RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780688|ref|YP_003065101.1| putative flagellar motor switch protein [Candidatus Liberibacter asiaticus str. psy62] (147 letters) >gnl|CDD|32070 COG1886, FliN, Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 136 Score = 74.7 bits (183), Expect = 9e-15 Identities = 37/113 (32%), Positives = 64/113 (56%), Gaps = 3/113 (2%) Query: 31 VSSPTNNSEMLIQKNDVDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQI 90 V ++ L+ K+ + + + +LE ++ DL+++IPV++ + LG M + Sbjct: 27 VPGSEATADSLLYKSVKEVAFAEVELTESTVLESLNESIDLLLDIPVRLSVELGRTKMPL 86 Query: 91 SNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 L+ L KG VI LDK GE VDI +N + I +GE+ ++++ FGVR+ EI Sbjct: 87 GELLALGKGSVIELDKLAGEPVDILVNGRLIGRGEVVVVDDK---FGVRITEI 136 >gnl|CDD|144589 pfam01052, SpoA, Surface presentation of antigens (SPOA). This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, pfam02154. Length = 77 Score = 62.9 bits (154), Expect = 3e-11 Identities = 23/75 (30%), Positives = 45/75 (60%), Gaps = 3/75 (4%) Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIM 129 + + ++PV+++ +LG + + L+NL GDVI LDK + V++ +N + I +GE+ ++ Sbjct: 3 EELSDVPVELEAVLGRTELTLGELLNLKVGDVIPLDKPAEDPVELYVNGRPIFRGELGVI 62 Query: 130 EEDDTHFGVRVIEIL 144 VR+ E+L Sbjct: 63 GG---KLAVRITELL 74 >gnl|CDD|32053 COG1868, FliM, Flagellar motor switch protein [Cell motility and secretion]. Length = 332 Score = 40.2 bits (94), Expect = 2e-04 Identities = 15/100 (15%), Positives = 44/100 (44%), Gaps = 4/100 (4%) Query: 48 DNISEPISSDSNNILEKSTDNF-DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDK 106 + +S + ++ + + + V+++ LG + + ++ L GDVI L+K Sbjct: 225 EKLSSRMQENTREKDPEWRKELRQQVQRVEVELEARLGEISLTLREILRLEVGDVIPLEK 284 Query: 107 RVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 + V +++ + + + V+++E++N+ Sbjct: 285 PADDRVTVSVGGKPKFLCQYGKSGG---QYAVKILELINS 321 >gnl|CDD|109627 pfam00577, Usher, Fimbrial Usher protein. This protein is involved in biogenesis of gram negative bacterial pili. Length = 784 Score = 28.4 bits (64), Expect = 0.81 Identities = 7/25 (28%), Positives = 12/25 (48%) Query: 111 SVDITINNQKIAKGEITIMEEDDTH 135 VD+ +N +K +I DD+ Sbjct: 33 LVDVYLNGEKKGSQDINFTANDDSK 57 >gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains 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. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 488 Score = 27.6 bits (62), Expect = 1.5 Identities = 19/94 (20%), Positives = 43/94 (45%), Gaps = 16/94 (17%) Query: 34 PTNNSEML-IQKNDVDNI--SEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQI 90 P + +L +Q ++D I ++ IS+D+ L+K + ++ P + + Sbjct: 195 PDAQTRLLALQSGEIDLIYGADGISADAFKQLKK-DKGYGTAVSEPTSTRFLA------- 246 Query: 91 SNLVNLSKGDVITLDKRVGESVDITINNQKIAKG 124 +N + D +V E+++ I+ + I+KG Sbjct: 247 ---LNTASE--PLSDLKVREAINYAIDKEAISKG 275 >gnl|CDD|146878 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. Length = 225 Score = 26.4 bits (59), Expect = 2.8 Identities = 7/41 (17%), Positives = 15/41 (36%), Gaps = 2/41 (4%) Query: 107 RVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147 + G+ + + + EI E V+++E L Sbjct: 18 KEGDEIKLFDGDGGEYLAEIE--EISKKSVLVKILEKLEVN 56 >gnl|CDD|144750 pfam01269, Fibrillarin, Fibrillarin. Length = 229 Score = 26.0 bits (58), Expect = 3.6 Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 4/35 (11%) Query: 111 SVDITINNQKIAKGEITIMEEDDTHFGVRVIEILN 145 S+D+T +++ E+ ++E G + E + Sbjct: 182 SIDVTKEPEEVFAREVEKLKE----EGFKPKEQVT 212 >gnl|CDD|32590 COG2520, COG2520, Predicted methyltransferase [General function prediction only]. Length = 341 Score = 26.0 bits (57), Expect = 3.7 Identities = 10/39 (25%), Positives = 17/39 (43%) Query: 42 IQKNDVDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQ 80 I+ N V+ EPI D+ + + +IM +P Sbjct: 231 IRLNKVEGRVEPILGDAREVAPELGVADRIIMGLPKSAH 269 >gnl|CDD|145730 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in chromatin proteins. Length = 158 Score = 25.7 bits (57), Expect = 5.0 Identities = 18/38 (47%), Positives = 20/38 (52%), Gaps = 6/38 (15%) Query: 90 ISNLVNLSKGDVITLDKRV----GESVDITINNQKIAK 123 ISN N KG I LDKRV D+ IN+ K AK Sbjct: 74 ISNWKN-PKGYTIPLDKRVAADGRGLQDVEIND-KFAK 109 >gnl|CDD|35153 COG5594, COG5594, Uncharacterized integral membrane protein [Function unknown]. Length = 827 Score = 24.9 bits (54), Expect = 8.2 Identities = 10/34 (29%), Positives = 14/34 (41%) Query: 3 KKVSKISYIKDNLEGRSMHIDNPLQDTNVSSPTN 36 KKV I Y L I+N + ++PT Sbjct: 325 KKVDAIDYYSAKLTKLDAEIENARKSLYENTPTK 358 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 0.313 0.131 0.351 Gapped Lambda K H 0.267 0.0776 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,543,693 Number of extensions: 69524 Number of successful extensions: 122 Number of sequences better than 10.0: 1 Number of HSP's gapped: 122 Number of HSP's successfully gapped: 16 Length of query: 147 Length of database: 6,263,737 Length adjustment: 85 Effective length of query: 62 Effective length of database: 4,426,972 Effective search space: 274472264 Effective search space used: 274472264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (24.1 bits)