RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780957|ref|YP_003065370.1| dihydrofolate reductase protein [Candidatus Liberibacter asiaticus str. psy62] (176 letters) >gnl|CDD|143949 pfam00186, DHFR_1, Dihydrofolate reductase. Length = 159 Score = 210 bits (538), Expect = 1e-55 Identities = 74/165 (44%), Positives = 102/165 (61%), Gaps = 6/165 (3%) Query: 5 EIILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRLLPGRTNI 64 I LI A+ +N VIG +PW + DLK FK+LT G P++MG +TF+SIGR LPGRTNI Sbjct: 1 MISLIVAVDKNGVIGKDNDLPWHLPEDLKHFKALTMGKPIIMGRKTFESIGRPLPGRTNI 60 Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITH 124 ++TR+ +A + S+ ++L LA+ ++IFIIGG EIY Q + A LY+T Sbjct: 61 VLTRNPDFKA---EGVEVVHSLEEALALAAGE--EEIFIIGGAEIYKQALPYADRLYLTE 115 Query: 125 IEKEIEGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIYDR 169 I+ E EGD FFP ID + W+ +E A E + Y FV Y+R Sbjct: 116 IDAEFEGDTFFPEIDLSEWELVSRE-EHPADEKNPYDYTFVTYER 159 >gnl|CDD|29264 cd00209, DHFR, Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis.. Length = 158 Score = 172 bits (437), Expect = 5e-44 Identities = 71/163 (43%), Positives = 94/163 (57%), Gaps = 7/163 (4%) Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIGRL-LPGRTNI 64 I LI A+ N VIG +PW + DLK FK TTGNPV+MG +TF+SI R LPGRTNI Sbjct: 1 ISLIVAVDENGVIGKDNKLPWHLPEDLKHFKKTTTGNPVIMGRKTFESIPRRPLPGRTNI 60 Query: 65 IITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTISLAHTLYITH 124 +++R + S+ ++L+LA T ++IF+IGG EIY Q + A LY+T Sbjct: 61 VLSR--QLDYQDAEGVEVVHSLEEALELAENTV-EEIFVIGGAEIYKQALPYADRLYLTR 117 Query: 125 IEKEIEGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIY 167 I E EGD FFP ID + W+ +E + E D Y F Y Sbjct: 118 IHAEFEGDTFFPEIDESEWELVSEEEVF---EEDGYSYTFETY 157 >gnl|CDD|30611 COG0262, FolA, Dihydrofolate reductase [Coenzyme metabolism]. Length = 167 Score = 137 bits (347), Expect = 1e-33 Identities = 63/170 (37%), Positives = 89/170 (52%), Gaps = 11/170 (6%) Query: 6 IILIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTGNPVVMGYRTFQSIG---RLLPGRT 62 IILI A++ + VIG +PW + DL FK+ T G PV+MG +T++S+ R LPGR Sbjct: 2 IILIVAVSLDGVIGRDNSLPWHLPEDLAHFKATTLGKPVIMGRKTYESLPGEWRPLPGRK 61 Query: 63 NIIITRDNTRRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGGEIYAQTIS--LAHTL 120 NI+++R+ + + SI ++L L K + IFIIGGGE+Y Q + LA L Sbjct: 62 NIVLSRNPDLKTEGG--VEVVDSIEEALLLLLKEEGEDIFIIGGGELYRQFLPAGLADEL 119 Query: 121 YITHIEKEI-EGDVFFPSIDSNIWKKQEKEIITSAGEGDDYPTRFVIYDR 169 +T I + EGD FP D W+ A E Y F Y+R Sbjct: 120 ILTIIPVLLGEGDTLFPEGDPADWE---LVSSEDADEKGGYFYTFESYER 166 >gnl|CDD|36538 KOG1324, KOG1324, KOG1324, Dihydrofolate reductase [Coenzyme transport and metabolism]. Length = 190 Score = 104 bits (260), Expect = 1e-23 Identities = 52/157 (33%), Positives = 90/157 (57%), Gaps = 16/157 (10%) Query: 8 LIAAITRNNVIGSCGGMPWKISSDLKRFKSLTTG-------NPVVMGYRTFQSI---GRL 57 L+ A++ N IG G +PW + S++K F+ +TT N V+MG +T++SI R Sbjct: 6 LVVALSPNMGIGKNGDLPWPLPSEMKYFRRVTTSTSDPSKKNAVIMGRKTWESIPEKFRP 65 Query: 58 LPGRTNIIITRDNTRRASVNPEAVLASSILDSLDLASKTGSK----KIFIIGGGEIYAQT 113 LPGR N++++R + L+SS+ +LDL + S +F+IGG E+Y++ Sbjct: 66 LPGRINVVLSRSLKEDFAPTENVFLSSSLESALDLLEEPPSSNSVEMVFVIGGSEVYSEA 125 Query: 114 IS--LAHTLYITHIEKEIEGDVFFPSIDSNIWKKQEK 148 ++ ++IT I + E D FFP+ID++ ++K +K Sbjct: 126 LNSPRCDAIHITEIFQSFECDTFFPAIDTSSYEKWDK 162 >gnl|CDD|30562 COG0213, DeoA, Thymidine phosphorylase [Nucleotide transport and metabolism]. Length = 435 Score = 30.2 bits (68), Expect = 0.29 Identities = 31/119 (26%), Positives = 48/119 (40%), Gaps = 25/119 (21%) Query: 18 IGSCGG--------MPWKISSDLKRFKSLTTGNPV-VMGYRTFQSIGRLLPGRTNIIITR 68 +G GG + D +F N V ++G QS G L P + R Sbjct: 115 LGHTGGTLDKLESIPGVNLELDEIKFIEQVKDNGVAIIG----QS-GNLAPADKKLYALR 169 Query: 69 DNTRRASVNPEAVLASSILDSLDLASKTGSKKIFI---IGGG---EIYAQTISLAHTLY 121 D T A+V+ ++ASSI+ S LA+ G+ I + +G G + LA + Sbjct: 170 DVT--ATVDSIPLIASSIM-SKKLAA--GADAIVLDVKVGSGAFMKTVEDARELAKAMV 223 >gnl|CDD|36395 KOG1180, KOG1180, KOG1180, Acyl-CoA synthetase [Lipid transport and metabolism]. Length = 678 Score = 26.8 bits (59), Expect = 3.4 Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%) Query: 21 CGGMPWKISSDLKRFKSLTTGNPVVMGY 48 GG P +S D +RF ++ PV+ GY Sbjct: 409 SGGAP--LSPDTQRFMNICFCCPVLQGY 434 >gnl|CDD|145065 pfam01715, IPPT, IPP transferase. This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37). Length = 253 Score = 26.5 bits (59), Expect = 3.6 Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 16/70 (22%) Query: 91 DLASKTGSKKIFIIGGGEIYAQTISLAHTLYITHIEKEIEGDVFFPSIDSNIWKKQEKEI 150 +A KI ++ GG LY + ++G PS D + K E+++ Sbjct: 48 AIAEIRARGKIPLLVGGT----------GLYFKAL---LDGLSDTPSADPKVRAKLEEQL 94 Query: 151 ITSAGEGDDY 160 G+DY Sbjct: 95 EE---LGNDY 101 >gnl|CDD|143445 cd07127, ALDH_PAD-PaaZ, Phenylacetic acid degradation proteins PaaZ (Escherichia coli) and PaaN (Pseudomonas putida)-like. Phenylacetic acid degradation (PAD) proteins PaaZ (Escherichia coli) and PaaN (Pseudomonas putida) are putative aromatic ring cleavage enzymes of the aerobic PA catabolic pathway. PaaZ mutants were defective for growth with PA as a sole carbon source due to interruption of the putative ring opening system. This CD is limited to bacterial monofunctional enzymes. Length = 549 Score = 26.7 bits (59), Expect = 3.9 Identities = 15/30 (50%), Positives = 16/30 (53%), Gaps = 4/30 (13%) Query: 17 VIGSCGGMP-WKISSDLKRFKSLTTGNPVV 45 VIG C P W L F SL TGNPV+ Sbjct: 199 VIG-CSTFPTWNGYPGL--FASLATGNPVI 225 >gnl|CDD|33084 COG3273, COG3273, Uncharacterized conserved protein [Function unknown]. Length = 204 Score = 26.4 bits (58), Expect = 4.6 Identities = 14/36 (38%), Positives = 17/36 (47%) Query: 72 RRASVNPEAVLASSILDSLDLASKTGSKKIFIIGGG 107 R V + LA L LDLA+ TG + I I G Sbjct: 121 VRVRVEKGSELAGKTLGELDLATNTGVRVIAIRRGE 156 >gnl|CDD|146850 pfam04414, tRNA_deacylase, D-aminoacyl-tRNA deacylase. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules. Length = 214 Score = 26.5 bits (59), Expect = 4.7 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%) Query: 76 VNPEAV--LASSILDSLDLASKTGSKKIFIIGGGEIYAQ---TISLAHTLYITHI 125 +P+A +A ++L++L + K IGGG YA I+L + HI Sbjct: 106 NDPDAAEAVAEAVLEALGKDEEEEVKPAVGIGGGH-YAPRFTDIALETEYAVGHI 159 >gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 311 Score = 26.5 bits (59), Expect = 4.8 Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 6/28 (21%) Query: 82 LASSILDSLDLASKTGSKKIFIIGGGEI 109 LA I +L KK+ +IG GE+ Sbjct: 168 LAEKIFGNL------KGKKVLVIGAGEM 189 >gnl|CDD|33705 COG3919, COG3919, Predicted ATP-grasp enzyme [General function prediction only]. Length = 415 Score = 26.1 bits (57), Expect = 5.5 Identities = 7/26 (26%), Positives = 11/26 (42%) Query: 90 LDLASKTGSKKIFIIGGGEIYAQTIS 115 D A K G K ++ G+ +S Sbjct: 64 RDFAEKHGLKGYLLVACGDGEVLLVS 89 >gnl|CDD|145023 pfam01661, Macro, Macro domain. This domain is an ADP-ribose binding module. It is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein. This domain is found in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alphaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria, and eukaryotes. Length = 117 Score = 26.0 bits (58), Expect = 5.6 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 12/84 (14%) Query: 21 CGGMPWKISSDLKRFKSLTTGNPVV-MGYRTFQSIGRLLPGRTNIIITR--DNTRRASVN 77 G + +LK+ TG VV G LP + +I T Sbjct: 22 AGPALLEECRELKKNGGCPTGEAVVTPGGN--------LPAK-YVIHTVGPIWRHGGGEE 72 Query: 78 PEAVLASSILDSLDLASKTGSKKI 101 E +LAS+ ++L+LA++ G K I Sbjct: 73 EEELLASAYRNALELANELGIKSI 96 >gnl|CDD|31391 COG1198, PriA, Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]. Length = 730 Score = 25.3 bits (55), Expect = 9.3 Identities = 11/25 (44%), Positives = 13/25 (52%) Query: 49 RTFQSIGRLLPGRTNIIITRDNTRR 73 R + + RL PG I I D TRR Sbjct: 495 RIEEELKRLFPGARIIRIDSDTTRR 519 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 0.137 0.396 Gapped Lambda K H 0.267 0.0765 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,120,784 Number of extensions: 106072 Number of successful extensions: 234 Number of sequences better than 10.0: 1 Number of HSP's gapped: 224 Number of HSP's successfully gapped: 18 Length of query: 176 Length of database: 6,263,737 Length adjustment: 87 Effective length of query: 89 Effective length of database: 4,383,754 Effective search space: 390154106 Effective search space used: 390154106 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 (21.7 bits) S2: 54 (24.5 bits)