RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780297|ref|YP_003064710.1| peptide deformylase [Candidatus Liberibacter asiaticus str. psy62] (170 letters) >gnl|CDD|144794 pfam01327, Pep_deformylase, Polypeptide deformylase. Length = 155 Score = 205 bits (525), Expect = 4e-54 Identities = 78/154 (50%), Positives = 108/154 (70%), Gaps = 1/154 (0%) Query: 4 KPLVIFPDPILRRVSRPIEKINSD-IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVID 62 P+V +PDP+LR+ ++P+E+ + + + LID+MLE MY+ +G+GLAA QIGV R+ VID Sbjct: 2 LPIVTYPDPVLRQKAKPVEEFDDEELKELIDDMLETMYAANGVGLAAPQIGVSKRIFVID 61 Query: 63 LQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQ 122 + D P+V INP+II+ S++ +EGCLS+P R +V+R ITVRY D N Sbjct: 62 VGDEDGEPEPLVLINPEIISASEETVEGEEGCLSVPGLRGEVERPKRITVRYQDLNGNEH 121 Query: 123 IIYADGLLATCLQHELDHLNGILFIDHLSRLKRD 156 + ADG LA LQHE+DHL+GILFID LS+LKR Sbjct: 122 ELEADGFLARVLQHEIDHLDGILFIDRLSKLKRL 155 >gnl|CDD|30591 COG0242, Def, N-formylmethionyl-tRNA deformylase [Translation, ribosomal structure and biogenesis]. Length = 168 Score = 203 bits (519), Expect = 1e-53 Identities = 83/167 (49%), Positives = 123/167 (73%), Gaps = 1/167 (0%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 M + +V +PDP LR+V++P+E+++ ++ LID+MLE MY+ +G+GLAA QIG+ R+ V Sbjct: 1 MAIREIVKYPDPRLRQVAKPVEEVDDELRQLIDDMLETMYAAEGVGLAAPQIGISKRIFV 60 Query: 61 IDLQDHAHRK-NPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNA 119 ID+++ K P+V INP+II+ S++ +EGCLS+P R +V+R ITV+Y+D N Sbjct: 61 IDVEEDGRPKEPPLVLINPEIISKSEETLTGEEGCLSVPGVRGEVERPERITVKYLDRNG 120 Query: 120 QHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLV 166 + Q + A+GLLA C+QHE+DHLNG+LFID LS LKRD + KK+ KL Sbjct: 121 KPQELEAEGLLARCIQHEIDHLNGVLFIDRLSPLKRDRLKKKLKKLK 167 >gnl|CDD|29602 cd00487, Pep_deformylase, Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents.. Length = 141 Score = 179 bits (457), Expect = 2e-46 Identities = 68/141 (48%), Positives = 101/141 (71%) Query: 6 LVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQD 65 +V +PDP+LR+ ++P+E+ + ++ LID+M E MY+ G+GLAA QIGV R+ VID+ D Sbjct: 1 IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPD 60 Query: 66 HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIY 125 +++ P+V INP+II S + +EGCLS+P YR +V+R +TVRY+D + + Sbjct: 61 EENKEPPLVLINPEIIESSGETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELE 120 Query: 126 ADGLLATCLQHELDHLNGILF 146 A+G LA C+QHE+DHLNGILF Sbjct: 121 AEGFLARCIQHEIDHLNGILF 141 >gnl|CDD|38347 KOG3137, KOG3137, KOG3137, Peptide deformylase [Translation, ribosomal structure and biogenesis]. Length = 267 Score = 119 bits (299), Expect = 4e-28 Identities = 54/162 (33%), Positives = 88/162 (54%), Gaps = 17/162 (10%) Query: 6 LVIFPDPILRRVSRPIEKI---NSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVID 62 +V + DP+LR ++ +++ + ++ NL+D M +VM TDG+GL+A Q+GV +L+V++ Sbjct: 81 IVEYGDPVLRAKAKRVDRAQIGDENLQNLVDAMFDVMRKTDGVGLSAPQVGVPVQLMVLE 140 Query: 63 LQDHAHRKNP--------------MVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSA 108 R+ P +V +NPK+ +SD + EGCLS+P + A+V R Sbjct: 141 PAGALCRECPEPGRAERQMEPFKLIVLVNPKLKKYSDKLVPFDEGCLSVPGFYAEVVRPQ 200 Query: 109 FITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHL 150 + + D + I A G A QHE DHL G+LF D + Sbjct: 201 SVKIDGRDITGERFSISASGWPARIFQHEYDHLEGVLFFDKM 242 >gnl|CDD|176203 cd08241, QOR1, Quinone oxidoreductase (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 323 Score = 28.6 bits (65), Expect = 0.98 Identities = 9/18 (50%), Positives = 11/18 (61%) Query: 44 GIGLAAVQIGVLYRLVVI 61 G+GLAAVQ+ VI Sbjct: 151 GVGLAAVQLAKALGARVI 168 >gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. This group has the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 345 Score = 28.0 bits (63), Expect = 1.5 Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%) Query: 44 GIGLAAVQIGVLY--RLVVIDLQDHA 67 G+GL+AV I R++ +D+ D Sbjct: 176 GVGLSAVMIASALGARVIAVDIDDDK 201 >gnl|CDD|29356 cd01172, RfaE_like, RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer membrane of gram-negative bacteria. RfaE consists of two domains, a sugar kinase domain, represented here, and a domain belonging to the cytidylyltransferase superfamily.. Length = 304 Score = 26.3 bits (58), Expect = 4.9 Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 4/71 (5%) Query: 31 LIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVY 90 LI+ + E + D + L+ GVL V+ L A V ++PK D+S Y Sbjct: 124 LIERIAERLPEADVVILSDYGKGVLTPRVIEALIAAARELGIPVLVDPK----GRDYSKY 179 Query: 91 QEGCLSIPDYR 101 + L P+ + Sbjct: 180 RGATLLTPNEK 190 >gnl|CDD|48606 cd03057, GST_N_Beta, GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Unlike mammalian GSTs which detoxify a broad range of compounds, the bacterial class Beta GSTs exhibit limited GSH conjugating activity with a narrow range of substrates. In addition to GSH conjugation, they also bind antibiotics and reduce the antimicrobial activity of beta-lactam drugs. The structure of the Proteus mirabilis enzyme reveals that the cysteine in the active site forms a covalent bond with GSH.. Length = 77 Score = 26.3 bits (58), Expect = 5.0 Identities = 9/28 (32%), Positives = 16/28 (57%) Query: 52 IGVLYRLVVIDLQDHAHRKNPMVFINPK 79 +G+ + LV +DL+ + + INPK Sbjct: 21 LGLPFELVRVDLRTKTQKGADYLAINPK 48 >gnl|CDD|48602 cd03053, GST_N_Phi, GST_N family, Class Phi subfamily; composed of plant-specific class Phi GSTs and related fungal and bacterial proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Phi GST subfamily has experience extensive gene duplication. The Arabidopsis and Oryza genomes contain 13 and 16 Phi GSTs, respectively. They are primarily responsible for herbicide detoxification together with class Tau GSTs, showing class specificity in substrate preference. Phi enzymes are highly reactive toward chloroacetanilide and thiocarbamate herbicides. Some Phi GSTs have other functions including transport of flavonoid pigments to the vacuole, shoot regeneration and GSH peroxidase activity.. Length = 76 Score = 25.9 bits (57), Expect = 5.7 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%) Query: 47 LAAVQIGVLYRLVVIDLQDHAHRKNPMVFINP--KIITFSD-DFSVYQ 91 L + GV Y LV +DL H+ + NP +I D D +++ Sbjct: 18 LCLEEKGVDYELVPVDLTKGEHKSPEHLARNPFGQIPALEDGDLKLFE 65 >gnl|CDD|146776 pfam04315, DUF462, Protein of unknown function, DUF462. This family consists of bacterial proteins of uncharacterized function. Length = 165 Score = 25.2 bits (56), Expect = 10.0 Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%) Query: 121 HQIIYADGLLATCLQHELDH 140 H+II+A G A+ L HE+ H Sbjct: 33 HRIIFAHGFFASAL-HEIAH 51 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 0.327 0.143 0.418 Gapped Lambda K H 0.267 0.0705 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,118,491 Number of extensions: 108950 Number of successful extensions: 306 Number of sequences better than 10.0: 1 Number of HSP's gapped: 302 Number of HSP's successfully gapped: 16 Length of query: 170 Length of database: 6,263,737 Length adjustment: 87 Effective length of query: 83 Effective length of database: 4,383,754 Effective search space: 363851582 Effective search space used: 363851582 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 54 (24.6 bits)