RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780687|ref|YP_003065100.1| flagellar C-ring protein [Candidatus Liberibacter asiaticus str. psy62] (318 letters) >gnl|CDD|32053 COG1868, FliM, Flagellar motor switch protein [Cell motility and secretion]. Length = 332 Score = 135 bits (342), Expect = 1e-32 Identities = 61/324 (18%), Positives = 128/324 (39%), Gaps = 16/324 (4%) Query: 4 QSIHKNTSPLHPI---LLARLTGKLGDKKTIEKISS--SLGYLYKKFLPKIFKEKMDLDV 58 + + L + K D+ + E++ + + + + L + V Sbjct: 15 SGVSEGVEELKEEDERKVKPYDFKRPDRFSKEQLRTLEIIHERFARLLTTSLSNLLRRSV 74 Query: 59 DISYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVITLLENLLGASHET 118 D+ S + I S + + S+ + +LV +++ L G Sbjct: 75 DVEVGSVDQMTYEEFIRSLPNPTILNLFSMKPLKGTALLEFDPSLVFIMVDRLFGGDGRF 134 Query: 119 IPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSN 178 + R L+ +E+++ + + +I L + + E P + + N Sbjct: 135 PAKPEGRELTDIEQRVITKLLERILEALKEAWNAVIELEPEIVRSETNPQFAQIV--SPN 192 Query: 179 EFVTTINMNMTIENVASSFVLIIPQETLLKTTLISLSSQNKSENQSED--LIDPFARKTY 236 E V I + + I N++ F + IP L LSS+ + + +D ++ Sbjct: 193 EIVVLITLEVEIGNLSGMFNICIPYSMLEP-IREKLSSRMQENTREKDPEWRKELRQQVQ 251 Query: 237 QLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTC---AILSANGKEIYSCELGRVG 293 ++ V ++ R+ TL++++ L++G VIP EK +S GK + C+ G+ G Sbjct: 252 RVEVELEARLGEISLTLREILRLEVGDVIPL---EKPADDRVTVSVGGKPKFLCQYGKSG 308 Query: 294 KNYTIRITDRINFDQKSLKNFLHK 317 Y ++I + IN +++SL L K Sbjct: 309 GQYAVKILELINSEEESLDELLPK 332 >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 = 53.3 bits (129), Expect = 9e-08 Identities = 21/74 (28%), Positives = 38/74 (51%) Query: 231 FARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELG 290 A + + V ++ + + TL +++ LK+G VIP + L NG+ I+ ELG Sbjct: 1 LAEELSDVPVELEAVLGRTELTLGELLNLKVGDVIPLDKPAEDPVELYVNGRPIFRGELG 60 Query: 291 RVGKNYTIRITDRI 304 +G +RIT+ + Sbjct: 61 VIGGKLAVRITELL 74 >gnl|CDD|32070 COG1886, FliN, Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 136 Score = 42.7 bits (100), Expect = 1e-04 Identities = 27/115 (23%), Positives = 47/115 (40%), Gaps = 9/115 (7%) Query: 189 TIENVASSFVLIIPQETLLKTTLISLSSQNKSENQSEDLIDPFARKTYQLNVNIDTRINL 248 E A S + +E ++ S+ +S N+S DL+ + V + + Sbjct: 29 GSEATADSLLYKSVKEVAFAEVELTESTVLESLNESIDLLL-------DIPVRLSVELGR 81 Query: 249 KKTTLKDVVTLKIGQVIPF-LHREKTCAILSANGKEIYSCELGRVGKNYTIRITD 302 K L +++ L G VI + IL NG+ I E+ V + +RIT+ Sbjct: 82 TKMPLGELLALGKGSVIELDKLAGEPVDIL-VNGRLIGRGEVVVVDDKFGVRITE 135 >gnl|CDD|39724 KOG4524, KOG4524, KOG4524, Uncharacterized conserved protein [Function unknown]. Length = 1014 Score = 32.7 bits (74), Expect = 0.13 Identities = 27/128 (21%), Positives = 52/128 (40%), Gaps = 7/128 (5%) Query: 70 FSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLV---ITLLENLLGASHETIPQLYNRS 126 II K N + +L+ + S C N+L LLE+L+ ++ P+L + Sbjct: 280 LKAIIPLRKHNNESVREALADFVSILLTRCENSLNNCEKHLLESLVHLENDENPKLPSHC 339 Query: 127 LSTVEKKLAKRTIAQISAVLNQCI---STTQESSPNLEDFYDIDYLK-KNTNRLSNEFVT 182 + +E + +L + S S +LE F ++D + + N+L Sbjct: 340 VKLLEVLNEQLHNKLSDIILFENAHRLSRLSFSITDLEKFAELDTMILEVVNKLFELLNE 399 Query: 183 TINMNMTI 190 +I++ I Sbjct: 400 SIHLPSLI 407 >gnl|CDD|37571 KOG2360, KOG2360, KOG2360, Proliferation-associated nucleolar protein (NOL1) [Cell cycle control, cell division, chromosome partitioning]. Length = 413 Score = 27.6 bits (61), Expect = 4.7 Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 8/41 (19%) Query: 245 RINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIY 285 RIN K T + + +L EK I E Y Sbjct: 135 RINTLKGTT--------DEALDYLDYEKWKMITELKPDEFY 167 >gnl|CDD|38832 KOG3626, KOG3626, KOG3626, Organic anion transporter [Secondary metabolites biosynthesis, transport and catabolism]. Length = 735 Score = 27.2 bits (60), Expect = 5.9 Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 9/94 (9%) Query: 80 NFVFSQASLSSWSSNFFIGCSNN----LVITLLENLLGASHETIPQLYNRSLSTVEKKL- 134 V S SL +S FFIGC ++ + + + SHE N S + Sbjct: 467 VIVCSVLSLLFYSLLFFIGCESSPVAGVTNSYEGSPAFTSHENPFSSCNSDCSCDTSEYE 526 Query: 135 ---AKRTIAQISAVLNQCISTTQESSPNLEDFYD 165 + I S C ++ S N + + Sbjct: 527 PVCGENGITYFSPCHAGCTESSGTSDGNT-IYTN 559 >gnl|CDD|35497 KOG0276, KOG0276, KOG0276, Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 794 Score = 27.2 bits (60), Expect = 6.0 Identities = 15/57 (26%), Positives = 26/57 (45%) Query: 257 VTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINFDQKSLKN 313 VT+K+G+ P + + I+ A EI + L VG + +R+ K L + Sbjct: 293 VTVKLGREEPAVSMDSNGKIIWAVHSEIQAVNLKSVGAQKEVTDGERLPLSVKELGS 349 >gnl|CDD|153057 cd00037, CLECT, C-type lectin (CTL)/C-type lectin-like (CTLD) domain. CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model. Length = 116 Score = 26.8 bits (59), Expect = 8.2 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 7/58 (12%) Query: 48 KIFKEKMDLDVDISYTSCQSGKFSH--IIHSFKEN-FVFSQASLSSWSSNFFIGCSNN 102 K EK+ + + C+S H IHS +EN F+ S S SS+ +IG ++ Sbjct: 4 KFSTEKLTWEE--AQEYCRS-LGGHLASIHSEEENDFLASLLK-KSSSSDVWIGLNDL 57 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 0.132 0.365 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,508,684 Number of extensions: 174436 Number of successful extensions: 417 Number of sequences better than 10.0: 1 Number of HSP's gapped: 413 Number of HSP's successfully gapped: 23 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 57 (25.7 bits)