RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780930|ref|YP_003065343.1| nodulation protein (outer membrane efflux protein) [Candidatus Liberibacter asiaticus str. psy62] (452 letters) >gnl|CDD|31727 COG1538, TolC, Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]. Length = 457 Score = 232 bits (593), Expect = 1e-61 Identities = 126/454 (27%), Positives = 226/454 (49%), Gaps = 23/454 (5%) Query: 14 LLAGCTVGPEYTKPHMPLLPTQFSIGNSKNLINIDTLKWWESFNDTSLNKLVKIALQQNL 73 LLAGC + P Y P +P + + WWE+FND LN+LV +AL N Sbjct: 3 LLAGCALLPPYLAP--AAVPAALAAAAAAAAAAAT---WWEAFNDAQLNQLVNLALAANP 57 Query: 74 TILQATERINAAKENILSVRADLFPSSYASISH-----------RFIPNLKTNSTGQLDS 122 + A + AA+ + RA L P AS S+ + + G + Sbjct: 58 DLRVAAAEVEAARAQLRIARAALLPQLSASASYTRQTLAGGPLSSTGTDRNSYGYGLSLA 117 Query: 123 DWKIDLFGQRRH-IESSLANLDSAYAQVDIAKLNVISKLIPSYIDARHFKERISIAHQIL 181 W +DLFG+ R + ++ A +A AQ++ A+L++ +++ +Y D +E++++A + L Sbjct: 118 SWLLDLFGRVRANVRAAEAAAKAARAQLEAARLSLAAEVATAYFDLLAAQEQLALAEETL 177 Query: 182 DLYKKNIELSHLKFTQGATSKLSLVKLEAEIKSIESDIPTLEKSFRMNVHNISTLLGYPA 241 ++ +EL+ ++ G ++L +++ EA++ S + + + + ++ LLG Sbjct: 178 AAAEEQLELAEKRYDAGLATRLDVLQAEAQLASARAQLAAAQAQLAQARNALARLLGLEP 237 Query: 242 TEFLHYMQKQSNNFQPNLYIPINIGIPADLIRNRPDIRYQEKKLADSVAKIGIAKSDLYP 301 E L P L + G+P++ + RPDI E +LA + A IG A++ P Sbjct: 238 GELL---DAPEPEALPALPPVLPDGLPSEALARRPDILAAEAQLAAANANIGAARAAFLP 294 Query: 302 SLSLNGSIALTH---DNSFPGYNTHWSFGPKLYLPIFDKGKIKSNIRRAESSAQEQYITW 358 +LSL S + F + WS GP L LPIFD G++++ +R+AE+ + Sbjct: 295 TLSLTASYGRSSTNLSGLFGSSSRSWSVGPGLSLPIFDGGRLRARVRQAEAQYDAALAQY 354 Query: 359 QETVLNAIKEVENALTSINEDKKIVTKLQHAVELHKKSMSLSMINYRQGRYSLLDILDIE 418 ++TVL A +EV +AL ++ + + L+ AVE ++++ L+ Y+ G +LLD+LD + Sbjct: 355 EQTVLTARQEVADALAALEAALEQLQALRQAVEAAQEALELARERYQAGVRTLLDVLDAQ 414 Query: 419 RATAKVEVDLSIAKRQLAKSYVDLYIAIGSGYNP 452 R + L A+ + V+LY A+G G++ Sbjct: 415 RTLLQARQALLQARYDYLVALVNLYKALGGGWDE 448 >gnl|CDD|145461 pfam02321, OEP, Outer membrane efflux protein. The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria. Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm. Length = 186 Score = 85.6 bits (212), Expect = 3e-17 Identities = 47/178 (26%), Positives = 86/178 (48%), Gaps = 2/178 (1%) Query: 272 IRNRPDIRYQEKKLADSVAKIGIAKSDLYPSLSLNGSIALTHDNSFPGYNTH--WSFGPK 329 + N PD++ E ++ + A I +AKS+ P LSL+G +NS G + S G Sbjct: 9 LENNPDLKAAEAEIEAARANIKLAKSEFLPDLSLSGGYGYNGNNSNGGGDDPRNGSVGLG 68 Query: 330 LYLPIFDKGKIKSNIRRAESSAQEQYITWQETVLNAIKEVENALTSINEDKKIVTKLQHA 389 L P+FD GK ++ ++ A++ + ++ EV A ++ K+ + + A Sbjct: 69 LSQPLFDGGKRRARVKAAKAQLEAAEAQLEQARRQLRLEVAQAYLNLLAAKEQLELAKQA 128 Query: 390 VELHKKSMSLSMINYRQGRYSLLDILDIERATAKVEVDLSIAKRQLAKSYVDLYIAIG 447 +EL ++++ L+ Y G SLLD+L E + ++L A+ L + L +G Sbjct: 129 LELAEEALELAEARYEAGLISLLDVLQAEVELLEARLELLEAEADLELARAQLEYLLG 186 Score = 79.5 bits (196), Expect = 2e-15 Identities = 41/186 (22%), Positives = 89/186 (47%), Gaps = 8/186 (4%) Query: 61 LNKLVKIALQQNLTILQATERINAAKENILSVRADLFPSSYASISHRFIPNLKTNSTGQL 120 L++L+ +AL+ N + A I AA+ NI +++ P S + + N Sbjct: 1 LDELLALALENNPDLKAAEAEIEAARANIKLAKSEFLPDLSLSGGYGYNGNNSNGGGDDP 60 Query: 121 DS-------DWKIDLFGQRRH-IESSLANLDSAYAQVDIAKLNVISKLIPSYIDARHFKE 172 + + G+RR ++++ A L++A AQ++ A+ + ++ +Y++ KE Sbjct: 61 RNGSVGLGLSQPLFDGGKRRARVKAAKAQLEAAEAQLEQARRQLRLEVAQAYLNLLAAKE 120 Query: 173 RISIAHQILDLYKKNIELSHLKFTQGATSKLSLVKLEAEIKSIESDIPTLEKSFRMNVHN 232 ++ +A Q L+L ++ +EL+ ++ G S L +++ E E+ ++ E + Sbjct: 121 QLELAKQALELAEEALELAEARYEAGLISLLDVLQAEVELLEARLELLEAEADLELARAQ 180 Query: 233 ISTLLG 238 + LLG Sbjct: 181 LEYLLG 186 >gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease HII. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 204 Score = 28.3 bits (64), Expect = 4.9 Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 6/29 (20%) Query: 422 AKVEVDLSIAKRQLAKSYVDLYIAIGSGY 450 AKVE D I +L + Y D GSGY Sbjct: 147 AKVERDREI--EELKEEYGD----FGSGY 169 >gnl|CDD|144459 pfam00873, ACR_tran, AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer. Length = 1021 Score = 27.6 bits (62), Expect = 8.1 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 3/54 (5%) Query: 324 WSFGPKLYLPIFDKGKIKSNIRRAESSAQEQYITWQETVLNAIK---EVENALT 374 + PK +LP D+G ++ + ++ +Q + V +K EVE+ Sbjct: 545 FVRIPKEFLPEEDEGVFVTSAQLPPGASLDQTQRVLKQVEKILKEKPEVESVFA 598 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 0.317 0.133 0.376 Gapped Lambda K H 0.267 0.0760 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,116,945 Number of extensions: 260270 Number of successful extensions: 644 Number of sequences better than 10.0: 1 Number of HSP's gapped: 639 Number of HSP's successfully gapped: 16 Length of query: 452 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 355 Effective length of database: 4,167,664 Effective search space: 1479520720 Effective search space used: 1479520720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (26.4 bits)