RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780398|ref|YP_003064811.1| dimethyladenosine transferase [Candidatus Liberibacter asiaticus str. psy62] (284 letters) >gnl|CDD|30380 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]. Length = 259 Score = 257 bits (658), Expect = 3e-69 Identities = 108/262 (41%), Positives = 148/262 (56%), Gaps = 11/262 (4%) Query: 21 PKKYMGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQ 80 P K +GQNFL+D N++ KI E++ G V+EIG G G LT+ LL AR V IE D+ Sbjct: 4 PNKRLGQNFLIDKNVIDKIVEAANISPGDNVLEIGPGLGALTEPLLERAAR-VTAIEIDR 62 Query: 81 QFFPILKDISSQHPNRLEIIQDDALKVDFEKFFNISSPIRIIANLPYNIGTRLLFNWISA 140 + +LK+ + + N L +I DALK DF P +++ANLPYNI + +LF + Sbjct: 63 RLAEVLKERFAPYDN-LTVINGDALKFDFPSLAQ---PYKVVANLPYNISSPILFKLLEE 118 Query: 141 DTWPPFWESLTLLFQKEVGERITAQKNSPHYGRLSVLTGWRTKATMMFDISPHVFFPSPK 200 + + L+ QKEV ER+ A+ S YGRLSVL + ++FD+ P F+P PK Sbjct: 119 KFII---QDMVLMVQKEVAERLVAKPGSKDYGRLSVLVQYYADVEIVFDVPPSAFYPPPK 175 Query: 201 VTSTVIHFIPHLNPIPCC--LESLKKITQEAFGKRRKTLRQSLKRLGG-ENLLHQAGIET 257 V S V+ +P E K + AF +RRKTLR +LK L G E +L AGI+ Sbjct: 176 VDSAVVRLVPKKEKPSPVKDEEKFFKFVKAAFSQRRKTLRNNLKNLFGLEEVLEAAGIDP 235 Query: 258 NLRAENLSIEDFCRITNILTDN 279 N RAENLS EDF ++ N L Sbjct: 236 NARAENLSPEDFLKLANALKGF 257 >gnl|CDD|36039 KOG0821, KOG0821, KOG0821, Predicted ribosomal RNA adenine dimethylase [RNA processing and modification]. Length = 326 Score = 162 bits (410), Expect = 1e-40 Identities = 92/290 (31%), Positives = 145/290 (50%), Gaps = 23/290 (7%) Query: 9 SLKTILSHYKIIPKKYMGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTL 68 +++ I+ Y++ K + QNFL+DL + KI + +G+L V EIG GPG +T+ +L Sbjct: 12 TIREIIKLYRLQAAKQLSQNFLMDLRLTDKIVKKAGNLTNAYVYEIGPGPGGITRSILNA 71 Query: 69 GARKVIVIEKDQQFFPILKDISSQHPNRLEIIQDDALKVDFEKFFNISS---------PI 119 +++V+EKD +F P L+ +S P +L I D L+ EK F+ S + Sbjct: 72 DVARLLVVEKDTRFIPGLQMLSEAAPGKLRIHHGDVLRFKIEKAFSESLKRPWEDDPPNV 131 Query: 120 RIIANLPYNIGTRLLFNWISADT-----WPPFWESLTLLFQKEVGERITAQKNSPHYGRL 174 II NLP+++ T L+ W+ + + +TL FQKEV ER+ A S RL Sbjct: 132 HIIGNLPFSVSTPLIIKWLENISCRDGPFVYGRTQMTLTFQKEVAERLCAPTGSKQRSRL 191 Query: 175 SVLTGWRTKATMMFDISPHVFFPSPKVTSTVIHFIPHLNP-IPCCLESLKKITQEAFGKR 233 SV++ + + M+F I F P P+V V+HF P P I + ++K+ + F R Sbjct: 192 SVMSQYLCEPRMIFTIPGQAFVPKPQVDVGVVHFTPLKQPKIEQPFKLVEKVVRNVFQFR 251 Query: 234 RKTLRQSLKRL--------GGENLLHQAGIETNLRAENLSIEDFCRITNI 275 +K + L+ L LL A I+ LR LSIE F + + Sbjct: 252 QKYCHRGLRTLFPEEQRLESTGRLLELADIDPTLRPRQLSIEQFKSLAEV 301 >gnl|CDD|109456 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase. Length = 258 Score = 159 bits (405), Expect = 7e-40 Identities = 73/263 (27%), Positives = 122/263 (46%), Gaps = 13/263 (4%) Query: 21 PKKYMGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQ 80 ++ GQNFL + ++ +I + + + TV+EIG G G LT+ L A++V+ IE D Sbjct: 4 GRRSYGQNFLTNKKVINRIVDKANLQESDTVLEIGPGKGALTEELAKR-AKQVVAIEIDP 62 Query: 81 QFFPILKDISSQHPNRLEIIQDDALKVDFEKFFNISSPIRIIANLPYNIGTRLLFNWISA 140 + L+ + HPN +E++ D LK F K P ++ N+PYNI T ++ + Sbjct: 63 RLAKRLQKKLALHPN-VEVVHQDFLKFSFPKHE----PFLVVGNIPYNITTPIVKKLLFE 117 Query: 141 DTWPPFWESLTLLFQKEVGERITAQKNSPHYGRLSVLTGWRTKATMMFDISPHVFFPSPK 200 + + L+ QKE R+ A+ S Y RL+VLT T ++ + F P PK Sbjct: 118 PRFG--RVKMLLVVQKEFARRLLARPGSKIYSRLTVLTEPFTDIKLVAKVPRSSFRPPPK 175 Query: 201 VTSTVIHFIPHLNPIPC--CLESLKKITQEAFGKRRKTLRQSLKRLGGENLLHQA---GI 255 V S ++ +P+ L+ + ++ F + ++L SL+RL + I Sbjct: 176 VDSALVRLERRDHPLLPVKDLKKYDYLVRKLFNGKGRSLFTSLRRLFPGGQVQALSKTRI 235 Query: 256 ETNLRAENLSIEDFCRITNILTD 278 N LS E + I L Sbjct: 236 NDNALVGKLSPEQWLTIFKELAK 258 >gnl|CDD|36038 KOG0820, KOG0820, KOG0820, Ribosomal RNA adenine dimethylase [RNA processing and modification]. Length = 315 Score = 117 bits (294), Expect = 4e-27 Identities = 63/224 (28%), Positives = 102/224 (45%), Gaps = 12/224 (5%) Query: 21 PKKYMGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQ 80 K GQ+ L + ++ +I E + V+E+G G GNLT LL G KV+ +E D Sbjct: 32 FNKDFGQHILKNPLVIDQIVEKADLKPTDVVLEVGPGTGNLTVKLLEAGK-KVVAVEIDP 90 Query: 81 QFFPILKDISSQHP--NRLEIIQDDALKVDFEKFFNISSPIRIIANLPYNIGTRLLFNWI 138 + L+ P +L+++ D LK D F+ ++NLPY I + L+F + Sbjct: 91 RMVAELEKRVQGTPKSGKLQVLHGDFLKTDL-PRFDG-----CVSNLPYQISSPLVFKLL 144 Query: 139 SADTWPPFWESLTLLFQKEVGERITAQKNSPHYGRLSVLTGWRTKATMMFDISPHVFFPS 198 P F ++ L+FQ+E R+ A+ Y RLS+ + T + + + F P Sbjct: 145 LHR--PVFRCAV-LMFQREFALRLVARPGDSLYCRLSINVQLLARVTHIMKVGKNNFRPP 201 Query: 199 PKVTSTVIHFIPHLNPIPCCLESLKKITQEAFGKRRKTLRQSLK 242 PKV S+V+ P P + + F ++ KTL K Sbjct: 202 PKVESSVVRIEPKNPRPPVDFHEWDGLLRICFLRKNKTLMAPFK 245 >gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).. Length = 107 Score = 44.7 bits (106), Expect = 3e-05 Identities = 16/91 (17%), Positives = 39/91 (42%), Gaps = 4/91 (4%) Query: 50 TVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKDISSQH-PNRLEIIQDDALKVD 108 V+++G G G L L + +V ++ + + ++ + +E+++ DA ++ Sbjct: 1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELP 60 Query: 109 FEKFFNISSPIRIIANLPYNIGTRLLFNWIS 139 E S II++ P + L ++ Sbjct: 61 PEAD---ESFDVIISDPPLHHLVEDLARFLE 88 >gnl|CDD|32444 COG2263, COG2263, Predicted RNA methylase [Translation, ribosomal structure and biogenesis]. Length = 198 Score = 41.0 bits (96), Expect = 4e-04 Identities = 19/70 (27%), Positives = 34/70 (48%) Query: 39 IAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKDISSQHPNRLE 98 +A G L+G TV+++GAG G L LGA +V+ ++ D + I + + + +E Sbjct: 37 VAYLRGDLEGKTVLDLGAGTGILAIGAALLGASRVLAVDIDPEALEIARANAEELLGDVE 96 Query: 99 IIQDDALKVD 108 + D Sbjct: 97 FVVADVSDFR 106 >gnl|CDD|33834 COG4076, COG4076, Predicted RNA methylase [General function prediction only]. Length = 252 Score = 38.8 bits (90), Expect = 0.001 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%) Query: 50 TVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPIL-KDISSQHPNRLEIIQDDALKVD 108 T ++GAG G L+ ++ A +VI IEKD + + +++ E++ DA D Sbjct: 35 TFADLGAGSGILS-VVAAHAAERVIAIEKDPKRARLAEENLHVPGDVNWEVVVGDARDYD 93 Query: 109 FEK 111 FE Sbjct: 94 FEN 96 >gnl|CDD|31989 COG1804, CaiB, Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]. Length = 396 Score = 34.9 bits (80), Expect = 0.024 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 5/39 (12%) Query: 42 SSGSLDGITVIEIG---AGPGNLTQMLLTLGARKVIVIE 77 G L+G+ VI++ AGP Q+L LGA VI +E Sbjct: 4 RKGPLEGLRVIDLAHVLAGPF-AGQLLADLGAE-VIKVE 40 >gnl|CDD|31263 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]. Length = 350 Score = 34.2 bits (78), Expect = 0.042 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 2/43 (4%) Query: 40 AESSGSLDGITVIEIGAGP-GNLTQMLLTL-GARKVIVIEKDQ 80 AE + G TV+ +GAGP G L L L GA VIV+++ Sbjct: 161 AERAAVRPGGTVVVVGAGPIGLLAIALAKLLGASVVIVVDRSP 203 >gnl|CDD|176193 cd08231, MDR_TM0436_like, Hypothetical enzyme TM0436 resembles the zinc-dependent alcohol dehydrogenases (ADH). This group contains the hypothetical TM0436 alcohol dehydrogenase from Thermotoga maritima, proteins annotated as 5-exo-alcohol dehydrogenase, and other members of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. MDR, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. Length = 361 Score = 32.6 bits (75), Expect = 0.14 Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%) Query: 48 GITVIEIGAGPGNLTQ--MLLTLGARKVIVIEKDQQ 81 G TV+ GAGP L GAR+VIVI+ + Sbjct: 178 GDTVVVQGAGPLGLYAVAAAKLAGARRVIVIDGSPE 213 >gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative L-iditol 2-dehydrogenase based on annotation of some members in this subgroup. L-iditol 2-dehydrogenase catalyzes the NAD+-dependent conversion of L-iditol to L-sorbose in fructose and mannose metabolism. This enzyme is related to sorbitol dehydrogenase, alcohol dehydrogenase, and other medium chain dehydrogenase/reductases. The zinc-dependent alcohol dehydrogenase (ADH-Zn)-like family of proteins is a diverse group of proteins related to the first identified member, class I mammalian ADH. This group is also called the medium chain dehydrogenases/reductase family (MDR) to highlight its broad range of activities and to distinguish from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal GroES-like catalytic domain. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Length = 343 Score = 32.2 bits (74), Expect = 0.16 Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 2/36 (5%) Query: 48 GITVIEIGAGPGNLTQMLLTL--GARKVIVIEKDQQ 81 G TV+ IGAGP L +L GARKVIV + ++ Sbjct: 166 GDTVLVIGAGPIGLLHAMLAKASGARKVIVSDLNEF 201 >gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Related proteins include threonine dehydrogenase, formaldehyde dehydrogenase, and butanediol dehydrogenase. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Horse liver alcohol dehydrogenase is a dimeric enzyme and each subunit has two domains. The NAD binding domain is in a Rossmann fold and the catalytic domain contains a zinc ion to which substrates bind. There is a cleft between the domains that closes upon formation of the ternary complex. Length = 343 Score = 32.2 bits (74), Expect = 0.17 Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 2/36 (5%) Query: 48 GITVIEIGAGP-GNLT-QMLLTLGARKVIVIEKDQQ 81 G TV+ IGAG G L Q L LGA++VI ++ D + Sbjct: 160 GDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDE 195 >gnl|CDD|37862 KOG2651, KOG2651, KOG2651, rRNA adenine N-6-methyltransferase [RNA processing and modification]. Length = 476 Score = 31.9 bits (72), Expect = 0.20 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 1/72 (1%) Query: 12 TILSHYKIIPKKYMGQNFLLDLNILKKIAESSGSLDGI-TVIEIGAGPGNLTQMLLTLGA 70 + S + +K++ ++ L ++ S GI V+++GAG G+L++ L Sbjct: 117 SQSSQLTALFRKHVRPKKQHEIRRLSELVSSISDFTGIDQVVDVGAGQGHLSRFLSLGYG 176 Query: 71 RKVIVIEKDQQF 82 V IE Q+ Sbjct: 177 LSVKAIEGSQRL 188 >gnl|CDD|145073 pfam01728, FtsJ, FtsJ-like methyltransferase. This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Length = 176 Score = 31.4 bits (72), Expect = 0.26 Identities = 13/28 (46%), Positives = 20/28 (71%) Query: 48 GITVIEIGAGPGNLTQMLLTLGARKVIV 75 G TV+++GA PG +Q+LL GA+ +V Sbjct: 22 GKTVLDLGAAPGGFSQVLLERGAKGRVV 49 >gnl|CDD|33744 COG3963, COG3963, Phospholipid N-methyltransferase [Lipid metabolism]. Length = 194 Score = 31.0 bits (70), Expect = 0.34 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%) Query: 37 KKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGAR--KVIVIEKDQQFFPILKDISSQHP 94 +K+A G+ V+E+G G G +T+ +L+ G R + IE F L Q Sbjct: 38 RKMASVIDPESGLPVLELGPGTGVITKAILSRGVRPESLTAIEYSPDFVCHLN----QLY 93 Query: 95 NRLEIIQDDALKVD 108 + II DA + Sbjct: 94 PGVNIINGDAFDLR 107 >gnl|CDD|30641 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure and biogenesis]. Length = 205 Score = 30.6 bits (69), Expect = 0.45 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 8/65 (12%) Query: 47 DGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKDISSQHPNRLEIIQDDALK 106 G+ V+++GA PG +Q+ ++ D P+ P + +Q D Sbjct: 45 PGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDIL--PM-----KPIPG-VIFLQGDITD 96 Query: 107 VDFEK 111 D + Sbjct: 97 EDTLE 101 >gnl|CDD|32589 COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]. Length = 256 Score = 30.6 bits (69), Expect = 0.45 Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 9/92 (9%) Query: 39 IAESSGSLDGITVIEIGAGPGNLTQMLLTL--GARKVIVIEKDQQFFPILKDISSQH--P 94 I G G V+E G G G LT L V E + F ++ S+ Sbjct: 86 IVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSEFGLG 145 Query: 95 NRLEIIQDDALKVDFEKFFNISSPIRIIANLP 126 +R+ + D + E+ + + +LP Sbjct: 146 DRVTLKLGDVREGIDEEDVD-----AVFLDLP 172 >gnl|CDD|31382 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]. Length = 245 Score = 30.2 bits (68), Expect = 0.74 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%) Query: 36 LKKIAESSG-SLDGITVIEIGAGPGNLTQMLLTLGARKVIVIE 77 L+K E + G V++IG+ G T +LL GA+ V ++ Sbjct: 67 LEKALEEFELDVKGKVVLDIGSSTGGFTDVLLQRGAKHVYAVD 109 >gnl|CDD|32445 COG2264, PrmA, Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]. Length = 300 Score = 29.9 bits (67), Expect = 0.87 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 7/82 (8%) Query: 46 LDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKDISSQH--PNRLEIIQDD 103 G TV+++G G G L LGA+KV+ ++ D Q ++ + + ++ Sbjct: 161 KKGKTVLDVGCGSGILAIAAAKLGAKKVVGVDIDPQAVEAARENARLNGVELLVQAKGFL 220 Query: 104 ALKVDFEKFFNISSPIRIIANL 125 L+V F++ I+AN+ Sbjct: 221 LLEVPENGPFDV-----IVANI 237 >gnl|CDD|32353 COG2170, COG2170, Uncharacterized conserved protein [Function unknown]. Length = 369 Score = 29.1 bits (65), Expect = 1.3 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 7/70 (10%) Query: 147 WESLTLLFQKEVGERITAQKNSPHYGRLSVLTGWRTKATMMFDISPHVFFPSPKVTSTVI 206 T F + + +P Y RL TG+ + + HV PSP ++ Sbjct: 86 CGGGTHPFADWRRQEVPD---NPRYQRLIERTGYLGRQMTVAGQHVHVGIPSPDDAMYLL 142 Query: 207 H----FIPHL 212 H ++PHL Sbjct: 143 HRLLRYVPHL 152 >gnl|CDD|32409 COG2227, UbiG, 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]. Length = 243 Score = 29.1 bits (65), Expect = 1.5 Identities = 14/41 (34%), Positives = 25/41 (60%) Query: 31 LDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGAR 71 L L+ ++++A L G+ V+++G G G L++ L LGA Sbjct: 43 LRLDYIREVARLRFDLPGLRVLDVGCGGGILSEPLARLGAS 83 >gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Length = 386 Score = 29.0 bits (66), Expect = 1.6 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 18/78 (23%) Query: 47 DGITVIEIGAGP-GNLTQML-LTLGARKVIVIEKDQQFFPILKDISSQHPNRLEIIQD-- 102 G TV G GP G LGA +VI I++ P RLE+ + Sbjct: 184 PGDTVAVWGCGPVGLFAARSAKLLGAERVIAIDR--------------VPERLEMARSHL 229 Query: 103 DALKVDFEKFFNISSPIR 120 A ++FE+ ++ +R Sbjct: 230 GAETINFEEVDDVVEALR 247 >gnl|CDD|176196 cd08234, threonine_DH_like, L-threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine, via NAD(H)-dependent oxidation. THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Length = 334 Score = 29.0 bits (66), Expect = 1.6 Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 2/35 (5%) Query: 48 GITVIEIGAGP-GNLTQMLLTL-GARKVIVIEKDQ 80 G +V+ GAGP G L LL L GA +V V E ++ Sbjct: 160 GDSVLVFGAGPIGLLLAQLLKLNGASRVTVAEPNE 194 >gnl|CDD|144557 pfam01012, ETF, Electron transfer flavoprotein domain. This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein. Length = 161 Score = 28.7 bits (65), Expect = 1.7 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%) Query: 32 DLNIL---KKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQ 80 DL L +++AE+ G +T + +G P +L +GA KV+V+E Sbjct: 17 DLEALEAARQLAEALGG--EVTAVVVGPVPAAAEALLAAMGADKVLVVEDPA 66 >gnl|CDD|36712 KOG1499, KOG1499, KOG1499, Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones, Transcription, Signal transduction mechanisms]. Length = 346 Score = 28.7 bits (64), Expect = 1.9 Identities = 12/28 (42%), Positives = 17/28 (60%) Query: 50 TVIEIGAGPGNLTQMLLTLGARKVIVIE 77 TV+++G G G L+ GARKV +E Sbjct: 63 TVLDVGCGTGILSMFAAKAGARKVYAVE 90 >gnl|CDD|30357 COG0007, CysG, Uroporphyrinogen-III methylase [Coenzyme metabolism]. Length = 244 Score = 28.3 bits (63), Expect = 2.4 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 16/66 (24%) Query: 51 VIEIGAGPGNLTQMLLTLGARKVI----VIEKDQQFFPILKDISSQHPNRLEIIQDDALK 106 V +GAGPG+ LLTL A + + V+ D+ + +++ L + + DA + Sbjct: 6 VYLVGAGPGDPG--LLTLRALRALQEADVVLYDRL---VPEEV-------LALARRDAER 53 Query: 107 VDFEKF 112 + K Sbjct: 54 IYVGKR 59 >gnl|CDD|36714 KOG1501, KOG1501, KOG1501, Arginine N-methyltransferase [General function prediction only]. Length = 636 Score = 28.5 bits (63), Expect = 2.4 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 2/47 (4%) Query: 33 LNILKKIAESSGSLDG--ITVIEIGAGPGNLTQMLLTLGARKVIVIE 77 L I K I E LD + V++IG G G L+ M + GA V E Sbjct: 50 LGIEKTITEPKHVLDIGKVFVLDIGTGTGLLSMMAVRAGADSVTACE 96 >gnl|CDD|36713 KOG1500, KOG1500, KOG1500, Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones, Transcription]. Length = 517 Score = 28.1 bits (62), Expect = 2.6 Identities = 15/53 (28%), Positives = 26/53 (49%) Query: 25 MGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIE 77 M Q+++ + I E+ V+++GAG G L+ GA+KV +E Sbjct: 155 MMQDYVRTGTYQRAILENHSDFQDKIVLDVGAGSGILSFFAAQAGAKKVYAVE 207 >gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like, 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members. This subgroup of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family has members identified as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase and alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. Length = 277 Score = 28.4 bits (64), Expect = 2.6 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 48 GITVIEIGAGP-GNLT-QMLLTLGARKVIVIE 77 G V +G G G L Q+ GAR+V+ ++ Sbjct: 98 GERVAVVGLGLVGLLAAQLAKAAGAREVVGVD 129 >gnl|CDD|109889 pfam00851, Peptidase_C6, Helper component proteinase. This protein is found in genome polyproteins of potyviruses. Length = 453 Score = 28.0 bits (63), Expect = 2.8 Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 23/98 (23%) Query: 193 HVFFPSPKVTSTVIHFIPHLNPIPCCLESLKKITQEAFGKR-RKTLRQSLKRLGGE---- 247 FP K+T C ++ K ++++ +R R L + L+ LG E Sbjct: 40 QALFPCGKITCKK------------CAQNYKNLSKDEIKERLRTRLMRQLEELGSEHPRF 87 Query: 248 ----NLLHQAGIETNLRAENLSIEDFCRITNILTDNQD 281 +L + ++ N+++E F IT ++ D Sbjct: 88 KHVRQVLER--LKQATNVTNMNLEAFSEITKLIGGRTD 123 >gnl|CDD|31085 COG0742, COG0742, N6-adenine-specific methylase [DNA replication, recombination, and repair]. Length = 187 Score = 28.3 bits (63), Expect = 2.8 Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 2/63 (3%) Query: 46 LDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKD--ISSQHPNRLEIIQDD 103 ++G V+++ AG G L L+ GA +V+ +EKD++ ILK+ + ++++D Sbjct: 42 IEGARVLDLFAGSGALGLEALSRGAARVVFVEKDRKAVKILKENLKALGLEGEARVLRND 101 Query: 104 ALK 106 AL+ Sbjct: 102 ALR 104 >gnl|CDD|32588 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]. Length = 209 Score = 27.9 bits (62), Expect = 3.7 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%) Query: 48 GITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQF 82 G V+EIG G G +L L +V+ IE+ ++ Sbjct: 73 GDRVLEIGTGSGYQAAVLARL-VGRVVSIERIEEL 106 >gnl|CDD|109450 pfam00392, GntR, Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor. Length = 64 Score = 27.2 bits (61), Expect = 5.6 Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 219 LESLKKITQEAFGKRRKTLRQSLKRLGGENLLH 251 L S +++ FG R T+R++L+RL E L+ Sbjct: 24 LPSEREL-AAEFGVSRTTVREALRRLEAEGLVE 55 >gnl|CDD|32723 COG2898, COG2898, Uncharacterized conserved protein [Function unknown]. Length = 538 Score = 27.2 bits (60), Expect = 5.7 Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 3/41 (7%) Query: 231 GKRRKTLRQSLKRLGGENL---LHQAGIETNLRAENLSIED 268 GKR + LRQ++ R E L + E +I D Sbjct: 327 GKRMRGLRQAVNRADREGLTFEIVPPDQSPAELDELRAISD 367 >gnl|CDD|144255 pfam00590, TP_methylase, Tetrapyrrole (Corrin/Porphyrin) Methylases. This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase. Length = 200 Score = 26.9 bits (60), Expect = 5.8 Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%) Query: 54 IGAGPGNLTQMLLTLGARKVI 74 +G GPG+ LLTL A + + Sbjct: 4 VGIGPGDPE--LLTLRALRAL 22 >gnl|CDD|145054 pfam01700, Orbi_VP3, Orbivirus VP3 (T2) protein. The orbivirus VP3 protein is part of the virus core and makes a 'subcore' shell made up of 120 copies of the 100K protein. VP3 particles can also bind RNA and are fundamental in the early stages of viral core formation. Also found in the family is structural core protein VP2 from broadhaven virus which is similar to VP3 in bluetongue virus. Orbivirus are part of the larger reoviridae which have a dsRNA genome of 10-12 linear segments; orbivirus found in this family include bluetongue virus and epizootic hemorrhagic disease virus. Length = 890 Score = 27.0 bits (60), Expect = 6.3 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 5/56 (8%) Query: 65 LLTLGARKVIVIEKDQQFFPILKDISSQHPNRLEIIQDDALKVDFEKFFNISSPIR 120 + +KV I + F IL DI + +E+ DAL VD + N+ S + Sbjct: 114 FYSTILKKVKFIRDEGSF--ILHDIPTHDHRGMEVADPDALGVDVK---NMLSSLT 164 >gnl|CDD|146308 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95. Length = 181 Score = 26.8 bits (60), Expect = 7.3 Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 21/104 (20%) Query: 44 GSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKD-ISSQHPNRLEIIQD 102 L G V+++ AG G L L+ GA V+ +EKD++ LK+ + + + D Sbjct: 40 FELGGARVLDLFAGSGALGLEALSRGASSVVFVEKDKKAVATLKENLEALGLEGAVLRMD 99 Query: 103 DALKVDFEKFFNISSPIRIIANLPYNIGTRLLFNWISADTWPPF 146 A L G F+ + D PP+ Sbjct: 100 AARA------------------LLRLAGKGPPFDLVFLD--PPY 123 >gnl|CDD|32702 COG2875, CobM, Precorrin-4 methylase [Coenzyme metabolism]. Length = 254 Score = 26.7 bits (59), Expect = 7.5 Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 2/25 (8%) Query: 50 TVIEIGAGPGNLTQMLLTLGARKVI 74 V IGAGPG+ L+T+ ++++ Sbjct: 4 KVYFIGAGPGDPD--LITVKGQRLL 26 >gnl|CDD|119429 cd05169, PIKKc_TOR, TOR (Target of rapamycin), catalytic domain; The TOR catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. TOR is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). TOR contains a rapamycin binding domain, a catalytic domain, and a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. It is also called FRAP (FK506 binding protein 12-rapamycin associated protein). TOR is a central component of the eukaryotic growth regulatory network. It controls the expression of many genes transcribed by all three RNA polymerases. It associates with other proteins to form two distinct complexes, TORC1 and TORC2. TORC1 is involved in diverse growth-related functions including protein synthesis, nutrient use and transport, autophagy and stress responses. TORC2 is involved in organizing cytoskeletal structures.. Length = 280 Score = 26.7 bits (60), Expect = 8.0 Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%) Query: 80 QQFFPILKDISS-QHPNRLEIIQDDALKVDF 109 F P+LK I S Q P RL I+ D + F Sbjct: 2 SSFDPVLKVIPSKQRPRRLTIVGSDGKEYKF 32 >gnl|CDD|37936 KOG2725, KOG2725, KOG2725, Cytochrome oxidase assembly factor COX15 [Posttranslational modification, protein turnover, chaperones]. Length = 411 Score = 26.5 bits (58), Expect = 9.0 Identities = 13/46 (28%), Positives = 18/46 (39%) Query: 131 TRLLFNWISADTWPPFWESLTLLFQKEVGERITAQKNSPHYGRLSV 176 TRL + +S W E Q+E E K SP + L+ Sbjct: 90 TRLTESGLSMVDWKLITEMKPPTSQEEWEEEFEKYKQSPEFKLLNS 135 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 0.138 0.409 Gapped Lambda K H 0.267 0.0731 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,440,879 Number of extensions: 182917 Number of successful extensions: 576 Number of sequences better than 10.0: 1 Number of HSP's gapped: 559 Number of HSP's successfully gapped: 51 Length of query: 284 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 191 Effective length of database: 4,254,100 Effective search space: 812533100 Effective search space used: 812533100 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: 57 (25.7 bits)