RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (268 letters) >gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and biogenesis]. Length = 242 Score = 235 bits (602), Expect = 7e-63 Identities = 94/241 (39%), Positives = 150/241 (62%), Gaps = 4/241 (1%) Query: 12 AKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSV 71 + I+LV+P NIG VARAM NF L++LRLVNPR G E+AR+ +A A ++++ Sbjct: 2 LENIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDILENA 60 Query: 72 RVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWG 131 ++ L+EA+AD + ATTAR+R+ + + P+EAA L E+ G V ++FGRER G Sbjct: 61 KIVDTLEEALADCDLVVATTARSRDLLRPLRTPREAAPELLEK-AKGGKVALVFGRERVG 119 Query: 132 LTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGE 191 LTNEE+AL + +++ P NP +PSLN++QAV ++++E + ++ E + ++ ATK E Sbjct: 120 LTNEELALCDVLVTIPANPDYPSLNLAQAVQVILYELRKAE-LAQEGSSGIEDELATKEE 178 Query: 192 LLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSR 251 L ++LE L+ G+ P KKK ++ L + R L EV +LRGI+ +++ + Sbjct: 179 LELLYEHLEELLDAIGFPDP-RKKKSLMRKLRRLLGRARLTSREVNILRGILRKIERRIK 237 Query: 252 Q 252 Sbjct: 238 G 238 >gnl|CDD|144253 pfam00588, SpoU_methylase, SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet. Length = 142 Score = 107 bits (270), Expect = 3e-24 Identities = 42/158 (26%), Positives = 76/158 (48%), Gaps = 21/158 (13%) Query: 14 GPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRD-GWPSEKARSSSANADCVIDSVR 72 +++L +PQ N+G +AR F L LV PR + KA +SA A + + Sbjct: 1 PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADLYNPKAIRASAGALFHLP-LV 59 Query: 73 VFSNLKEAIADLH----FIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRE 128 + NL+EA+ DL +I AT+ + + ++ K V ++FG E Sbjct: 60 IVDNLEEALKDLKEAGYWIIATSLKGKPLYEIDFPKK---------------VALVFGNE 104 Query: 129 RWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVW 166 GL+NE + L + ++ P++ SLN++ A ++++ Sbjct: 105 GTGLSNEVLELCDRLVRIPMSGEVESLNVAVAAAIILY 142 >gnl|CDD|30912 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure and biogenesis]. Length = 260 Score = 41.5 bits (97), Expect = 2e-04 Identities = 32/152 (21%), Positives = 62/152 (40%), Gaps = 23/152 (15%) Query: 21 DPQLGENIGMVARAMWNFNLTQLRLVNPR-DGWPSEKARSSSANADCVIDSVRVFSNLKE 79 DP N+G + R F + + L R D + R+S+ A + +RV + + Sbjct: 119 DPH---NLGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGAAF-HVPVIRVTNLART 174 Query: 80 AIADLH----FIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 + L ++ AT+ + PK+ A+V G E GL+ Sbjct: 175 LLELLKEAGFWVVATSLDGEVDLYETDLPKKTALV--------------LGNEGEGLSRL 220 Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167 + ++ ++ P+ SLN+S A ++++E Sbjct: 221 LLEHADQLVRIPMAGKVESLNVSVAAGILLYE 252 >gnl|CDD|30568 COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]. Length = 155 Score = 36.7 bits (85), Expect = 0.006 Identities = 32/154 (20%), Positives = 58/154 (37%), Gaps = 15/154 (9%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVID-SVRVFS 75 I+L P++ N G + R +L L+ P G+ + R A D S+ Sbjct: 5 IVLYQPEIPPNTGNIIRTCAATG-AELHLIEPL-GFDLDDKRLKRAGLDYHEKASLTEHD 62 Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 +L+ + + + + F + ++FG E GL E Sbjct: 63 SLEAFLEA----------EPIGGRLFALTTKGTTTYTDVSFQKGDY-LLFGPESRGLPEE 111 Query: 136 EI-ALSNAIISFPVNPLFPSLNISQAVLLMVWEC 168 + A + I P+ P SLN+S V ++++E Sbjct: 112 ILDAAPDRCIRIPMRPGVRSLNLSNTVAVVLYEA 145 >gnl|CDD|176209 cd08247, AST1_like, AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast. This group contains members identified in targeting of yeast membrane proteins ATPase. AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast, identified as a multicopy suppressor of pma1 mutants which cause temperature sensitive growth arrest due to the inability of ATPase to target to the cell surface. This family is homologous to the medium chain family of dehydrogenases and reductases. Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of an beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. Length = 352 Score = 30.3 bits (69), Expect = 0.50 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%) Query: 35 MWNFNLTQLRLVNPRDGWPSEKARS--SSANADCVIDSVRVFSNLKEAIADL 84 +W++N Q L++P W EK + IDSV F + KEA L Sbjct: 290 LWSYNY-QFFLLDPNADWI-EKCAELIADGKVKPPIDSVYPFEDYKEAFERL 339 >gnl|CDD|143948 pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain. Length = 155 Score = 29.5 bits (67), Expect = 0.92 Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 2/51 (3%) Query: 43 LRLVNPRDGWPSEK--ARSSSANADCVIDSVRVFSNLKEAIADLHFIYATT 91 + LV P+ P + + S+ V +L+EA+ +Y Sbjct: 31 VVLVAPKGLPPDPELVDEAKKNALKSGGISITVTDDLEEALKGADVVYTDR 81 >gnl|CDD|30427 COG0078, ArgF, Ornithine carbamoyltransferase [Amino acid transport and metabolism]. Length = 310 Score = 28.6 bits (64), Expect = 1.8 Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 7/69 (10%) Query: 25 GENIG---MVARAMWNFNLTQLRLVNPRDGWPSEKARS-SSANADCVIDSVRVFSNLKEA 80 G N+ ++A A ++ R+ P+ P + + NA + + + +EA Sbjct: 162 GNNVANSLLLAAAKLGMDV---RIATPKGYEPDPEVVEKAKENAKESGGKITLTEDPEEA 218 Query: 81 IADLHFIYA 89 + +Y Sbjct: 219 VKGADVVYT 227 >gnl|CDD|35746 KOG0526, KOG0526, KOG0526, Nucleosome-binding factor SPN, POB3 subunit [Transcription, Replication, recombination and repair, Chromatin structure and dynamics]. Length = 615 Score = 27.2 bits (60), Expect = 4.5 Identities = 16/61 (26%), Positives = 23/61 (37%) Query: 39 NLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNF 98 L ++R P D E A + V+ V S + +AI I T R R + Sbjct: 159 GLMEMRFHIPEDQEDGEDRDKVEAFYENVLAKADVSSAVGDAIVSFEEILCLTPRGRYDI 218 Query: 99 K 99 K Sbjct: 219 K 219 >gnl|CDD|31437 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function prediction only]. Length = 358 Score = 27.2 bits (60), Expect = 5.3 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%) Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFI--RPELMREEV 236 SFLD E+ E R Y ++ D++ + + RPE +REE Sbjct: 111 SFLDPEEVPREARRYIL---ERISENDNVKEVVVESRPEFIREER 152 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 0.318 0.133 0.380 Gapped Lambda K H 0.267 0.0753 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,117,920 Number of extensions: 161127 Number of successful extensions: 354 Number of sequences better than 10.0: 1 Number of HSP's gapped: 349 Number of HSP's successfully gapped: 12 Length of query: 268 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 176 Effective length of database: 4,275,709 Effective search space: 752524784 Effective search space used: 752524784 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: 56 (25.3 bits)