RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780202|ref|YP_003064615.1| hypothetical protein CLIBASIA_00435 [Candidatus Liberibacter asiaticus str. psy62] (211 letters) >gnl|CDD|30947 COG0602, NrdG, Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]. Length = 212 Score = 138 bits (349), Expect = 1e-33 Identities = 74/227 (32%), Positives = 99/227 (43%), Gaps = 31/227 (13%) Query: 1 MKLYSIKEIFLTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFCDTD-FVGIQG 59 Y I EIF ++QGEG + GR +VF RF+GCNL C CDT Sbjct: 1 QMKYRIVEIFDSIQGEGKNIGRPSVFVRFAGCNLR-----------CPGCDTKYTWDFNY 49 Query: 60 TKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV-PLIQALNKRGFEIAVET 118 K G AD I + + R LTGGEPLLQ ++ L++ L + GF IA+ET Sbjct: 50 GKPGT---PMSADEILADIKSLGYKARGVSLTGGEPLLQPNLLELLELLKRLGFRIALET 106 Query: 119 NGTIEPP--QGIDWICVSPKAG------CDLKIKGGQELKLVFPQVNVSPEN------YI 164 NGTI ID + VSPK+ D + G +K V+ +V + + Sbjct: 107 NGTIPVWTGYTIDELTVSPKSDKSLLSAIDEVLVDGDFIKFVYAKVLADRGSANQRVLRL 166 Query: 165 GFDFERFSLQPMDGPFLEENTNLAISYCFQNPKWRLSVQTHKFIGIR 211 + L P L++ L RLS QTHK +GI Sbjct: 167 AESLKPVVLVPQPISRLDKLVKLCARLAI-RLNVRLSPQTHKLLGIN 212 >gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Length = 165 Score = 48.7 bits (116), Expect = 1e-06 Identities = 33/123 (26%), Positives = 55/123 (44%), Gaps = 28/123 (22%) Query: 31 GCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVL 90 GCNL +C +C + +G KG + +++ + +E G +L Sbjct: 6 GCNL-----------RCTYCAFPSIRARG-KGRELSPEEILEEAKELARLG---VEVVIL 50 Query: 91 TGGEPLLQVDVP-----LIQALNKRGFEIAVETNGTIEPPQ--------GIDWICVSPKA 137 TGGEPLL D+ L++ G I +ETNGT+ + G+D + +S ++ Sbjct: 51 TGGEPLLLPDLVELLERLLKLEELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQS 110 Query: 138 GCD 140 G D Sbjct: 111 GDD 113 >gnl|CDD|31373 COG1180, PflA, Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]. Length = 260 Score = 41.4 bits (97), Expect = 2e-04 Identities = 26/107 (24%), Positives = 44/107 (41%), Gaps = 20/107 (18%) Query: 22 RVAVFCRFSGCNLWSGREQDRLSAQCRFCDT-DFVGIQGTKGGRYNVDQLADLIEEQWIT 80 R++VF GCNL +C +C + G ++ Sbjct: 37 RLSVF--LQGCNL-----------RCPYCQNPEISQRGREVSGEEVSPEVLVDKAFY--- 80 Query: 81 GEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAVETNGTIEPP 125 + G +GGEP LQ + + L++A +RG +A++TNG + P Sbjct: 81 -SESGGGVTFSGGEPTLQAEFALDLLRAAKERGLHVALDTNGFLPPE 126 >gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.. Length = 204 Score = 39.6 bits (92), Expect = 6e-04 Identities = 33/117 (28%), Positives = 43/117 (36%), Gaps = 30/117 (25%) Query: 31 GCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEG--RYC 88 GCNL C FC GR + KE Sbjct: 6 GCNL-----------NCGFC------SNPASKGRGPESPPEIEEILDIVLEAKERGVEVV 48 Query: 89 VLTGGEPLLQVDVP--LIQAL-NKRGFEIAVETNGTIE--------PPQGIDWICVS 134 +LTGGEPLL ++ L + GFEI++ETNGT+ G+D + VS Sbjct: 49 ILTGGEPLLYPELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVS 105 >gnl|CDD|32721 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]. Length = 322 Score = 37.9 bits (88), Expect = 0.002 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 5/83 (6%) Query: 41 DRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD 100 DR + +C +C + K +++++ L+ G ++ R LTGGEPLL+ D Sbjct: 19 DRCNFRCTYCMPEGPLAFLPKEELLSLEEIRRLVRAFAELGVEKVR---LTGGEPLLRKD 75 Query: 101 VP-LIQALNKRG-FEIAVETNGT 121 + +I L + G ++++ TNG Sbjct: 76 LDEIIARLARLGIRDLSLTTNGV 98 >gnl|CDD|31698 COG1509, KamA, Lysine 2,3-aminomutase [Amino acid transport and metabolism]. Length = 369 Score = 31.8 bits (72), Expect = 0.15 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 6/58 (10%) Query: 41 DRLSAQCRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLL 97 + CR+C FVG + D+ D +I E R +L+GG+PL Sbjct: 119 GVCAVYCRYCFRRRFVGQDNQGFNKEEWDKALD-----YIAAHPEIREVLLSGGDPLS 171 >gnl|CDD|30881 COG0535, COG0535, Predicted Fe-S oxidoreductases [General function prediction only]. Length = 347 Score = 30.0 bits (66), Expect = 0.54 Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 15/103 (14%) Query: 42 RLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV 101 R + C+ C + G + ++ +I+E GE + TGGEPLL+ D+ Sbjct: 28 RCNLACKHC---YAEAGKKLPGELSTEEDLRVIDELAELGEIP--VVIFTGGEPLLRPDL 82 Query: 102 PLI--QALNKRGFEIAVETNGTIEPPQ--------GIDWICVS 134 I A K G +++ TNGT+ + G+D++ +S Sbjct: 83 LEIVEYARKKGGIRVSLSTNGTLLTEEVLEKLKEAGLDYVSIS 125 >gnl|CDD|31645 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit (corrinoid Fe-S protein) [Energy production and conversion]. Length = 467 Score = 29.1 bits (65), Expect = 0.80 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%) Query: 51 DTDFVGIQ-GTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV 101 DT + + GG+ +++ DLIEE I + R V+ G LQ D+ Sbjct: 386 DTGGLAVDVSVAGGQLTGEKVKDLIEETGIEDKVNHRVLVIPGLAARLQGDI 437 >gnl|CDD|39417 KOG4216, KOG4216, KOG4216, Steroid hormone nuclear receptor [Transcription]. Length = 479 Score = 29.2 bits (65), Expect = 0.83 Identities = 15/63 (23%), Positives = 26/63 (41%) Query: 87 YCVLTGGEPLLQVDVPLIQALNKRGFEIAVETNGTIEPPQGIDWICVSPKAGCDLKIKGG 146 YC T GE V + + L + + +ET +E I W + + + KG Sbjct: 221 YCSFTNGETSPTVSMAELDHLAQNIIKSHLETQYLLEELHQITWQTFDQEEIENYQNKGR 280 Query: 147 QEL 149 +E+ Sbjct: 281 EEM 283 >gnl|CDD|37025 KOG1814, KOG1814, KOG1814, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. Length = 445 Score = 28.5 bits (63), Expect = 1.4 Identities = 9/30 (30%), Positives = 14/30 (46%) Query: 25 VFCRFSGCNLWSGREQDRLSAQCRFCDTDF 54 V+C + C L ++ R A C C+ F Sbjct: 274 VYCPRACCQLPVKQDPGRALAICSKCNFAF 303 >gnl|CDD|176115 cd08423, PBP2_LTTR_like_6, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 200 Score = 28.3 bits (64), Expect = 1.7 Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 15/60 (25%) Query: 63 GRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQALNKRGFE--IAVETNG 120 GR V LADL +E WI G G C L++A GF IA E + Sbjct: 91 GREEVA-LADLADEPWIAGC-PGSPCHRW-----------LVRACRAAGFTPRIAHEADD 137 >gnl|CDD|29617 cd01570, NAPRTase_A, Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi).. Length = 327 Score = 28.2 bits (63), Expect = 1.9 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 9/60 (15%) Query: 67 VDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVETN 119 +D L I EG V+ EPLL V+ PLI+A LN F+ + T Sbjct: 77 LDYLRGFRFTGTIYAIPEGE--VVFPNEPLLTVEGPLIEAQLLETLLLNLINFQTLIATK 134 >gnl|CDD|73175 COG1964, COG1964, Predicted Fe-S oxidoreductases [General function prediction only]. Length = 475 Score = 27.9 bits (62), Expect = 2.3 Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 2/33 (6%) Query: 90 LTGGEPLLQVDVP-LIQALNKRGFE-IAVETNG 120 TGGEP L+ D+ +I+ + G++ + + TNG Sbjct: 116 FTGGEPTLRDDLIEIIKIAREEGYDHVQLNTNG 148 >gnl|CDD|163647 cd07404, MPP_MS158, Microscilla MS158 and related proteins, metallophosphatase domain. MS158 is an uncharacterized Microscilla protein with a metallophosphatase domain. Microscilla proteins MS152, and MS153 are also included in this family. The domain present in members of this family 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 = 166 Score = 27.3 bits (61), Expect = 3.0 Identities = 10/31 (32%), Positives = 11/31 (35%), Gaps = 1/31 (3%) Query: 26 FCRFSGCNLWSGREQDRLSAQCRFCDTDFVG 56 + R G LWS A R DF G Sbjct: 68 YVRIIGTTLWSDISLFGE-AAARMRMNDFRG 97 >gnl|CDD|99911 cd05569, PTS_IIB_fructose, PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-phosphate ester in to the cytoplasm in preparation for metabolism primarily via glycolysis. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include fructose, chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, and a sensory system with similarity to the bacterial bgl system.. Length = 96 Score = 26.3 bits (59), Expect = 5.9 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 103 LIQALNKRGFEIAVETNGTI 122 L +A K G+EI VET G++ Sbjct: 21 LEKAAKKLGWEIKVETQGSL 40 >gnl|CDD|144342 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This family are structurally different from the alpha/ beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of (S)-2-haloacid dehalogenase from Pseudomonas sp. CBS3. The rest of the fold is composed of the core alpha/beta domain. Length = 190 Score = 26.1 bits (57), Expect = 7.4 Identities = 8/26 (30%), Positives = 15/26 (57%) Query: 101 VPLIQALNKRGFEIAVETNGTIEPPQ 126 ++AL +RG ++A+ TNG + Sbjct: 103 REALKALKERGIKVAILTNGDRANAE 128 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 0.322 0.142 0.450 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,695,135 Number of extensions: 138523 Number of successful extensions: 277 Number of sequences better than 10.0: 1 Number of HSP's gapped: 270 Number of HSP's successfully gapped: 20 Length of query: 211 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 121 Effective length of database: 4,318,927 Effective search space: 522590167 Effective search space used: 522590167 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 (21.9 bits) S2: 55 (25.2 bits)