RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780367|ref|YP_003064780.1| ribonuclease protein [Candidatus Liberibacter asiaticus str. psy62] (281 letters) >gnl|CDD|31486 COG1295, Rbn, Predicted membrane protein [Function unknown]. Length = 303 Score = 130 bits (327), Expect = 5e-31 Identities = 84/274 (30%), Positives = 147/274 (53%), Gaps = 4/274 (1%) Query: 7 IVFDIIYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQ-FVPTVIDV 65 + D++ A+E F E+DG +A+ ++ LLS+FP ++ +L GF AH + ++ + Sbjct: 15 GILDLLRRALERFNEDDGSLLAAALAYYTLLSLFPLLLVVFSLLGFFLAHPILLEDLLFI 74 Query: 66 VFGAWPEVIAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEM 125 + PE A I D + L+ L ++ + A + +SNG+ ALR +LN+ +RV Sbjct: 75 IANLLPEQAADVIEDYLKNFLSQSRGSLLSLGLVVALWTASNGMSALRDALNKIWRVKPR 134 Query: 126 RSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFF--PALGNLLLIIWNGRIY 183 RS+ RL+S + L + L+ + V P+AL + F P L+LI+ R+ Sbjct: 135 RSFIRRRLLSLFWTLGTLLPLLFALLLSVVGPIALQALLLRFGLPFFDVLVLILLRLRLL 194 Query: 184 ATMLALFIGLIFVHLFLPAAKSKIMS-ILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMY 242 ++L L +G ++ FLP + +LPG + I + +G LF +Y+ F+ YS+ Y Sbjct: 195 VSLLLLTLGFFLLYRFLPNVRVLKWRDVLPGALLAAILFELGKYLFGYYLSNFANYSSTY 254 Query: 243 AGLASIMTCLVFLYMLGVFFILGAELNASMIIYY 276 L S++ L++LY+ + +LGAELNA++ Y Sbjct: 255 GALGSVIILLLWLYISALIILLGAELNATLSEYK 288 >gnl|CDD|146329 pfam03631, Ribonuclease_BN, Ribonuclease BN-like family. This family contains integral membrane proteins with 5 to 6 predicted transmembrane spans. The family include ribonuclease BN that is involved in tRNA maturation. This family of proteins does not seem to contain any completely conserved polar residues that would be expected in a nuclease enzyme, suggesting that many members of this family may not have this catalytic activity (Bateman A pers. obs.). Length = 255 Score = 124 bits (313), Expect = 3e-29 Identities = 74/253 (29%), Positives = 133/253 (52%), Gaps = 4/253 (1%) Query: 21 EEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAH-QFVPTVIDVVFGAWPEVIAKPIT 79 E+D +A+ ++ LLS+FP ++ L G G ++D++ PE A+ I Sbjct: 2 EDDLSLLAAALAYYTLLSLFPLLLVLLALLGLFGGPPALQEQLLDLLAEVLPEEAAELIE 61 Query: 80 DEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYV 139 D + ++L + GL + L + +S G ALR +LNR Y V E RS+ RL+S G Sbjct: 62 DILQRLLTQASLGLLGLGVLL--WSASGGFAALRRALNRIYGVKEKRSFLRRRLLSLGLT 119 Query: 140 LLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIYATMLALFIGLIFVHLF 199 LL + L++ + V +P AL + LG +++ R ++L L + ++ F Sbjct: 120 LLLGLLLLLSLLLSVFLP-ALLGILLLGLGLGLATVLLQLLRWLVSLLLLTLLFALLYRF 178 Query: 200 LPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCLVFLYMLG 259 LP K + + LPG + + W++ + F+ Y+ F+ Y++ Y L +++ L++LY+ Sbjct: 179 LPNRKVRWRAALPGALLAAVLWLLLSYGFSLYLSNFANYNSTYGSLGALIVLLLWLYLSA 238 Query: 260 VFFILGAELNASM 272 + +LGAELNA++ Sbjct: 239 LILLLGAELNAAL 251 >gnl|CDD|30822 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and metabolism]. Length = 917 Score = 35.0 bits (80), Expect = 0.027 Identities = 37/225 (16%), Positives = 81/225 (36%), Gaps = 19/225 (8%) Query: 12 IYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAWP 71 +Y I+ F+ ++ +L++ + +F I+++ + P Sbjct: 697 VYVNIKKFI-----LYLLSKNVGEVLTLLIYSLFNLFFLPLTPLQL---LWINLLTDSLP 748 Query: 72 EV---IAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSW 128 + + P +D + + P +GLF + A I + + + Sbjct: 749 ALALGVEDPESDVMKRPPRGPEEGLFNRKIFWRFILIIGLLSA--ILFILTFLLYLLGFI 806 Query: 129 YITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIYATMLA 188 T + LL + ++ + + + LA+ + F L ++++ + L Sbjct: 807 ANTLGLDLFQALLQTTAFTVLVLIQLLLTLAVRSRGRPF-----LSSLLFSNKYLWLALL 861 Query: 189 LFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIV 233 + I L + +FLP KI P +F W+ + L YIV Sbjct: 862 VIIILQLLIIFLPPLNLKIFQPTPLSLFEWL-IAIAVALLLLYIV 905 >gnl|CDD|32387 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]. Length = 890 Score = 32.1 bits (73), Expect = 0.18 Identities = 28/131 (21%), Positives = 50/131 (38%), Gaps = 25/131 (19%) Query: 120 YRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWN 179 +R SW L++ LA+ + + F + + ++ LG L++ + Sbjct: 387 WRPKIQGSWSRDYLVAILICALATAIAIQLDKFFDLANIVMLFL------LGVLVVAVLT 440 Query: 180 GRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYS 239 GR A + AL L+F + F +T+ AV Y+VTF+ Sbjct: 441 GRWPAVLAALLSVLVFNYFFTEP------------RYTF------AVSDPQYLVTFAVML 482 Query: 240 TMYAGLASIMT 250 + A L +T Sbjct: 483 AV-ALLTGNLT 492 >gnl|CDD|39049 KOG3845, KOG3845, KOG3845, MLN, STAR and related lipid-binding proteins [Lipid transport and metabolism]. Length = 241 Score = 29.6 bits (66), Expect = 0.91 Identities = 19/132 (14%), Positives = 30/132 (22%), Gaps = 10/132 (7%) Query: 12 IYDAIEHFVEE-DGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAW 70 +Y+ +E + D W + FI G+ + V T + Sbjct: 83 VYNMLEKIQKNTDIWTSEFDSFNVDIFRPRVFIDSGSVFRLEHMINIPVTTCVS-----R 137 Query: 71 PEVIAKPITDE----ILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMR 126 + AK I V VP I A +F R + Sbjct: 138 AFLSAKVILVRGYNHPCGVFCVPLPIEPFILAWLREWFLDLRGLPQENVGERPEARTLVN 197 Query: 127 SWYITRLISFGY 138 Sbjct: 198 FELAPLKAPKAL 209 >gnl|CDD|145481 pfam02357, NusG, Transcription termination factor nusG. Length = 90 Score = 28.8 bits (65), Expect = 1.8 Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 1/40 (2%) Query: 176 IIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVI 215 + NG+ LF G +FV + L KI S PGV Sbjct: 37 VRKNGKKKKVERPLFPGYVFVRMDLNDETWKIRST-PGVS 75 >gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 895 Score = 28.0 bits (62), Expect = 3.1 Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 8/63 (12%) Query: 51 GFLGAHQFVPTVIDVVFGAWPEVIAKP------ITDEILQVLAVPAKGLFTISALAAAYF 104 GF VP V++ + A+PE+ P I +E Q L +G +A Sbjct: 330 GFFS--TLVPVVVETLGDAFPELKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELG 387 Query: 105 SSN 107 SS Sbjct: 388 SSK 390 >gnl|CDD|177097 CHL00206, ycf2, Ycf2; Provisional. Length = 2281 Score = 28.0 bits (62), Expect = 3.3 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 6/66 (9%) Query: 193 LIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCL 252 LI+ HL P + + SIL ++ V G ++ TH + S + I + + Sbjct: 1329 LIWTHLRSPNVREFLYSIL------FLLLVAGYLVRTHLLFVSRASSELQTEFEKIKSLM 1382 Query: 253 VFLYML 258 + YM+ Sbjct: 1383 IPSYMI 1388 >gnl|CDD|31348 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme metabolism / Lipid metabolism]. Length = 627 Score = 27.8 bits (62), Expect = 3.8 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 7/63 (11%) Query: 35 ALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAWPEVIAKPITDEILQVLAVPAKGLF 94 A+L+ + +A L A+ TV+D F KP+ + +L LA + Sbjct: 505 AILAFGTMLPEALKVAEKLNAYGISVTVVDPRF-------VKPLDEALLLELAKSHDLVV 557 Query: 95 TIS 97 T+ Sbjct: 558 TLE 560 >gnl|CDD|38926 KOG3722, KOG3722, KOG3722, Lipocalin-interacting membrane receptor (LIMR) [Defense mechanisms]. Length = 538 Score = 27.6 bits (61), Expect = 3.9 Identities = 27/127 (21%), Positives = 52/127 (40%), Gaps = 16/127 (12%) Query: 145 TLVIMSFVFVAIPLALAYVRKFFPALGNLLLI--IWNGRIYATMLALFIGLIFVHLFLPA 202 ++++ F ++ + L Y ++ N LI +WN + L+LF+ L F + F+ + Sbjct: 80 AVLLLPFSIISNEVLLLYPGNYYIQWLNGSLIHGLWNLVFLFSNLSLFVLLPFAYFFIES 139 Query: 203 ---AKSKI-----------MSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASI 248 A SK + +L ++ + WV A+L S L + Sbjct: 140 EGFAGSKKGILQRIYETMVILMLLALLVLGLVWVASAILDYPKAQFESFLDLWSVYLPYL 199 Query: 249 MTCLVFL 255 +C+ FL Sbjct: 200 YSCVSFL 206 >gnl|CDD|144001 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e. Length = 129 Score = 27.1 bits (61), Expect = 5.9 Identities = 10/29 (34%), Positives = 17/29 (58%) Query: 90 AKGLFTISALAAAYFSSNGVEALRISLNR 118 A G + + AL ++ +EA RI++NR Sbjct: 26 AFGDYGLKALEPGRITARQIEAARIAINR 54 >gnl|CDD|176177 cd08488, PBP2_AmpR, The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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 = 191 Score = 26.7 bits (59), Expect = 6.6 Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 10/62 (16%) Query: 68 GAWPEVIAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRS 127 GAW + A + + L L P A + R +L R+YR E Sbjct: 56 GAWHGIDATRLFEAPLSPLCTPE----------LARQLREPADLARHTLLRSYRADEWPQ 105 Query: 128 WY 129 W+ Sbjct: 106 WF 107 >gnl|CDD|32008 COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]. Length = 458 Score = 26.4 bits (58), Expect = 9.4 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 5/76 (6%) Query: 124 EMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIY 183 E W+ ++ GYV L + +++M VF++I A+A + LG + L+ ++ Sbjct: 61 ETIDWF--NIVGNGYVRL--LQMIVMPLVFISILSAIAKLDNA-SKLGKISLLTIGTLLF 115 Query: 184 ATMLALFIGLIFVHLF 199 T +A IG++ LF Sbjct: 116 TTAIAALIGILVALLF 131 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 0.144 0.449 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,648,969 Number of extensions: 209140 Number of successful extensions: 1478 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1416 Number of HSP's successfully gapped: 291 Length of query: 281 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 188 Effective length of database: 4,254,100 Effective search space: 799770800 Effective search space used: 799770800 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: 39 (21.5 bits) S2: 57 (25.7 bits)