives = 16/41 (39%) Query: 69 EHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILN 109 E + L I PD + L YMR + + N L+ Sbjct: 190 EELEEYAELLERINPDFVELKTYMRPGASRYRLPRSNMPLH 230 >gnl|CDD|37712 KOG2501, KOG2501, KOG2501, Thioredoxin, nucleoredoxin and related proteins [General function prediction only]. Length = 157 Score = 26.4 bits (58), Expect = 5.2 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 3/77 (3%) Query: 22 QATKKNDYPAEIVGVFSDNSNAQGLVKARKEKVPTFPIPYKDYISR---REHEKAILMQL 78 + K N P E+V V SD + IP+ D + + ++E + L Sbjct: 60 EELKDNAAPFEVVFVSSDRDEESLDEYMLEHHGDWLAIPFGDDLIQKLSEKYEVKGIPAL 119 Query: 79 SSIQPDLICLAGYMRLL 95 ++PD + RLL Sbjct: 120 VILKPDGTVVTEDARLL 136 >gnl|CDD|163628 cd07385, MPP_YkuE_C, Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain. YkuE is an uncharacterized Bacillus subtilis protein with a C-terminal metallophosphatase domain and an N-terminal twin-arginine (RR) motif. An RR-signal peptide derived from the Bacillus subtilis YkuE protein can direct Tat-dependent secretion of agarase in Streptomyces lividans. This is an indication that YkuE is transported by the Bacillus subtilis Tat (Twin-arginine translocation) pathway machinery. YkuE belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 223 Score = 26.5 bits (59), Expect = 5.5 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 8/57 (14%) Query: 61 YKDYISRREHEKAILMQLSSIQPDLICLAGYMRLLSRDFVESYKNKILNIHPSLLPL 117 ++SR E+ + +++++PDL+ L G D V+ + + + L L Sbjct: 12 LGPFVSRERLERLVEK-INALKPDLVVLTG-------DLVDGSVDVLELLLELLKKL 60 >gnl|CDD|99778 cd00322, FNR_like, Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H).. Length = 223 Score = 25.9 bits (57), Expect = 7.7 Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 4/38 (10%) Query: 7 VIFISGEG---TNMLSLIQATKKNDYPAEIVGVFSDNS 41 V+ I+G G T S+++ + EI ++ + Sbjct: 100 VVLIAG-GIGITPFRSMLRHLAADKPGGEITLLYGART 136 >gnl|CDD|145103 pfam01770, Folate_carrier, Reduced folate carrier. The reduced folate carrier (a transmembrane glycoprotein) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy, such as methotrexate (MTX). Mammalian cells have an absolute requirement for exogenous folates which are needed for growth, and biosynthesis of macromolecules. Length = 410 Score = 26.1 bits (58), Expect = 7.8 Identities = 7/30 (23%), Positives = 10/30 (33%) Query: 79 SSIQPDLICLAGYMRLLSRDFVESYKNKIL 108 S + +RLL Y N +L Sbjct: 218 ESGGLEKFSRLSVLRLLWYHLKSCYSNPLL 247 >gnl|CDD|37394 KOG2183, KOG2183, KOG2183, Prolylcarboxypeptidase (angiotensinase C) [Posttranslational modification, protein turnover, chaperones, General function prediction only]. Length = 492 Score = 25.7 bits (56), Expect = 9.2 Identities = 8/31 (25%), Positives = 15/31 (48%) Query: 83 PDLICLAGYMRLLSRDFVESYKNKILNIHPS 113 D + + R+++RDF ++ N I S Sbjct: 206 EDTVPKDVFYRIVTRDFKDASPNCRNTIRKS 236 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.135 0.384 Gapped Lambda K H 0.267 0.0757 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,357,107 Number of extensions: 114744 Number of successful extensions: 261 Number of sequences better than 10.0: 1 Number of HSP's gapped: 257 Number of HSP's successfully gapped: 19 Length of query: 205 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 116 Effective length of database: 4,340,536 Effective search space: 503502176 Effective search space used: 503502176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (24.9 bits)