RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780837|ref|YP_003065250.1| putative restriction endonuclease S subunit [Candidatus Liberibacter asiaticus str. psy62] (426 letters) >gnl|CDD|31076 COG0732, HsdS, Restriction endonuclease S subunits [Defense mechanisms]. Length = 391 Score = 70.5 bits (171), Expect = 9e-13 Identities = 75/407 (18%), Positives = 152/407 (37%), Gaps = 31/407 (7%) Query: 25 WKVVPIKRFTKLNTGRTS------ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTV 78 WK + + ++ G+T G DI + ++DV+ ++ Sbjct: 1 WKELKLGDIGEIIRGKTPSTESPLNYGSDIPILTVKDVKGRYSVKGNNGIIGKKLS---- 56 Query: 79 SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIE 138 + A L + L + + L L+PK P+ L +LL + ++ Sbjct: 57 YLIAGLGPLGELVRAGLGDVAYVNGKLSINQGCLSLRPKKKEPKSLFLYLLLKLELKLLK 116 Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK 198 + G+T+ + + IP+P+PPL EQ + I +D LI + IELL+ Sbjct: 117 SGAGGSTIPNLSKSSLKEIPIPLPPLEEQ----QAIAKILSTLDDLIELLEKLIELLEAI 172 Query: 199 KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT--KLIESNI 256 KQ L + TKG +K +P+ W+V +V ++ L + Sbjct: 173 KQKLFKELFTKGKYLLNNIKS--------IPEDWKVIKLKDIVEIISGGTKIKPLEKGVN 224 Query: 257 LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGII 316 +S ++ E N + S I ++I L + ++ A + + Sbjct: 225 VSYGKNPVLNGGEPNNGDIVKLSRIDNFIYGLKLSGGKYITLSSSGATIGIAIINNGTLK 284 Query: 317 TSAY-----MAVKPHGIDSTYLAWLMRSYDLCKVF-YAMGSGLRQSLKFEDVKRLPVLVP 370 + ++ +L + + S K+ L + ++ +P+ +P Sbjct: 285 FILSQGIGILRIENKVEGEKFLYYYLSSEFFKKIIKKVSKGSTIPRLNKKLLEEIPIPIP 344 Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTG 417 P++EQ I +++ ID+L + + LK++ + +TG Sbjct: 345 PLEEQQKIAEILSALDKLIDIL-NRKPAELEALKKQLDYLLNKLLTG 390 Score = 42.0 bits (97), Expect = 3e-04 Identities = 49/216 (22%), Positives = 89/216 (41%), Gaps = 10/216 (4%) Query: 2 KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61 K +K + I +IP+ WKV+ +K ++ +G T + Sbjct: 175 KLFKELFTKGKYLLNNIKSIPEDWKVIKLKDIVEIISGGTKIKPLEKGVNVSYGKNPVLN 234 Query: 62 KYLPKDGNSRQSDTSTVSIFAKGQ-----ILYGKLGPYLRKAIIAD--FDGICSTQFLVL 114 P +G+ + I+ I G + AII + I S +L Sbjct: 235 GGEPNNGDIVKLSRIDNFIYGLKLSGGKYITLSSSGATIGIAIINNGTLKFILSQGIGIL 294 Query: 115 QPKD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172 + ++ + L +L S + I+ + +G+T+ + K + IP+PIPPL EQ I E Sbjct: 295 RIENKVEGEKFLYYYLSSEFFKKIIKKVSKGSTIPRLNKKLLEEIPIPIPPLEEQQKIAE 354 Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208 + A ID L + +E LK++ L++ ++T Sbjct: 355 ILSALDKLIDILNRKPAE-LEALKKQLDYLLNKLLT 389 >gnl|CDD|144860 pfam01420, Methylase_S, Type I restriction modification DNA specificity domain. This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits. Length = 167 Score = 53.9 bits (130), Expect = 9e-08 Identities = 37/187 (19%), Positives = 67/187 (35%), Gaps = 28/187 (14%) Query: 22 PKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75 P W+ + ++ G+T E+G YI D+ +G + Sbjct: 1 PVDWEEFKLGEIFEIKKGKTLSKKELRENG-KYPYITAGDLNNGVIGGVGYIKKK----- 54 Query: 76 STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ 135 IF IL + D + VL PK+ +L + + Sbjct: 55 ----IFPGNSILIS-SNGSIGYVFYRDKPFFANQDVKVLIPKNNELLNKFLYLFLKTILK 109 Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195 +++ + G+ + K + + +P+PPL EQ + IA+ ++ L IEL Sbjct: 110 KLKKLKFGSGQPKLNKKRLKELKIPLPPLEEQ-----QKIAD--ILEQL----DATIELE 158 Query: 196 KEKKQAL 202 K+K L Sbjct: 159 KKKLAEL 165 >gnl|CDD|34136 COG4457, SrfB, Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]. Length = 1014 Score = 28.4 bits (63), Expect = 3.7 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 5/72 (6%) Query: 105 GICSTQFLVLQ-PKDVLPELLQGWLLSI--DVTQRIEAICEGATMSHADWKGIGNIPMPI 161 + + QF +L P + L LS D+T +A+CE D + P + Sbjct: 732 ELPAGQFSILDVPLAIDLSQLHECFLSGDYDITGVFDALCEAINHYDCDVLLLTGRPSRL 791 Query: 162 PPLAEQVLIREK 173 P + Q L R Sbjct: 792 PGV--QALFRHL 801 >gnl|CDD|38525 KOG3315, KOG3315, KOG3315, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 191 Score = 28.4 bits (63), Expect = 4.2 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 12/85 (14%) Query: 244 LNRKNTKL------IESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297 ++ TK+ I S + +G KLE N + TY I+D +V FI Sbjct: 78 GQKRETKILGILQFIHSTVWKYLFGKEADKLEKAN-----DDDRTYMIIDKEPLVNTFIS 132 Query: 298 LQNDKRSLRSAQVMERGIITSAYMA 322 + + +L A + GII + Sbjct: 133 VPKENGTLNCAAFVA-GIIEAVLDN 156 >gnl|CDD|35289 KOG0066, KOG0066, KOG0066, eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]. Length = 807 Score = 28.1 bits (62), Expect = 4.8 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%) Query: 152 KGIGNIPMPIPPLAEQVLIREKIIA-ETVRIDTLITERIRFIELLKEKKQALVSYIVTKG 210 K I + IPP + +L ++++A T IDT++ + + LL+E+ + L+S I Sbjct: 308 KHIAARALAIPPNIDVLLCEQEVVADSTSAIDTVLKADKKRLALLEEEAK-LMSQIEEGD 366 Query: 211 LNPDVKMKDSGIE 223 ++K+ E Sbjct: 367 TTAAERLKEVADE 379 >gnl|CDD|38899 KOG3695, KOG3695, KOG3695, Uncharacterized conserved protein [Function unknown]. Length = 825 Score = 27.3 bits (60), Expect = 8.8 Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 9/65 (13%) Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235 AE I I ER F +L AL S + + G +W L+PD W Sbjct: 225 AENKSIGEYIAERTSFCPVLTTGLSALYS---------SLPREILGDDWHRLLPDDWLEI 275 Query: 236 PFFAL 240 PF AL Sbjct: 276 PFLAL 280 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 0.319 0.138 0.400 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,203,076 Number of extensions: 278079 Number of successful extensions: 519 Number of sequences better than 10.0: 1 Number of HSP's gapped: 515 Number of HSP's successfully gapped: 10 Length of query: 426 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 330 Effective length of database: 4,189,273 Effective search space: 1382460090 Effective search space used: 1382460090 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (26.6 bits)