RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781095|ref|YP_003065508.1| UDP-N-acetylenolpyruvoylglucosamine reductase [Candidatus Liberibacter asiaticus str. psy62] (318 letters) >gnl|CDD|31154 COG0812, MurB, UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]. Length = 291 Score = 308 bits (791), Expect = 1e-84 Identities = 121/291 (41%), Positives = 166/291 (57%), Gaps = 3/291 (1%) Query: 20 KFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLPS-DIPITIVGLGSNILVRDA 78 + + N PLK+ T FR GG AEV+ +P+DI +LK L + D+P+ I+G GSN+LVRD Sbjct: 2 RIKTNVPLKRYTTFRIGGPAEVLVEPRDIEELKAALKYAKAEDLPVLILGGGSNLLVRDG 61 Query: 79 GIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGG 138 GI GVV++L F IE + + GA L AL +G+ G F GIPGS+GG Sbjct: 62 GIGGVVIKLGKLNFIEIEGDDGL-IEAGAGAPWHDLVRFALENGLSGLEFLAGIPGSVGG 120 Query: 139 AAYMNAGANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYRSSEITK-DLIITHVVLRG 197 A MNAGA E S +V V +DR G + E+L + YR+S K L++ V + Sbjct: 121 AVIMNAGAYGVEISDVLVSVEVLDRDGEVRWLSAEELGFGYRTSPFKKEYLVVLSVEFKL 180 Query: 198 FPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAK 257 I AA+ + RE QPI + GS FKNP G A LIE++G +G GGA+ Sbjct: 181 TKGDPEDILAAMCAIRRRRELKQPIDLPSAGSFFKNPVGDFAGWLIEEAGLKGYRIGGAQ 240 Query: 258 ISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLGDFFD 308 +SE H NF+IN NAT D+ L E VR++V + GI LE E+K +G+ + Sbjct: 241 VSEKHANFLINTGNATAKDVLDLIEHVRQRVLEKFGIELEPEVKIIGESGE 291 >gnl|CDD|111727 pfam02873, MurB_C, UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain. Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. Length = 103 Score = 118 bits (298), Expect = 2e-27 Identities = 47/104 (45%), Positives = 63/104 (60%), Gaps = 1/104 (0%) Query: 201 SQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISE 260 Q I+ A R++ QP K GSTFKNP G +A LIE++G +G + GGA++SE Sbjct: 1 PQQILKAMKKIR-QTRKSTQPYKFPNAGSTFKNPEGFAAGWLIEEAGLKGYQIGGAQVSE 59 Query: 261 LHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLG 304 H NF+IN NAT D+ L VR+ VF + GI LE E+K +G Sbjct: 60 KHANFIINTGNATAEDVVDLIRHVRQTVFEKFGIWLEPEVKIIG 103 >gnl|CDD|144965 pfam01565, FAD_binding_4, FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. Length = 138 Score = 56.4 bits (137), Expect = 8e-09 Identities = 34/140 (24%), Positives = 56/140 (40%), Gaps = 11/140 (7%) Query: 39 AEVMFQPQDIHDLKYFLTLLPS-DIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEV 97 + +P+ ++ + L +P+ + G GS+ L+ DA GVVL LS + I Sbjct: 1 PAAVVRPESEEEVAAIVRLANEHGLPVLVRGGGSS-LLGDAVTGGVVLDLSR--LNGILE 57 Query: 98 RNHCEMI--VGARCSGKSLANSALRHG-IGGFHFFYGIPGSIGGAAYMNAGANNCE---- 150 + V A + L + G + G GIPG++GGA N G E Sbjct: 58 IDPENGTATVEAGVTLGDLVRALAAKGLLLGLEPGSGIPGTVGGAIATNGGGYGSEKYGL 117 Query: 151 TSQYVVEVHGIDRKGNQHVI 170 T V+ + + G + Sbjct: 118 TRDNVLSLEVVLADGEVVRL 137 >gnl|CDD|33712 COG3930, COG3930, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 434 Score = 34.6 bits (79), Expect = 0.037 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 9/79 (11%) Query: 132 IPGSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYRSSEITKDLIIT 191 + + A M GA+ + ++ HG DR+ + + R YR TKD Sbjct: 305 LANRVLACAAMLDGADFLDVFHFLTREHGFDREDAFNNVLR-----VYRGGGFTKD---- 355 Query: 192 HVVLRGFPESQNIISAAIA 210 + LRGF + + A Sbjct: 356 AIYLRGFILILDHLQLGGA 374 >gnl|CDD|31876 COG1690, RtcB, Uncharacterized conserved protein [Function unknown]. Length = 432 Score = 31.1 bits (70), Expect = 0.38 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 7/65 (10%) Query: 132 IPGSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYRSSEITKDLIIT 191 IPGS+G A+Y+ G N E + HG R V+ R K + E+ L T Sbjct: 330 IPGSMGTASYIVRGVGNEEA--FGSTSHGAGR-----VLSRTAAKRKLSGKEVQDALKAT 382 Query: 192 HVVLR 196 +V+R Sbjct: 383 GIVVR 387 >gnl|CDD|35996 KOG0777, KOG0777, KOG0777, Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]. Length = 322 Score = 30.0 bits (67), Expect = 0.83 Identities = 13/27 (48%), Positives = 15/27 (55%) Query: 116 NSALRHGIGGFHFFYGIPGSIGGAAYM 142 NS LR G H YG+P +I A YM Sbjct: 80 NSPLRRGQPVAHSIYGVPSTINTANYM 106 >gnl|CDD|38076 KOG2865, KOG2865, KOG2865, NADH:ubiquinone oxidoreductase, NDUFA9/39kDa subunit [Energy production and conversion]. Length = 391 Score = 29.5 bits (66), Expect = 1.3 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 14/89 (15%) Query: 104 IVGARCSG----KSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVH 159 +G + +++A++ G GG GI ++ GA +YVV Sbjct: 30 GASNHLNGPDPCRYSSSAAMKKGTGGRSSVSGIVATVFGATGF--------LGRYVVNKL 81 Query: 160 GIDRKGNQHVIPREQLKYQYRSSEITKDL 188 + G+Q +IP +Y R ++ DL Sbjct: 82 A--KMGSQVIIPYRGDEYDPRHLKVMGDL 108 >gnl|CDD|153386 cd07949, PCA_45_Doxase_B_like_1, The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase. This subfamily is composed of proteins of unknown function with similarity to the B subunit of Protocatechuate 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. Length = 276 Score = 29.3 bits (66), Expect = 1.5 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 10/50 (20%) Query: 235 TGHSAWQLIEKSGCRGLEFG---------GAKISELHCNFMINADN-ATG 274 T +S +L+E +G +G+EF G ++ E+H N+ I N A G Sbjct: 222 TKYSIEELVELAGTQGVEFLMWIAMRGALGDEVREVHRNYHIPISNTAAG 271 >gnl|CDD|143499 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Length = 365 Score = 29.2 bits (66), Expect = 1.5 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 7/74 (9%) Query: 57 LLPSDIP--ITIVGLGSNI---LVRDAGIRGVVLRLSNAGFSNIE--VRNHCEMIVGARC 109 ++PS I I VG+ SN +VR+AG G +LR+ A S IE + + E ++G+ Sbjct: 44 VMPSIIAQNIPCVGITSNEEARVVREAGFTGKILRVRTATPSEIEDALAYNIEELIGSLD 103 Query: 110 SGKSLANSALRHGI 123 + + + A RHG Sbjct: 104 QAEQIDSLAKRHGK 117 >gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria. Length = 374 Score = 28.3 bits (64), Expect = 2.6 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 9/45 (20%) Query: 94 NIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGG 138 + R+ +M + + G +LAN+ G+G H G+ G IGG Sbjct: 227 DAAARD--DMALASLLGGIALANA----GLGAVH---GLAGPIGG 262 >gnl|CDD|36296 KOG1080, KOG1080, KOG1080, Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics, Transcription]. Length = 1005 Score = 27.7 bits (61), Expect = 4.1 Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 3/43 (6%) Query: 277 LEYLGEQVRKKVFNQSGILLEWE-IKR--LGDFFDHQIVDATK 316 +EY GE VR + + E I L D +VDATK Sbjct: 893 IEYRGELVRSSIADLREARYERMGIGDSYLFRIDDEVVVDATK 935 >gnl|CDD|37756 KOG2545, KOG2545, KOG2545, Conserved membrane protein [Function unknown]. Length = 543 Score = 27.3 bits (60), Expect = 5.2 Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%) Query: 46 QDI-HDLKYFLTLLPSDIPITIVGLGSNILVRDAGIR 81 Q + +D +Y+ + S++ + I+ G +IL D GIR Sbjct: 407 QKLTYDFQYYQMEVHSNVRVLILSEGRSILPADLGIR 443 >gnl|CDD|32881 COG3067, NhaB, Na+/H+ antiporter [Inorganic ion transport and metabolism]. Length = 516 Score = 26.8 bits (59), Expect = 8.1 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 8/55 (14%) Query: 36 GGNAEVMFQPQDI--------HDLKYFLTLLPSDIPITIVGLGSNILVRDAGIRG 82 GG ++ +PQ++ H ++FL + P +P+ I GL + +LV G Sbjct: 216 GGVMTMVGEPQNLIIAKQAGWHFGEFFLRMAPVTVPVLICGLLTCLLVEKFRWFG 270 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 0.140 0.423 Gapped Lambda K H 0.267 0.0728 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,929,006 Number of extensions: 208348 Number of successful extensions: 441 Number of sequences better than 10.0: 1 Number of HSP's gapped: 436 Number of HSP's successfully gapped: 20 Length of query: 318 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 224 Effective length of database: 4,232,491 Effective search space: 948077984 Effective search space used: 948077984 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)