RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780644|ref|YP_003065057.1| hypothetical protein CLIBASIA_02655 [Candidatus Liberibacter asiaticus str. psy62] (289 letters) >gnl|CDD|185150 PRK15235, PRK15235, outer membrane fimbrial usher protein SefC; Provisional. Length = 814 Score = 30.1 bits (67), Expect = 0.67 Identities = 12/37 (32%), Positives = 19/37 (51%) Query: 90 QAVEYEKPYSTVIANLTDSHQKYATNIATYMPIGEEF 126 Q Y PYST + +L D + KY+ I Y + ++ Sbjct: 317 QVQNYTVPYSTPVLSLPDGYSKYSVTIGRYREVNNDY 353 >gnl|CDD|132534 TIGR03495, phage_LysB, phage lysis regulatory protein, LysB family. Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin. Length = 135 Score = 28.1 bits (63), Expect = 2.5 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 15/84 (17%) Query: 127 AHSLSARIASSENAQVIEALYDIVKNRNDIMLLTKYGESLQILRRLTQETEKHINNLQDK 186 + A +AS N + L + RN+ E+ LR+ + + + + Sbjct: 35 LKAQQAELASKAN--QLIVLL-ALAKRNE--------EAQAQLRQQLAQARALLAQREQR 83 Query: 187 I--LQDRAKEIKHWYDTLIPHPDD 208 I L+ ++++ W DT P PDD Sbjct: 84 IERLKRENEDLRRWADT--PLPDD 105 >gnl|CDD|162709 TIGR02110, PQQ_syn_pqqF, coenzyme PQQ biosynthesis probable peptidase PqqF. In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Length = 696 Score = 27.5 bits (61), Expect = 4.3 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 6/96 (6%) Query: 6 EKLKEACDVATDSIRSFFMQAKPYILPALSKEEQ--KSLKYFFLPEN---TLCQKFFNAF 60 L + F P L A +E +S+ +L ++ L F+A Sbjct: 247 AGLPATARDNVTLLCEFLQDEAPGGLLAQLRERGLAESVAATWLYQDAGQALLALEFSAR 306 Query: 61 DRHATAGIEIKKTMNATLQFLQKVPTADPQAVEYEK 96 A A +I++ + L L + A+ Y + Sbjct: 307 CISAAAAQQIEQLLTQWLGALAEQTWAEQLE-HYAQ 341 >gnl|CDD|161982 TIGR00657, asp_kinases, aspartate kinase. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. This may be a feature of a number of closely related forms, including a paralog from B. subtilis. Length = 441 Score = 27.3 bits (61), Expect = 5.0 Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 2/98 (2%) Query: 181 NNLQDKILQDRAKEIKHWYDTLIPHPDDSSPNSGVSFDIMEPGHEKTNIYALSYGEQMSA 240 ++ + + R K I+ + LIP + +++ + LS+GE++SA Sbjct: 59 GPSKEFLEKIREKHIEI-LERLIPQAIAEELKRLLDAELVLEEKPREMDRILSFGERLSA 117 Query: 241 PANLSECQ-LNCLGLAVWGSCAPLLNNHHLALSFSIIQ 277 + + L +++ G A +L + + + II+ Sbjct: 118 ALLSAALEELGVKAVSLLGGEAGILTDSNFGRARVIIE 155 >gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. These proteins are found in P. falciparum, P. vivax and P. yoelii. Length = 2757 Score = 27.3 bits (60), Expect = 5.2 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%) Query: 139 NAQVIEALYDIVKNRNDIMLLTKYGESLQILRRLTQETEKHINNLQDKILQDRAKEIKHW 198 +I L D K+ N+ L+ K E+ +I+ LT+ NN IL + +I ++ Sbjct: 2210 KKHMISILADATKDHNN--LIEKEKEATKIINNLTELFTIDFNNADADILHNNKIQIIYF 2267 Query: 199 YDTL 202 L Sbjct: 2268 NSEL 2271 >gnl|CDD|130083 TIGR01010, BexC_CtrB_KpsE, polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export. Length = 362 Score = 27.0 bits (60), Expect = 5.9 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 12/60 (20%) Query: 144 EALYDIVKNRNDIMLLTKYG------------ESLQILRRLTQETEKHINNLQDKILQDR 191 EA Y K R + + + G E+ +I +RL +E E+ IN L ++ +D Sbjct: 112 EAFYRYYKKRLSVDVDSVSGILTLNVTAFDAEEAQKINQRLLKEGERLINRLNERARKDT 171 >gnl|CDD|180515 PRK06291, PRK06291, aspartate kinase; Provisional. Length = 465 Score = 26.8 bits (60), Expect = 6.9 Identities = 8/12 (66%), Positives = 11/12 (91%) Query: 230 YALSYGEQMSAP 241 Y LS+GE++SAP Sbjct: 124 YILSFGERLSAP 135 >gnl|CDD|152763 pfam12328, Rpp20, Rpp20 subunit of nuclear RNase MRP and P. The nuclear RNase P of Saccharomyces cerevisiae is made up of at least nine protein subunits; Pop1, Pop3, Pop4, Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these subunits seem to be present also in the RNase MRP, with the exception of Rpr2 (Rpp21) which is unique to RNase P. Human nuclear RNase P and MRP appear to contain at least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although there is recent evidence that not all of these subunits are shared between P and MRP. Archaeal RNase P has at least four protein subunits homologous to eukaryotic RNase P/MRP proteins. In the yeast RNase P, Pop6 and Pop7 (the Rpp20 homologue) interact with each other and they are both interaction partners of Pop4; in the human MRP Rpp25 and Rpp20 interact with each other and Rpp25 binds to Rpp29 (Pop4). Length = 120 Score = 26.9 bits (60), Expect = 7.0 Identities = 8/32 (25%), Positives = 16/32 (50%) Query: 53 CQKFFNAFDRHATAGIEIKKTMNATLQFLQKV 84 QK + ++ AT+ E+ K + L++V Sbjct: 21 IQKLLDKAEKRATSSEELAKDRKNGGKKLEEV 52 >gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed. Length = 1068 Score = 26.5 bits (59), Expect = 7.9 Identities = 10/15 (66%), Positives = 10/15 (66%), Gaps = 2/15 (13%) Query: 218 DIMEPGHE--KTNIY 230 DI PGHE K NIY Sbjct: 28 DIESPGHEQKKANIY 42 >gnl|CDD|177917 PLN02278, PLN02278, succinic semialdehyde dehydrogenase. Length = 498 Score = 26.6 bits (59), Expect = 8.3 Identities = 7/19 (36%), Positives = 14/19 (73%) Query: 190 DRAKEIKHWYDTLIPHPDD 208 +R+K ++ WYD +I + +D Sbjct: 85 ERSKILRRWYDLIIANKED 103 >gnl|CDD|162167 TIGR01034, metK, S-adenosylmethionine synthetase. Tandem isozymes of this S-adenosylmethionine synthetase in E. coli are designated MetK and MetX. Length = 377 Score = 26.6 bits (59), Expect = 8.7 Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 1/25 (4%) Query: 112 YATNIA-TYMPIGEEFAHSLSARIA 135 YATN MP+ AH L R A Sbjct: 122 YATNETPELMPLPITLAHKLLKRAA 146 >gnl|CDD|129550 TIGR00458, aspS_arch, aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). Length = 428 Score = 26.3 bits (58), Expect = 9.6 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 16/76 (21%) Query: 162 YGESLQILRR----------LTQETEKHINNLQDKI--LQDRAKEIKHWYDTLIPHPDDS 209 Y E++++ L+ E EK + D + + D EI+ +Y PD+ Sbjct: 280 YDEAIEMANAKGVEIGWGEDLSTEAEKALGEEMDGLYFITDWPTEIRPFYTM----PDED 335 Query: 210 SPNSGVSFDIMEPGHE 225 +P SFD+M E Sbjct: 336 NPEISKSFDLMYRDLE 351 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.131 0.383 Gapped Lambda K H 0.267 0.0686 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,509,067 Number of extensions: 270274 Number of successful extensions: 578 Number of sequences better than 10.0: 1 Number of HSP's gapped: 578 Number of HSP's successfully gapped: 18 Length of query: 289 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 197 Effective length of database: 4,006,537 Effective search space: 789287789 Effective search space used: 789287789 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 (25.8 bits)