RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780862|ref|YP_003065275.1| NADH dehydrogenase subunit J [Candidatus Liberibacter asiaticus str. psy62] (199 letters) >gnl|CDD|177129 MTH00057, ND6, NADH dehydrogenase subunit 6; Provisional. Length = 186 Score = 127 bits (320), Expect = 3e-30 Identities = 73/178 (41%), Positives = 107/178 (60%), Gaps = 7/178 (3%) Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66 FYLF+ IIS +V++ NP++SV LI AF +A+ LF+LL EF+A+I L+VYVGA+ Sbjct: 4 LFYLFALGVIISGIMVISALNPVHSVLWLIVAFTSASALFILLEVEFIALIFLIVYVGAI 63 Query: 67 IVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVF 126 + FLF+IMML++ F IG++ L +S + S+ ++ + F Sbjct: 64 AILFLFVIMMLNLTDLEGGGDMSNYLPAGFIIGVVF--LFEVSSGISLLSSGTKIGQWDF 121 Query: 127 -----KGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDIKRQDISKQ 179 K +N+E +G+VLYT Y Y ++ FILL++MIGAIVL +IKRQDI Q Sbjct: 122 PNWIEKESNIEVLGRVLYTDYYYLFILASFILLVAMIGAIVLTHDLIIEIKRQDIFIQ 179 >gnl|CDD|31181 COG0839, NuoJ, NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]. Length = 166 Score = 100 bits (250), Expect = 3e-22 Identities = 62/168 (36%), Positives = 100/168 (59%), Gaps = 2/168 (1%) Query: 1 MVMQSLFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLV 60 M++++L FYLF+ +AI + VV +NP+YS L ++ A LF LLGAEF+ ++ ++ Sbjct: 1 MMIETLAFYLFAVLAIAFALGVVLAKNPVYSALYLALTLLSIAALFFLLGAEFLGVVQVL 60 Query: 61 VYVGAVIVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGE 120 VYVGAV+V FLF++MML++D RG + +G++ L++ + V S Sbjct: 61 VYVGAVMVLFLFVVMMLNVDGAEVREEGLRGKPLAALVGLVLLALLIISV--AVVSGAFV 118 Query: 121 LSRLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHR 168 N++ +G VL+T Y P E++ +LL++M+GAIVL R R Sbjct: 119 PPSNPAAIGNIKALGSVLFTDYLLPFELASVLLLVAMVGAIVLARRER 166 >gnl|CDD|177103 MTH00021, ND6, NADH dehydrogenase subunit 6; Validated. Length = 188 Score = 98.6 bits (246), Expect = 9e-22 Identities = 56/187 (29%), Positives = 95/187 (50%), Gaps = 12/187 (6%) Query: 11 FSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFF 70 FS I S +V++ NP++S+F L+ FVN+A F+LLG +F+A++ L++YVGA+ + F Sbjct: 2 FSLGIIGSGIMVISALNPVHSIFWLVVVFVNSAVFFILLGLDFLALMFLIIYVGAIAILF 61 Query: 71 LFIIMMLDIDIEVAEPRKKR--------GFLGSFFIGILAAELIVCASNFMVFSAEGELS 122 LF+IM+L++ + G + A + V + Sbjct: 62 LFVIMLLNLTDFPPAFGGEADMTNYIPIGLIIGTLFFSEIASSWLIIGGPYVERWDLAFP 121 Query: 123 RLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDI----KRQDISK 178 + +N+E +G++LY Y ++ FILL++MIGAIVL ++ K+QDI Sbjct: 122 WFLISYHNIEALGRILYITCYYLFLLASFILLVAMIGAIVLTQEPGSEVGPLSKKQDIFF 181 Query: 179 QLESNPD 185 Q+ Sbjct: 182 QISRANS 188 >gnl|CDD|177256 MTH00213, ND6, NADH dehydrogenase subunit 6; Provisional. Length = 239 Score = 61.8 bits (150), Expect = 1e-10 Identities = 27/51 (52%), Positives = 40/51 (78%) Query: 27 NPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFFLFIIMML 77 N + SVF LI F+ ++GLF++LG EF+ +I L+VYVGA+ + FLF+IMM+ Sbjct: 22 NFLASVFWLILTFIGSSGLFIVLGMEFLGLIFLIVYVGAICIIFLFVIMMI 72 Score = 44.5 bits (105), Expect = 2e-05 Identities = 22/38 (57%), Positives = 26/38 (68%) Query: 128 GNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLML 165 G N+E IG VLY Y Y + FILL++MIGAIVL L Sbjct: 196 GTNLEAIGSVLYINYYYAFILVSFILLVAMIGAIVLGL 233 >gnl|CDD|176959 CHL00016, ndhG, NADH dehydrogenase subunit 6. Length = 182 Score = 59.1 bits (144), Expect = 8e-10 Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 10/168 (5%) Query: 4 QSLFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYV 63 I+ S VV + NPIYS FSL V + ++LL A+FVA L++YV Sbjct: 8 HDFLLVFLGSGLILGSLGVVLLTNPIYSAFSLGLVLVCISLFYILLNADFVAAAQLLIYV 67 Query: 64 GAVIVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMV--------F 115 GA+ V +F +M ++ E ++ G ++ L ++ + Sbjct: 68 GAINVLIIFAVMFMN-GPEYSKDFNLWTV-GDGITSLVCTSLFFSLITTILDTSWYGIIW 125 Query: 116 SAEGELSRLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVL 163 + +NV+ IG L T + P E+ ILL+++IGAI + Sbjct: 126 TTRSNQIIEQDLISNVQQIGIHLSTDFLLPFELISIILLVALIGAITV 173 >gnl|CDD|144188 pfam00499, Oxidored_q3, NADH-ubiquinone/plastoquinone oxidoreductase chain 6. Length = 140 Score = 51.9 bits (125), Expect = 1e-07 Identities = 41/148 (27%), Positives = 73/148 (49%), Gaps = 9/148 (6%) Query: 16 IISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFFLFIIM 75 I+SS LV+ +NPIY SLI ++ + L LLG+ ++ +I +VYVG ++V FL+++ Sbjct: 1 ILSSLLVLFSKNPIYLGLSLILLSLSLSLLLFLLGSSWLGLILFLVYVGGILVLFLYVVS 60 Query: 76 MLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVFKGNNVENIG 135 + P +K F +L L+ F + + S +NV + Sbjct: 61 LS--------PNEKFKFKKGSKFLLLLLLLLFILLLFFLLFSNLSFSLNSISSSNVNLLS 112 Query: 136 KVLYTQYAYPLEISGFILLLSMIGAIVL 163 +LY+ + + +LL+++IG I L Sbjct: 113 -LLYSSNSLIFILLSLLLLIALIGVIKL 139 >gnl|CDD|177120 MTH00045, ND6, NADH dehydrogenase subunit 6; Validated. Length = 162 Score = 38.0 bits (89), Expect = 0.002 Identities = 43/166 (25%), Positives = 69/166 (41%), Gaps = 8/166 (4%) Query: 8 FYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVI 67 FYLF + + S LV +P YS L+ ++ L LLG F+A++ L++Y+G ++ Sbjct: 3 FYLFLILMLFGSTLVFYSLSPYYSALGLVLVSLSGCLLLSLLGLSFLALLLLLIYMGGML 62 Query: 68 VFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVFK 127 V F++ AE LG + L L V S E + Sbjct: 63 VVFVY------SSALSAERYPSVSNLGEVLVLSLLLSLWVFISFDNFL--ELSNNNWSLV 114 Query: 128 GNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDIKR 173 + LY L + GFILL++++ A+V+ H R Sbjct: 115 SLSDLVGSSELYNSGGLYLLLGGFILLVALVVALVISFGHEYSSLR 160 >gnl|CDD|177257 MTH00214, ND6, NADH dehydrogenase subunit 6; Provisional. Length = 168 Score = 35.0 bits (81), Expect = 0.013 Identities = 15/71 (21%), Positives = 33/71 (46%) Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66 F +L F ++ +V + +P + L+ + L L G F+ +I ++Y+G + Sbjct: 4 FVFLLMFGFLLGLMMVASSPSPYFGALGLVLLALLGCFLLLSHGNSFLGLILFLIYLGGM 63 Query: 67 IVFFLFIIMML 77 +V F + + Sbjct: 64 LVVFSYSAALA 74 >gnl|CDD|177176 MTH00115, ND6, NADH dehydrogenase subunit 6; Provisional. Length = 174 Score = 35.1 bits (82), Expect = 0.013 Identities = 20/64 (31%), Positives = 35/64 (54%) Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66 F +L ++ V + +P Y V SL+ A V G+ + LG FV+++ +VY+G + Sbjct: 4 FVFLLGVCFVLGVVGVASNPSPYYGVVSLVLASVFGCGVLVSLGGSFVSLVLFLVYLGGM 63 Query: 67 IVFF 70 +V F Sbjct: 64 LVVF 67 >gnl|CDD|31751 COG1563, COG1563, Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]. Length = 87 Score = 31.4 bits (71), Expect = 0.18 Identities = 17/69 (24%), Positives = 33/69 (47%) Query: 6 LFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGA 65 L YL + + ++S+ L + R+ + +V + + AA L+ LL A VA+ +V G Sbjct: 10 LIEYLITILLLLSALLAIFQRDLLNAVIASGVLSLLAALLYTLLLAPDVALTEALVGAGL 69 Query: 66 VIVFFLFII 74 + + Sbjct: 70 STAVYAIAL 78 >gnl|CDD|37045 KOG1834, KOG1834, KOG1834, Calsyntenin [Extracellular structures]. Length = 952 Score = 28.5 bits (63), Expect = 1.2 Identities = 13/44 (29%), Positives = 25/44 (56%) Query: 150 GFILLLSMIGAIVLMLRHRRDIKRQDISKQLESNPDNSIVMVKV 193 GF++ + ++G + + HRR +RQ K E + D+S + + V Sbjct: 838 GFLVFMVVLGVLRIRDAHRRRRRRQKRQKDGEMDWDDSALTITV 881 >gnl|CDD|34870 COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]. Length = 309 Score = 27.3 bits (60), Expect = 2.9 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 6/80 (7%) Query: 7 FFYLFSFMAIISSFLVVTV------RNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLV 60 FFY F I+ + +V+ + + G LL F+ L+ Sbjct: 154 FFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLL 213 Query: 61 VYVGAVIVFFLFIIMMLDID 80 +++ +I+ L I + I Sbjct: 214 LFLIYLILNNLTTIEFIQIS 233 >gnl|CDD|176167 cd08478, PBP2_CrgA, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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 = 199 Score = 27.3 bits (61), Expect = 3.1 Identities = 19/52 (36%), Positives = 21/52 (40%), Gaps = 6/52 (11%) Query: 106 IVCASNFMVFS--AEGELSRLVFKGNNV---ENIGKVLYTQYAYPLEISGFI 152 I C S+FM AEG L L F + I V Y A L I FI Sbjct: 146 IACLSDFMTDKDIAEGRLIPL-FAEQTSDVRQPINAVYYRNTALSLRIRCFI 196 >gnl|CDD|35387 KOG0165, KOG0165, KOG0165, Microtubule-associated protein Asp [Cytoskeleton]. Length = 1023 Score = 26.2 bits (57), Expect = 6.3 Identities = 10/41 (24%), Positives = 19/41 (46%) Query: 159 GAIVLMLRHRRDIKRQDISKQLESNPDNSIVMVKVKSGKGI 199 A V++ +H R +S + S P V ++++S I Sbjct: 217 KAAVVLQKHLMHKLRAFLSAKHFSQPTMLKVYLQIRSSVII 257 >gnl|CDD|37277 KOG2066, KOG2066, KOG2066, Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]. Length = 846 Score = 26.0 bits (57), Expect = 7.2 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 3/41 (7%) Query: 147 EISGFILLLSMIG---AIVLMLRHRRDIKRQDISKQLESNP 184 +I I+LL ++ AI L+L +R I ++ +QLE NP Sbjct: 548 QIKDQIVLLMLLDSKKAIDLLLDNRDSISPSEVVEQLEDNP 588 >gnl|CDD|29942 cd00949, FBP_aldolase_I_bact, Fructose-1.6-bisphosphate aldolase found in gram +/- bacteria. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). The enzyme is member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates.. Length = 292 Score = 26.0 bits (57), Expect = 7.9 Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 6/94 (6%) Query: 103 AELIVCASNFMVFSAEGELSRLVFKGNNVENIGKVLYTQYAYPLEI--SGFILLLSMIGA 160 EL++ A VF G R V K N + I V+ Q+ +I G + ++ Sbjct: 122 DELLMRAKEKGVF---GTKMRSVIKEANPKGIAAVVDQQFELAKQILSHGLVPIIEPEVD 178 Query: 161 IVLMLRHR-RDIKRQDISKQLESNPDNSIVMVKV 193 I + + I + +I K L+ P+ VM+K+ Sbjct: 179 IHSADKAKCEAILKAEILKHLDKLPEGQQVMLKL 212 >gnl|CDD|145271 pfam01997, Translin, Translin family. Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes Translin-associated protein X, which was found to interact with translin with yeast two-hybrid screen. Length = 186 Score = 25.6 bits (57), Expect = 8.8 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 12/69 (17%) Query: 114 VFSAEGELSRLVFKGNNVENIGKVLYTQYAYPLEISGFI----LLLSMIGAIVLMLRHRR 169 +F GEL R + ++ Y PLEI F+ ++ LR + Sbjct: 113 LFDLTGELMRFA-----LNSVTL---GDYERPLEILEFMEELYAGFRLLNLKNDGLRKKL 164 Query: 170 DIKRQDISK 178 D+ R + K Sbjct: 165 DVLRYSLEK 173 >gnl|CDD|39167 KOG3964, KOG3964, KOG3964, Phosphatidylglycerolphosphate synthase [Lipid transport and metabolism]. Length = 469 Score = 25.7 bits (56), Expect = 8.8 Identities = 11/24 (45%), Positives = 16/24 (66%) Query: 88 KKRGFLGSFFIGILAAELIVCASN 111 ++R FL S ++G L EL+ C SN Sbjct: 52 QRRIFLASLYLGKLERELVDCLSN 75 >gnl|CDD|35427 KOG0206, KOG0206, KOG0206, P-type ATPase [General function prediction only]. Length = 1151 Score = 25.6 bits (56), Expect = 9.9 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 2/81 (2%) Query: 1 MVMQSLFFYLFSFMAIISSFLVVTVRNPIYS-VFSLIFAFVNAAGLFLLLGAEFVA-MIT 58 + +++ ++ + + I S L+ V IYS + I G+ L + + Sbjct: 997 IALETSYWTWINHIVIWGSILLWFVFLFIYSELTPAISTPDPFYGVAEHLLSSPSFWLTL 1056 Query: 59 LVVYVGAVIVFFLFIIMMLDI 79 L+ V A++ F++ + Sbjct: 1057 LLTVVAALLPDFVYKSLQRTF 1077 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 0.333 0.147 0.408 Gapped Lambda K H 0.267 0.0657 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,374,076 Number of extensions: 134594 Number of successful extensions: 977 Number of sequences better than 10.0: 1 Number of HSP's gapped: 934 Number of HSP's successfully gapped: 273 Length of query: 199 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 110 Effective length of database: 4,340,536 Effective search space: 477458960 Effective search space used: 477458960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 bits) S2: 55 (25.1 bits)